Trends and hotspots in gastrointestinal neoplasms risk assessment: A bibliometric analysis from 1984 to 2022.

BACKGROUND: Gastrointestinal neoplasm (GN) significantly impact the global cancer burden and mortality, necessitating early detection and treatment. Understanding the evolution and current state of research in this field is vital. AIM: To conducts a comprehensive bibliometric analysis of publications from 1984 to 2022 to elucidate the trends and hotspots in the GN risk assessment research, focusing on key contributors, institutions, and thematic evolution. METHODS: This study conducted a bibliometric analysis of data from the Web of Science Core Collection database using the "bibliometrix" R package, VOSviewer, and CiteSpace. The analysis focused on the distribution of publications, contributions by institutions and countries, and trends in keywords. The methods included data synthesis, network analysis, and visualization of international collaboration networks. RESULTS: This analysis of 1371 articles on GN risk assessment revealed a notable evolution in terms of research focus and collaboration. It highlights the United States' critical role in advancing this field, with significant contributions from institutions such as Brigham and Women's Hospital and the National Cancer Institute. The last five years, substantial advancements have been made, representing nearly 45% of the examined literature. Publication rates have dramatically increased, from 20 articles in 2002 to 112 in 2022, reflecting intensified research efforts. This study underscores a growing trend toward interdisciplinary and international collaboration, with the Journal of Clinical Oncology standing out as a key publication outlet. This shift toward more comprehensive and collaborative research methods marks a significant step in addressing GN risks. CONCLUSION: This study underscores advancements in GN risk assessment through genetic analyses and machine learning and reveals significant geographical disparities in research emphasis. This calls for enhanced global collaboration and integration of artificial intelligence to improve cancer prevention and treatment accuracy, ultimately enhancing worldwide patient care.

Leveraging error-prone algorithm-derived phenotypes: Enhancing association studies for risk factors in EHR data.

OBJECTIVES: It has become increasingly common for multiple computable phenotypes from electronic health records (EHR) to be developed for a given phenotype. However, EHR-based association studies often focus on a single phenotype. In this paper, we develop a method aiming to simultaneously make use of multiple EHR-derived phenotypes for reduction of bias due to phenotyping error and improved efficiency of phenotype/exposure associations. MATERIALS AND METHODS: The proposed method combines multiple algorithm-derived phenotypes with a small set of validated outcomes to reduce bias and improve estimation accuracy and efficiency. The performance of our method was evaluated through simulation studies and real-world application to an analysis of colon cancer recurrence using EHR data from Kaiser Permanente Washington. RESULTS: In settings where there was no single surrogate performing uniformly better than all others in terms of both sensitivity and specificity, our method achieved substantial bias reduction compared to using a single algorithm-derived phenotype. Our method also led to higher estimation efficiency by up to 30% compared to an estimator that used only one algorithm-derived phenotype. DISCUSSION: Simulation studies and application to real-world data demonstrated the effectiveness of our method in integrating multiple phenotypes, thereby enhancing bias reduction, statistical accuracy and efficiency. CONCLUSIONS: Our method combines information across multiple surrogates using a statistically efficient seemingly unrelated regression framework. Our method provides a robust alternative to single-surrogate-based bias correction, especially in contexts lacking information on which surrogate is superior.

Develop and validate a computable phenotype for the identification of Alzheimer's disease patients using electronic health record data.

INTRODUCTION: Alzheimer's disease (AD) is often misclassified in electronic health records (EHRs) when relying solely on diagnosis codes. This study aimed to develop a more accurate, computable phenotype (CP) for identifying AD patients using structured and unstructured EHR data. METHODS: We used EHRs from the University of Florida Health (UFHealth) system and created rule-based CPs iteratively through manual chart reviews. The CPs were then validated using data from the University of Texas Health Science Center at Houston (UTHealth) and the University of Minnesota (UMN). RESULTS: Our best-performing CP was "patient has at least 2 AD diagnoses and AD-related keywords in AD encounters," with an F1-score of 0.817 at UF, 0.961 at UTHealth, and 0.623 at UMN, respectively. DISCUSSION: We developed and validated rule-based CPs for AD identification with good performance, which will be crucial for studies that aim to use real-world data like EHRs. Highlights: Developed a computable phenotype (CP) to identify Alzheimer's disease (AD) patients using EHR data.Utilized both structured and unstructured EHR data to enhance CP accuracy.Achieved a high F1-score of 0.817 at UFHealth, and 0.961 and 0.623 at UTHealth and UMN.Validated the CP across different demographics, ensuring robustness and fairness.

