TFTG: A comprehensive database for human transcription factors and their targets

Transcription factors (TFs) are major contributors to gene transcription, especially in controlling cell-specific gene expression and disease occurrence and development. Uncovering the relationship between TFs and their target genes is critical to understanding the mechanism of action of TFs. With the development of high-throughput sequencing techniques, a large amount of TF-related data has accumulated, which can be used to identify their target genes. In this study, we developed TFTG (Transcription Factor and Target Genes) database (http://tf.liclab.net/TFTG), which aimed to provide a large number of available human TF-target gene resources by multiple strategies, besides performing a comprehensive functional and epigenetic annotations and regulatory analyses of TFs. We identified extensive available TF-target genes by collecting and processing TF-associated ChIP-seq datasets, perturbation RNA-seq datasets and motifs. We also obtained experimentally confirmed relationships between TF and target genes from available resources. Overall, the target genes of TFs were obtained through integrating the relevant data of various TFs as well as fourteen identification strategies. Meanwhile, TFTG was embedded with user-friendly search, analysis, browsing, downloading and visualization functions. TFTG is designed to be a convenient resource for exploring human TF-target gene regulations, which will be useful for most users in the TF and gene expression regulation research.

Advances in therapeutic cancer vaccines: Harnessing immune adjuvants for enhanced efficacy and future perspectives

Preventive cancer vaccines are highly effective in preventing viral infection-induced cancer, but advances in therapeutic cancer vaccines with a focus on eliminating cancer cells through immunotherapy are limited. To develop therapeutic cancer vaccines, the integration of optimal adjuvants is a potential strategy to enhance or complement existing therapeutic approaches. However, conventional adjuvants do not satisfy the criteria of clinical trials for therapeutic cancer vaccines. To improve the effects of adjuvants in therapeutic cancer vaccines, effective vaccination strategies must be formulated and novel adjuvants must be identified. This review offers an overview of the current advancements in therapeutic cancer vaccines and highlights in situ vaccination approaches that can be synergistically combined with other immunotherapies by harnessing the adjuvant effects. Additionally, the refinement of adjuvant systems using cutting-edge technologies and the elucidation of molecular mechanisms underlying immunogenic cell death to facilitate the development of innovative adjuvants have been discussed.

A contrastive learning approach to integrate spatial transcriptomics and histological images

The rapid growth of spatially resolved transcriptomics technology provides new perspectives on spatial tissue architecture. Deep learning has been widely applied to derive useful representations for spatial transcriptome analysis. However, effectively integrating spatial multi-modal data remains challenging. Here, we present ConGcR, a contrastive learning-based model for integrating gene expression, spatial location, and tissue morphology for data representation and spatial tissue architecture identification. Graph convolution and ResNet were used as encoders for gene expression with spatial location and histological image inputs, respectively. We further enhanced ConGcR with a graph auto-encoder as ConGaR to better model spatially embedded representations. We validated our models using 16 human brains, four chicken hearts, eight breast tumors, and 30 human lung spatial transcriptomics samples. The results showed that our models generated more effective embeddings for obtaining tissue architectures closer to the ground truth than other methods. Overall, our models not only can improve tissue architecture identification's accuracy but also may provide valuable insights and effective data representation for other tasks in spatial transcriptome analyses.

Angiopoietin-2, vascular endothelial growth factor family, and heparin binding endothelial growth factor are associated with subclinical atherosclerosis in rheumatoid arthritis

Introduction

Patients with RA are at a higher risk of developing CV diseases than the general population. The precise mechanisms are still unknown. We evaluated the associations between 8 plasma growth factors (GFs) (angiopoietin-2, EGF, HB-EGF, PLGF, TGF-α, VEGFa, VEGFc, and VEGFd) and subclinical arteriosclerosis in RA patients.

Materials and methods

A total of 199 patients with RA treated at the Hospital Universitari Sant Joan de Reus (Spain) between 2011 and 2015 were included in this cross-sectional study. Carotid intima media thickness (cIMT), carotid plaque presence (cPP) and pulse wave velocity (PWV) were measured. GFs were measured with Bio-Plex Pro Human Cancer Biomarker Panel 2 (Bio-Rad). Multivariate models and partial least square discriminant analysis (PLS-DA) were used for analysis (RStudio, version 4.0.1).

