bluuebunny/crossref_metadata_2025 huggingface dataset:
Construction and validation of a prognostic nutritional index-based nomogram for predicting pathological complete response in breast cancer: a two-center study of 1,170 patients
Authors: Qu Fanli , Luo Yaxi , Peng Yang , Yu Haochen , Sun Lu , Liu Shengchun , Zeng Xiaohua
Published: January 2024

Background

Pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) is associated with favorable outcomes in breast cancer patients. Identifying reliable predictors for pCR can assist in selecting patients who will derive the most benefit from NAC. The prognostic nutritional index (PNI) serves as an indicator of nutritional status and systemic immune competence. It has emerged as a prognostic biomarker in several malignancies; however, its predictive value for pCR in breast cancer remains uncertain. The objective of this study is to assess the predictive value of pretreatment PNI for pCR in breast cancer patients.

Methods

A total of 1170 patients who received NAC in two centers were retrospectively analyzed. The patients were divided into three cohorts: a training cohort (n=545), an internal validation cohort (n=233), and an external validation cohort (n=392). Univariate and multivariate analyses were performed to assess the predictive value of PNI and other clinicopathological factors. A stepwise logistic regression model for pCR based on the smallest Akaike information criterion was utilized to develop a nomogram. The C-index, calibration plots and decision curve analysis (DCA) were used to evaluate the discrimination, calibration and clinical value of the model.

Results

Patients with a high PNI (≥53) had a significantly increased pCR rate (OR 2.217, 95% CI 1.215-4.043, p=0.009). Tumor size, clinical nodal status, histological grade, ER, Ki67 and PNI were identified as independent predictors and included in the final model. A nomogram was developed as a graphical representation of the model, which incorporated the PNI and five other factors (AIC=356.13). The nomogram demonstrated satisfactory calibration and discrimination in the training cohort (C-index: 0.816, 95% CI 0.765-0.866), the internal validation cohort (C-index: 0.780, 95% CI 0.697-0.864) and external validation cohort (C-index: 0.714, 95% CI 0.660-0.769). Furthermore, DCA indicated a clinical net benefit from the nomogram.

Conclusion

The pretreatment PNI is a reliable predictor for pCR in breast cancer patients. The PNI-based nomogram is a low-cost, noninvasive tool with favorable predictive accuracy for pCR, which can assist in determining individualized treatment strategies for breast cancer patients.
Drug survival of IL-12/23, IL-17 and IL-23 inhibitors for moderate-to-severe plaque psoriasis: a retrospective multicenter real-world experience on 5932 treatment courses – IL PSO (Italian landscape psoriasis)
Authors: Gargiulo Luigi , Ibba Luciano , Malagoli Piergiorgio , Balato Anna , Bardazzi Federico , Burlando Martina , Carrera Carlo G. , Damiani Giovanni , Dapavo Paolo , Dini Valentina , Gaiani Francesca M. , Girolomoni Giampiero , Guarneri Claudio , Lasagni Claudia , Loconsole Francesco , Marzano Angelo V. , Megna Matteo , Mercuri Santo R. , Travaglini Massimo , Costanzo Antonio , Narcisi Alessandra
Published: January 2024

Introduction

The development of several effective biological drugs for moderate-to-severe plaque psoriasis has dramatically changed the lives of patients. Despite the wide use of interleukin (IL) inhibitors, limited data are available to date regarding long-term treatment persistence.

Method

This multicenter retrospective real-world study evaluated 5932 treatment courses across 5300 patients, all treated with interleukin inhibitors. Drug survival was expressed by using the Kaplan-Meier estimator for each biological drug at 6, 12, 24, 36 and 48 months. We also stratified by discontinuation associated with primary or secondary ineffectiveness.

Results

In our study, the most prescribed drugs were secukinumab (1412), ixekizumab (1183), and risankizumab (977). After four years of follow-up, risankizumab emerged as the treatment with the highest drug survival overall, as 91.6% of patients were still on treatment. The overall probability of drug survival at four years was comparable for tildrakizumab (83.5%), ixekizumab (82.6%), guselkumab (82.4%) and brodalumab (81.8%). When evaluating only patients who discontinued the treatment because of ineffectiveness, once again risankizumab was the molecule with the highest drug survival at 4 years (93.4%), this time followed by ixekizumab (87%). Our study, in which all IL inhibitors were adequately represented, confirmed a slightly better treatment persistence for IL-23 inhibitors, consistent with other real-world studies.