Perioperative Transcutaneous Electrical Acupoint Stimulation Reduces Postoperative Pain in Patients Undergoing Thoracoscopic Surgery: A Randomized Controlled Trial.

Objectives: This study aimed to determine the effects of perioperative transcutaneous electrical acupoint stimulation (TEAS) on postoperative pain management in patients undergoing thoracic surgery. Methods: In the prospective, randomized, controlled study, a total of 84 patients undergoing video-assisted thoracoscopic surgery (VATS) were randomly allocated to the TEAS group (Group T) or control group (Group C). Patients in the Group T received TEAS at Neiguan (PC6) and Hegu (LI4) acupoints for 30 min before anesthesia induction and 30 min after thoracoscopic surgery. Patients in the Group C received the same placement of electrodes but without electrical stimulation. The numeric rating scale (NRS) pain score, remifentanil consumption, demand for rescue analgesics and incidence of postoperative nausea and vomiting (PONV), patient satisfaction, and the levels of plasma ß-endorphin (EP) and IL-6 were recorded. Results: Patients in the Group T had significantly lower NRS pain scores at 6 h, 12 h, 24 h, and 48 h after surgery than those in the Group C. Compared with Group C, patients in Group T had lower remifentanil consumption during operation, lower demand for rescue analgesics and lower rate of PONV within 24 h after surgery. Patients in Group T also had lower IL-6 content, higher ß-EP content and higher satisfaction degree than those in the Group C. Conclusions: Perioperative TEAS significantly decreased postoperative pain and rescued analgesia requirements and the incidence of PONV in patients undergoing thoracoscopic surgery, with a higher patient satisfaction. This trial is registered with ChiCTR2100051841.

Elucidating genetic and molecular basis of altered higher-order brain structure-function coupling in major depressive disorder.

Previous studies have shown that major depressive disorder (MDD) patients exhibit structural and functional impairments, but few studies have investigated changes in higher-order coupling between structure and function. Here, we systematically investigated the effect of MDD on higher-order coupling between structural connectivity (SC) and functional connectivity (FC). Each brain region was mapped into embedding vector by the node2vec algorithm. We used support vector machine (SVM) with the brain region embedding vector to distinguish MDD patients from health controls (HCs) and identify the most discriminative brain regions. Our study revealed that MDD patients had decreased higher-order coupling in connections between the most discriminative brain regions and local connections in rich-club organization and increased higher-order coupling in connections between the ventral attentional network and limbic network compared with HCs. Interestingly, transcriptome-neuroimaging association analysis demonstrated the correlations between regional rSC-FC coupling variations between MDD patients and HCs and α/ß-hydrolase domain-containing 6 (ABHD6), ß 1,3-N-acetylglucosaminyltransferase-9(ß3GNT9), transmembrane protein 45B (TMEM45B), the correlation between regional dSC-FC coupling variations and retinoic acid early transcript 1E antisense RNA 1(RAET1E-AS1), and the correlations between regional iSC-FC coupling variations and ABHD6, ß3GNT9, katanin-like 2 protein (KATNAL2). In addition, correlation analysis with neurotransmitter receptor/transporter maps found that the rSC-FC and iSC-FC coupling variations were both correlated with neuroendocrine transporter (NET) expression, and the dSC-FC coupling variations were correlated with metabotropic glutamate receptor 5 (mGluR5). Further mediation analysis explored the relationship between genes, neurotransmitter receptor/transporter and MDD related higher-order coupling variations. These findings indicate that specific genetic and molecular factors underpin the observed disparities in higher-order SC-FC coupling between MDD patients and HCs. Our study confirmed that higher-order coupling between SC and FC plays an important role in diagnosing MDD. The identification of new biological evidence for MDD etiology holds promise for the development of innovative antidepressant therapies.