Results

Multivariate models showed that angiopoietin-2 was associated with cPP and PWV in the overall cohort (OR = 1.53 and β = 0.20, respectively). VEGFc (β = 0.29), VEGFa (β = 0.26) and HB-EGF (β = 0.22) were also associated with PWV. VEGFa (OR = 2.36), VEGFd (OR = 2.29), EGF (OR = 2.62), PLGF (OR = 2.54), and HB-EGF (OR = 2.24) were associated with cPP in men. According to PLS-DA, GFs were able to distinguish between patients with and without cPP in the overall cohort, male cohort, and female cohort. In women, angiopoietin-2 was associated with PWV (β = 0.18).

Conclusions

The selected GFs were closely related to atherosclerosis in patients with RA and are potential predictors of CV disease in patients with RA.

Insulin-related traits and prostate cancer: A Mendelian randomization study

Investigating the causal relationship between insulin secretion and prostate cancer (PCa) development is challenging due to the multifactorial nature of PCa, which complicates the isolation of the specific impact of insulin-related factors. We conducted a Mendelian randomization (MR) study to investigate the associations between insulin secretion-related traits and PCa. We used 36, 60, 56, 23, 48, and 49 single nucleotide polymorphisms (SNPs) as instrumental variables for fasting insulin, insulin sensitivity, proinsulin, and proinsulin in nondiabetic individuals, individuals with diabetes, and individuals receiving exogenous insulin, respectively. These SNPs were selected from various genome-wide association studies. To clarify the causal relationship between insulin-related traits and PCa, we utilized a multivariable MR analysis to adjust for obesity and body fat percentage. Additionally, two-step Mendelian randomization was conducted to assess the role of insulin-like growth factor 1 (IGF-1) in the relationship between proinsulin and PCa. Two-sample MR analysis revealed strong associations between genetically predicted fasting insulin, insulin sensitivity, proinsulin, and proinsulin in nondiabetic individuals and the development of PCa. After adjustment for obesity and body fat percentage using multivariable MR analysis, proinsulin remained significantly associated with PCa, whereas other factors were not. Furthermore, two-step MR analysis demonstrated that proinsulin acts as a negative factor in prostate carcinogenesis, largely independent of IGF-1. This study provides evidence suggesting that proinsulin may act as a negative factor contributing to the development of PCa. Novel therapies targeting proinsulin may have potential benefits for PCa patients, potentially reducing the need for unnecessary surgical treatments.

The clinical efficacy of powder air-polishing in the non-surgical treatment of peri-implant diseases: A systematic review and meta-analysis

Peri-implant diseases, characterized by inflammatory conditions affecting peri-implant tissues, encompass peri-implant mucositis and peri-implantitis. Peri-implant mucositis is an inflammatory lesion limited to the mucosa around an implant, while peri-implantitis extends from the mucosa to the supporting bone, causing a loss of osseointegration. For non-surgical treatments, we tested the null hypothesis that the presence or absence of air-polishing made no difference. The study focused on randomized controlled trials (RCTs) comparing air-polishing with mechanical or ultrasonic debridement, evaluating outcomes such as bleeding on probing (BOP), probing depth (PD), plaque index/plaque score (PI/PS), clinical attachment level (CAL), bone loss, and mucosal recession (MR). Two independent reviewers conducted data extraction and quality assessments, considering short-term (<6 months) and long-term (≥6 months) follow-up periods. After screening, ten articles were included in the meta-analysis. In nonsurgical peri-implant disease management, air-polishing moderately mitigated short-term PI/PS for peri-implant mucositis and showed a similar improvement in long-term BOP and bone loss for peri-implantitis compared to the control group. The Egger test found no evidence of publication bias except for the long-term PI/PS of peri-implant mucositis. Leave-one-out analysis confirmed the stability of the results. The findings highlight the need for future research with longer-term follow-up and high-quality, multi-center, large-sample RCTs.