Conclusion

Our experience showed that IL-23 inhibitors, and risankizumab in particular, had a higher probability of drug survival overall during a 4-year follow-up. Risankizumab and ixekizumab were less likely to be discontinued because of ineffectiveness after four years.
Role of CD1d and iNKT cells in regulating intestinal inflammation
Authors: Lee Sung Won , Park Hyun Jung , Van Kaer Luc , Hong Seokmann
Published: January 2024

Invariant natural killer T (iNKT) cells, a subset of unconventional T cells that recognize glycolipid antigens in a CD1d-dependent manner, are crucial in regulating diverse immune responses such as autoimmunity. By engaging with CD1d-expressing non-immune cells (such as intestinal epithelial cells and enterochromaffin cells) and immune cells (such as type 3 innate lymphoid cells, B cells, monocytes and macrophages), iNKT cells contribute to the maintenance of immune homeostasis in the intestine. In this review, we discuss the impact of iNKT cells and CD1d in the regulation of intestinal inflammation, examining both cellular and molecular factors with the potential to influence the functions of iNKT cells in inflammatory bowel diseases such as Crohn’s disease and ulcerative colitis.
The potential role of Hippo pathway regulates cellular metabolism via signaling crosstalk in disease-induced macrophage polarization
Authors: An Yina , Tan Shuyu , Yang Jingjing , Gao Ting , Dong Yanjun
Published: January 2024

Macrophages polarized into distinct phenotypes play vital roles in inflammatory diseases by clearing pathogens, promoting tissue repair, and maintaining homeostasis. Metabolism serves as a fundamental driver in regulating macrophage polarization, and understanding the interplay between macrophage metabolism and polarization is crucial for unraveling the mechanisms underlying inflammatory diseases. The intricate network of cellular signaling pathway plays a pivotal role in modulating macrophage metabolism, and growing evidence indicates that the Hippo pathway emerges as a central player in network of cellular metabolism signaling. This review aims to explore the impact of macrophage metabolism on polarization and summarize the cell signaling pathways that regulate macrophage metabolism in diseases. Specifically, we highlight the pivotal role of the Hippo pathway as a key regulator of cellular metabolism and reveal its potential relationship with metabolism in macrophage polarization.
Learning and unlearning voicing assimilation
Authors: Bárkányi Zsuzsanna , G. Kiss Zoltán
Published: January 2024

This study investigates how postlexical phonological processes are acquired in multilingual speech, namely, how learners cope with conflicting demands in the production and perception of the voicing patterns in their non-native languages, what impact lexical knowledge has on learner behavior, and to what extent existing speech learning models can account for it. To investigate this, 14 Hungarian native speakers, proficient sequential learners of Spanish and English, took part in two types of experiment. The production experiments examined regressive voicing assimilation between obstruents and when the trigger was a sonorant consonant (presonorant voicing) word-internally and across word-boundary. At word level, we compared various lexical groups: non-cognates, double cognates and triple cognates (inhibitory, facilitative, and cognates with conflicting information). The perception experiments aimed to find out whether learners notice the voicing assimilations mentioned. The results showed that participants failed to learn presonorant voicing and failed to block regressive voicing assimilation despite perceiving the latter as linguistically relevant. Data also revealed that there is no direct link between perception and production, and that cognate status had a limited effect, but in triple cognates the primacy of the native language was dominant. Thus, it is concluded that in laryngeal postlexical processes the native language plays the primary role, neither the other non-native language, nor linguistic proximity seems to be decisive. Our data can be best accounted for by the Scalpel Model extended to phonological acquisition.
Oxygen isotopic fractionation during dissolved oxygen consumption in the bottom layer of the Ulleung Basin, East/Japan Sea
Authors: Kim Yeseul , Kang Dong-Jin
Published: January 2024

The interpretation of decline in dissolved oxygen (DO) in the oxygenated bottom water of the Ulleung Basin (UB), southwest of the East/Japan Sea has been challenging because of the integrated influence of various DO-consuming processes. Therefore, the stable oxygen isotopic fractionation of DO was investigated to enhance our understanding of the distinct DO consumption observed in the bottom layers of the center of the UB. We explored the relationship between DO and its oxygen isotope composition (δ18ODO) using data collected at a station located in the center of the UB in 2020, 2021, and 2022. An unforeseen decrease in δ18ODO in the bottom layer (> 1800 m) where DO was depleted was discovered. The overall DO consumption in the mesopelagic water layer (300–1000 m), primarily attributed to water column respiration, exhibited an isotopic fractionation factor (α) with 0.985 ± 0.001 in the δ18ODO/[O2] relationship. The consumptive isotope fractionation factor in the bottom waters near the sediments (approximately 2146 m) showed a value slightly higher (0.988 ± 0.002) than that in the mesopelagic water layer. This isotopic signature is likely due to a smaller fractionation in the bottom waters relative to the mesopelagic water. The isotopic evidence suggests the involvement of mineral oxidation associated with excess dissolved Mn and Fe in the bottom waters because mineral oxidation exhibits a smaller fractionation effect than respiration. Our study demonstrates that DO depletion results from multiple consumption processes, including respiration, mineral oxidation, and diffusive transport, and the isotopic behavior provides evidence that mineral oxidation significantly influences DO consumption.
Failure modes and mechanical properties of double-layer rock-like composite specimens with a single fissure under triaxial compression
Authors: Xiao Taoli , Xu Ke , Lu Yifan , She Haicheng
Published: January 2024

Introduction: Geotechnical engineering disasters often result from instability failures in layered and heterogeneous fissured rock masses. However, the key mechanisms governing mechanical properties and crack propagation in these rock masses remain unclear.

Methods: This study presents triaxial compression tests on double-layer rock-like specimens composed of limestone and sandstone materials, containing a single fissure, to investigate the effects of fissure angles and positions on the strength and failure modes of these double-layer specimens under varying confining pressure.

