bluuebunny/crossref_metadata_2025 huggingface dataset:
Interpretable machine learning-based prediction of 28-day mortality in ICU patients with sepsis: a multicenter retrospective study
Authors: Shen Li , Wu Jiaqiang , Lan Jianger , Chen Chao , Wang Yi , Li Zhiping
Published: January 2025

Background

Sepsis is a major cause of mortality in intensive care units (ICUs) and continues to pose a significant global health challenge, with sepsis-related deaths contributing substantially to the overall burden on healthcare systems worldwide. The primary objective was to construct and evaluate a machine learning (ML) model for forecasting 28-day all-cause mortality among ICU sepsis patients.

Methods

Data for the study was sourced from the eICU Collaborative Research Database (eICU-CRD) (version 2.0). The main outcome was 28-day all-cause mortality. Predictor selection for the final model was conducted using the least absolute shrinkage and selection operator (LASSO) regression analysis and the Boruta feature selection algorithm. Five machine learning algorithms including logistic regression (LR), decision tree (DT), extreme gradient boosting (XGBoost), support vector machine (SVM), and light gradient boosting machine (lightGBM) were employed to construct models using 10-fold cross-validation. Model performance was evaluated using AUC, accuracy, sensitivity, specificity, recall, and F1 score. Additionally, we performed an interpretability analysis on the model that showed the most stable performance.

Results

The final study cohort comprised 4564 patients, among whom 568 (12.4%) died within 28 days of ICU admission. The XGBoost algorithm demonstrated the most reliable performance, achieving an AUC of 0.821, balancing sensitivity (0.703) and specificity (0.798). The top three risk predictors of mortality included APACHE score, serum lactate levels, and AST.

Conclusion

ML models reliably predicted 28-day mortality in critically ill sepsis patients. Of the models evaluated, the XGBoost algorithm exhibited the most stable performance in identifying patients at elevated mortality risk. Model interpretability analysis identified crucial predictors, potentially informing clinical decisions for sepsis patients in the ICU.
Design of a TSR-based project learning strategy for biochemistry undergraduate teaching and research labs: a case study
Authors: Reaux Camille R. , Meche Shelby A. , Grider Jordan M. , Dhanabal Soundharya , Milon Tarikul I. , Chen Feng , Xu Wu
Published: January 2025

Given the exponential growth of biochemical data and deep effect of computational methods on life sciences, there is a need to rethink undergraduate curricula. A project-oriented learning approach based on the Triangular Spatial Relationship (TSR) algorithm has been developed. The TSR-based method was designed for protein 3D structural comparison, motif discovery and probing molecular interactions. The uniqueness of the method benefits students’ learning of big data and computational methods. Specifically, students learn (i) how to search proteins of interest from the PDB archive, (ii) basic supercomputer skills, (iii) how to prepare datasets, (iv) how to perform protein structure and sequence analyses, (v) how to interpret the results, visualize protein structures and make graphs. Five specific strategies have been developed to achieve students’ highest potentials. (i) This lab exercise is designed as a project-oriented learning approach. (ii) The skills-first and concept-second approach is used. (iii) Students choose the proteins based on their interests. (iv) Students are encouraged to learn from each other to promote student–student interactions. (v) Students are required to write a report and/or present their studies. To assess students’ performance, we have developed an assessment rubric that includes (i) demonstration of supercomputer skills in job script preparation, submission and monitoring, (ii) skills in preparation of datasets, (iii) data analytical skills, (iv) project report, (v) presentation, and (vi) integration of the TSR-based method with other computational methods (e.g., molecular 3D structural visualization and protein sequence analysis). This project has been introduced in undergraduate biochemistry research and teaching labs for 4 years. Most students have learned the basic supercomputer skills as well as structure data analysis skills. Students’ feedback is positive and encouraging. It can be further developed as a module for an integrated computational chemistry lecture course.
Genetic insights and therapeutic avenues: unraveling the role of polyunsaturated fatty acids as mediators between hypothyroidism and Von Willebrand disease through Mendelian randomization
Authors: Zhou Wenting , He Rui , Ou Ruwei
Published: January 2025

Background

Previous observational studies have shown that Hypothyroidism is associated with Von Willebrand Disease (VWD), but the causal relationship has not been confirmed because of conflicting findings and confounding by mixing factors. There are also some studies suggesting that polyunsaturated fatty acids (PUFA) may be one of the potential mediators. In this study, we used a Mendelian randomization study to analyze the causal relationship between Hypothyroidism and VWD and to investigate whether polyunsaturated fatty acids mediate the effects of Hypothyroidism on VWD.

Methods

Using a large publicly available genome-wide association study of predominantly European ancestry to obtain data on Hypothyroidism, VWD, and PUFA, we conducted a two-sample Mendelian randomization study to assess the causal relationship between Hypothyroidism and VWD and assess the potential role of Polyunsaturated fatty acids in mediating the causal pathway between Hypothyroidism and VWD. Finally, we also inferred reverse causality between VWD and Hypothyroidism. Inverse variance weighting (IVW) was the primary analytical method.

Results

We found that Hypothyroidism may be negatively causally associated with the development of VWD and that PUFA have a role in mediating role in this process (the ratio of the mediating effect: 24.33%). The causal effects of Hypothyroidism and PUFA on VWD remained significant (p < 0.05) after correction of each other by MVMR.