Unraveling the hidden complexity: Exploring dental tissues through single-cell transcriptional profiling

Understanding the composition and function of cells constituting tissues and organs is vital for unraveling biological processes. Single-cell analysis has allowed us to move beyond traditional methods of categorizing cell types. This innovative technology allows the transcriptional and epigenetic profiling of numerous individual cells, leading to significant insights into the development, homeostasis, and pathology of various organs and tissues in both animal models and human samples. In this review, we delve into the outcomes of major investigations using single-cell transcriptomics to decipher the cellular composition of mammalian teeth and periodontal tissues. The recent single-cell transcriptome-based studies have traced in detail the dental epithelium-ameloblast lineage and dental mesenchyme lineages in the mouse incisors and the tooth germ of both mice and humans; unraveled the microenvironment, the identity of niche cells, and cellular intricacies in the dental pulp; shed light on the molecular mechanisms orchestrating root formation; and characterized cellular dynamics of the periodontal ligament. Additionally, cellular components in dental pulps were compared between healthy and carious teeth at a single-cell level. Each section of this review contributes to a comprehensive understanding of tooth biology, offering valuable insights into developmental processes, niche cell identification, and the molecular secrets of the dental environment.

EM-COGLOAD: An investigation into age and cognitive load detection using eye tracking and deep learning

Alzheimer's Disease is the most prevalent neurodegenerative disease, and is a leading cause of disability among the elderly. Eye movement behaviour demonstrates potential as a non-invasive biomarker for Alzheimer's Disease, with changes detectable at an early stage after initial onset. This paper introduces a new publicly available dataset: EM-COGLOAD (available at https://osf.io/zjtdq/, DOI: 10.17605/OSF.IO/ZJTDQ). A dual-task paradigm was used to create effects of declined cognitive performance in 75 healthy adults as they carried out visual tracking tasks. Their eye movement was recorded, and time series classification of the extracted eye movement traces was explored using a range of deep learning techniques. The results of this showed that convolutional neural networks were able to achieve an accuracy of 87.5% when distinguishing between eye movement under low and high cognitive load, and 76% when distinguishing between the oldest and youngest age groups.

Mind the gap: Comparing parents' information needs about impending preterm birth to current clinical practices using a mixed methods approach

Objective

To identify parents' information needs about impending very preterm birth and compare these needs to current information practices in the Netherlands.

Methods

Step 1: We surveyed N = 203 parents of preterm infants to assess their information needs. Data were analyzed using inductive thematic analysis. Step 2a: We collected information resources from hospitals (N = 9 NICUs) and via an online search. These materials were analyzed using deductive thematic analysis. Step 2b: We compared findings from Steps 1-2a.

Results

We identified four themes pertaining to parents' information needs: (1) participation in care, (2) emotional wellbeing, (3) experience/success stories, and (4) practical information about prematurity. Clinicians' communicative skills and time were considered prerequisites for optimal information-provision. Notably, hospital resources provided mainly medical information about prematurity with some emphasis on participation in care, while parent associations mainly focused on emotional wellbeing and experience/success stories.

Conclusion

While parents demonstrate clear information needs about impending very preterm birth, current information resources satisfy these partially.

Innovation

Our multidisciplinary research team included both scholars and veteran NICU parents. As such, we identified parents' information needs bottom-up. These parent-driven insights will be used to design an innovative, tailored information platform for parents about impending very preterm birth.

Machine learning judged neutral facial expressions as key factors for a "good therapist" within the first five minutes: An experiment to simulate online video counselling

Objective

Machine learning models were employed to discern patients' impressions from the therapists' facial expressions during a virtual online video counselling session.

Methods

Eight therapists simulated an online video counselling session for the same patient. The facial emotions of the therapists were extracted from the session videos; we then utilized a random forest model to determine the therapist's impression as perceived by the patients.

Results

The therapists' neutral facial expressions were important controlling factors for patients' impressions. A predictive model with three neutral facial features achieved an accuracy of 83% in identifying patients' impressions.

Conclusions

Neutral facial expressions may contribute to patient impressions in an online video counselling environment with spatiotemporal disconnection.

Innovation

Expression recognition techniques were applied innovatively to an online counselling setting where therapists' expressions are limited. Our findings have the potential to enhance psychiatric clinical practice using Information and Communication Technology.