Results and Discussion: The experimental results reveal that the intact composite rock approaches the strength of sandstone but is deformation-limited by limestone. Under constant confining pressure (σ3 = 5 MPa), the fissure angle affects initial crack initiation, and fissure position dictates the failure mode and extent, while increased confining pressure induces overall shear failure in the composite rock, with the failure mode being predominantly influenced by confining pressure. Concerning mechanical deformation, augmenting the fissure angle and confining pressure substantially enhances the elasticity and ductility of the composite rock. Regarding volumetric deformation, the extent of volume shrinkage in the composite rock is influenced by both fissure angle and confining pressure, while volume expansion is influenced by fissure position. Under uniaxial compression, fissured composite rock exhibits the most unstable crack propagation, resulting in early failure. Triaxial compression shows that a higher fissure angle stabilizes crack propagation while confining pressure variation affects stability only when the fissure is in limestone. When the fissure is in sandstone, crack propagation stability remains at its highest. Furthermore, an increase in fissure angle, higher confining pressure, and changes in fissure position from sandstone through the contact interface to limestone contribute to an increasing trend in the peak strength and elastic modulus of the composite rock. Fissure-induced rock degradation is primarily influenced by the fissure angle. These findings are significant for guiding engineering construction and design, providing valuable insights to geotechnical engineers, and enhancing safety in rock engineering projects.
Obstetric Medicine: the protocol for a prospective three-dimensional cohort study to assess maternity care for women with pre-existing conditions (ForMaT)
Authors: Jost Elena , Kosian Philipp , Greiner Gregory Gordon , Icks Andrea , Schmitz Marie-Therese , Schmid Matthias , Merz Waltraut M.
Published: January 2024

Background

Pregnancies in women with pre-existing medical conditions are on the rise. These pregnancies are characterized by an increased rate of maternal and perinatal complications, which can result in higher health care expenditures and altered pregnancy experiences. The purpose of this study is to integrally analyze maternity care for women with pre-existing conditions in the framework of a risk-adapted, interdisciplinary care by recording three substantial parts of maternity care: (1) maternal and perinatal outcome; (2) hospital costs and reimbursements covering the period from preconception counseling or initial antenatal visit to discharge after birth; and (3) women’s experience of reproductive choice and becoming a mother in the presence of a pre-existing condition.

Methods

In this observational, prospective, longitudinal, and monocentric cohort study, we aim to include a total of 1,500 women over a recruitment period of 15 months. Women registering for care at the Department of Obstetrics and Prenatal Medicine, University Hospital Bonn, Germany, are allocated to three groups based on their health and risk status: women with pre-existing conditions, as well as healthy women with obstetric risk factor and healthy women with a low-risk pregnancy. Participants are observed from time of initial consultation until discharge after birth. Analysis focuses on (1) maternal and perinatal outcome, especially rate of severe maternal and neonatal morbidity; (2) costs and reimbursements; and (3) surveys to capture of women’s experience and health-related quality of life during the time of reproductive choice, pregnancy, and childbirth in the presence of pre-existing medical conditions.

Discussion

With its complex three-dimensional design, the ForMaT-Trial is aiming to provide a comprehensive analysis of pregnancy and childbirth in women with pre-existing conditions. The results may serve as a basis for counseling and care of these women. By analyzing costs of specialized care, data for discussing reimbursement are generated. Lastly, our results may increase awareness for the perception of reproductive choice, pregnancy and motherhood in this continuously rising population.

Clinical trial registration: German Clinical Trials Register, DRKS00030061, October 28, 2022.
A multi-institute, follow-up, observational study measuring nursing students’ adherence to infection prevention and control protocols in Saudi Arabia
Authors: Albarmawi Marwa , Al Hadid Lourance , Alnjadat Rafi , Aljabery Ahmad
Published: January 2024

Background

Nursing students learn principles of infection prevention and control (IPC) and hand hygiene (HH) in clinical courses, and their learning is reflected in their practice.

Objectives

The knowledge, attitude, and practice of principles of IPC and HH of the students were measured prior to and after attending an educational workshop. The adherence of the students to the IPC and HH protocols at the hospital was also observed.

Methods

This study included a pretest-posttest time series follow-up and an observational part. During the first part of the study, students attended a workshop, which was preceded by a pretest. It was then followed by a posttest directly after finishing the workshop and in 12 weeks. Participants were submitted to an observational part by a trained observer to document certain skills taught earlier during the workshop.

Settings

Students from three nursing schools in Saudi Arabia participated in the study.

Participants

A total number of 130 completed the study protocol, and 100 completed the observation part.

Results

Students were found to experience an improvement in their knowledge, beliefs, and commitment scales after the workshop. The attitude scale remained relatively unchanged over different tests. Most students performed the skills properly and adequately, but some failed to perform certain skills, like hand rub, and the proper use of disinfectants.
Chronic post-surgical pain after knee arthroplasty: a role of peripheral nerve blocks
Authors: Sreckovic Svetlana , Ladjevic Nebojsa , Milicic Biljana , Tulic Goran , Milovanovic Darko , Djukanovic Marija , Kadija Marko
Published: January 2024

Introduction

Peripheral nerve blocks are an efficient method of pain control after total knee arthroplasty (TKA), but there is no report of their impact on chronic post-surgical pain (CPSP).