Conclusion

Our study unveils a novel negative correlation between hypothyroidism and VWD, further enriched by the discovery of partial mediation by PUFA. This groundbreaking finding not only advances our comprehension of VWD etiology but also opens promising avenues for its control and treatment. By elucidating the intricate interplay between hypothyroidism, PUFA, and VWD, our research pioneers a paradigm shift in therapeutic approaches, offering fresh perspectives for the management of this complex disorder.
DLBWE-Cys: a deep-learning-based tool for identifying cysteine S-carboxyethylation sites using binary-weight encoding
Authors: Luo Zhengtao , Wang Qingyong , Xia Yingchun , Zhu Xiaolei , Yang Shuai , Xu Zhaochun , Gu Lichuan
Published: January 2025

Cysteine S-carboxyethylation, a novel post-translational modification (PTM), plays a critical role in the pathogenesis of autoimmune diseases, particularly ankylosing spondylitis. Accurate identification of S-carboxyethylation modification sites is essential for elucidating their functional mechanisms. Unfortunately, there are currently no computational tools that can accurately predict these sites, posing a significant challenge to this area of research. In this study, we developed a new deep learning model, DLBWE-Cys, which integrates CNN, BiLSTM, Bahdanau attention mechanisms, and a fully connected neural network (FNN), using Binary-Weight encoding specifically designed for the accurate identification of cysteine S-carboxyethylation sites. Our experimental results show that our model architecture outperforms other machine learning and deep learning models in 5-fold cross-validation and independent testing. Feature comparison experiments confirmed the superiority of our proposed Binary-Weight encoding method over other encoding techniques. t-SNE visualization further validated the model’s effective classification capabilities. Additionally, we confirmed the similarity between the distribution of positional weights in our Binary-Weight encoding and the allocation of weights in attentional mechanisms. Further experiments proved the effectiveness of our Binary-Weight encoding approach. Thus, this model paves the way for predicting cysteine S-carboxyethylation modification sites in protein sequences. The source code of DLBWE-Cys and experiments data are available at: https://github.com/ztLuo-bioinfo/DLBWE-Cys.
Understanding the impacts of drought on peanuts (Arachis hypogaea L.): exploring physio-genetic mechanisms to develop drought-resilient peanut cultivars
Authors: Pokhrel Sameer , Kharel Prasanna , Pandey Swikriti , Botton Stephanie , Nugraha Gema Takbir , Holbrook Corley , Ozias-Akins Peggy
Published: January 2025

Peanut is a vital source of protein, particularly in the tropical regions of Asian and African countries. About three-quarters of peanut production occurs worldwide in arid and semi-arid regions, making drought an important concern in peanut production. In the US about two-thirds of peanuts are grown in non-irrigated lands, where drought accounts for 50 million USD loss each year. The looming threat of climate change exacerbates this situation by increasing erratic rainfall. Drought not only reduces yield but also degrades product quality. Peanuts under drought stress exhibit higher levels of pre-harvest aflatoxin contamination, a toxic fungal metabolite detrimental to both humans and animals. One way to sustain peanut production in drought-prone regions and address pre-harvest aflatoxin contamination is by developing drought-tolerant peanut cultivars, a process that can be accelerated by understanding the underlying physiological and genetic mechanisms for tolerance to drought stress. Different physiological attributes and genetic regions have been identified in drought-tolerant cultivars that help them cope with drought stress. The advent of precise genetic studies, artificial intelligence, high-throughput phenotyping, bioinformatics, and data science have significantly improved drought studies in peanuts. Yet, breeding peanuts for drought tolerance is often a challenge as it is a complex trait significantly affected by environmental conditions. Besides technological advancements, the success of drought-tolerant cultivar development also relies on the identification of suitable germplasm and the conservation of peanut genetic variation.
The development and maintenance of immunity against visceral leishmaniasis
Authors: Tiwari Rahul , Kumar Awnish , Singh Vishal Kumar , Rajneesh  , Chauhan Shashi Bhushan , Sundar Shyam , Nylén Susanne , Engwerda Christian , Kumar Rajiv
Published: January 2025

Understanding the development and maintenance of immunological memory is important for efforts to eliminate parasitic diseases like leishmaniasis. Leishmaniasis encompasses a range of pathologies, resulting from infection with protozoan parasites belonging to the subgenera Leishmania and Viannia of the genus Leishmania. A striking feature of these infections is that natural or drug-mediated cure of infection generally confers life-long protection against disease. The generation of protective T cell responses are necessary to control Leishmania infections. CD4+ T helper (Th) cells orchestrate immune responses in leishmaniasis and IFNγ+ Tbet+ CD4+ T (Th1) cells are required for the activation of phagocytes to kill captured or resident parasites, while other Th cell subset, including FoxP3+ natural regulatory T cells and Th2 cells can promote disease progression by suppressing the activities of Th1 cells. Upon resolution of a primary Leishmania infection, different subsets of CD4+ T cells, including tissue-resident memory T cells, effector memory T cells, central memory T cells, and short-lived effector T cells, help to confer resistance against reinfection. To maintain long-term protective Leishmania-specific CD4+ T cells responses, it is believed that persistent parasites or re-exposure to parasites at regular intervals is required (concomitant immunity). Despite the advances in our understanding about the immune responses during leishmaniasis, the generation of long-lasting protective immunity via vaccination has yet to be achieved. In this review, we summarize our current understanding about the formation and maintenance of immunological memory and control of leishmaniasis at the individual and population level. We will focus on Indian visceral leishmaniasis and discuss T cell responses that contribute to susceptibility to leishmaniasis, parasite persistence in populations and the environment, as well as describing advances in the development of leishmaniasis vaccines aimed at inducing protective CD4+ T cell responses.
Comprehensive analysis of the prognostic, immunological, and diagnostic roles of SIRT1 in pan-cancer and its validation in KIRC
Authors: Liu Qi , Sun Songxian , Zhou Chunxiang , Xu Houxi
Published: January 2025