[Clinical characteristics and prognosis of acute gastrointestinal injury in patients with sepsis-associated acute respiratory distress syndrome].

OBJECTIVE: To observe the clinical characteristics and prognosis of patients with acute respiratory distress syndrome (ARDS) in sepsis combined with acute gastrointestinal injury (AGI) of different grades, and to further explore the risk factors associated with the poor prognosis of patients. METHODS: The clinical data of patients with septic ARDS admitted to the intensive care unit (ICU) of Tianjin First Central Hospital from March to October 2023 were collected. According to the 2012 European Association of Critical Care Medicine AGI definition and grading criteria, the patients were categorized into AGI grade 0- IV groups. The clinical characteristics and 28-day clinical outcomes of the patients were observed; the risk factors related to the prognosis of patients with septic ARDS combined with AGI were analyzed by using univariate and multivariate Logistic regression; and the receiver operator characteristic curve (ROC curve) and calibration curves were plotted to evaluate the predictive value of each risk factor on the prognosis of patients with septic ARDS combined with AGI. RESULTS: A total of 92 patients with septic ARDS were enrolled, including 7 patients in the AGI 0 group, 20 patients in the AGI I group, 38 patients in the AGI II group, 23 patients in the AGI III group, and 4 patients in the AGI IV group. The incidence of AGI was 92.39%. With the increase of AGI grade, the ARDS grade increased, and acute physiology and chronic health evaluation II (APACHE II), sequential organ failure assessment (SOFA), intra-abdominal pressure (IAP), white blood cell count (WBC), neutrophil count (NEU), lymphocyte count (LYM), lymphocyte percentage (LYM%), and 28-day mortality all showed a significant increasing trend, while the oxygenation index (PaO2/FiO2) showed a significant decreasing trend (all P < 0.05). Pearson correlation analysis showed that APACHE II score, SOFA score, and ARDS classification were positively correlated with patients' AGI grade (Pearson correlation index was 0.386, 0.473, and 0.372, respectively, all P < 0.001), and PaO2/FiO2 was negatively correlated with patients' AGI grade (Pearson correlation index was -0.425, P < 0.001). Among the patients with septic ARDS combined with AGI, there were 68 survivors and 17 deaths at 28 days. The differences in APACHE II score, SOFA score, ARDS grade, AGI grade, PaO2/FiO2, IAP, AGI 7-day worst value, length of ICU stay, and total length of hospital stay between the survival and death groups were statistically significant. Univariate Logistic regression analysis showed that SOFA score [odds ratio (OR) = 1.350, 95% confidence interval (95%CI) was 1.071-1.702, P = 0.011], PaO2/FiO2 (OR = 0.964, 95%CI was 0.933-0.996, P = 0.027) and AGI 7-day worst value (OR = 2.103, 95%CI was 1.194-3.702, P = 0.010) were the risk factors for 28-day mortality in patients with septic ARDS combined with AGI. Multivariate Logistic regression analysis showed that SOFA score (OR = 1.384, 95%CI was 1.153-1.661, P < 0.001), PaO2/FiO2 (OR = 0.983, 95%CI was 0.968-0.999, P = 0.035) and AGI 7-day worst value (OR = 1.992, 95%CI was 1.141-3.478, P = 0.015) were the independent risk factors for 28-day mortality in patients with septic ARDS combined with AGI. ROC curve analysis showed that SOFA score, PaO2/FiO2 and AGI 7-day worst value had predictive value for the 28-day prognosis of patients with septic ARDS combined with AGI. The area under the ROC curve (AUC) was 0.824 (95%CI was 0.697-0.950), 0.760 (95%CI was 0.642-0.877) and 0.721 (95%CI was 0.586-0.857), respectively, all P < 0.01; when the best cut-off values of the above metrics were 5.50 points, 163.45 mmHg (1 mmHg≈0.133 kPa), and 2.50 grade, the sensitivities were 94.1%, 94.1%, 31.9%, respectively, and the specificities were 80.9%, 67.6%, 88.2%, respectively. CONCLUSIONS: The incidence of AGI in patients with septic ARDS is about 90%, and the higher the AGI grade, the worse the prognosis of the patients. SOFA score, PaO2/FiO2 and AGI 7-day worst value have a certain predictive value for the prognosis of patients with septic ARDS combined with AGI, among which, the larger the SOFA score and AGI 7-day worst value, and the smaller the PaO2/FiO2, the higher the patients' mortality.