Methods

This prospective observational study aimed to assess adductor canal block (ACB) and IPACK block (blocks vs. no blocks) on opioid consumption, postoperative pain score, chronic post-surgical pain 2 years after TKA.

Results

166 patients (82 vs. 84) were analyzed. Opioid consumption was less in the group with blocks (9.74 ± 3.87 mg vs. 30.63 ± 11.52 mg) (p < 0.001). CPSP was present in 20.24% of patients in the group without blocks and 6.1% of patients with blocks (p = 0.011). Predictor variables of CPSP included pain before surgery (cut-off of 5.5), pain at rest (cut-off of 2.35), pain during active movement (cut-off: 2.5), and opioid consumption (cut-off: 8 mg).

Conclusion

Peripheral nerve blocks provide adequate analgesia, significantly decrease opioid consumption, improve functional outcomes, and reduce CPSP 2 years after surgery.
Opportunities and challenges of traditional Chinese medicine doctors in the era of artificial intelligence
Authors: Li Wenyu , Ge Xiaolei , Liu Shuai , Xu Lili , Zhai Xu , Yu Linyong
Published: January 2024

With the exponential advancement of artificial intelligence (AI) technology, the realm of medicine is experiencing a paradigm shift, engendering a multitude of prospects and trials for healthcare practitioners, encompassing those devoted to the practice of traditional Chinese medicine (TCM). This study explores the evolving landscape for TCM practitioners in the AI era, emphasizing that while AI can be helpful, it cannot replace the role of TCM practitioners. It is paramount to underscore the intrinsic worth of human expertise, accentuating that artificial intelligence (AI) is merely an instrument. On the one hand, AI-enabled tools like intelligent symptom checkers, diagnostic assistance systems, and personalized treatment plans can augment TCM practitioners’ expertise and capacity, improving diagnosis accuracy and treatment efficacy. AI-empowered collaborations between Western medicine and TCM can strengthen holistic care. On the other hand, AI may disrupt conventional TCM workflow and doctor-patient relationships. Maintaining the humanistic spirit of TCM while embracing AI requires upholding professional ethics and establishing appropriate regulations. To leverage AI while retaining the essence of TCM, practitioners need to hone holistic analytical skills and see AI as complementary. By highlighting promising applications and potential risks of AI in TCM, this study provides strategic insights for stakeholders to promote the integrated development of AI and TCM for better patient outcomes. With proper implementation, AI can become a valuable assistant for TCM practitioners to elevate healthcare quality.
Development and usability testing of a patient digital twin for critical care education: a mixed methods study
Authors: Rovati Lucrezia , Gary Phillip J. , Cubro Edin , Dong Yue , Kilickaya Oguz , Schulte Phillip J. , Zhong Xiang , Wörster Malin , Kelm Diana J. , Gajic Ognjen , Niven Alexander S. , Lal Amos
Published: January 2024

Background

Digital twins are computerized patient replicas that allow clinical interventions testing in silico to minimize preventable patient harm. Our group has developed a novel application software utilizing a digital twin patient model based on electronic health record (EHR) variables to simulate clinical trajectories during the initial 6 h of critical illness. This study aimed to assess the usability, workload, and acceptance of the digital twin application as an educational tool in critical care.

Methods

A mixed methods study was conducted during seven user testing sessions of the digital twin application with thirty-five first-year internal medicine residents. Qualitative data were collected using a think-aloud and semi-structured interview format, while quantitative measurements included the System Usability Scale (SUS), NASA Task Load Index (NASA-TLX), and a short survey.

Results

Median SUS scores and NASA-TLX were 70 (IQR 62.5–82.5) and 29.2 (IQR 22.5–34.2), consistent with good software usability and low to moderate workload, respectively. Residents expressed interest in using the digital twin application for ICU rotations and identified five themes for software improvement: clinical fidelity, interface organization, learning experience, serious gaming, and implementation strategies.

Conclusion

A digital twin application based on EHR clinical variables showed good usability and high acceptance for critical care education.
Abdominal venous thromboses: detection of the JAK2 p.V617F mutation by next-generation ultradeep sequencing—A prevalence study of patients in Mecklenburg-West Pomerania (2017–2021)
Authors: Henze Larissa , Grunwald Luise , Felser Sabine , Witte Maria , Grosse-Thie Christina , Roolf Catrin , Murua Escobar Hugo , Junghanss Christian
Published: January 2024

Background

Abdominal venous thromboses are rare thrombotic events with heterogeneous etiologies. They are related to myeloproliferative neoplasms (MPNs) in some patients and can occur as first signs of the disease. MPNs are characterized by mutations in the genes of Janus kinase 2 (JAK2), myeloproliferative leukemia virus oncogene (MPL), and calreticulin (CALR).

Methods

Within the prospective trial “Prevalence of JAK2 mutations in patients with abdominal venous thromboses” (JAK2 MV study; German Clinical Trials Register: DRKS00026943), the peripheral blood of patients with abdominal venous thromboses in Mecklenburg-West Pomerania, a federal state located in north-east Germany, was analyzed by next-generation ultradeep sequencing for MPN-associated mutations. Clinical characteristics and blood cell counts were also of interest. The primary endpoint was the detection of the mutation JAK2 p.V617F. Secondary endpoints were the detection of other acquired variants of JAK2, as well as MPL and CALR.