Background

Disturbances in DNA damage repair may lead to cancer. SIRT1, an NAD+-dependent deacetylase, plays a crucial role in maintaining cellular homeostasis through the regulation of processes such as histone posttranslational modifications, DNA repair, and cellular metabolism. However, a comprehensive exploration of SIRT1’s involvement in pan-cancer remains lacking. Our study aimed to analyze the role of SIRT1 in pan-cancer to gain a more comprehensive understanding of its role in multiple malignancies.

Methods

We systematically examined the role of SIRT1 in pan-cancer by analyzing data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. Various tools, including R, Cytoscape, HPA, Archs4, TISIDB, cBioPortal, STRING, GSCALite, and CancerSEA, were used to integrate and analyze SIRT1 gene expression, prognosis, protein interactions, signaling pathways, immune infiltration, and other relevant information. Furthermore, we validated the differential expression of SIRT1 in normal human kidney cells and kidney cancer cell lines via experimental verification.

Results

SIRT1 expression was significantly reduced in various cancers and was different across molecular and immune subtypes. SIRT1 is intricately linked to numerous cancer pathways. In most cancer types, increased SIRT1 expression is positively associated with eosinophils, helper T cells, central memory T cells, effector memory T cells, γδ T cells, and Th2 cells. SIRT1 expression is significantly correlated with immune regulatory factors across various cancer types. Quantitative reverse transcription polymerase chain reaction (qRT–PCR) and Western blot (WB) analyses confirmed that SIRT1 is differentially expressed in kidney renal clear cell carcinoma (KIRC).

Conclusions

Using an integrative approach involving bioinformatics analysis and experimental validation, we clarified the potential roles and mechanisms of SIRT1 in pan-cancer, providing a theoretical basis for the development of SIRT1-targeted therapies in clinical applications.
Identification of an immunological signature of long COVID syndrome
Authors: Guerrera Gisella , Sambucci Manolo , Timperi Eleonora , Picozza Mario , Misiti Andrea , Placido Roberta , Corbisiero Silvia , D’Orso Silvia , Termine Andrea , Fabrizio Carlo , Gargano Francesca , Eleuteri Sharon , Marchioni Luisa , Bordoni Veronica , Coppola Luigi , Iannetta Marco , Agrati Chiara , Borsellino Giovanna , Battistini Luca
Published: January 2025

Introduction

Acute COVID-19 infection causes significant alterations in the innate and adaptive immune systems. While most individuals recover naturally, some develop long COVID (LC) syndrome, marked by persistent or new symptoms weeks to months after SARS-CoV-2 infection. Despite its prevalence, there are no clinical tests to distinguish LC patients from those fully recovered. Understanding the immunological basis of LC is essential for improving diagnostic and treatment approaches.

Methods

We performed deep immunophenotyping and functional assays to examine the immunological profiles of LC patients, individuals with active COVID-19, recovered patients, and healthy donors. This analysis assessed both innate and adaptive immune features, identifying potential biomarkers for LC syndrome. A Binomial Generalized Linear Model (BGLM) was used to pinpoint immune features characterizing LC.

Results

COVID-19 patients exhibited depletion of innate immune cell subsets, including plasmacytoid and conventional dendritic cells, classical, non-classical, and intermediate monocytes, and monocyte-derived inflammatory dendritic cells. Elevated basal inflammation was observed in COVID-19 patients compared to LC patients, whose immune profiles were closer to those of healthy donors and recovered individuals. However, LC patients displayed persistent immune alterations, including reduced T cell subsets (CD4, CD8, Tregs) and switched memory B cells, similar to COVID-19 patients. Through BGLM, a unique adaptive immune signature for LC was identified, featuring memory CD8 and gd T cells with low proliferative capacity and diminished expression of activation and homing receptors.

Discussion

The findings highlight a unique immunological signature associated with LC syndrome, characterized by persistent adaptive immune dysregulation. While LC patients displayed recovery in innate immune profiles comparable to healthy and Recovered individuals, deficits in T cell and memory B cell populations were evident, differentiating LC from full recovery. These findings provide insights into LC pathogenesis and may support the development of diagnostic tools and targeted therapies.
Measuring metalinguistic awareness among heritage speakers in the US-based L3 context
Authors: Fiorenza Elisa , Travers Will
Published: January 2025