Assessing genotoxic effects of chemotherapy agents by a robust in vitro assay based on mass spectrometric quantification of γ-H2AX in HepG2 cells.

Chemotherapy has already proven widely effective in treating cancer. Chemotherapeutic agents usually include DNA damaging agents and non-DNA damaging agents. Assessing genotoxic effect is significant during chemotherapy drug development, since the ability to attack DNA is the major concern for DNA damaging agents which relates to the therapeutic effect, meanwhile genotoxicity should also be evaluated for chemotherapy agents' safety especially for non-DNA damaging agents. However, currently applicability of in vitro genotoxicity assays is hampered by the fact that genotoxicity results have comparatively high false positive rates. γ-H2AX has been shown to be a bifunctional biomarker reflecting both DNA damage response and repair. Previously, we developed an in vitro genotoxicity assay based on γ-H2AX quantification using mass spectrometry. Here, we employed the assay to quantitatively assess the genotoxic effects of 34 classic chemotherapy agents in HepG2 cells. Results demonstrated that the evaluation of cellular γ-H2AX could be an effective approach to screen and distinguish types of action of different classes of chemotherapy agents. In addition, two crucial indexes of DNA repair kinetic curve, i.e., k (speed of γ-H2AX descending) and t50 (time required for γ-H2AX to drop to half of the maximum value) estimated by our developed online tools were employed to further evaluate nine representative chemotherapy agents, which showed a close association with therapeutic index or carcinogenic level. The present study demonstrated that mass spectrometric quantification of γ-H2AX may be an appropriate tool to preliminarily evaluate genotoxic effects of chemotherapy agents.

Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.

Dissecting the regulatory mechanisms controlling mammalian transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm in human and mouse cells. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA-binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered a link between DDX3X and nuclear export. For hundreds of RNA metabolism genes, most transcripts with retained introns were degraded by the nuclear exosome, while the remaining molecules were exported with stable cytoplasmic lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, machine learning identified molecular features that predicted the diverse life cycles of mRNAs.

Sulfur-based fluorescent probes for biological analysis: A review.

The widespread adoption of small-molecule fluorescence detection methodologies in scientific research and industrial contexts can be ascribed to their inherent merits, including elevated sensitivity, exceptional selectivity, real-time detection capabilities, and non-destructive characteristics. In recent years, there has been a growing focus on small-molecule fluorescent probes engineered with sulfur elements, aiming to detect a diverse array of biologically active species. This review presents a comprehensive survey of sulfur-based fluorescent probes published from 2017 to 2023. The diverse repertoire of recognition sites, including but not limited to N, N-dimethylthiocarbamyl, disulfides, thioether, sulfonyls and sulfoxides, thiourea, thioester, thioacetal and thioketal, sulfhydryl, phenothiazine, thioamide, and others, inherent in these sulfur-based probes markedly amplifies their capacity for detecting a broad spectrum of analytes, such as metal ions, reactive oxygen species, reactive sulfur species, reactive nitrogen species, proteins, and beyond. Owing to the individual disparities in the molecular structures of the probes, analogous recognition units may be employed to discern diverse substrates. Subsequent to this classification, the review provides a concise summary and introduction to the design and biological applications of these probe molecules. Lastly, drawing upon a synthesis of published works, the review engages in a discussion regarding the merits and drawbacks of these fluorescent probes, offering guidance for future endeavors.

Polyketides from the mangrove-derived fungus Penicillium robsamsonii HNNU0006.