TAK-242 improves sepsis-associated acute kidney injury in rats by inhibiting the TLR4/NF-κB signaling pathway

OBJECTIVE

This study was designed to observe the effect of toll-like receptor 4 (TLR4)/nuclear factor kappa-B (NF-κB) pathway activity on sepsis-associated acute kidney injury (SA-AKI), thereby providing new considerations for the prevention and treatment of SA-AKI.

METHODS

The rats were divided into Sham, cecal ligation and puncture (CLP), CLP + vehicle, and CLP + TAK-242 groups. Except the Sham group, a model of CLP-induced sepsis was established in other groups. After 24 h, the indicators related to kidney injury in blood samples were detected. The pathological changes in the kidneys were observed by hematoxylin-eosin staining, and tubular damage was scored. Oxidative stress-related factors, mitochondrial dysfunction-related indicators in each group were measured; the levels of inflammatory factors in serum and kidney tissue of rats were examined. Finally, the expression of proteins related to the TLR4/NF-κB signaling pathway was observed by western blot.

RESULTS

Compared with the CLP + vehicle and CLP + TAK-242 groups, the CLP + TAK-242 group reduced blood urea nitrogen (BUN), creatinine (Cr), cystatin-C (Cys-C), reactive oxygen species (ROS), malondialdehyde (MDA), and inflammatory factors levels (p < 0.01), as well as increased superoxide dismutase (SOD) activity of CLP rats (p < 0.01). Additionally, TAK-242 treatment improved the condition of CLP rats that had glomerular and tubular injuries and mitochondrial disorders (p < 0.01). Further mechanism research revealed that TAK-242 can inhibit the TLR4/NF-κB signaling pathway activated by CLP (p < 0.01). Above indicators after TAK-242 treatment were close to those of the Sham group.

CONCLUSION

TAK-242 can improve oxidative stress, mitochondrial dysfunction, and inflammatory response by inhibiting the activity of TLR4/NF-κB signaling pathway, thereby preventing rats from SA-AKI.

Gene choice in cancer cells is exclusive in ion transport but concurrent in DNA replication

Cancers share common cellular and physiological features. Little is known about whether distinctive gene expression patterns can be displayed at the single-cell level by gene families in cancer cells. The expression of gene homologs within a family can exhibit concurrence and exclusivity. Concurrence can promote all-or-none expression patterns of related genes and underlie alternative physiological states. Conversely, exclusive gene families express the same or similar number of homologs in each cell, allowing a broad repertoire of cell identities to be generated. We show that gene families involved in the cell-cycle and antigen presentation are expressed concurrently. Concurrence in the DNA replication complex MCM reflects the replicative status of cells, including cell lines and cancer-derived organoids. Exclusive expression requires precise regulatory mechanism, but cancer cells retain this form of control for ion homeostasis and extend it to gene families involved in cell migration. Thus, the cell adhesion-based identity of healthy cells is transformed to an identity based on migration in the population of cancer cells, reminiscent of epithelial-mesenchymal transition.

A hypoxia-derived gene signature to suggest cisplatin-based therapeutic responses in patients with cervical cancer

Cervical cancer remains a significant global public health concern, often exhibits cisplatin resistance in clinical settings. Hypoxia, a characteristic of cervical cancer, substantially contributes to cisplatin resistance. To evaluate the therapeutic efficacy of cisplatin in patients with cervical cancer and to identify potential effective drugs against cisplatin resistance, we established a hypoxia-inducible factor-1 (HIF-1)-related risk score (HRRS) model using clinical data from patients treated with cisplatin. Cox and LASSO regression analyses were used to stratify patient risks and prognosis. Through qRT-PCR, we validated nine potential prognostic HIF-1 genes that successfully predict cisplatin responsiveness in patients and cell lines. Subsequently, we identified fostamatinib, an FDA-approved spleen tyrosine kinase inhibitor, as a promising drug for targeting the HRRS-high group. We observed a positive correlation between the IC50 values of fostamatinib and HRRS in cervical cancer cell lines. Moreover, fostamatinib exhibited potent anticancer effects on high HRRS groups in vitro and in vivo. In summary, we developed a hypoxia-related gene signature that suggests cisplatin response prediction in cervical cancer and identified fostamatinib as a potential novel treatment approach for resistant cases.