Metalinguistic awareness is considered by many to be a crucial ingredient for successful adult foreign-language acquisition. Researchers further suggest that it helps bilinguals learning a third language (L3) even more than it does monolinguals learning their second language (L2). In response to a recently proposed hypothesis that differences in metalinguistic awareness may be responsible for the variation in L3 grammatical development often witnessed amongst bilingual university students, and that teaching methods should accordingly be modified as a result, research that actually measures these varying levels of metalinguistic awareness has now become urgently needed. However, due to a lack of standardized assessments and an inability to converge on how best to measure this set of abilities in adults, few studies have yet attempted to operationalize this variable in the US-based L3 context, and those that did adopted diverse methods, raising issues of comparability. For multilingual language learners, especially those who grew up speaking a heritage language, the challenge that researchers face is whether to measure metalinguistic awareness in a native language, a prior-learned L2 (if one such language exists), the learner's current target language, or a language unknown to the learner entirely. This article highlights these methodological complexities and calls for a principled approach to measuring metalinguistic awareness before implementing any pedagogical changes in terms of how third languages are taught.
Hook, line, and social media: crowd-sourced images reveal size and species patterns of ocean sunfishes (Tetraodontiformes, Molidae) from California to Alaska
Authors: Mowatt-Larssen Tor , Thys Tierney M. , Hildering Jackie , Caldera Eric J. , Biesack Ellen E. , McDowell Jan R. , Nyegaard Marianne
Published: January 2025

Taxonomic confusion and limited data have impeded species-level biogeographic analyses of the world’s largest bony fishes, ocean sunfishes (Molidae; ‘molids’), in many ecosystems. However, recent advances in molid taxonomy and the emergence of photo-based community-science platforms provide an opportunity to revisit species-level biogeography. In this study, we use crowd-sourced images of 1,213 ocean sunfishes to determine if molid morphology visible in citizen-science images permits reliable species determination. From the ensuing data, we describe patterns in molid size structure and species composition from 1,178 molids observed in the Alaska and California Current Systems (ACS and CCS, respectively). Molids <1 m total length (TL) were commonly reported in the CCS, particularly off the central coast of California, suggesting this area may function as a molid nursery. Molids >1 m TL were more commonly observed in both the CCS and cooler ACS, which suggests larger molids occupy a larger thermal range (ontogenetic habitat expansion) than smaller individuals. Overall, Mola mola was the most frequently observed species in both the ACS and CCS; however, the persistent occurrence of Mola tecta in both current systems suggests a range extension for this otherwise Southern Hemisphere species. The species identity of six M. tecta specimens from California and Alaska were verified with genetic analysis. Finally, two Mola alexandrini confirmed in the southern portion of the CCS represent the first records of this species in the Northeast Pacific Ocean.
Frailty index, frailty phenotype and 6-year mortality trends in the FRASNET cohort
Authors: Damanti Sarah , De Lorenzo Rebecca , Citterio Lorena , Zagato Laura , Brioni Elena , Magnaghi Cristiano , Simonini Marco , Ruggiero Maria Pia , Santoro Simona , Senini Eleonora , Messina Marco , Farina Francesca , Festorazzi Costanza , Vitali Giordano , Manunta Paolo , Manfredi Angelo Andrea , Lanzani Chiara , Rovere-Querini Patrizia
Published: January 2025

Background

Frailty, a geriatric syndrome associated with adverse outcomes, lacks a universal definition. No consensus exists on the most effective frailty scale for predicting mortality.

Methods

This prospective observational study followed community-dwelling volunteers for 6 years. Frailty was measured with the Frailty Index (FI) and the Frailty Phenotype (FP). Concordance was assessed using Cohen’s Kappa coefficients. Age-and sex-adjusted Cox regression analyses were conducted to evaluate the association with mortality.

Results

Out of 1,114 participants (median age 72 years, IQR 69–77), 186 were classified as frail by the FI, 13 by the FP and 48 by both definitions. The concordance between the two measures was fair (κ = 0.26). Thirty-nine individuals died during the follow-up period. The FI showed a stronger association with mortality (HR 75.29, 95% CI 8.12–697.68, p < 0.001) compared to the FP (HR 3.3, 95% CI 1.45–7.51, p = 0.004). Individuals classified as frail by both definitions had the highest mortality risk and the highest FI scores (median 0.36).

Conclusion

Definitions of frailty identify different individuals as frail. The FI was more closely related to mortality than the FP. Individuals classified as frail according to both definitions displayed the highest complexity (corresponding also ho higher FI scores) and the greatest mortality. The FI demonstrated a more accurate ability to predict mortality due to its comprehensive nature.
Shared signaling pathways and comprehensive therapeutic approaches among diabetes complications
Authors: Ebrahimi Moein , Ahmadieh Hamid , Rezaei Kanavi Mozhgan , Safi Sare , Alipour-Parsa Saeed , Advani Soroor , Sorenson Christine M. , Sheibani Nader
Published: January 2025

The growing global prevalence of diabetes mellitus (DM), along with its associated complications, continues to rise. When clinically detected most DM complications are irreversible. It is therefore crucial to detect and address these complications early and systematically in order to improve patient care and outcomes. The current clinical practice often prioritizes DM complications by addressing one complication while overlooking others that could occur. It is proposed that the commonly targeted cell types including vascular cells, immune cells, glial cells, and fibroblasts that mediate DM complications, might share early responses to diabetes. In addition, the impact of one complication could be influenced by other complications. Recognizing and focusing on the shared early responses among DM complications, and the impacted cellular constituents, will allow to simultaneously address all DM-related complications and limit adverse treatment impacts. This review explores the current understanding of shared pathological signaling mechanisms among DM complications and recognizes new concepts that will benefit from further investigation in both basic and clinical settings. The ultimate goal is to develop more comprehensive treatment strategies, which effectively impact DM complications in multiple organs and improve patient care and outcomes.
Candida tropicalis spondylitis in a non-tropical immunocompetent patient: a case report and review of the literature
Authors: Yang Hong , Wang Xin , Zhu Weijian , Zhou Bei
Published: January 2025

Background

Tropical Candida spondylitis is an uncommon cause of lower back pain in patients, especially in non-tropical areas or in patients not at risk of immunocompromise.