Seven polyketides, including an undescribed depsidone (1) and six previously reported 3,6,8-trihydroxy-1-methylxanthone (2), 7-hydroxy-2-(2-hydroxypropyl)-5-methylchromone (3), methyl3-chloro-6-hydroxy-2-(4-hy-droxy-2-methoxy-6-methylphenoxy)-4- methoxybenzoate (4), xylarianin A (5), 4,5-dihydroxy-6-(6'-methylsalicyloxy)-2-hydro-xymethyl-2-cyclohexen-1-one (6) and alternariol (7), have been isolated from cultures of the mangrove-derived fungus Penicillium robsamsonii HNNU0006. The structure of compound 1 was elucidated by extensive spectroscopic analysis and X-ray crystallography. Furthermore, all the compounds were evaluated their cytotoxic activities, and compounds 1 and 7 showed weak cytotoxicity against two cell lines Vero and A549 with IC50 values ranging from 95.6 and 296.5 µM, relative to the positive control Etoposide phosphate with IC50 values of 24.5 and 18.7 µM, respectively.

Phosphoribosylpyrophosphate synthetase as a metabolic valve advances Methylobacterium/Methylorubrum phyllosphere colonization and plant growth.

The proficiency of phyllosphere microbiomes in efficiently utilizing plant-provided nutrients is pivotal for their successful colonization of plants. The methylotrophic capabilities of Methylobacterium/Methylorubrum play a crucial role in this process. However, the precise mechanisms facilitating efficient colonization remain elusive. In the present study, we investigate the significance of methanol assimilation in shaping the success of mutualistic relationships between methylotrophs and plants. A set of strains originating from Methylorubrum extorquens AM1 are subjected to evolutionary pressures to thrive under low methanol conditions. A mutation in the phosphoribosylpyrophosphate synthetase gene is identified, which converts it into a metabolic valve. This valve redirects limited C1-carbon resources towards the synthesis of biomass by up-regulating a non-essential phosphoketolase pathway. These newly acquired bacterial traits demonstrate superior colonization capabilities, even at low abundance, leading to increased growth of inoculated plants. This function is prevalent in Methylobacterium/Methylorubrum strains. In summary, our findings offer insights that could guide the selection of Methylobacterium/Methylorubrum strains for advantageous agricultural applications.

Construction of nursing-sensitive quality indicators for acute poisoning in emergency departments: An e-Delphi study.

AIMS: The aim of the study was to develop a set of nursing-sensitive quality indicators for acute poisoning in emergency departments. DESIGN: A two-round e-Delphi study was conducted from July to November 2023. METHODS: Subject-matter experts from 19 tertiary hospitals across four provinces of China participated in the survey. Potential indicators identified through a literature review were rated on a 5-point Likert scale and comments solicited. Descriptive statistics were used to demonstrate convergence of expert opinion, and consensus was reached in two rounds. Weights of each indicator were determined by analytic hierarchy process. There were 20 expert responses in Round 1 and 18 in Round 2. RESULTS: After two rounds, experts reached a consensus on definitions, calculation formulas, and data collection methods for these indicators. Three primary and 11 secondary indicators were included in the final nursing-sensitive quality indicators for acute poisoning in the emergency department. CONCLUSION: A set of indicators about acute poisoning care, applicable to the Chinese context, was developed in collaboration with emergency nurse specialists. IMPLICATIONS FOR THE PROFESSION AND PATIENT CARE: The lack of supervision of the nursing quality for acute poisoning leads to great variability in clinical practice in different medical institutions. The results can help in their standardization in China and in other countries lacking regulation. Our study also offers nursing managers a concrete and operable evaluation tool for quality supervision. Normative nursing behaviours are conducive to increase safety and enhance patients' experience of medical treatment. IMPACT: The indicators identified in this study closely approach clinical practice and exhibit the characteristics of sensitivity and practicality. Although developed in the Chinese healthcare system, there is potential for adoption or adaption in other healthcare settings. REPORTING METHOD: This study was reported in line with the Conducting and REporting of DElphi studies (CREDE) guidance on Delphi studies. PATIENT OR PUBLIC CONTRIBUTION: No patient or public contribution in this study. CONTRIBUTION TO THE WIDER GLOBAL CLINICAL COMMUNITY: The nursing quality of acute poisoning in emergency departments remains a growing attention, but the relevant assessment tools are lack. This study provides a set of nursing-sensitive quality indicators for acute poisoning to guide the quality monitoring of nursing managers. Study recommendations have broad applicability to all healthcare professionals who are engaged in emergency nursing.

