bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of the mental health promotion seminar ‘Coping with stress’ in the undergraduate medical curriculum of the Medical University of Vienna
Authors: Till Benedikt , Hofhansl Angelika , Niederkrotenthaler Thomas
Published: January 2024

Background

High prevalence rates of distress and burnout in medical students are well-documented in mental health literature. Different types of interventions have been developed in the past in order to reduce stress in medical undergraduate students and promote better coping skills. There is, however, a paucity of studies that have tested the effectiveness of these interventions. This study aimed to examine the effect of different versions of the seminar ‘Coping with stress’, which was implemented in the first year of the undergraduate curriculum of the Medical University of Vienna in the summer semester of 2018, on students’ mental health.

Methods

Invitations to participate in the study were sent via email to six cohorts of students from the Medical University of Vienna. Two cohorts participated in the onsite version of the seminar ‘Coping with stress’, whereas two cohorts participated in the online version of the seminar, and two cohorts received no intervention (control group). Data on burnout risk, life satisfaction, stress, and knowledge about available help resources were collected via online questionnaires from n = 137 students before and after the curriculum module that contained the seminar.

Results

Medical students who participated in the onsite seminar reported a reduction of some aspects of burnout, a decrease in stress, and an increase in knowledge about available help resources. No such effect was seen in the control group. Participants of the online seminar experienced a similar increase in knowledge about available help resources, but no changes in other outcomes.

Conclusions

The findings support the notion that the onsite seminar of ‘Coping with stress’ had a positive impact on medical students’ mental health and is a useful addition to the medical curriculum by promoting mental health literacy.

Trial registration

This research has been registered in the German Clinical Trial Registry with the registration number DRKS00018981 and the registration date 14/11/2019.
Dirichlet process mixture models to impute missing predictor data in counterfactual prediction models: an application to predict optimal type 2 diabetes therapy
Authors: Cardoso Pedro , Dennis John M. , Bowden Jack , Shields Beverley M. , McKinley Trevelyan J. ,   the MASTERMIND Consortium
Published: January 2024

Background

The handling of missing data is a challenge for inference and regression modelling. A particular challenge is dealing with missing predictor information, particularly when trying to build and make predictions from models for use in clinical practice.

Methods

We utilise a flexible Bayesian approach for handling missing predictor information in regression models. This provides practitioners with full posterior predictive distributions for both the missing predictor information (conditional on the observed predictors) and the outcome-of-interest. We apply this approach to a previously proposed counterfactual treatment selection model for type 2 diabetes second-line therapies. Our approach combines a regression model and a Dirichlet process mixture model (DPMM), where the former defines the treatment selection model, and the latter provides a flexible way to model the joint distribution of the predictors.

Results

We show that DPMMs can model complex relationships between predictor variables and can provide powerful means of fitting models to incomplete data (under missing-completely-at-random and missing-at-random assumptions). This framework ensures that the posterior distribution for the parameters and the conditional average treatment effect estimates automatically reflect the additional uncertainties associated with missing data due to the hierarchical model structure. We also demonstrate that in the presence of multiple missing predictors, the DPMM model can be used to explore which variable(s), if collected, could provide the most additional information about the likely outcome.

Conclusions

When developing clinical prediction models, DPMMs offer a flexible way to model complex covariate structures and handle missing predictor information. DPMM-based counterfactual prediction models can also provide additional information to support clinical decision-making, including allowing predictions with appropriate uncertainty to be made for individuals with incomplete predictor data.
The impact of night shift stress and sleep disturbance on nurses quality of life: case in Palestine Red Crescent and Al-Ahli Hospital
Authors: AL-hrinat Jebril , Al-Ansi Abdullah M. , Hendi Aseel , Adwan Ghadeer , Hazaimeh Manar
Published: January 2024

Background

Nurses play a vital role in providing round-the-clock care to patients, but the challenges associated with working night shifts can have significant implications for their well-being and quality of life.

Methods

This cross-sectional study aimed to investigate the impact of night shift stress and sleep disturbance on the quality of life among nurses working in Palestine Red Crescent Society and Al-Ahli Hospital. Convenience sampling was used to recruit 189 full-time registered nurses with at least one year of job experience. The participants completed a questionnaire assessing night shift stress, sleep disturbance, and quality of life. Descriptive statistics, correlation analysis, and path analysis were conducted to analyze the data.

Results

The results reveal that quality of life has positive and low relationship with both night shift stress and sleep disturbances. Results also reveal that night shift stress had a direct negative impact on the quality of life of nurses. Sleep disturbance was found to mediate the relationship between night shift stress and quality of life, indicating that higher levels of night shift stress were associated with increased sleep disturbance, which, in turn, led to poorer quality of life outcomes.