Results

A total of 68 patients with abdominal venous thromboses were included from February 2017 to January 2021, with splanchnic veins affected in 65 patients. The mutation JAK2 p.V617F was present in 13 patients (19%), with four patients showing low variant allele frequencies (VAF 0.1% to 1.9%). The time interval from the thrombotic event to analysis was longer for patients with the mutation. The mutation MPL p.W515R was detected in three cases, all of them with low VAF. One patient among them had a concurrent mutation of JAK2 p.V617F. The mutations CALR type I or type II were not found.

Discussion

By analyzing peripheral blood for the mutation JAK2 p.V617F, an important cause of these rare thrombotic events can be identified. The development of a diagnostic workup with next-generation ultradeep sequencing for the analysis of the JAK2 p.V617F mutation and further mutations has the potential to better understand the etiology of abdominal venous thromboses in individual patients in regional clinical care, as abdominal venous thromboses are diagnosed by various medical disciplines.
Long-term phosphorus fertilization reveals the phosphorus limitation shaping the soil micro-food web stability in the Loess Plateau
Authors: Li Liangliang , Luo Zhuzhu , Li Lingling , Niu Yining , Zhang Yaoquan , He Renyuan , Liu Jiahe , Nian Lili
Published: January 2024

The intricate decomposition pathways within soil micro-food webs are vital for cycling soil organic carbon and nutrients, influencing the quality, productivity, and sustainability of soil systems. However, the impact of diverse phosphorus addition on these organic decomposition pathways still needs to be explored. In an 8-year experiment, phosphorus (P) fertilizer was added at varying levels (0 kg ha−1, CK; 60 kg ha−1, P60; 120 kg ha−1, P120; and 180 kg ha−1, P180), to investigate the response of the soil micro-food web. The results revealed a significant effect of phosphorus addition on soil microorganisms and nematodes, with P60 exerting a greater influence than other treatments. At P60, the Shannon index of nematodes and fungi surpassed other treatments, indicating higher diversity, while the Shannon index of bacteria was lower. The Chao1 index of bacteria and fungi at P60 was higher, contrasting with the lower index for nematodes. Metabolic footprints of bacterivores and omnivores–predators (BFMF and OPMF) were higher at P60, while metabolic footprints of fungivores and plant parasites (FFMF and PPMF) were lower, signifying altered energy flow. Functional metabolic footprints and energy flow analysis unveiled a stable soil micro-food web structure at P60, with enhanced energy conversion efficiency. Network analysis illustrated positive correlations between fungi, fungivorous nematodes (FF), and omnivorous-predatory nematodes (OP) at P60, while P120 and P180 showed positive correlations among bacteria, bacterivorous nematodes (BF), and OP. Path analysis underscored the higher contribution rate of BF-C, FF-C, and OP-C to soil organic carbon at P60 compared with P120 and P180. These findings suggest that nutrient interactions between fungi and nematodes regulate soil micro-food web decomposition under low phosphorus concentrations. In contrast, interactions between bacteria and nematodes dominate at high phosphorus concentrations. The study indicates that adding phosphorus has nuanced bottom-up effects, intricately shaping the structure and activity of the pathways and underscoring the need for a comprehensive understanding of nutrient dynamics in soil ecosystems.
Effectiveness assessment of using water environmental microHI to predict the health status of wild fish
Authors: Yang Haile , Zhong Jia , Leng Xiaoqian , Wu Jinming , Cheng Peilin , Shen Li , Wu Jinping , Li Pengcheng , Du Hao
Published: January 2024

Aquatic wildlife health assessment is critically important for aquatic wildlife conservation. However, the health assessment of aquatic wildlife (especially aquatic wild animals) is difficult and often accompanied by invasive survey activities and delayed observability. As there is growing evidence that aquatic environmental microbiota could impact the health status of aquatic animals by influencing their symbiotic microbiota, we propose a non-invasive method to monitor the health status of wild aquatic animals using the environmental microbiota health index (microHI). However, it is unknown whether this method is effective for different ecotype groups of aquatic wild animals. To answer this question, we took a case study in the middle Yangtze River and studied the water environmental microbiota and fish gut microbiota at the fish community level, population level, and ecotype level. The results showed that the gut microHI of the healthy group was higher than that of the unhealthy group at the community and population levels, and the overall gut microHI was positively correlated with the water environmental microHI, whereas the baseline gut microHI was species-specific. Integrating these variations in four ecotype groups (filter-feeding, scraper-feeding, omnivorous, and carnivorous), only the gut microHI of the carnivorous group positively correlated with water environmental microHI. Alcaligenaceae, Enterobacteriaceae, and Achromobacter were the most abundant groups with health-negative-impacting phenotypes, had high positive correlations between gut sample group and environment sample group, and had significantly higher abundance in unhealthy groups than in healthy groups of carnivorous, filter-feeding, and scraper-feeding ecotypes. Therefore, using water environmental microHI to indicate the health status of wild fish is effective at the community level, is effective just for carnivorous fish at the ecotype level. In the middle Yangtze River, Alcaligenaceae, Enterobacteriaceae (family level), and Achromobacter (genus level) were the key water environmental microbial groups that potentially impacted wild fish health status. Of course, more data and research that test the current hypothesis and conclusion are encouraged.
Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation
Authors: Yao Junpeng , Yan Xiangyun , Li Yanqiu , Chen Yaoyao , Xiao Xianjun , Zhou Siyuan , Zhang Wei , Wang Lu , Chen Min , Zeng Fang , Li Ying
Published: January 2024