Case presentation

A 65-year-old woman presented with a six-month history of poorly managed low back pain, now accompanied by numbness and pain in both lower extremities. Her medical history was significant for tertiary hypertension. Inflammatory markers were mildly elevated. MRI fluid sequences revealed lamellar enhancement of the L4-5 vertebral bodies, narrowing of the intervertebral space, peripheral soft tissue edema, and spinal canal compression. After 3 weeks of empirical anti-tuberculosis therapy, the patient’s symptoms did not improve, prompting posterior lesion debridement and autologous iliac bone grafting with pedicle screw fixation. Postoperatively, disc tissue cultures and next-generation sequencing (NGS) identified Candida tropicalis. The patient was subsequently treated with a six-week course of voriconazole, resulting in symptomatic improvement, with no recurrence observed during follow-up.

Conclusion

The imaging and clinical presentation of Candida tropicalis spondylitis can closely mimic that of tuberculous spondylitis, particularly in patients without clear risk factors for immune compromise. This overlap in presentation often complicates the differential diagnosis, leading to potential delays in appropriate treatment.
Ischemic colitis presenting as a colonic mass: a case report and diagnostic challenges
Authors: Xu Lin , Wu Yuqi , Li Shangjin , Chen Xinbo , Zhang Dong , Chen Boqian , Guo Shaoju
Published: January 2025

Ischemic colitis (IC) is a multifaceted condition that often manifests with nonspecific symptoms such as abdominal pain and bloody diarrhea, particularly in older adults with vascular risk factors. Diagnosis is supported by elevated levels of white blood cells, lactate, and C-reactive protein (CRP). Computed tomography (CT) imaging typically reveals wall thickening and fat stranding in watershed areas. Colonoscopy may demonstrate mucosal erythema, ulceration, or necrosis. IC can be differentiated from inflammatory bowel disease (IBD), diverticulitis, and colorectal cancer based on symptom patterns and imaging findings. The absence of specific biomarkers can complicate diagnosis, potentially causing delays. Illustrating these challenges is the case of a 53-year-old male patient who arrived at the hospital exhibiting abdominal pain and diarrhea. Enhanced CT scans and colonoscopy identified a mass in the ileocecal region of the colon, and subsequent tissue biopsy revealed ischemic lesions in the submucosa. Initially diagnosed with IC, the patient’s symptoms gradually improved with conservative treatment, which included antibiotics, fluid resuscitation, and bowel rest. Follow-up endoscopy showed significant lesion improvement, and no recurrence was detected during subsequent follow-ups. This case illustrates the healing process of IC as manifested by colon mass under endoscopy. Also, it highlights the critical importance of timely diagnosis and personalized treatment strategies in atypical presentations to improve patient outcomes.
Advances in genetic diagnosis and therapy of hereditary heart disease: a bibliometric review from 2004 to 2024
Authors: Ma Huixi , Wang Yun , Jia Yang , Xie Linjun , Liu Lini , Zhang Dingyi , Ma Xinyue , Guo Yingkun , Xu Rong
Published: January 2025

Hereditary heart disease (HHD) is a series of cardiac disorders associated with monogenic or polygenic abnormalities and is one of the leading causes of sudden death, particularly in young adults. The updated European Cardiology guideline for cardiomyopathies provides the first comprehensive summary of genotyping, imaging, and therapy recommendations for inherited cardiomyopathies, but still lacks a comprehensive discussion of research advances and future trends in genetic diagnosis and therapy of HHD. Our research aims to fill this gap. Bibliometric analysis software (CiteSpace 6.3.R1, VOSviewer 1.6.18, and Scimago Graphica) was used to analyze the general information, trends, and emerging foci of HHD in the past 20 years, including author, country, institution, keyword, and so on. There were 5,757 publications were screened and aggregated in the database, including 1876 reviews and 3,881 articles. Hypertrophic cardiomyopathy (HCM), arrhythmogenic cardiomyopathy (ACM), Brugada syndrome (BrS), myocardial amyloidosis, and Fabry disease (FD) were the main types of HHD that were explored in greater depth. Moreover, new diagnostic methods, clinical cohorts, and genetically targeted therapies for HHD patients are key research hotspots. The relationship between the pathogenicity of genes and prognosis will become increasingly important for therapy.
Developments and clinical experiences in collagenase chemonucleolysis for lumbar disc herniation: a narrative review
Authors: Zhang Hao , Zhang Chi , Li Lin , Hu Ming-liang , Zhao Jian-ning , Zheng Zhang , Ding Wen-feng
Published: January 2025