Conclusion

These findings highlight the importance of addressing night shift stress and sleep disturbance among nurses to enhance their well-being and improve the quality of care provided to patients. In conclusion, this study contributes to the existing literature by demonstrating the detrimental effects of night shift stress and sleep disturbance on the quality of life of nurses. It emphasizes the importance of implementing interventions and creating supportive work environments that address the unique challenges faced by nurses working night shifts.
Comparing microbiotas of foals and their mares’ milk in the first two weeks after birth
Authors: Mienaltowski Michael J. , Callahan Mitchell , De La Torre Ubaldo , Maga Elizabeth A.
Published: January 2024

Background

The mare-foal relationship is essential for the well-being and growth of a foal. Mare’s milk provides a foal with nutrients, protective immunity, and microbes. Within the first two weeks of life, there is a risk for a foal to suffer from diarrhea, particularly “foal heat diarrhea” which happens at about the time of a mare’s estrus cycle but is more likely due to transitions in the microbiota in the foal’s gastrointestinal (GI) tract. We hypothesized that this GI microbiota transition could be caused by changes in lysozyme and microbial populations in the mare’s milk. To test this hypothesis, fifteen mare-foal pairs were followed in the first 15 days post-foaling. Every other day milk was collected from mares and rectal swabs were collected from foals. Lysozyme activity in the mare’s milk was measured using a fluorescence assay. Microbial DNA was isolated from the milk and swabs and the V4 domain of 16 S rRNA genes were PCR amplified and sequenced using Illumina MiSeq technology. Microbial populations were analyzed using DADA2 and phyloseq within R.

Results

Mare’s milk lysozyme activity peaked for samples at Day 1 and levels dropped to 72.5% of Day 1 activity by Day 15; however, microbial populations in the mare’s milk did not vary significantly over the two weeks. Furthermore, levels of microbial diversity found in foal rectal swabs were initially similar to microbial diversity seen in mare’s milk; however, over the first fifteen days, diversity increased for the foal rectal swab microbiota and swab microbial populations differed from milk microbes. A transition occurred shifting from microbes from the phylum Proteobacteria early in rectal swabs to those primarily from the phyla Firmicutes and Bacteroidota after the first few days post-foaling. These phyla contained several families and genera of microbes that promote utilization of milk components in healthy gut transition. Microbial abundance levels correlated more with days post-parturition than with lysozyme activity and mare’s milk microbial populations.

Conclusions

The findings suggest that much of the microbial populations responsible for the transition of the foal’s gut comes from sources outside of mare’s milk species and levels of lysozyme activity.
A novel prognostic signature and therapy guidance for hepatocellular carcinoma based on STEAP family
Authors: Fu Dongxue , Zhang Xian , Zhou Yi , Hu Shanshan
Published: January 2024

Background

The six-transmembrane epithelial antigen of prostate (STEAP) family members are known to be involved in various tumor-related biological processes and showed its huge potential role in tumor immunotherapy.

Methods

Biological differences were investigated through Gene set enrichment analysis (GSEA) and tumor microenvironment analysis by CIBERSORT. Tumor mutation burden (TMB), immunotherapy response and chemotherapeutic drugs sensitivity were estimated in R.

Results

We established a prognostic signature with the formula: risk score = STEAP1 × 0.3994 + STEAP4 × (− 0.7596), which had a favorable concordance with the prediction. The high-risk group were enriched in cell cycle and RNA and protein synthesis related pathways, while the low-risk group were enriched in complement and metabolic related pathways. And the risk score was significantly correlated with immune cell infiltration. Most notably, the patients in the low-risk group were characterized with increased TMB and decreased tumor immune dysfunction and exclusion (TIDE) score, indicating that these patients showed better immune checkpoint blockade response. Meanwhile, we found the patients with high-risk were more sensitive to some drugs related to cell cycle and apoptosis.

Conclusions

The novel signature based on STEAPs may be effective indicators for predicting prognosis, and provides corresponding clinical treatment recommendations for HCC patients based on this classification.
Immune checkpoint inhibitors in gastrointestinal malignancies: an Umbrella review
Authors: Noori Maryam , Jafari-Raddani Farideh , Davoodi-Moghaddam Zeinab , Delshad Mahda , Safiri Saeid , Bashash Davood
Published: January 2024

In the Modern era, immune checkpoint inhibitors (ICIs) have been the cornerstone of success in the treatment of several malignancies. Despite remarkable therapeutic advances, complex matrix together with significant molecular and immunological differences have led to conflicting outcomes of ICI therapy in gastrointestinal (GI) cancers. As far we are aware, to date, there has been no study to confirm the robustness of existing data, and this study is the first umbrella review to provide a more comprehensive picture about ICIs’ efficacy and safety in GI malignancies. Systematic search on PubMed, Scopus, Web of Science, EMBASE, and Cochrane library identified 14 meta-analyses. The pooled analysis revealed that ICIs application, especially programmed death-1 (PD-1) inhibitors such as Camrelizumab and Sintilimab, could partially improve response rates in patients with GI cancers compared to conventional therapies. However, different GI cancer types did not experience the same efficacy; it seems that hepatocellular carcinoma (HCC) and esophageal cancer (EC) patients are likely better candidates for ICI therapy than GC and CRC patients. Furthermore, application of ICIs in a combined-modal strategy are perceived opportunity in GI cancers. We also assessed the correlation of PD-L1 expression as well as microsatellite status with the extent of the response to ICIs; overall, high expression of PD-L1 in GI cancers is associated with better response to ICIs, however, additional studies are required to precisely elaborate ICI responses with respect to microsatellite status in different GI tumors. Despite encouraging ICI efficacy in some GI cancers, a greater number of serious and fatal adverse events have been observed; further highlighting the fact that ICI therapy in GI cancers is not without cost, and further studies are required to utmost optimization of this approach in GI cancers.
A serum panel of three microRNAs may serve as possible biomarkers for kidney renal clear cell carcinoma
Authors: Wen Zhenyu , Li Yingqi , Zhao Zhengping , Li Rongkang , Li Xinji , Lu Chong , Sun Chen , Chen Wenkang , Ge Zhenjian , Ni Liangchao , Lai Yongqing
Published: January 2024

Background

Although non-invasive radiological techniques are widely applied in kidney renal clear cell carcinoma (KIRC) diagnosis, more than 50% of KIRCs are detected incidentally during the diagnostic procedures to identify renal cell carcinoma (RCC). Thus, sensitive and accurate KIRC diagnostic methods are required. Therefore, in this study, we aimed to identify KIRC-associated microRNAs (miRNAs).