Comprehensive analysis of the clinical significance and molecular mechanism of T-box transcription factor 3 in osteosarcoma.

Background: T-box transcription factor 3 (TBX3) has been implicated in various malignant tumors, while its exact involvement in osteosarcoma (OS) remains unknown. Methods: Utilizing microarray data and bulk and single-cell RNA-seq data and qRT-PCR, we compared TBX3 mRNA expression levels in different stages of OS. Diagnostic ability testing and prognosis analysis were conducted to better understand the clinical importance of TBX3. Enrichment analysis was performed using gene groups with biological functions similar to TBX3 in different stages of OS to investigate the potential role of TBX3 in OS progression. In addition, we predicted medications targeted at TBX3 and identified downstream target genes to gain a comprehensive understanding of its therapeutic direction and regulatory mechanism. Results: TBX3 expression was highly upregulated in OS and was predominantly expressed in osteoblastic OS cells, with higher expression levels in metastatic tissues. TBX3 expression appeared somewhat suitable for discriminating between OS and normal samples, as well as different stages of OS. We found that TBX3 increased the malignant development of OS by altering cell cycle and cell adhesion molecules; exisulind and tacrolimus, which are targeted small-molecule medicines, were anticipated to counteract this dysregulation. The expression of CCNA2 could potentially be regulated by TBX3, contributing to OS advancement. Conclusion: TBX3 emerges as a potential biomarker for OS. In-depth research into its underlying molecular processes may offer new perspectives on treating OS.

3D-Printed Biomimetic Hydroxyapatite Composite Scaffold Loaded with Curculigoside for Rat Cranial Defect Repair.

The treatment of various large bone defects has remained a challenge for orthopedic surgeons for a long time. Recent research indicates that curculigoside (CUR) extracted from the curculigo plant exerts a positive influence on bone formation, contributing to fracture healing. In this study, we employed emulsification/solvent evaporation techniques to successfully fabricate poly(ε-caprolactone) nanoparticles loaded with curculigoside (CUR@PM). Subsequently, using three-dimensional (3D) printing technology, we successfully developed a bioinspired composite scaffold named HA/GEL/SA/CUR@PM (HGSC), chemically cross-linked with calcium chloride, to ensure scaffold stability. Further characterization of the scaffold's physical and chemical properties revealed uniform pore size, good hydrophilicity, and appropriate mechanical properties while achieving sustained drug release for up to 12 days. In vitro experiments demonstrated the nontoxicity, good biocompatibility, and cell proliferative properties of HGSC. Through alkaline phosphatase (ALP) staining, Alizarin Red S (ARS) staining, cell migration assays, tube formation assays, and detection of angiogenic and osteogenic gene proteins, we confirmed the HGSC composite scaffold's significant angiogenic and osteoinductive capabilities. Eight weeks postimplantation in rat cranial defects, Micro-computed tomography (CT) and histological observations revealed pronounced angiogenesis and new bone growth in areas treated with the HGSC composite scaffold. These findings underscore the scaffold's exceptional angiogenic and osteogenic properties, providing a solid theoretical basis for clinical bone repair and demonstrating its potential in promoting vascularization and bone regeneration.

Abnormalities in emotion regulation are associated with negative, but not positive or disorganized schizotypy: An experience sampling study.

BACKGROUND: Schizotypy, a multidimensional construct with positive, negative, and disorganized dimensions, represents a vulnerability marker for the development of schizophrenia. Although there has been increasing evidence linking schizotypy to emotion regulation (ER) deficits, the specific association between different schizotypal dimensions and alterations in ER strategy use in daily life remains poorly understood. METHODS: Using the experience sampling method (ESM), the present study examined the associations between positive, negative, and disorganized schizotypy and ER strategy use in daily life in a nonclinical young adult sample (N = 258). Participants were instructed to report their ER strategy use 5 times a day for 14 days. Four adaptive ER strategies (reflection, reappraisal, social sharing, and distraction) and two maladaptive ER strategies (suppression and rumination) were included. RESULTS: Multilevel modeling analyses showed that positive schizotypal traits predicted greater use of adaptive ER strategies, while negative schizotypal traits predicted less use of adaptive ER strategies and more frequent use of emotional suppression in daily life. No associations between disorganized schizotypal traits and any ER strategy use were found. CONCLUSION: Schizotypy dimensions are differentiated by preferences for different ER strategies in daily life. The findings suggest a strong association between negative schizotypy and notable dysfunctions in ER, emphasizing the significance of negative schizotypy as a vulnerability factor for psychosis.