While dysbiosis within the intestinal ecosystem has been associated with functional constipation (FC), the mechanisms underlying the interactions between FC and the microbiome remain poorly elucidated. Recent investigations suggested that host microRNAs (miRNAs) can modulate bacterial growth and influence the composition of the gut microbiome. To explore the connection between gut microbiota and fecal miRNAs in FC patients, we initially employed 16S rRNA sequencing to assess the gut microbial landscape in 30 FC patients and 30 healthy controls (HCs). The α-diversity within the FC group exhibited some alterations, and the β-diversity significantly differed, signifying distinctive variations in gut microbiota composition between FC patients and HCs. Subsequently, we identified 44 differentially expressed (DE) miRNAs in feces from FC patients and HCs. Through correlation analysis between DE miRNAs and FC-associated microbiota, we detected an interaction involving nine DE miRNAs (miR-205-5p, miR-493-5p, miR-215-5p, miR-184, miR-378c, miR-335-5p, miR-514a-3p, miR-141-3p, and miR-34c-5p) with seven bacterial genera (Oscillibacter, Escherichia.Shigella, UCG.002, Lachnospiraceae_NK4A136_group, Lachnospiraceae_UCG.010, Eubacterium_ruminantium_group and Megamonas), as evidenced by a co-occurrence network. Further, a comprehensive panel of seven diagnostic biomarkers (Oscillibacter, Escherichia.Shigella, UCG.002, miR-205-5p, miR-493-5p, miR-215-5p, and Lachnospiraceae_NK4A136_group) demonstrated robust discriminatory capacity in predicting FC status when integrated into a random forest model (AUC = 0.832, 95% CI: 65.73–98.88). Microbiomes correlating with DE miRNAs exhibited enrichment in distinct predicted metabolic categories. Moreover, miRNAs correlated with FC-associated bacteria were found to be enriched in signaling pathways linked to colonic contractility, including Axon guidance, PI3K-Akt signaling pathway, MAPK signaling pathway, and Hippo signaling pathway. Our study offers a comprehensive insight into the global relationship between microbiota and fecal miRNAs in the context of FC, presenting potential targets for further experimental validation and therapeutic interventions.
Microbes on the “peachy spots” of ancient Kaihua paper: microbial community and functional analysis
Authors: Zhou Yanjun , Shi Yan , Huang Yanyan , Zhong Jiang
Published: January 2024

Kaihua paper is a type of precious hand-made paper in China that has been used throughout Chinese history. Due to its extraordinary whiteness and fine texture, it was adopted by the imperial palace in the reign of Emperor Kang Xi and Yong Zheng of the Qing Dynasty of China in the 17th and 18th century. It is stained by a special type of yellowish-brown spot after years of storage, which is called a “peachy spot.” The formation of such spots remains unclear, although complicated physicochemical processes or microbial activities might be involved. We performed nondestructive sampling and high-throughput sequencing on peachy spot surfaces, unstained areas, and air samples in the stack room to analysis the the bacterial and fungal communities, and performed prediction of functional genes of the bacterial communities. The results showed that peachy spot formation was mainly related to bacterial communities rather than fungal communities. Significantly more potential acid- producing, acidophilic or cellulase-producing bacteria, such as, Streptococcus, Staphylococcus, and Lysinibacillus, and pigment-producing bacteria, such as Methylobacterium and Rubrobacter, were identified in the peachy spot samples. Prediction of the functional genes of the bacterial community also suggested the production of acidic substance pigments. These findings provide new insights into the pigment formation mechanism in ancient paper and open an opportunity to develop new strategies to preserve the ancient paper documents.
Antimicrobial resistance and genetic diversity of Klebsiella pneumoniae strains from different clinical sources in horses
Authors: Gravey Francois , Sévin Corinne , Castagnet Sophie , Foucher Nathalie , Maillard Karine , Tapprest Jackie , Léon Albertine , Langlois Bénédicte , Le Hello Simon , Petry Sandrine
Published: January 2024

Introduction

Klebsiella pneumoniae is a major cause of infections and reproductive disorders among horses, ranked in recent French studies as the sixth most frequently isolated bacterial pathogen in equine clinical samples. The proportion of multidrug-resistant (MDR) K. pneumoniae is therefore significant in a context where MDR K. pneumoniae strains are considered a major global concern by the World Health Organization.