Methods

This three-phase study included 224 participants (112 each of patients with KIRC and healthy controls (NCs)). RT-qPCR was used to evaluate miRNA expression in KIRC and NC samples. Receiver operating characteristic (ROC) curves and the area under the ROC curve (AUC) were used to predict the usefulness of serum miRNAs in KIRC diagnosis. In addition, we performed survival and bioinformatics analyses.

Results

We found that miR-1-3p, miR-129-5p, miR-146b-5p, miR-187-3p, and miR-200a-3p were significantly differentially expressed in patients with KIRC. A panel consisting of three miRNAs (miR-1-3p, miR-129-5p, and miR-146b-5p) had an AUC of 0.895, ranging from 0.848 to 0.942. In addition, using the GEPIA database, we found that the miRNAs were associated with CREB5. According to the survival analysis, miR-146b-5p overexpression was indicative of a poorer prognosis in patients with KIRC.

Conclusions

The identified three-miRNA panel could serve as a non-invasive indicator for KIRC and CREB5 as a potential target gene for KIRC treatment.
Lipid changes during endocrine therapy in early-stage breast cancer patients: A real-world study
Authors: Li Yuechong , Deng Zixi , Wang Yingjiao , Shen Songjie
Published: January 2024

Background

Endocrine drugs may affect lipid metabolism in breast cancer (BC) patients. This study explores lipid changes in early-stage BC patients taking different endocrine drugs.

Methods

The changing trend of blood lipid during endocrine therapy in 2756 BC patients from January 2013 to December 2021 was retrospectively analyzed. The changes in four lipid parameters were assessed by the Generalized Linear Mixed Model, including total cholesterol (TC), triglycerides (TG), low-density lipoprotein (LDL-C), and high-density lipoprotein (HDL-C). These parameters were quantified at baseline and at 6, 12, 18, 24, 36, 48, 60, and 72 months after endocrine therapy initiation. Furthermore, a subgroup analysis according to menopausal status or medication types was conducted.

Results

A total of 1201 patients taking aromatase inhibitors (AIs), including anastrozole (ANA), letrozole (LET), or exemestane (EXE), and 1555 patients taking toremifene (TOR) were enrolled. TC and TG levels showed a significantly elevated trend during 5 years of treatment (P < 0.05). HDL-C levels increased from baseline in the TOR group (P < 0.05). Compared with the postmenopausal AI group, the increasing trends of TC, TG, and LDL-C in the premenopausal AI group were more evident with the extension of time (β = 0.105, 0.027, 0.086, respectively). Within 3 years, TC, TG, and LDL-C levels in the ANA and LET groups were significantly higher than baseline (P < 0.05). Moreover, the levels of TG in the EXE group were significantly lower than that in the ANA or LET group (P < 0.05), but this significant difference disappeared after 3 years.

Conclusions

AIs significantly influenced lipid profiles more than TOR. AIs had a greater effect on blood lipids in premenopausal patients. Steroidal AIs (EXE) may affect lipid levels less than nonsteroidal AIs (ANA and LET).
Recent trends in preparation and biomedical applications of iron oxide nanoparticles
Authors: Meng Yu Qing , Shi Ya Nan , Zhu Yong Ping , Liu Yan Qing , Gu Li Wei , Liu Dan Dan , Ma Ang , Xia Fei , Guo Qiu Yan , Xu Cheng Chao , Zhang Jun Zhe , Qiu Chong , Wang Ji Gang
Published: January 2024

The iron oxide nanoparticles (IONPs), possessing both magnetic behavior and semiconductor property, have been extensively used in multifunctional biomedical fields due to their biocompatible, biodegradable and low toxicity, such as anticancer, antibacterial, cell labelling activities. Nevertheless, there are few IONPs in clinical use at present. Some IONPs approved for clinical use have been withdrawn due to insufficient understanding of its biomedical applications. Therefore, a systematic summary of IONPs’ preparation and biomedical applications is crucial for the next step of entering clinical practice from experimental stage. This review summarized the existing research in the past decade on the biological interaction of IONPs with animal/cells models, and their clinical applications in human. This review aims to provide cutting-edge knowledge involved with IONPs’ biological effects in vivo and in vitro, and improve their smarter design and application in biomedical research and clinic trials.

Graphical Abstract
Comparison of medical students' considerations in choosing a specialty: 2020 vs. 2009/10
Authors: Schroeder Hanna , Shacham Alon , Amar Shimon , Weissman Charles , Schroeder Josh E.
Published: January 2024

Background

Workforce shortage in healthcare and particularly in physicians poses a threat to healthcare delivery and its quality. In comparison to other OECD countries, Israel currently has a small number of medical graduates relative to its number of physicians, naturally emphasizing the importance of ensuring that this population chooses to remain in medicine. Understanding what is most important to medical students can help improve working conditions in residency. Such information is particularly needed to facilitate policy planning that will encourage the next generation of physicians to specialize in medical fields that are experiencing shortages. We hypothesized that between 2009/2010 and 2020, there were significant changes in medical students' preferences regarding their considerations for choosing a medical specialty.