A Study of Biomedical Relation Extraction Using GPT Models.

Relation Extraction (RE) is a natural language processing (NLP) task for extracting semantic relations between biomedical entities. Recent developments in pre-trained large language models (LLM) motivated NLP researchers to use them for various NLP tasks. We investigated GPT-3.5-turbo and GPT-4 on extracting the relations from three standard datasets, EU-ADR, Gene Associations Database (GAD), and ChemProt. Unlike the existing approaches using datasets with masked entities, we used three versions for each dataset for our experiment: a version with masked entities, a second version with the original entities (unmasked), and a third version with abbreviations replaced with the original terms. We developed the prompts for various versions and used the chat completion model from GPT API. Our approach achieved a F1-score of 0.498 to 0.809 for GPT-3.5-turbo, and a highest F1-score of 0.84 for GPT-4. For certain experiments, the performance of GPT, BioBERT, and PubMedBERT are almost the same.

Integration of C3H15-mediated transcriptional and post-transcriptional regulation confers plant thermotolerance in Arabidopsis.

Heat stress is an environmental factor that significantly threatens crop production worldwide. Nevertheless, the molecular mechanisms governing plant responses to heat stress are not fully understood. Plant zinc finger CCCH proteins have roles in stress responses as well as growth and development through protein-RNA, protein-DNA, and protein-protein interactions. Here, we reveal an integrated multi-level regulation of plant thermotolerance that is mediated by the CCCH protein C3H15 in Arabidopsis. Heat stress rapidly suppressed C3H15 transcription, which attenuated C3H15-inhibited expression of its target gene HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2), a central regulator of heat stress response (HSR), thereby activating HEAT SHOCK COGNATE 70 (HSC70.3) expression. The RING-type E3 ligase MED25-BINDING RING-H2 PROTEIN 2 (MBR2) was identified as an interacting partner of C3H15. The mbr2 mutant was susceptible to heat stress compared to wild-type plants, whereas plants overexpressing MBR2 showed increased heat tolerance. MBR2-dependent ubiquitination mediated the degradation of phosphorylated C3H15 protein in the cytoplasm, which was enhanced by heat stress. Consistently, heat sensitivities of C3H15 overexpression lines increased in MBR2 loss-of-function and decreased in MBR2 overexpression backgrounds. Heat stress-induced accumulation of HSC70.3 promoted MBR2-mediated degradation of C3H15 protein, implying that an auto-regulatory loop involving C3H15, HSFA2, and HSC70.3 regulates HSR. Heat stress also led to the accumulation of C3H15 in stress granules (SGs), a kind of cytoplasmic RNA granule. This study advances our understanding of the mechanisms plants use to respond to heat stress, which will facilitate technologies to improve thermotolerance in crops.

The Research of a Large-Scale Analysis Platform for MNS Blood Group Identification Based on Long-Read Sequencing.

