Online Version Research Articles

Mapping and candidate gene analysis of QTLs for grain shape in a rice chromosome segment substitution line Z485 and breeding of SSSLs.

The online version contains supplementary material available at 10.1007/s11032-024-01480-x.

GhWER controls fiber initiation and early elongation by regulating ethylene signaling pathway in cotton (Gossypium hirsutum).

The online version contains supplementary material available at 10.1007/s11032-024-01477-6.

A novel framework for online supervised learning with feature selection

Current online learning methods suffer issues such as lower convergence rates and limited capability to select important features compared to their offline counterparts. In this paper, a novel framework for online learning based on running averages is proposed. Many popular offline regularised methods such as Lasso, Elastic Net, Minimax Concave Penalty (MCP), and Feature Selection with Annealing (FSA) have their online versions introduced in this framework. The equivalence between the proposed online methods and their offline counterparts is proved, and then novel theoretical true support recovery and convergence guarantees are provided for some of the methods in this framework. Numerical experiments indicate that the proposed methods enjoy high true support recovery accuracy and a faster convergence rate compared with conventional online and offline algorithms. Finally, applications to large datasets are presented, where again the proposed framework shows competitive results compared to popular online and offline algorithms.

#1204 Measuring needling experience: development and validation of the Needling Patient Reported Experience Measure (NPREM)

Abstract Background and Aims Most people on haemodialysis rely on having reliable access to their vascular system, often via surgically created arteriovenous fistula or graft. At the beginning of each dialysis session, needles must be inserted. While ‘needling’ is a key step, an annual UK survey shows that needling is one of the lowest scoring areas of reported experience for individuals receiving haemodialysis in a kidney centre or satellite unit. Qualitative research indicates that needling can be painful and cause anxiety. Although an emerging area of research, no validated measures exist which assess patient reported experience of needling. We aimed to develop a questionnaire which reliably measures needling experience. The Needling Patient Reported Experience Measure (NPREM) was developed over multiple phases consisting of qualitative interviews with patients, item generation involving a multidisciplinary expert group including experts by experience, cognitive interviewing and pilot testing. Here we report the results of the final validation phase. Methods Seven NHS kidney centres participated in the validation phase (aiming for 500 participants). Between February-April 2023, participants completed either online or paper versions of the questionnaire. A subset of participants (aiming for 80-120) completed a follow-up questionnaire pack (NPREM, Change of Circumstances) 2-4 weeks after the first to assess the reliability of the scale over time. Analyses included a full evaluation of the scale psychometric properties and factor analyses to assess dimensional structure. Correlations with other validated measures (Vascular Access Quality of Life [VASQoL], EuroQol 5 Dimension [EQ5D-5L], and Patient Activation Measure [PAM]) were used to assess the convergent and divergent validity of the NPREM. Results 468 people participated (sample characteristics: male 66%, mean age 66 years (SD 14), White 75%, access via fistula 95%, first access 76%), of which 99 completed the follow-up. Overall, the NPREM showed good internal consistency (Cronbach's alpha = 0.94) and moderate to strong inter-item correlations. Factor analyses indicated that needling experience was a unidimensional construct, with one strong, main factor. Follow-up scores were strongly correlated (r = 0.89) with participants’ initial NPREM responses, demonstrating high reliability. Evidence of convergent validity was seen in the strong correlations between the NPREM and 1) the VASQoL (r = 0.60) and 2) the Overall Needling Experience question (r = 0.79). NPREM did not correlate with the EQ-5D (r = −0.31), the EQ-5D overall health (r = 0.24) or PAM (0.17), demonstrating divergent validity. The research team reviewed all items and themes reaching a consensus on items included, resulting in the validated 28-item NPREM (v 1.0), across five themes of care (Communicating with the Team, My Fistula/Graft and Needling, Steps in Needling, Working Together, My Personal Experience) plus Overall Needling Experience. Conclusion These results indicate that the NPREM offers a robust needling-specific tool to measure patient experience in those receiving haemodialysis. It addresses a gap by offering a way for kidney care providers to assess needling experience, both as a whole and across themes of care, which may facilitate meaningful service improvements. When published, the NPREM will be publicly available and free to use.