Methods

We compared cross-sectional data from questionnaire-based surveys of 5th year medical students performed in 2009–2010 and 2020 at two Israeli universities.

Results

Of the 335 medical students who responded (237 and 98 in 2009/2010 and 2020, respectively) those in 2020 were 2.26 less likely vs. those in 2009/2010, to choose a residency for its high-paying potential (P < 0.05), and had significantly more interest in residencies with greater teaching opportunity (98.8% vs 82.9%, P < 0.05), increased responsibility and chances to make clinical decisions on their own (67.9% vs 51.6%, P < 0.05). Criteria important to both the 2009/2010 and 2020 students were choosing a bedside specialty (70.2%vs 67.9%, NS), and an interesting and challenging specialty (95.2%v s 91.3%, NS).

Conclusions

These results partially supported our hypothesis that medical students' preferences have changed over the years, though there are fundamental factors that apparently reflect medical students’ nature that do not change over time.
Central 5-HTergic hyperactivity induces myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS)-like pathophysiology
Authors: Lee Jin-Seok , Kang Ji-Yun , Park Samuel-Young , Hwang Seung-Ju , Bae Sung-Jin , Son Chang-Gue
Published: January 2024

Objectives

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a significant medical challenge, with no indisputable pathophysiological mechanism identified to date.

Methods

Based on clinical clues, we hypothesized that 5-hydroxytryptamine (5-HT) hyperactivation is implicated in the pathogenic causes of ME/CFS and the associated symptoms. We experimentally evaluated this hypothesis in a series of mouse models.

Results

High-dose selective serotonin reuptake inhibitor (SSRI) treatment induced intra- and extracellular serotonin spillover in the dorsal raphe nuclei of mice. This condition resulted in severe fatigue (rota-rod, fatigue rotating wheel and home-cage activity tests) and ME/CFS-associated symptoms (nest building, plantar and open field test), along with dysfunction in the hypothalamic-pituitary-adrenal (HPA) axis response to exercise challenge. These ME/CFS-like features induced by excess serotonin were additionally verified using both a 5-HT synthesis inhibitor and viral vector for Htr1a (5-HT1A receptor) gene knockdown.

Conclusions

Our findings support the involvement of 5-HTergic hyperactivity in the pathophysiology of ME/CFS. This ME/CFS-mimicking animal model would be useful for understanding ME/CFS biology and its therapeutic approaches.
Single-cell transcriptome sequencing reveals aberrantly activated inter-tumor cell signaling pathways in the development of clear cell renal cell carcinoma
Authors: Zhang Junfeng , Liu Fuzhong , Guo Wenjia , Bi Xing , Yuan Shuai , Shayiti Fuerhaiti , Pan Ting , Li Kailing , Chen Peng
Published: January 2024

Background

Aberrant intracellular or intercellular signaling pathways are important mechanisms that contribute to the development and progression of cancer. However, the intercellular communication associated with the development of ccRCC is currently unknown. The purpose of this study was to examine the aberrant tumor cell-to-cell communication signals during the development of ccRCC.

Methods

We conducted an analysis on the scRNA-seq data of 6 ccRCC and 6 normal kidney tissues. This analysis included sub clustering, CNV analysis, single-cell trajectory analysis, cell–cell communication analysis, and transcription factor analysis. Moreover, we performed validation tests on clinical samples using multiplex immunofluorescence.

Results

This study identified eleven aberrantly activated intercellular signaling pathways in tumor clusters from ccRCC samples. Among these, two of the majors signaling molecules, MIF and SPP1, were mainly secreted by a subpopulation of cancer stem cells. This subpopulation demonstrated high expression levels of the cancer stem cell markers POU5F1 and CD44 (POU5F1hiCD44hiE.T), with the transcription factor POU5F1 regulating the expression of SPP1. Further research demonstrated that SPP1 binds to integrin receptors on the surface of target cells and promotes ccRCC development and progression by activating potential signaling mechanisms such as ILK and JAK/STAT.

Conclusion

Aberrantly activated tumor intercellular signaling pathways promote the development and progression of ccRCC. The cancer stem cell subpopulation (POU5F1hiCD44hiE.T) promotes malignant transformation and the development of a malignant phenotype by releasing aberrant signaling molecules and interacting with other tumor cells.
Bone marrow graft versus peripheral blood graft in haploidentical hematopoietic stem cells transplantation: a retrospective analysis in1344 patients of SFGM-TC registry
Authors: Lacan Claire , Lambert Jérôme , Forcade Edouard , Robin Marie , Chevallier Patrice , Loron Sandrine , Bulabois Claude-Éric , Orvain Corentin , Ceballos Patrice , Daguindau Etienne , Charbonnier Amandine , Chalandon Yves , Bernard Marc , Simand Célestine , Rubio Marie-Thérèse , Turlure Pascal , Maertens Johan , Huynh Anne , Loschi Michael , Bay Jacques-Olivier , Guillerm Gaëlle , Alani Mustafa , Castilla-Llorente Cristina , Poiré Xavier , Chantepie Sylvain , Maillard Natacha , Beguin Yves , Marçais Ambroise , Cornillon Jérôme , Malfuson Jean-Valère , Maury Sébastien , Meuleman Nathalie , Villate Alban , Bekadja Mohammed-Amine , Walter-Petrich Anouk , Jacque Nathalie , Srour Micha , Devillier Raynier , Nguyen Stéphanie
Published: January 2024