Acceptability and usability of the Planning Advance Care Together (PACT) website for improving patients' engagement in advance care planning

Objectives

Most prior advance care planning (ACP) interventions lack integration of the social context of patients' ACP process, which patients indicate is critically important. The current study developed the Planning Advance Care Together (PACT) website to foster inclusion of loved ones in the ACP process.

Methods

To provide feedback about the PACT website, patients with advanced cancer (N = 11), their caregivers (N = 11), and experts (N = 10) participated in semi-structured interviews. Patients and caregivers also completed standardized ratings of acceptability and usability.

Results

Overall, patient (n = 11) and caregiver (n = 11) ratings of acceptability and usability of the website exceeded benchmark cut-offs (≥24 on the Acceptability E-Scale and ≥ 68 on the System Usability Scale). Patients, caregivers, and experts liked the topic of ACP but felt that it could be emotionally challenging. They recommended focusing more on planning and less on end of life. They appreciated being able to include loved ones and recommended adding resources for caregivers.

Conclusions

Study findings support the preliminary usability and acceptability of the PACT website. Findings will be used to inform a modified prototype of the PACT website that is interactive and ready for field testing with patients with advanced cancer and their loved ones.

Innovation

We utilized a novel application of the shared mind framework to support patients with advanced cancer in engaging their loved ones in the ACP process.

Retrospective review of treatment outcomes and costs in children with sleep disordered breathing assessed with multi-channel studies

Current UK guidance on OSA management recommends only selective use of sleep studies - when there is diagnostic uncertainty, in children with comorbidities or to evaluate perioperative risk in those with suspected severe OSA. Routine use of sleep studies to confirm a diagnosis of obstructive sleep apnoea (OSA) in children before adenotonsillectomy is not currently recommended. We report the findings of a novel paediatric sleep service based on routine use of multi-channel sleep studies (MCSS) before adenotonsillectomy and present the results of a service evaluation assessing the impact of our practise on treatment outcomes and cost. We conducted a retrospective study of 264 children with sleep disordered breathing seen in our centre between July 2018-June 2019, using medical records and a sleep study database to determine treatment outcomes and costs. Using responses from a questionnaire completed by otolaryngologists for a separate prospective study, we compare our costs with estimates of those associated with a standard UK model of care i.e. with selective use of sleep studies. We estimate that our routine use of MCSS reduced the number of adenotonsillectomies by 44 % but at higher monetary costs than those estimated for the standard model of care. We note however, that reconfiguring our service to arrange a sleep study before the initial appointment, rather than after, would result in the service being cost neutral compared with the standard model. We also estimate that use of home multi-channel studies in our service would bring a significant cost saving (∼£50,000 - £80,000 per annum) compared to standard care.

Dopamine, an exogenous quorum sensing signaling molecule or a modulating factor in Pseudomonas aeruginosa?

Pseudomonas aeruginosa is recognized globally as an opportunistic pathogen of considerable concern due to its high virulence and pathogenicity, especially in immunocompromised individuals. While research has identified several endogenous quorum sensing (QS) signaling molecules that enhance the virulence and pathogenicity of P. aeruginosa, investigations on exogenous QS signaling molecules or modulating factors remain limited. This study found that dopamine serves as an exogenous QS signaling molecule or modulating factor of P. aeruginosa PAO1, enhancing the production of virulence factors and biofilms. Compared to the control group, treatment with 40 μM dopamine resulted in a 33.1 % increase in biofilm formation, 68.1 % increase in swimming mobility, 63.1 % increase in swarming mobility, 147.2 % increase in the signaling molecule 3-oxo-C12-HSL, and 50.5 %, 28.5 %, 27.0 %, and 33.2 % increases in the virulence factors alginate, rhamnolipids, protease, and pyocyanin, respectively. This study further explored the mechanism of dopamine regulating the biofilm formation and virulence of P. aeruginosa PAO1 through transcriptome and metabolome. Transcriptomic analysis showed that dopamine promoted the expression of virulence genes psl, alg, lasA, rhlABC, rml, and phz in P. aeruginosa PAO1. Metabolomic analysis revealed changes in the concentrations of tryptophan, pyruvate, ethanolamine, glycine, 3-hydroxybutyric acid, and alizarin. Furthermore, KEGG enrichment analysis of altered genes and metabolites indicated that dopamine enhanced phenylalanine, tyrosine, and tryptophan in P. aeruginosa PAO1. The results of this study will contribute to the development of novel exogenous QS signaling molecules or modulating factors and advance our understanding of the interactions between P. aeruginosa and the host environment.