Lumbar disc herniation (LDH) affects millions globally, with annual healthcare costs exceeding $100 billion in the United States alone, driving increasing interest in minimally invasive radiological interventions as treatment alternatives. This narrative review examines developments in collagenase chemonucleolysis for LDH, integrating a literature analysis with clinical experience. Key advancements include the transition from single-agent to combination therapies, exploration of diverse injection routes, and the progression from C-arm fluoroscopy to multi-slice CT guidance. The synergistic use of collagenase, oxygen-ozone, and anti-inflammatory analgesics has enhanced efficacy. Safety measures such as aspiration tests, contrast agent tests, and lidocaine tests implemented to mitigate procedural risks. However, challenges persist, including non-standardized dosages and potential complications arising from intradiscal injections. Future research should focus on establishing accreditation systems, refining patient selection criteria, optimizing drug dosages, and exploring advanced image-guided technologies. While chemonucleolysis offers advantages such as minimal invasiveness and cost-effectiveness, its complexity necessitates a multidisciplinary approach. Key findings demonstrate that combination therapy achieves superior outcomes compared to monotherapy, with long-term efficacy rates reaching 90% and 6-month success rates of 95%. Additionally, CT guidance has significantly improved procedural precision and safety compared to traditional fluoroscopy. This review provides insights for clinicians and researchers, highlighting the potential of chemonucleolysis in LDH management to ensure its safe and effective integration into mainstream treatment protocols.
The potential benefits of radiotherapy in elderly patients with early-stage triple-negative breast cancer
Authors: Xu Zheng , Qin Chengdong , Cao Binxiao , Ruan Pengcheng , Zhang Mianhao , Chen Guidong
Published: January 2025

Background

Breast cancer (BC) is the most common cancer in women in the U.S. and a leading cause of cancer-related deaths. The incidence rises with age, especially in women over 70. Older patients often face multiple comorbidities, complicating treatment decisions. This study will analyze the role of radiotherapy (RT) in early-stage triple-negative breast cancer (TNBC) among elderly patients using the SEER database to assess its impact on survival outcomes.

Methods

The patients aged 70+ with T1-2N0-1M0 TNBC were selected from the SEER database (2010–2015) according to specific inclusion and exclusion criteria. Statistical analyses involved chi-square tests, propensity score matching (PSM), and Cox regression to identify risk factors. A nomogram was developed, and Kaplan-Meier analysis compared overall (OS) and breast cancer-specific survival (BCSS) across different groups.

Results

A total of 3,024 elderly patients with early-stage TNBC were analyzed. After employing PSM to eliminate baseline differences, survival analysis indicated that the breast-conserving surgery (BCS) group could benefit from RT (OS, HR = 0.68, p < 0.001; BCSS, HR = 0.64, p = 0.001). Cox regression analysis on the non-RT cohort within the BCS group identified age, tumor grade, and T stage as independent risk factors. Subsequently, a nomogram was developed to stratify patients and found that RT significantly improved OS and BCSS in the intermediate-risk (OS, HR = 0.49, 95% CI = 0.34–0.71, p = 0.001; BCSS, HR = 0.40, 95% CI = 0.21–0.77, p = 0.018) and high-risk group (OS, HR = 0.67, 95% CI = 0.55–0.81, p < 0.001; BCSS, HR = 0.61, 95% CI = 0.45–0.83, p = 0.007), while showing no significant benefit in the low-risk group (all p-values > 0.05).

Conclusion

RT significantly improves OS and BCSS in early-stage TNBC patients after BCS, particularly for intermediate to high-risk individuals, while low-risk patients may omit it.
Phage WO diversity and evolutionary forces associated with Wolbachia-infected crickets
Authors: Luo Qing-Chen , Li Yue-Yuan , Ren Ye-Song , Yang Xiao-Hui , Zhu Dao-Hong
Published: January 2025

Introduction

Phage WO represents the sole bacteriophage identified to infect Wolbachia, exerting a range of impacts on the ecological dynamics and evolutionary trajectories of its host. Given the extensive prevalence of Wolbachia across various species, phage WO is likely among the most prolific phage lineages within arthropod populations. To examine the diversity and evolutionary dynamics of phage WO, we conducted a screening for the presence of phage WO in Wolbachia-infected cricket species from China.

Methods

The presence of phage WO was detected using a PCR-based methodology. To elucidate the evolutionary forces driving phage WO diversity, analyses of intragenic recombination were conducted employing established recombination techniques, and horizontal transmission was investigated through comparative phylogenetic analysis of the phages and their hosts.

Results and discussion

Out of 19 cricket species infected with Wolbachia, 18 species were found to harbor phage WO. Notably, 13 of these 18 cricket species hosted multiple phage types, with the number of types ranging from two to 10, while the remaining five species harbored a single phage type. Twelve horizontal transmission events of phage WO were identified, wherein common phage WO types were shared among different Wolbachia strains. Notably, each phage WO horizontal transfer event was associated with distinct Wolbachia supergroups, specifically supergroups A, B, and F. Previous studies have found that four Wolbachia strains infect two to five species of crickets. However, among these cricket species, in addition to the shared phage WO types, all harbored species-specific phage WO types. This suggests that Wolbachia in crickets may acquire phage WO types through horizontal viral transfer between eukaryotes, independent of Wolbachia involvement. Furthermore, nine putative recombination events were identified across seven cricket species harboring multiple phage types. These findings suggest that horizontal transmission and intragenic recombination have played a significant role in the evolution of the phage WO genome, effectively enhancing the diversity of phage WO associated with crickets.
Comparative evaluation of specimen type and processing conditions for studying oyster microbiomes
Authors: Almuhaideb Esam , Hasan Nur A. , Grim Christopher , Rashed Shah Manzur , Parveen Salina
Published: January 2025