The use of peripheral blood (PB) or bone marrow (BM) stem cells graft in haploidentical hematopoietic stem cell transplantation with post-transplant cyclophosphamide (PTCy) for graft-versus-host disease (GVHD) prophylaxis remains controversial. Moreover, the value of adding anti-thymoglobulin (ATG) to PTCy is unknown. A total of 1344 adult patients received an unmanipulated haploidentical transplant at 37 centers from 2012 to 2019 for hematologic malignancy. We compared the outcomes of patients according to the type of graft, using a propensity score analysis. In total population, grade II–IV and III–IV acute GVHD (aGVHD) were lower with BM than with PB. Grade III–IV aGVHD was lower with BM than with PB + ATG. All outcomes were similar in PB and PB + ATG groups. Then, in total population, adding ATG does not benefit the procedure. In acute leukemia, myelodysplastic syndrome and myeloproliferative syndrome (AL-MDS-MPS) subgroup receiving non-myeloablative conditioning, risk of relapse was twice greater with BM than with PB (51 vs. 22%, respectively). Conversely, risk of aGVHD was greater with PB (38% for aGVHD II–IV; 16% for aGVHD III–IV) than with BM (28% for aGVHD II–IV; 8% for aGVHD III–IV). In this subgroup with intensified conditioning regimen, risk of relapse became similar with PB and BM but risk of aGVHD III–IV remained higher with PB than with BM graft (HR = 2.0; range [1.17–3.43], p = 0.012).
The association between patent foramen ovale and unexplained syncope in pediatric patients
Authors: Zou Runmei , Wang Shuo , Liu Ping , Chen Donghai , Yan Jun , Cai Hong , Wang Yuwen , Wang Cheng
Published: January 2024

Background

Patent foramen ovale (PFO) is associated with transient ischemia attack (TIA) or stroke, paradoxical embolism, and migraines. PFO closure decreases the recurrent incidence of cerebral ischemic events and reduces the incidence of syncope in adults. However, whether PFO is associated with syncope in pediatric patients has not been investigated.

Methods

1001 pediatric patients (aged 4 to 17 years, mean age 10.31 ± 2.61 years, 519 males) who complained of unexplained syncope, palpitation, headache, dizziness and chest pain and were hospitalized in the Syncope Ward, The Second Xiangya Hospital, Central South University between January 2013 and April 2022 were recruited. Children with definite etiology of syncope, neurological, cardiogenic, psychological and other system diseases were excluded. PFO was measured by transthoracic echocardiography and right-heart contrast echocardiography was performed to identify the presence of right-to-left shunting. The demographic data and medical records were retrospectively reviewed and analyzed.

Results

276 cases were included in the simple syncope group, 379 cases in the headache/dizziness group, 265 cases in the chest pain group, and 81 cases in the palpitation group. The incidence of PFO between the four groups was insignificant (4.71%, 4.74%, 4.15%, 6.17%, respectively, P = 0.903). Multivariate Logistic regression demonstrated that PFO is not associated with the increased risk of syncope (P = 0.081).

Conclusion

PFO may not increase the risk of syncope in pediatric patients. Further study may include a large and multicenter sample to investigate the association between PFO and unexplained syncope.
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
Authors: Viner Coby , Ishak Charles A. , Johnson James , Walker Nicolas J. , Shi Hui , Sjöberg-Herrera Marcela K. , Shen Shu Yi , Lardo Santana M. , Adams David J. , Ferguson-Smith Anne C. , De Carvalho Daniel D. , Hainer Sarah J. , Bailey Timothy L. , Hoffman Michael M.
Published: January 2024

Background

Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Current models of transcription factor binding tend not to take DNA modifications into account, while the recent few that do often have limitations. This makes a comprehensive and accurate profiling of transcription factor affinities difficult.

Results

Here, we develop methods to identify transcription factor binding sites in modified DNA. Our models expand the standard /// DNA alphabet to include cytosine modifications. We develop Cytomod to create modified genomic sequences and we also enhance the MEME Suite, adding the capacity to handle custom alphabets. We adapt the well-established position weight matrix (PWM) model of transcription factor binding affinity to this expanded DNA alphabet. Using these methods, we identify modification-sensitive transcription factor binding motifs. We confirm established binding preferences, such as the preference of ZFP57 and C/EBPβ for methylated motifs and the preference of c-Myc for unmethylated E-box motifs.

Conclusions

Using known binding preferences to tune model parameters, we discover novel modified motifs for a wide array of transcription factors. Finally, we validate our binding preference predictions for OCT4 using cleavage under targets and release using nuclease (CUT&RUN) experiments across conventional, methylation-, and hydroxymethylation-enriched sequences. Our approach readily extends to other DNA modifications. As more genome-wide single-base resolution modification data becomes available, we expect that our method will yield insights into altered transcription factor binding affinities across many different modifications.
Upregulation of PD-1/PD-L1 and downregulation of immune signaling pathways lead to more severe visceral leishmaniasis in undernutrition mice
Authors: He Jinlei , Zhang Jianhui , Liao Xuechun , Xiao Yuying , Li Jiao , Zheng Zhiwan , Chen Dali , Chen Jianping
Published: January 2024

Background

Leishmaniasis is mainly prevalent in tropical and subtropical developing countries, where chronic undernutrition often co-exists. Undernutrition is reported to promote the progression of leishmaniasis, but its immune mechanisms have not been fully elucidated.