Assessing the Factor Structure and Construct Validity of the Beck Depression Inventory (BDI-II) in a Korean Preschool Teacher Sample

Preschool teachers are at high risk of depression. Therefore, emphasis should be placed on evaluating a valid and reliable instrument to measure depressive symptomatology for this population. One such promising instrument is the Beck Depression Inventory (BDI-II), a 21-item self-report measure designed to assess the presence and severity of depression. Although the tool’s psychometric properties have been analyzed in different samples, they have not been validated with a Korean preschool teacher sample. Hence, this study sought to evaluate the psychometric properties of the Korean version of the BDI-II in a sample of Korean preschool teachers. The study participants comprised 252 Korean preschool teachers (243 women and 9 men) with an average age of 33.5 years (SD = 10.3, range = 21-59). The participants completed the Korean version of the BDI-II online. Confirmatory factor analysis was performed to examine the psychometric properties of the BDI-II. Six models based on the literature were tested, including single-factor, correlated two- and three-factor, and bifactor models. The reliability and validity of the BDI-II were also analyzed. The bifactor model demonstrated the best data fit with an overarching vital general depression factor that coexists with comparatively weak specific cognitive, affective, and somatic factors. Internal consistency, measured using McDonald’s omega coefficients, was adequate in all cases. Using a validated screening instrument such as the BDI-II may allow clinicians to better detect depression among preschool teachers because of its conciseness and satisfactory psychometric properties. Since a bifactor model confirmed the unidimensionality of the BDI-II, the scores of specific factors should not be used in isolation. However, clinical assessment may benefit from its subscales if they are used in conjunction with total scores.

Erratum: 16. Diabetes Care in the Hospital: Standards of Care in Diabetes—2024 Abridged for Primary Care Professionals. Clin Diabetes 2024;42:222 (doi: 10.2337/cd24-a016)

A table on the perioperative care of people with diabetes in the abridged version of section 16 of the American Diabetes Association’s Standards of Care in Diabetes—2024 contained typographical errors. The corrected version is as follows. The online version of this article (https://doi.org/10.2337/cd24-a016) has been updated to reflect this change. Perioperative Care A1C and glucose goals Elective surgery A1C goal: <8% (63.9 mmol/L) Blood glucose goal within 4 hours of surgery: 100–180 mg/dL (5.6–10.0 mmol/L) Medication adjustments Hold metformin on the day of surgery. Discontinue sodium–glucose cotransporter 2 inhibitors 3–4 days before surgery. Hold other oral glucose-lowering agents the morning of the surgery or procedure. There are few data on the safe use and/or influence of glucagon-like peptide 1 receptor agonists on glycemia and delayed gastric emptying in the perioperative period. Individualize plan based on clinical scenario and procedure/surgery. Insulin therapy adjustments Give half of NPH dose or 75–80% of long-acting analog insulin or adjust insulin pump basal rates based on diabetes type and clinical judgment.

Stacked probability plots of the extended illness-death model using constant transition hazards - an easy to use shiny app.

Extended illness-death models (a specific class of multistate models) are a useful tool to analyse situations like hospital-acquired infections, ventilation-associated pneumonia, and transfers between hospitals. The main components of these models are hazard rates and transition probabilities. Calculation of different measures and their interpretation can be challenging due to their complexity. By assuming time-constant hazards, the complexity of these models becomes manageable and closed mathematical forms for transition probabilities can be derived. Using these forms, we created a tool in R to visualize transition probabilities via stacked probability plots. In this article, we present this tool and give some insights into its theoretical background. Using published examples, we give guidelines on how this tool can be used. Our goal is to provide an instrument that helps obtain a deeper understanding of a complex multistate setting. While multistate models (in particular extended illness-death models), can be highly complex, this tool can be used in studies to both understand assumptions, which have been made during planning and as a first step in analysing complex data structures. An online version of this tool can be found at https://eidm.imbi.uni-freiburg.de/ .

Isolation, chemical characterization, antimicrobial activity, and molecular docking studies of 2,6-dimethoxy benzoquinone isolated from medicinal plant Flacourtia jangomas.

The online version contains supplementary material available at 10.1007/s13205-024-04002-w.

An immunoinformatic approach for developing a multi-epitope subunit vaccine against Monkeypox virus.

The online version contains supplementary material available at 10.1007/s40203-024-00220-5.

Corrigendum to “The effect of topical endometrial scratching on pregnancy outcome in women with previous failure of intrauterine insemination: A non-randomized clinical trial” [Int J Reprod BioMed 2021; 19: 465-470

The publisher has been informed of an error that occurred on page 465 in which the first author affiliation order is incorrect and should be replaced with each other. On behalf of the author, the publisher wishes to apologize for this error. The online version of article has been updated on 31 March 2024 and can be found at https://doi.org/10.18502/ijrm.v19i5.9256.

Investigating the potential of mono-chalcone compounds in targeting breast cancer receptors through network pharmacology, molecular docking, molecular dynamics simulation, antiproliferative effects, and gene expressions.