Deep learning of antibody epitopes using positional permutation vectors

Background

The accurate computational prediction of B cell epitopes can vastly reduce the cost and time required for identifying potential epitope candidates for the design of vaccines and immunodiagnostics. However, current computational tools for B cell epitope prediction perform poorly and are not fit-for-purpose, and there remains enormous room for improvement and the need for superior prediction strategies.

Results

Here we propose a novel approach that improves B cell epitope prediction by encoding epitopes as binary positional permutation vectors that represent the position and structural properties of the amino acids within a protein antigen sequence that interact with an antibody. This approach supersedes the traditional method of defining epitopes as scores per amino acid on a protein sequence, where each score reflects each amino acids predicted probability of partaking in a B cell epitope antibody interaction. In addition to defining epitopes as binary positional permutation vectors, the approach also uses the 3D macrostructure features of the unbound protein structures, and in turn uses these features to train another deep learning model on the corresponding antibody-bound protein 3D structures. This enables the algorithm to learn the key structural and physiochemical features of the unbound protein and embedded epitope that initiate the antibody binding process helping to eliminate "induced fit" biases in the training data. We demonstrate that the strategy predicts B cell epitopes with improved accuracy compared to the existing tools. Additionally, we show that this approach reliably identifies the majority of experimentally verified epitopes on the spike protein of SARS-CoV-2 not seen by the model during training and generalizes in a very robust manner on dissimilar data not seen by the model during training.

Conclusions

With the approach described herein, a primary protein sequence and a query positional permutation vector encoding a putative epitope is sufficient to predict B cell epitopes in a reliable manner, potentially advancing the use of computational prediction of B cell epitopes in biomedical research applications.

Reliability of a short diet and vitamin supplement questionnaire for retrospective collection of maternal nutrient intake

Background

Gestational nutrition can protect against adverse neurodevelopmental outcomes.

Objectives

We developed a short tool for collecting maternal nutritional intake during pregnancy to facilitate research in this area and compared its retrospective use to prospectively-collected food frequency questionnaires (FFQ).

Methods

Maternal nutritional intake was retrospectively assessed using three versions (full interview, full self-administered online, and shortened interview) of the Early Life Exposure Assessment Tool (ELEAT) among participants of the MARBLES pregnancy cohort study of younger siblings of autistic children. Retrospective responses were compared with responses to supplement questions and the validated 2005 Block FFQ prospectively collected in MARBLES during pregnancies 2-7 years prior. ELEAT nutrient values were calculated using reported food intake frequencies and nutrient values from the USDA nutrient database. Correlations between retrospectively- and prospectively-reported intake were evaluated using Kappa coefficients, Youden's J, and Spearman Rank Correlation Coefficients (rs).

Results

MARBLES FFQ dietary intakes were compared among 54 women who completed the ELEAT full form including 12 online, and among 23 who completed the ELEAT short form. Correlations across most foods were fair to moderate. Most ELEAT quantified nutrient values were moderately correlated (rs = 0.3-0.6) with those on the Block FFQ. Supplement questions in both MARBLES and the ELEAT were completed by 114 women. Kappas were moderate for whether or not supplements were taken, but modest for timing. Correlations varied by version and child diagnosis or concerns, and were higher when mothers completed the ELEAT when their child was 4 years old or younger.

Conclusions

With recall up to several years, ELEAT dietary and supplement module responses were modestly to moderately reliable and produced nutrient values moderately correlated with prospectively-collected measures. The ELEAT dietary and vitamin supplements modules can be used to rank participants in terms of intake of several nutrients relevant for neurodevelopment.