Methods

In this study, we used a genomic approach to characterize a population of 119 equine K. pneumoniae strains collected by two laboratories specialized in animal health in Normandy (France). We describe the main antibiotic resistance profiles and acquired resistance genes, and specify the proportion of virulence-encoding genes carried by these strains. The originality of our panel of strains lies in the broad collection period covered, ranging from 1996 to 2020, and the variety of sample sources: necropsies, suspected bacterial infections (e.g., genital, wound, allantochorion, and umbilical artery samples), and contagious equine metritis analyses.

Results

Our results reveal a remarkable level of genomic diversity among the strains studied and we report the presence of 39% MDR and 9% hypervirulent strains (including 5% that are both MDR and hypervirulent).

Discussion

These findings clearly emphasize the importance of improving the surveillance of K. pneumoniae in routine equine diagnostic tests to detect high-risk MDR-hypervirulent Klebsiella pneumoniae strains. The circulation of these worrisome strains reveals that they are not being detected by the simple K1, K2, and K5 serotype approach currently implemented in the French horse-breeding sector.
Oral administration of resveratrol reduces oxidative stress generated in the hippocampus of Wistar rats in response to consumption of ethanol
Authors: Navarro-Cruz Addí Rhode , Juárez-Serrano Daniel , Cesar-Arteaga Ivan , Kammar-García Ashuin , Guevara-Díaz Jorge Alberto , Vera-López Obdulia , Lazcano-Hernández Martin , Pérez-Xochipa Ivonne , Segura-Badilla Orietta
Published: January 2024

Introduction

Chronic ethanol intake has been found to favor hippocampal deterioration and alter neuronal morphological maturation; resveratrol has been suggested as an antioxidant that may counteract these effects. The objective of this study was to analyze the effect of resveratrol on oxidative stress markers, endogenous antioxidant system in the hippocampus, and the behavior of male Wistar rats administered different concentrations of ethanol.

Methods

The animals, at 3 months old, were randomly distributed into 11 study groups (n = 6/group), orally administered (5 days on, 2 days off) with water (control), ethanol (10, 20, 30, 40 or 50%), or ethanol (10, 20, 30, 40 or 50%) plus resveratrol (10 mg/Kg/day) for 2 months. Subsequently, the production of nitrites, malondialdehyde, and 4-hydroxy-alkenal (HNE) and the enzymatic activity of catalase and superoxide dismutase (SOD) were quantified.

Results

The levels of nitric oxide and lipid peroxidation products were significantly increased in each ethanol concentration and were statistically different compared to the control group; however, resveratrol significantly reduced oxidative stress caused by high ethanol concentration. The SOD and CAT did not present significant changes with respect to the controls in any of the study groups. In the different concentrations of ethanol used, GR increases significantly in the groups administered with resveratrol but not GPx. Resveratrol was shown to maintain the results similar to the control at most ethanol concentrations.

Discussion

Our results suggest that resveratrol prevents oxidative stress induced by ethanol in the hippocampus by decreasing cellular lipid peroxidation, but does not prevent the activation of catalase or SOD enzymes; however, allows glutathione to be kept active and in adequate concentrations in its reduced form and avoids alterations in the locomotor system.
Beyond correlation: optimal transport metrics for characterizing representational stability and remapping in neurons encoding spatial memory
Authors: Aoun Andrew , Shetler Oliver , Raghuraman Radha , Rodriguez Gustavo A. , Hussaini S. Abid
Published: January 2024

Introduction

Spatial representations in the entorhinal cortex (EC) and hippocampus (HPC) are fundamental to cognitive functions like navigation and memory. These representations, embodied in spatial field maps, dynamically remap in response to environmental changes. However, current methods, such as Pearson's correlation coefficient, struggle to capture the complexity of these remapping events, especially when fields do not overlap, or transformations are non-linear. This limitation hinders our understanding and quantification of remapping, a key aspect of spatial memory function.

Methods

We propose a family of metrics based on the Earth Mover's Distance (EMD) as a versatile framework for characterizing remapping.

Results

The EMD provides a granular, noise-resistant, and rate-robust description of remapping. This approach enables the identification of specific cell types and the characterization of remapping in various scenarios, including disease models. Furthermore, the EMD's properties can be manipulated to identify spatially tuned cell types and to explore remapping as it relates to alternate information forms such as spatiotemporal coding.

Discussion

We present a feasible, lightweight approach that complements traditional methods. Our findings underscore the potential of the EMD as a powerful tool for enhancing our understanding of remapping in the brain and its implications for spatial navigation, memory studies and beyond.
The cortico-striatal circuitry in autism-spectrum disorders: a balancing act
Authors: Soghomonian Jean-Jacques
Published: January 2024

The basal ganglia are major targets of cortical inputs and, in turn, modulate cortical function via their projections to the motor and prefrontal cortices. The role of the basal ganglia in motor control and reward is well documented and there is also extensive evidence that they play a key role in social and repetitive behaviors. The basal ganglia influence the activity of the cerebral cortex via two major projections from the striatum to the output nuclei, the globus pallidus internus and the substantia nigra, pars reticulata. This modulation involves a direct projection known as the direct pathway and an indirect projection via the globus pallidus externus and the subthalamic nucleus, known as the indirect pathway. This review discusses the respective contribution of the direct and indirect pathways to social and repetitive behaviors in neurotypical conditions and in autism spectrum disorders.
A lightweight mixup-based short texts clustering for contrastive learning
Authors: Xu Qiang , Zan HaiBo , Ji ShengWei
Published: January 2024