The online version contains supplementary material available at 10.1007/s13205-024-03991-y.

Victims of a Human Tragedy or “Objects” of Migrant Smuggling? Media Framing of Greece’s Deadliest Migrant Shipwreck in Pylos’ Dark Waters

Refugee and migration crises has been an integral part of the continuous and successive crises that the world has been experiencing. Media has played a crucial role in shaping public opinion over migration and asylum-seeking. Within this context, this paper aims to discuss Greek media coverage of the migrant shipwreck off the Greek coast of Pylos, in June 2023, in which more than 600 people mostly from Syria, Egypt, and Pakistan are thought to have drowned. Based on data from a quantitative content analysis and a sample of news stories stemming from the online version of five Greek news media outlets, representing diverse political spaces, a broader set of criteria for content analysis, including the absence of refugee and migrant voice in media content, dehumanization, absence of solutions and context, among many others, was used in order to explore how the Greek media framed what has been labeled as one of the deadliest migrant shipwrecks in the Mediterranean. Results revealed (i) frames of dehumanization, (ii) insufficient reporting of injustice and discrimination stemming from (state) structures and practices, and an (iii) overemphasis on migrant smuggling.

How Technology, Health Information Seeking, and Socioeconomic Factors Are Associated With Coronavirus Disease 2019 Vaccination Readiness in Estonians Over 50 Years?

Despite the proven effectiveness of COVID-19 vaccines in preventing severe illness, many individuals, including older adults who are most susceptible to the virus, have opted against vaccination. Various factors could shape vaccination decisions, including seeking health information (HI). The internet is the primary source of HI today; however, older adults are often referred to as those missing out on digital benefits. The study explores the correlations between information and communication technology (ICT) use, online HI seeking, socioeconomic factors, and COVID-19 vaccination readiness among individuals aged 50 and above in Estonia. The survey data were gathered from 501 people aged 50 and older after the first lockdown in 2020. The outcomes revealed that vaccination readiness positively correlated with factors such as higher educational attainment, greater income, male gender, access to ICT, a readiness to employ digital technologies for health-related purposes, a greater demand for HI, and a higher frequency of seeking it online. There was some discrepancy in the preference of HI sources; for example, vaccination consenters preferred online versions of professional press publications and specific health portals. Based on the findings, it is advisable to encourage older adults to utilize the internet and new technology for health-related purposes. This practice expands the range of information sources available to them, ultimately enabling better decision-making regarding their health behaviors.

Identification of potential marine bioactive compounds from brown seaweeds towards BACE1 inhibitors: molecular docking and molecular dynamics simulations approach.

The online version contains supplementary material available at 10.1007/s40203-024-00210-7.

Abstract PO1-14-11: Different molecular processes are associated with recurrence in the clinical high- genomic low risk (cH/gL) and clinical low- genomic high risk (cL/gH) groups of the MINDACT clinical trial