Interaction of noncoding RNAs with hippo signaling pathway in cancer cells and cancer stem cells

The Hippo signaling pathway has a regulatory function in the organogenesis process and cellular homeostasis, switching the cascade reactions of crucial kinases acts to turn off/on the Hippo pathway, altering the downstream gene expression and thereby regulating proliferation, apoptosis, or stemness. Disruption of this pathway can lead to the occurrence of various disorders and different types of cancer. Recent findings highlight the importance of ncRNAs, such as microRNA, circular RNA, and lncRNAs, in modulating the Hippo pathway. Defects in ncRNAs can disrupt Hippo pathway balance, increasing tumor cells, tumorigenesis, and chemotherapeutic resistance. This review summarizes ncRNAs' inhibitory or stimulatory role in - Hippo pathway regulation in cancer and stem cells. Identifying the relation between ncRNAs and the components of this pathway could pave the way for developing new biomarkers in the treatment and diagnosis of cancers.

Findings on dietary characteristics among Haitian immigrants and the threat of food insecurity: A scoping review

Objectives

This study aimed to map and describe the available evidence on dietary characteristics and diet-related health conditions among Haitian immigrants across the globe.

Study design

Scoping review.

Methods

This review was based on the international guide Preferred Reporting Items for Systematic review and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). The searches were conducted in several electronic databases in July 2023. Reports focusing on diet, nutrition, and diet-related health conditions among international Haitian immigrants published in English, Portuguese, French, or Spanish with no year limit were included. The data extracted was tabulated and presented in a narrative summary.

Results

Database search retrieved 502 records, of which 30 met the inclusion criteria. The categories that emerged from the analysis were: food consumption patterns and trends, food and nutrition insecurity, cultural identity, and diet-related health conditions. Findings suggest: available evidence underrepresents Latin America and the Caribbean context; research gaps related to adolescents and the elderly and also to noncommunicable diseases except obesity; changes in food consumption after immigration towards less healthy eating; the Haitian immigrant's preference for healthy and traditional eating patterns; many experiences of food insecurity related to poverty, unemployment, and lack of social support, especially in host countries in Latin America and the Caribbean; and a high prevalence of obesity, especially among women.

Conclusions

Further research is required in countries in Latin America, mainly. Diet-related chronic diseases, adolescents, and the elderly should be targeted for further research. We recommend: longitudinal and qualitative research; field action reports describing local and global strategies to manage Haitian migration-related food and nutrition issues; culturally appropriate dietary interventions; and policies to protect and support the most vulnerable Haitian immigrants to have their fundamental right to adequate food guaranteed, reducing health inequalities.

Structural and functional prediction, evaluation, and validation in the post-sequencing era

The surge of genome sequencing data has underlined substantial genetic variants of uncertain significance (VUS). The decryption of VUS discovered by sequencing poses a major challenge in the post-sequencing era. Although experimental assays have progressed in classifying VUS, only a tiny fraction of the human genes have been explored experimentally. Thus, it is urgently needed to generate state-of-the-art functional predictors of VUS in silico. Artificial intelligence (AI) is an invaluable tool to assist in the identification of VUS with high efficiency and accuracy. An increasing number of studies indicate that AI has brought an exciting acceleration in the interpretation of VUS, and our group has already used AI to develop protein structure-based prediction models. In this review, we provide an overview of the previous research on AI-based prediction of missense variants, and elucidate the challenges and opportunities for protein structure-based variant prediction in the post-sequencing era.

Impact of a patient and family participation education program on hospital nurses' attitudes and competencies: A controlled before-after study

Objective

We designed a Patient and Family Participation Education Program (PFEP) with the aim of fostering a positive attitude and enhancing the competencies of hospital nurses required for effective patient and family participation in care.

Methods

In a Dutch university hospital, we conducted a before-after study. The PFEP comprising three courses: family conversation, supporting shared decision-making, and health literacy. We assessed nursing attitudes using the FINC-NA questionnaire and competencies with a separate questionnaire before and three months after the program. Changes in attitudes and competencies were analyzed using regression analysis.

Results

Twenty-two nurses participated in the education group, and 58 participated as controls.After three months, the change scores for the education group were statistically significantly higher on the total attitude score (FINC-NA) compared to the control group. Moreover, in six out of twelve competencies, the education group demonstrated significantly higher scores than the control group.

Conclusion

The educational program appeared effective in promoting nurses' attitudes and feelings of competencies towards patient and family-centered care.

