Online Version Research Articles

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.

A cross-cultural study of differential item functioning analysis of beliefs about Language Learning Inventory (BALLI)

This research examines students' beliefs about language learning by evaluating the measurement equivalence of the beliefs about Language Learning Inventory (BALLI). The graded response model (GRM) was used to examine differential item functioning (DIF) in the BALLI across four different countries, namely: Iran, Malaysia, Indonesia, and Bangladesh. The sample was drawn from 1613, including 500 males and 1113 females who completed the online version of the BALLI, comprising five subscales of beliefs about foreign language aptitude, the difficulty of language learning, the nature of language learning, learning and communication strategies, and motivations and expectations. Most BALLI items showed non-uniform DIF. This finding implies that students in different countries had different perceptions of the BALLI items. Therefore, researchers should be very cautious about using the BALLI in different countries. This cross-cultural comparison may generate new insights into revising the BALLI items or developing another scale to compare students' beliefs about language learning in different countries.

Identification of two plastid transit peptides for construction of pollen-inactivation system in rice.

The online version contains supplementary material available at 10.1007/s11032-024-01471-y.

Piriformospora indica suppresses the symptoms produced by Banana bract mosaic virus by inhibiting its replication and manipulating chlorophyll and carotenoid biosynthesis and degradation in banana.

The online version contains supplementary material available at 10.1007/s13205-024-03983-y.

Deciphering variations, identification of marker-trait associations and candidate genes for seed oil content under terminal heat stress in Indian mustard (Brassica junceaL. Czern & Coss) germplasm stock.

The online version contains supplementary material available at 10.1007/s13205-024-03985-w.

Identification of QTLs responsible for culturability, and fine-mapping of QTL qCBT9 related to callus browning derived from Dongxiang common wild rice (Oryza rufipogon Griff.).

The online version contains supplementary material available at 10.1007/s11032-024-01470-z.

Digitalization of anesthesiology and resuscitation services: multicenter questionnaire study

OBJECTIVE: To substantiate recommendations for the implementation of the concept and technologies of digitalization of the anesthesiology and resuscitation (A&R) service in multidisciplinary hospitals to solve the problem of ensuring the safety of patients and medical personnel. MATERIALS AND METHODS: The study presents data on the implementation of information technology in the practice of the A&R service based on information received from 235 anesthesiology and resuscitation specialists working in leadership positions in various categories of healthcare institutions. Method of collecting information: experts independently completed the online version of the questionnaire. Sampling principle: intentional. Survey period: April 12, 2023 — August 4, 2023. RESULTS: In 87 % of hospitals the medical information system (MIS) of the A&R service is part of the hospital’s MIS. Only in 23 % of hospitals all workstations of the anesthesiologist-resuscitator are connected to the MIS. Logging into a personal electronic workplace using access rights on any of the hospital’s personal computers was confirmed by 87 % of respondents. Hospitals in which anesthesiology and resuscitation equipment are not integrated into the MIS account for 89 %. In the case of branches with a local A&R information system, equipment in 44 % of similar branches is connected to it. Only in 51 % of hospitals the A&R receives data from the laboratory information system, the integration rates with the radiological information system are even lower and amount to only 34 %. The study revealed a significant problem with the introduction of clinical recommendations, drug reference books, as well as prevention and manipulation protocols, various requirements and, in particular, scales/indices for assessing the condition of patients into the MIS. CONCLUSIONS: For the full functioning of the MIS, organizational solutions are needed that are aimed at implementing the tasks, primary and future. The development and application of modern MIS in anesthesiology and resuscitation will contribute to the further development of the specialty and ensure patient safety and adequate quality of medical care. It is necessary to unify the requirements for MIS developers according to the main components in the functionality.