Metagenomic sequencing is increasingly being employed to understand the assemblage and dynamics of the oyster microbiome. Specimen collection and processing steps can impact the resultant microbiome composition and introduce bias. To investigate this systematically, a total of 54 farmed oysters were collected from Chesapeake Bay between May and September 2019. Six different specimen types and processing methods were evaluated for microbial community composition using shotgun metagenomics, namely fresh oyster homogenate (FOH), oyster homogenate after simulated temperature abuse (AOH), Luria broth-enriched oyster homogenate (EOH), dissected stomach homogenate (DSH), hemolymph (HLM), and stomach-gut content (SGC). In general, DSH, EOH, and FOH yielded the highest DNA concentration, while EOH had the highest microbial reads, followed by DSH, HLM, and FOH. HLM produced the highest bacterial species alpha diversity, followed by AOH, EOH, and SGC. Although alpha diversities did not differ significantly, beta-diversity measurements showed significant dissimilarity among methods (p < 0.05) indicating that the specimen types and processing steps do play an important role in representing the composition of the bacterial community. Bacterial species that had the highest log mean abundance included Cyanobium sp. PCC 7001 in FOH, Vibrio vulnificus in AOH, EOH, and DSH, and lastly Synechococcus sp. CB0205 in the DSH, HML, and SGC samples. EOH displayed higher bacterial hits, distinct microbial composition, and higher values of bacterial, phages, and antimicrobial resistance gene reads. Therefore, if studying the overall oyster microbial community, prioritizing optimum specimen collection and processing methods that align with the overall goal of the study is recommended.
Efficacy and safety of laser acupuncture on osteoarthritis: a systematic review and meta-analysis
Authors: Wen Xiangdong , Zhang Guojiang , Cui Jinquan , Tang Yuzhe , Meng Qi , Su Yang , An Senbo , Sun Shui
Published: January 2025

Objectives

To perform a meta-analysis of previous studies investigating the effects of laser acupuncture on osteoarthritis.

Study design

Systematic review and meta-analysis.

Methods

Randomized controlled trials (RCTS) on laser acupuncture for osteoarthritis were searched in the databases of PubMed, Embase, Cochrane Library, and Web of Science with a search deadline of 24 December 2023. After identifying 11 studies, we used Stata 15.0 to analyze the data.

Results

In the 11 studies identified, 931 patients were analyzed. Results showed that laser acupuncture significantly improved patients’ pain and function compared to the placebo laser group. There were significant differences in VAS pain scores[SMD = −0.924, 95% CI (−1.200, −0.649), p = 0.000], WOMAC pain scores[SMD = −0.425, 95% CI (−0.652, −0.199), p = 0.000], WOMAC function scores[SMD = −0.307, 95% CI (−0.548, −0.065), p = 0.013], WOMAC stiffness scores[SMD = −0.235, 95% CI (−0.388, −0.083), p = 0.002] between the laser acupuncture group and the placebo laser group. The therapeutic effect of laser acupuncture disappeared at 8 weeks. In subgroup analysis, patients who received laser acupuncture with specific parameters had better VAS scores and WOMAC scores than patients in other subgroups.

Conclusion

The application of laser acupuncture can improve knee pain and function in patients with osteoarthritis in the short term. It is recommended to use a laser with a power greater than 100 mW and a wavelength greater than 1,000 nm. CO2 lasers and solid-state lasers were shown to be more effective in the results than other types of lasers.
RL-QPSO net: deep reinforcement learning-enhanced QPSO for efficient mobile robot path planning
Authors: Jing Yang , Weiya Li
Published: January 2025

Introduction

Path planning in complex and dynamic environments poses a significant challenge in the field of mobile robotics. Traditional path planning methods such as genetic algorithms, Dijkstra's algorithm, and Floyd's algorithm typically rely on deterministic search strategies, which can lead to local optima and lack global search capabilities in dynamic settings. These methods have high computational costs and are not efficient for real-time applications.

Methods

To address these issues, this paper presents a Quantum-behaved Particle Swarm Optimization model enhanced by deep reinforcement learning (RL-QPSO Net) aimed at improving global optimality and adaptability in path planning. The RL-QPSO Net combines quantum-inspired particle swarm optimization (QPSO) and deep reinforcement learning (DRL) modules through a dual control mechanism to achieve path optimization and environmental adaptation. The QPSO module is responsible for global path optimization, using quantum mechanics to avoid local optima, while the DRL module adjusts strategies in real-time based on environmental feedback, thus enhancing decision-making capabilities in complex high-dimensional scenarios.