Innovation

A blended education program focusing on patient and family has potential value for implementation in hospital care settings, especially for hospitals aiming to cultivate a more patient- and family-centered environment.

Turkish adaptation of the maternal cognition about infant sleep questionnaire

Background

Exploring early childhood sleep problems requires a detailed understanding of parental beliefs and cognitions related to infant sleep. There is a need for validated measures to investigate the cognitions of Turkish mothers about infant sleep however no scale measuring parental perceptions related to infant sleep behaviors in Turkish is available. We aimed to culturally adapt the Maternal Cognitions about Infant Sleep Questionnaire (MCISQ) in Turkish.

Methods

Subjects were recruited from an internet sample through social media. Internal consistency was evaluated by Cronbach's alpha, and test-retest reliability was determined by Pearson's correlation test and paired t-test. For factorial validity, the principal component factor analysis was performed for the components of MCISQ.

Results

A total of 417 mothers, most aged between 25 and 29 years (47.8 %), participated in the study. Infants' age ranged between 6 and 18 months, with a mean of 10.5 ± 3.9 months. Factor analysis revealed four factors after removal of item 11: Anger, doubt, safety, limit setting. Cronbach's alpha was 0.85. A subgroup of 32 mothers completed MCISQ three weeks after the initial administration. Total mean scores showed a significantly strong correlation (p:<0.01, r:0.82). Higher scores were noted in both total and subscale scores in infants with maternally reported sleep problems (p:<0.01).

Conclusion

Findings suggest a four-factor solution for MCISQ in Turkish mothers with infants aged 6-18 months. The adapted Turkish version is composed of 19 items with good reliability. Factor structure and items included in the subscales differed from the original study, highlighting the cultural factors related to maternal perceptions about infant sleep.

Application of one-piece endodontic crowns fabricated with CAD-CAM system to molars

Computer-aided design-computer-aided manufacturing (CAD-CAM) systems have been widely used as a fabrication method for restorations because of their high efficiency and accuracy, which significantly reduces fabrication time. However, molars with insufficient clearance or short clinical crown lengths require retention holes or grooves on the preparation, making it difficult to replicate the shapes with the CAM milling system. In these cases, restorations using the lost-wax method are selected. This article focuses on one-piece endodontic crowns (endocrowns) fabricated with a CAD-CAM system (CAD-CAM endocrowns), in which their posts and crowns are integrated. Articles from July 2012 to August 2023 were searched in PubMed with the keyword "endocrown". This review discusses the application of CAD-CAM endocrowns to molars from the viewpoint of model experiment (fracture resistance, adaptation) and clinical research. This technique, which allows margins and internal gaps to be set within the clinically acceptable range, is reported to be an effective way of restoring molars with high survival rates in clinical research.

Splicing inhibition mediated by reduced splicing factors and helicases is associated with the cellular response of lung cancer cells to cisplatin

Lung cancer's mortality is predominantly linked to post-chemotherapy recurrence, driven by the reactivation of dormant cancer cells. Despite the critical role of these reactivated cells in cancer recurrence and metastasis, the molecular mechanisms governing their therapeutic selection remain poorly understood. In this study, we conducted an integrative analysis by combining PacBio single molecule real-time (SMRT) sequencing with short reads Illumina RNA-seq. Our study revealed that cisplatin-induced dormant and reactivated cancer cells exhibited a noteworthy reduction in gene transcripts and alternative splicing events. Particularly, the differential alternative splicing events were found to be overlapping with the differentially expression genes and enriched in genes related to cell cycle and cell division. Utilizing ENCORI database and correlation analysis, we identified key splicing factors, including SRSF7, SRSF3, PRPF8, and HNRNPC, as well as RNA helicase such as EIF4A3, DDX39A, DDX11, and BRIP1, which were associated with the observed reduction in alternative splicing and subsequent decrease in gene expression. Our study demonstrated that lung cancer cells reduce gene transcripts through diminished alternative splicing events mediated by specific splicing factors and RNA helicase in response to the chemotherapeutic stress. These findings provide insights into the molecular mechanisms underlying the therapeutic selection and reactivation of dormant cancer cells. This discovery opens a potential avenue for the development of therapeutic strategies aimed at preventing cancer recurrence following chemotherapy.