Methods

To simulate chronic undernutrition of patients in epidemic areas and explore the immune mechanism of undernutrition promoting leishmaniasis, BALB/c mouse models with different nutritional imbalances were established, including undernutrition 75%, undernutrition 65% and obesity mouse models. After infection with Leishmania donovani in these model mice, we focused on evaluating the progress of leishmaniasis in the spleen and liver, the expression of important immunosuppressive and immunoactivation molecules, and changes of spleen transcriptome. The immune signaling pathways enriched by differentially expressed genes and hub genes were analyzed.

Results

The results showed that among the mouse infection models, undernutrition 75% + infection group had the highest parasite load in the spleen and liver at the 8th week post-infection, possibly due to the continuous increase of PD-1, PD-L1 and TCR. Spleen RNA-seq results suggested that some immune signaling pathways were downregulated in undernutrition 75% + infection group, including neutrophil extracellular trap formation, IL-17 signaling pathway, natural killer cell-mediated cytotoxicity, etc. Among them, neutrophil extracellular trap formation pathway had the largest number of downregulated genes. This also explained why undernutrition 75% + infection group had the highest parasite load. Through PPI network analysis, hub genes such as Lcn2, Ltf, Mpo, Dnaja1, Hspa1a, Hspa1b and Hsph1 were screened out and might play important roles in the process of undernutrition promoting leishmaniasis.

Conclusions

Undernutrition upregulated PD-1 and PD-L1 expression and downregulated immune signaling pathways in mice with visceral leishmaniasis. The signaling pathways and hub genes may serve as drug targets or intervention targets for the treatment of leishmaniasis patients with undernutrition.

Graphical Abstract
A novel detection method based on MIRA-CRISPR/Cas13a-LFD targeting the repeated DNA sequence of Trichomonas vaginalis
Authors: Yang Zhenke , Wang Jinghui , Qi Yiming , Shi Yiping , Li Fakun , Wang Weijuan , Tian Xiaowei , Mei Xuefang , Zhang Zhenchao , Wang Shuai
Published: January 2024

Background

Trichomonas vaginalis is a protozoan parasite, widely recognized as the most prevalent non-viral sexually transmitted infection (STI) globally. This infection is linked to various complications, including pelvic inflammatory disease, adverse pregnancy outcomes, and an increased risk of acquiring HIV. Current molecular detection methods for T. vaginalis are often costly and technically challenging.

Methods

We developed a novel detection method for T. vaginalis using a multi-enzyme isothermal rapid amplification–clustered regularly interspaced short palindromic repeats (MIRA-CRISPR)/Cas13a-lateral flow device (LFD). This assay targets the repeated DNA sequence (GenBank: L23861.1) of T. vaginalis and is performed at a constant temperature of 37 °C for approximately 1 hour.

Results

The detection limit of genomic DNA (gDNA) using our protocol was 1 × 10–4 ng/μl. Specificity was confirmed by the absence of cross-reaction with gDNA from various other microorganisms such as Staphylococcus aureus, Lactobacillus taiwanensis, Escherichia coli, Monilia albicans, Giardia lamblia, or Toxoplasma gondii. Among 30 clinical samples tested, the positive rates of T. vaginalis detection were 33.33% (10/30) by wet mount microscopy, 40% (12/30) by nested polymerase chain reaction (PCR), 40% (12/30) by MIRA-CRISPR/Cas13a-LFD, and 40% (12/30) by the culture method. Compared with the culture method, the gold standard for diagnosing trichomoniasis, wet mount microscopy showed a sensitivity of 83.3% and moderate diagnostic agreement (kappa value = 0.87). Both nested PCR and MIRA-CRISPR/Cas13a-LFD exhibited 100% sensitivity and excellent diagnostic agreement (kappa value = 1).

Conclusions

The MIRA-CRISPR/Cas13a-LFD method is a convenient, rapid, stable, and accurate diagnostic tool for detecting T. vaginalis. This method has the potential to enhance the diagnosis and management of vaginitis, offering a significant improvement over existing diagnostic techniques.

Graphical Abstract
Development and validation of a predictive model based on clinical and MpMRI findings to reduce additional systematic prostate biopsy
Authors: Cheng Xueqing , Chen Yuntian , Xu Jinshun , Cai Diming , Liu Zhenhua , Zeng Hao , Yao Jin , Song Bin
Published: January 2024

Objectives

To develop and validate a predictive model based on clinical features and multiparametric magnetic resonance imaging (mpMRI) to reduce unnecessary systematic biopsies (SBs) in biopsy-naïve patients with suspected prostate cancer (PCa).

Methods

A total of 274 patients who underwent combined cognitive MRI-targeted biopsy (MRTB) with SB were retrospectively enrolled and temporally split into development (n = 201) and validation (n = 73) cohorts. Multivariable logistic regression analyses were used to determine independent predictors of clinically significant PCa (csPCa) on cognitive MRTB, and the clinical, MRI, and combined models were established respectively. Area under the receiver operating characteristic curve (AUC), calibration plots, and decision curve analyses were assessed.

Results

Prostate imaging data and reporting system (PI-RADS) score, index lesion (IL) on the peripheral zone, age, and prostate-specific antigen density (PSAD) were independent predictors and included in the combined model. The combined model achieved the best discrimination (AUC 0.88) as compared to both the MRI model incorporated by PI-RADS score, IL level, and zone (AUC 0.86) and the clinical model incorporated by age and PSAD (AUC 0.70). The combined model also showed good calibration and enabled great net benefit. Applying the combined model as a reference for performing MRTB alone with a cutoff of 60% would reduce 43.8% of additional SB, while missing 2.9% csPCa.