The objective of this study was to devise a novel approach for determining MNS blood group utilizing long-read sequencing (LRS) and to identify intricate genome variations associated with this blood group system. In this study, a total of 60 blood samples were collected from randomly selected Chinese Han blood donors. The amplification of the full-length sequences of GYPA exon 2-7 (11 kb) and GYPB exon 2-6 (7 kb) was conducted on the blood samples obtained from these 60 donors. Subsequently, the sequencing of these amplified sequences was performed using the PacBio platform. The obtained sequencing data were then compared with the reference sequence of the human genome (GRCh38) utilizing the pbmm2 software, resulting in the acquisition of the haploid sequences of GYPA and GYPB. The serological typing prediction was conducted using the International Society of Blood Transfusion (ISBT) database, while the analysis of SNVs sites was performed using deepvariant v1.2.0 software and reference sequence alignment. A total of 60 samples yielded unambiguous high-quality haplotypes, which can serve as a standardized reference sequence for molecular biology typing of MNSs in the Chinese population. In a total of 60 serological samples, the LRS method successfully identified the M, N, S, and s blood group antigens by analyzing specific genetic variations (c.59, c.71, c.72 for GYPA, and c.143 for GYPB), which aligned with the results obtained through conventional serological techniques. 4 Mur samples that had been previously validated through serology and molecular biology were successfully confirmed, and complete haploid sequences were obtained. Notably, one of the Mur samples exhibited a novel breakpoint, GYP (B1-136-B ψ 137-212-A213-229-B230-366), thereby representing a newly identified subtype. Single molecule sequencing, which eliminates the necessity for PCR amplification, effectively encompasses GC and high repeat regions, enhancing accuracy in quantifying mutations with low abundance or frequency. By employing LRS analysis of the core region of GYPA and GYPB, diverse genotypes of MNS can be precisely and reliably identified in a single assay. This approach presents a comprehensive, expeditious, and precise novel method for the categorization and investigation of MNS blood group system.

Me-LLaMA: Foundation Large Language Models for Medical Applications.

Recent advancements in large language models (LLMs) such as ChatGPT and LLaMA have hinted at their potential to revolutionize medical applications, yet their application in clinical settings often reveals limitations due to a lack of specialized training on medical-specific data. In response to this challenge, this study introduces Me-LLaMA, a novel medical LLM family that includes foundation models - Me-LLaMA 13/70B, along with their chat-enhanced versions - Me-LLaMA 13/70B-chat, developed through continual pre-training and instruction tuning of LLaMA2 using large medical datasets. Our methodology leverages a comprehensive domain-specific data suite, including a large-scale, continual pre-training dataset with 129B tokens, an instruction tuning dataset with 214k samples, and a new medical evaluation benchmark (MIBE) across six critical medical tasks with 12 datasets. Our extensive evaluation using the MIBE shows that Me-LLaMA models achieve overall better performance than existing open-source medical LLMs in zero-shot, few-shot and supervised learning abilities. With task-specific instruction tuning, Me-LLaMA models outperform ChatGPT on 7 out of 8 datasets and GPT-4 on 5 out of 8 datasets. In addition, we investigated the catastrophic forgetting problem, and our results show that Me-LLaMA models outperform other open-source medical LLMs in mitigating this issue. Me-LLaMA is one of the largest open-source medical foundation LLMs that use both biomedical and clinical data. It exhibits superior performance across both general and medical tasks compared to other open-source medical LLMs, rendering it an attractive choice for medical AI applications. We release our models, datasets, and evaluation scripts at: https://github.com/BIDS-Xu-Lab/Me-LLaMA.

Sensitive Detection and Differentiation of Biologically Active Ricin and Abrin in Complex Matrices via Specific Neutralizing Antibody-Based Cytotoxicity Assay.

Ricin and abrin are highly potent plant-derived toxins, categorized as type II ribosome-inactivating proteins. High toxicity, accessibility, and the lack of effective countermeasures make them potential agents in bioterrorism and biowarfare, posing significant threats to public safety. Despite the existence of many effective analytical strategies for detecting these two lethal toxins, current methods are often hindered by limitations such as insufficient sensitivity, complex sample preparation, and most importantly, the inability to distinguish between biologically active and inactive toxin. In this study, a cytotoxicity assay was developed to detect active ricin and abrin based on their potent cell-killing capability. Among nine human cell lines derived from various organs, HeLa cells exhibited exceptional sensitivity, with limits of detection reaching 0.3 ng/mL and 0.03 ng/mL for ricin and abrin, respectively. Subsequently, toxin-specific neutralizing monoclonal antibodies MIL50 and 10D8 were used to facilitate the precise identification and differentiation of ricin and abrin. The method provides straightforward and sensitive detection in complex matrices including milk, plasma, coffee, orange juice, and tea via a simple serial-dilution procedure without any complex purification and enrichment steps. Furthermore, this assay was successfully applied in the unambiguous identification of active ricin and abrin in samples from OPCW biotoxin exercises.