Traditional text clustering based on distance struggles to distinguish between overlapping representations in medical data. By incorporating contrastive learning, the feature space can be optimized and applies mixup implicitly during the data augmentation phase to reduce computational burden. Medical case text is prevalent in everyday life, and clustering is a fundamental method of identifying major categories of conditions within vast amounts of unlabeled text. Learning meaningful clustering scores in data relating to rare diseases is difficult due to their unique sparsity. To address this issue, we propose a contrastive clustering method based on mixup, which involves selecting a small batch of data to simulate the experimental environment of rare diseases. The contrastive learning module optimizes the feature space based on the fact that positive pairs share negative samples, and clustering is employed to group data with comparable semantic features. The module mitigates the issue of overlap in data, whilst mixup generates cost-effective virtual features, resulting in superior experiment scores even when using small batch data and reducing resource usage and time overhead. Our suggested technique has acquired cutting-edge outcomes and embodies a favorable strategy for unmonitored text clustering.
Association of non-contrast CT markers with long-term functional outcome in deep intracerebral hemorrhage
Authors: Kölbl Kathrin , Hock Stefan W. , Xu Mingming , Sembill Jochen A. , Mrochen Anne , Balk Stefanie , Lang Stefan , Volbers Bastian , Engelhorn Tobias , Kallmünzer Bernd , Kuramatsu Joji B.
Published: January 2024

Objective

Hematoma expansion (HE) is the most important therapeutic target during acute care of patients with intracerebral hemorrhage (ICH). Imaging biomarkers such as non-contrast CT (NCCT) markers have been associated with increasing risk for HE. The aim of the present study was to evaluate the influence of NCCT markers with functional long-term outcome and with HE in patients with deep (basal ganglia and thalamus) ICH who represent an important subgroup of patients at the highest risk for functional deterioration with HE due to the eloquence of the affected brain region.

Methods

From our prospective institutional database, all patients maximally treated with deep ICH were included and retrospectively analyzed. NCCT markers were recorded at diagnostic imaging, ICH volume characteristics were volumetrically evaluated, and all patients received follow-up imaging within 0–48 h. We explored associations of NCCT makers with unfavorable functional outcome, defined as modified Rankin scale 4–6, after 12 months and with HE. Bias and confounding were addressed by multivariable regression modeling.

Results

In 322 patients with deep ICH, NCCT markers were distributed as follows: irregular shape: 69.6%, heterogenous density: 55.9%, hypodensities: 52.5%, island sign: 19.3%, black hole sign: 11.5%, and blend sign: 4.7%. Upon multivariable regression analyses, independent associations were documented with the functional outcome for irregular shape (aOR: 2.73, 95%CI: 1.42–5.22, p = 0.002), heterogenous density (aOR: 2.62, 95%CI: 1.40–4.90, p = 0.003) and island sign (aOR: 2.54, 95%CI: 1.05–6.14, p = 0.038), and with HE for heterogenous density (aOR: 5.01, 95%CI: 1.93–13.05, p = 0.001) and hypodensities (aOR: 3.75, 95%CI: 1.63–8.62, p = 0.002).

Conclusion

NCCT markers are frequent in deep ICH patients and provide important clinical implications. Specifically, markers defined by diverging intra-hematomal densities provided associations with a 5-times higher risk for HE and a 2.5-times higher likelihood for unfavorable functional long-term outcome. Hence, these markers allow the identification of patients with deep ICH at high risk for clinical deterioration due to HE.
The expert's knowledge combined with AI outperforms AI alone in seizure onset zone localization using resting state fMRI
Authors: Kamboj Payal , Banerjee Ayan , Boerwinkle Varina L. , Gupta Sandeep K. S.
Published: January 2024

We evaluated whether integration of expert guidance on seizure onset zone (SOZ) identification from resting state functional MRI (rs-fMRI) connectomics combined with deep learning (DL) techniques enhances the SOZ delineation in patients with refractory epilepsy (RE), compared to utilizing DL alone. Rs-fMRI was collected from 52 children with RE who had subsequently undergone ic-EEG and then, if indicated, surgery for seizure control (n = 25). The resting state functional connectomics data were previously independently classified by two expert epileptologists, as indicative of measurement noise, typical resting state network connectivity, or SOZ. An expert knowledge integrated deep network was trained on functional connectomics data to identify SOZ. Expert knowledge integrated with DL showed a SOZ localization accuracy of 84.8 ± 4.5% and F1 score, harmonic mean of positive predictive value and sensitivity, of 91.7 ± 2.6%. Conversely, a DL only model yielded an accuracy of <50% (F1 score 63%). Activations that initiate in gray matter, extend through white matter, and end in vascular regions are seen as the most discriminative expert-identified SOZ characteristics. Integration of expert knowledge of functional connectomics can not only enhance the performance of DL in localizing SOZ in RE but also lead toward potentially useful explanations of prevalent co-activation patterns in SOZ. RE with surgical outcomes and preoperative rs-fMRI studies can yield expert knowledge most salient for SOZ identification.