Conclusions

The combined model based on clinical and mpMRI findings improved csPCa prediction and might be useful in making a decision about which patient could safely avoid unnecessary SB in addition to MRTB in biopsy-naïve patients.

Critical relevance statement

The combined model based on clinical and mpMRI findings improved csPCa prediction and might be useful in making a decision about which patient could safely avoid unnecessary SB in addition to MRTB in biopsy-naïve patients.

Key points

• Age, PSAD, PI-RADS score, and peripheral index lesion were independent predictors of csPCa.

• Risk models were used to predict the probability of detecting csPCa on cognitive MRTB.

• The combined model might reduce 43.8% of unnecessary SBs, while missing 2.9% csPCa.

Graphical Abstract
Impact of point-of-care clinical decision support on referrer behavior, imaging volume, patient radiation dose exposure, and sustainability
Authors: Schranz Amy L. , Ryan Dave T. , David Raegan , McNeill Graeme , Killeen Ronan P.
Published: January 2024

Objectives

When referring patients to radiology, it is important that the most appropriate test is chosen to avoid inappropriate imaging that may lead to delayed diagnosis, unnecessary radiation dose, worse patient outcome, and poor patient experience. The current radiology appropriateness guidance standard at our institution is via access to a standalone web-based clinical decision support tool (CDST). A point-of-care (POC) CDST that incorporates guidance directly into the physician workflow was implemented within a subset of head and neck cancer specialist referrers. The purpose of this audit was to evaluate the imaging pathway, pre- and post-implementation to assess changes in referral behavior.

Methods

CT and MRI neck data were collected retrospectively to examine the relationship between imaging referrals pre- and post-POC CDST implementation. Effective radiation dose and estimated carbon emissions were also compared.

Results

There was an overall reduction in absolute advanced imaging volume by 8.2%, and a reduction in duplicate CT and MRI imaging by 61%, p < 0.0001. There was also a shift in ordering behavior in favor of MRI (OR [95% CI] = 1.50 [1.02–2.22], p = 0.049). These changes resulted in an effective radiation dose reduction of 0.27 mSv per patient, or 13 equivalent chest x-rays saved per patient, p < 0.0001. Additionally, the reduction in unnecessary duplicate imaging led to a 13.5% reduction in carbon emissions, p = 0.0002.

Conclusions

Implementation of the POC CDST resulted in a significant impact on advanced imaging volume, saved effective dose, and reduction in carbon emissions.

Critical relevance statement

The implementation of a point-of-care clinical decision support tool may reduce multimodality ordering and advanced imaging volume, manifesting in reduced effective dose per patient and reduced estimated carbon emissions. Widespread utilization of the point-of-care clinical decision support tool has the potential to reduce imaging wait times.

Key points

• Implementation of the point-of-care clinical decision support tool reduced the number of patients who simultaneously had a CT and MRI ordered for the same clinical indication compared to a standalone web-based clinical decision support tool.

• The point-of-care clinical decision support tool reduced the absolute number of CT/MRI scans requested compared to the standalone web-based clinical decision support tool.

• Utilization of the point-of-care clinical decision support tool led to a significant reduction in the effective dose per patient compared to the standalone web-based clinical decision support tool.

Graphical Abstract
Economic evaluation of percutaneous cryoablation vs conventional surgery in extra-abdominal desmoid tumours in the Spanish healthcare system
Authors: Narvaez José Antonio , Bernabeu Daniel , Muntaner Lorenzo , Gomez Fernando , Martel José , Castellano María del Mar , García-Marcos Raúl , Britel Reda , Oyagüez Itziar , Tejado Nerea , Ortiz-Cruz Eduardo
Published: January 2024

Background

Desmoid tumours (DTs) or deep fibromatosis are benign soft-tissue tumours, sometimes locally aggressive, requiring intervention on some cases. Surgery has been the gold standard, but new less invasive techniques such as percutaneous cryoablation have proved their effectiveness, reducing health resources and complications. The study aimed to compare the total cost of percutaneous cryoablation and conventional surgery for patients with extra-abdominal and/or abdominal wall DTs, candidates for local ablative treatment in Spain.

Methods

A cost-analysis model was developed. An expert panel provided data about resource consumption for the percutaneous cryoablation technique and validated the epidemiology used for target population estimation. Unitary resources cost (€ 2022) derived from local cost databases. A retrospective analysis of 54 surgical cases in 3 Spanish hospitals was performed to estimate the cost of conventional surgery based on the cost of the Diagnosis-Related group (DRG) codes identified on this patient sample, weighted by each DRG proportion. The total cost for each alternative included intervention cost and complications cost, considering debridement required in 4.5% of cases with percutaneous cryoablation and minor surgery for surgical site infection in 18.0% for conventional surgery.

Results

The total cost for percutaneous cryoablation (€ 5774.78/patient-year) was lower than the total cost for conventional surgery (€ 6780.98/patient-year), yielding cost savings up to € 80,002 in 1 year for the entire cohort of 80 patients with DTs eligible for intervention estimated in Spain. One-way sensitivity analyses confirmed the results’ robustness.

Conclusion

Percutaneous cryoablation versus conventional surgery would yield cost savings for the management of DT patients in Spain.

Critical relevance statement

This manuscript provides insight into the economic impact derived from the savings related to the use of percutaneous cryoablation for desmoid-type tumours from the perspective of the Spanish National Healthcare System, providing useful information for the health decision-making process.