Abstract Background: Despite the growing understanding of estrogen receptor positive/HER2-negative (ER+/HER2-) breast cancer (BC) biology, many unknowns remain regarding the mechanisms of disease recurrence. While several multigene prognostic signatures have shown clinical utility in identifying those patients at high or low genomic risk of recurrence, they can present with some limitations. In this retrospective analysis of the MINDACT trial, we interrogated the available transcriptomic data to understand which biological characteristics of the tumor are associated with recurrence in patients from the clinical high- genomic low risk (cH/gL) and clinical low- genomic high risk (cL/gH) groups (where the clinical and genomic risk were defined by a modified version of Adjuvant Online! and the 70-gene signature, respectively). Methods: These analyses focused on the subset of patients with ER+/HER2- tumors of no special type (NST) who received endocrine therapy (which comprised the majority of this NST ER+/HER2- sub-cohort) and for which central pathology and gene expression data were available (n= 1245). Scores of gene expression modules associated with key biological processes in breast cancer defined in a collection of previous publications were computed from the gene expression matrix using the formula described in Desmedt et al. (Clin. Cancer Res. 2008). Gene Set Variation Analysis method (R package ‘GSVA’ – version 1.40.1) was used to derive the enrichment scores of fifty hallmark gene sets available in the ‘H’ collection of the MSigDB database (version 7.5.1). Survival analyses were performed for disease-free survival (DFS) and distant recurrence-free survival (DRFS). Univariable and multivariable regression models, implemented by Cox regression and Fine-Gray subdistribution hazard regression methods, were performed to evaluate the association of enrichment of hallmarks and gene modules with DFS and DRFS, respectively (covariates =age, nodal status, KI67, tumor size, chemotherapy, radiotherapy). Results: DFS event occurred in 150/913 (16.4%) and 51/332 (15.4%) NST ER+/HER2- patients in the cH/gL and cL/gH groups, respectively. DRFS event occurred in 70/913 (7.7%) and 21/332 (6.3%) NST ER+/HER2- patients in the cH/gL and cL/gH groups, respectively. In the cH/gL group, we observed an association of hallmarks related to cell cycle and downregulation of gene modules related to lymphocyte-centric immune activities with worse prognosis (Table). For the cL/gH, we did not observe an association between hallmarks related to cell cycle and worse prognosis but an enrichment of hallmarks related to PI3K/AKT/mTOR signaling as well as several metabolic hallmarks related to insulin activities (Table). Of interest, in this group of patients, higher scores of the HER2-associated gene expression signature were also associated with worse prognosis. Across the two groups effects were more pronounced for DRFS than DFS. Conclusion: Different molecular processes are associated with progression in these two distinct groups of patients. The association of hallmarks related to cell cycle with survival in the cH/gL group supports the observation that adjuvant chemotherapy could benefit a subset of these patients. In the cL/gH group, the association of signatures associated with PI3K pathway and HER2 can have potential clinical relevance given their current targetability in the metastatic setting. This retrospective study is funded by the Breast Cancer Research Foundation. Table. Representative hallmarks and gene expression modules independently associated with prognosis in NST ER+/HER2- patients in the cH/gL group and in the cL/gH group #p-values reported were not corrected for multiple testing Citation Format: Christine Desmedt, Ha-Linh Nguyen, François Richard, Marion Maetens, Coralie Poncet, Laura De Meulemeester, Kim Aalders, Mauro Delorenzi, Suzette Delaloge, Jean-Yves Pierga, Etienne Brain, Suzan Vrijaldenhoven, Peter A Neijenhuis, Emiel Rutgers, Florentine Hilbers, Laura Van ’t Veer, Giuseppe Viale, Christos Sotiriou, Martine Piccart, Fatima Cardoso. Different molecular processes are associated with recurrence in the clinical high- genomic low risk (cH/gL) and clinical low- genomic high risk (cL/gH) groups of the MINDACT clinical trial [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-14-11.

OsAAP8 mutation leads to significant improvement in the nutritional quality and appearance of rice grains.

The online version contains supplementary material available at 10.1007/s11032-024-01473-w.

A novel functional allele of Ehd3 controls flowering time in rice.

The online version contains supplementary material available at 10.1007/s11032-024-01472-x.

The artificial neural network selects saccharides from natural sources a promise for potential FimH inhibitor to prevent UTI infections.

The online version contains supplementary material available at 10.1007/s40203-024-00212-5.

Efficient dual-frequency SSVEP brain-computer interface system exploiting interocular visual resource disparities

Here, we present a novel dual-frequency steady-state visual evoked potential (SSVEP) brain-computer interface (BCI) system with a unique human–computer interaction (HCI) feature that utilizes distinct visual resource disparities between the two eyes. By leveraging subtle differences in electroencephalography (EEG) responses due to binocular disparity, our system effectively distinguishes identical frequency targets. We conducted a two-phase validation: initial offline experiments confirmed EEG differences from interocular disparity, followed by global optimization to refine the SSVEP coding and spatial arrangement, allowing for 40 distinct targets within 20 frequency combinationes. A tailored binocular-task-related component analysis (bTRCA) algorithm was developed, achieving a maximum individual information transmission rate (ITR) of 338.32 bits/min offline and an average of 224.96 bits/min, with the online version reaching an average ITR of 234.13 bits/min. These results indicate that this system is a leading candidate for dual-frequency SSVEP BCIs, opening new prospects for HCI applications.

An Investigation of the Impact of Online and In-Person Delivery of Undergraduate Biology Instruction

Online learning is a well-established and growing, yet controversial and widely criticized, component of higher education. In this study, in-person and online versions of an undergraduate introductory biology class were compared to determine whether the online version of the course promoted student performance as well as the in-person course. Student survey responses were also analyzed to identify which teaching modality students perceived to be most effective at promoting learning, and to determine which components of the course were perceived by students to be most effective. No statistically significant difference was observed in exam scores or course grades between the two course modalities. Interestingly, some course components, such as completing virtual labs, were perceived to be more effective in the online version of the course, while others, such as participating in class discussions, were ranked as more effective for the in-person course offering; other components were ranked as similarly effective in both versions of the course. Therefore, this study provides evidence that online education can be effective if appropriately designed and implemented, and it provides a framework for strengthening the effectiveness of online education in the future.