Results and discussion

Experiments were conducted on multiple datasets, including Cityscapes, NYU Depth V2, Mapillary Vistas, and ApolloScape, and the results showed that RL-QPSO Net outperforms traditional methods in terms of accuracy, computational efficiency, and model complexity. This method demonstrated significant improvements in accuracy and computational efficiency, providing an effective path planning solution for real-time applications in complex environments for mobile robots. In the future, this method could be further extended to resource-limited environments to achieve broader practical applications.
Modeling analysis of depolarization-assisted afterdischarge in hippocampal mossy fibers
Authors: Kamiya Haruyuki
Published: January 2025

A strong repetitive stimulus can occasionally enhance axonal excitability, leading to the generation of afterdischarge. This afterdischarge outlasts the stimulus period and originates either from the physiological spike initiation site, typically the axon initial segment, or from ectopic sites for spike generation. One of the possible mechanisms underlying the stimulus-induced ectopic afterdischarge is the local depolarization due to accumulated potassium ions surrounding the axonal membranes of the distal portion. In this study, the mechanisms were explored by computational approaches using a simple model of hippocampal mossy fibers implemented with the structure of en passant axons and experimentally obtained properties of ionic conductances. When slight depolarization of distal axons was given in conjunction with the high-frequency stimulus, robust afterdischarges were triggered after cessation of the repetitive stimulus and lasted for a prolonged period after the stimulus. Each spike during the afterdischarge recorded from distal axons precedes that recorded from the soma, suggesting that the afterdischarge was ectopically generated from distal axons and propagated antidromically toward the soma. Notably, when potassium channels in the model are replaced with non-inactivating ones, repetitive stimuli fail to induce afterdischarge. These results suggested that the inactivating property of axonal potassium channels plays a crucial role in generating the afterdischarge. Accumulated inactivation of potassium channels during strong repetitive stimulation may alter mossy fiber excitability, leading to ectopic afterdischarges from sites distinct from the physiological spike initiation region.
Morinda officinalis oligosaccharides alleviate chronic unpredictable mild stress-induced depression through the BDNF/TrkB/CREB pathway and symptoms of sexual dysfunction in mice
Authors: He Mengjie , Hu Mengying , Wang Tingqiao , Zuo Zeping , Li Hongkai , Zhao Zhiwei , Hao Yunwen , Dai Xueling , Wang Jianfang , Sun Yaxuan
Published: January 2025

Background

In recent years, depression has become a global public health concern, and one of the common concomitant symptoms are diminished sexual motivation and impaired sexual performance. The aim of this study was to investigate the potential effects of Morinda officinalis oligosaccharides (MOO) on depression and its concomitant symptom, sexual dysfunction.

Methods

Chronic unpredictable mild stress (CUMS)-induced depression model was constructed, and the effects of MOO on depression and sexual abilities were evaluated.

Results

The results revealed that MOO was able to alleviate CUMS-induced depression-like behavior in mice, to inhibit hippocampal neuron apoptosis, to reverse monoamine neurotransmitter imbalance, increase Brain-derived neurotrophic factor (BDNF) expression levels in the hippocampus, to modulate the composition and distribution of gut microbiota, and to increase the abundance of probiotics after continuous gavage of MOO for 28 days. MOO further confirmed that sexual dysfunction is closely related to the development of depression by improving the lack of sexual motivation and low sexual performance in CUMS-induced depressed mice, modulating the disruption of sex hormone secretion in serum, and alleviating sperm morphology and functional defects in the epididymis.

Conclusion

These findings on MOO provide a basis for exploring its antidepressant mechanism, its use to improve hypogonadotropic symptoms, and for future development of new antidepressant drug to improves hypogonadotropic symptoms.
Neural differentiation in perspective: mitochondria as early programmers
Authors: Farahani Ramin M.
Published: January 2025

Neural differentiation during development of the nervous system has been extensively studied for decades. These efforts have culminated in the generation of a detailed map of developmental events that appear to be associated with emergence of committed cells in the nervous system. In this review the landscape of neural differentiation is revisited by focusing on abiotic signals that play a role in induction of neural differentiation. Evidence is presented regarding a chimeric landscape whereby abiotic signals generated by mitochondria orchestrate early events during neural differentiation. This early stage, characterised by mitochondrial hyperactivity, in turn triggers a late stage of differentiation by reprogramming the activity of biotic signals.
Case report: Resolution of VIPoma-related symptoms with peptide receptor radionuclide therapy
Authors: Cengiz Turgut Bora , Kulkarni Raksha , Corbett Virginia , Ghesani Nasrin V. , Wolin Edward , Ghesani Munir V.
Published: January 2025

Peptide receptor radionuclide therapy (PRRT) is used for the management of neuroendocrine tumors (NETs) not responsive to somatostatin analogs. In this case series, we report two patients with pancreatic vasoactive intestinal peptide (VIP)-secreting NETs (VIPomas) not responsive to any other therapies who achieved symptomatic control and a significant decrease in serum VIP levels with PRRT during their hospital stay. Two patients with VIPomas were admitted to the hospital with multiple prior hospital admissions after going through multiple lines of therapy. The first patient was a 47-year-old woman with a grade 2 pancreatic VIP-secreting NET. She was treated with somatostatin analogs and chemotherapy; however, she experienced recurrent symptoms and complications leading to two hospital admissions, one of which included an intensive care unit (ICU) admission. The patient was treated with lutetium-177 DOTATATE while in the hospital, which led to the resolution of the symptoms and a marked decline in serum VIP levels, and she was able to be discharged from the hospital after 147 days of hospitalization (16 days after PRRT). The second patient was a 27-year-old man who was diagnosed with a well-differentiated grade 3 pancreatic VIPoma. He also suffered from severe diarrhea and was not responsive to any form of therapy, including liver embolization. He was also treated with PRRT on admission, which led to immediate resolution of his symptoms and a decrease in tumor markers. In conclusion, 177Lu-DOTATATE is an effective treatment for highly symptomatic VIPoma. Inpatient administration of PRRT can rapidly reduce diarrhea and fluid and electrolyte complications of VIP secretion and may shorten hospital stays.