Key points

• Desmoid tumours are locally aggressive and may require local therapy.

• Percutaneous cryoablation procedure is less invasive than the conventional surgery.

• Cost comparison shows savings associated to percutaneous cryoablation use.

Graphical Abstract
Uncovering impaired mitochondrial and lysosomal function in adipose-derived stem cells from obese individuals with altered biological activity
Authors: Wang Bo , Zhang Ge , Hu Yuwen , Mohsin Ali , Chen Zhimin , Hao Weijie , Li Zhanxia , Gao Wei-Qiang , Guo Meijin , Xu Huiming
Published: January 2024

Background

Adipose-derived stem cells (ADSCs) have been extensively used in preclinical and clinical trials for treating various diseases. However, the differences between ADSCs from lean individuals (L-ADSCs) and those from obese individuals (O-ADSCs) have not been thoroughly investigated, particularly regarding their mitochondrial and lysosomal functions. Therefore, this study aims to evaluate the differences between L-ADSCs and O-ADSCs in terms of cell biological activity, mitochondria, and lysosomes.

Methods

We first isolated and cultured L-ADSCs and O-ADSCs. We then compared the differences between the two groups in terms of biological activity, including cell proliferation, differentiation potential, and their effect on the polarization of macrophages. Additionally, we observed the mitochondrial and lysosomal morphology of ADSCs using an electronic microscope, MitoTracker Red, and lysotracker Red dyes. We assessed mitochondrial function by examining mitochondrial membrane potential and membrane fluidity, antioxidative ability, and cell energy metabolism. Lysosomal function was evaluated by measuring autophagy and phagocytosis. Finally, we performed transcriptome analysis of the ADSCs using RNA sequencing.

Results

The biological activities of O-ADSCs were decreased, including cell immunophenotypic profiles, cell proliferation, and differentiation potential. Furthermore, compared to L-ADSCs, O-ADSCs promoted M1-type macrophage polarization and inhibited M2-type macrophage polarization. Additionally, the mitochondrial morphology of O-ADSCs was altered, with the size of the cells becoming smaller and mitochondrial fragments increasing. O-ADSCs also exhibited decreased mitochondrial membrane potential and membrane fluidity, antioxidative ability, and energy metabolism. With respect to lysosomes, O-ADSCs contained ungraded materials in their lysosomes, enhanced lysosomal permeability, and reduced autophagy and phagocytosis ability. RNA sequence analysis indicated that the signalling pathways related to cell senescence, cancer, and inflammation were upregulated, whereas the signalling pathways associated with stemness, cell differentiation, metabolism, and response to stress and stimuli were downregulated.

Conclusions

This study indicates that ADSCs from individuals (BMI > 30 kg/m2) exhibit impaired mitochondrial and lysosomal function with decreased biological activity.
Good manufacturing practice production of human corneal limbus-derived stromal stem cells and in vitro quality screening for therapeutic inhibition of corneal scarring
Authors: Santra Mithun , Geary Moira L. , Rubin Elizabeth , Hsu Michael Y. S. , Funderburgh Martha L. , Chandran Christine , Du Yiqin , Dhaliwal Deepinder K. , Jhanji Vishal , Yam Gary Hin-Fai
Published: January 2024

Background

Mesenchymal stem cells in the adult corneal stroma (named corneal stromal stem cells, CSSCs) inhibit corneal inflammation and scarring and restore corneal clarity in pre-clinical corneal injury models. This cell therapy could alleviate the heavy reliance on donor materials for corneal transplantation to treat corneal opacities. Herein, we established Good Manufacturing Practice (GMP) protocols for CSSC isolation, propagation, and cryostorage, and developed in vitro quality control (QC) metric for in vivo anti-scarring potency of CSSCs in treating corneal opacities.

Methods

A total of 24 donor corneal rims with informed consent were used—18 were processed for the GMP optimization of CSSC culture and QC assay development, while CSSCs from the remaining 6 were raised under GMP-optimized conditions and used for QC validation. The cell viability, growth, substrate adhesion, stem cell phenotypes, and differentiation into stromal keratocytes were assayed by monitoring the electric impedance changes using xCELLigence real-time cell analyzer, quantitative PCR, and immunofluorescence. CSSC’s conditioned media were tested for the anti-inflammatory activity using an osteoclastogenesis assay with mouse macrophage RAW264.7 cells. In vivo scar inhibitory outcomes were verified using a mouse model of anterior stromal injury caused by mechanical ablation using an Algerbrush burring.

Results

By comparatively assessing various GMP-compliant reagents with the corresponding non-GMP research-grade chemicals used in the laboratory-based protocols, we finalized GMP protocols covering donor limbal stromal tissue processing, enzymatic digestion, primary CSSC culture, and cryopreservation. In establishing the in vitro QC metric, two parameters—stemness stability of ABCG2 and nestin and anti-inflammatory ability (rate of inflammation)—were factored into a novel formula to calculate a Scarring Index (SI) for each CSSC batch. Correlating with the in vivo scar inhibitory outcomes, the CSSC batches with SI < 10 had a predicted 50% scar reduction potency, whereas cells with SI > 10 were ineffective to inhibit scarring.

Conclusions

We established a full GMP-compliant protocol for donor CSSC cultivation, which is essential toward clinical-grade cell manufacturing. A novel in vitro QC–in vivo potency correlation was developed to predict the anti-scarring efficacy of donor CSSCs in treating corneal opacities. This method is applicable to other cell-based therapies and pharmacological treatments.