bluuebunny/crossref_metadata_2025 huggingface dataset:
Fog in western coastal ecosystems: inter-disciplinary challenges and opportunities with example concepts from the Pacific Northwest, USA
Authors: Dye Alex , Rauschenbach Sonya , de Szoeke Simon , Igel Adele L. , Jin Yufang , Kim John B. , Krawchuk Meg A. , Maes Kenneth , O’Neill Larry , Paw U Kyaw Tha , Samelson Roger , Shaw David C. , Still Christopher
Published: November 2024

Coastal fog occurs along many of the world’s west coast continental environments. It is particularly consequential during summer when an increased frequency of fog co-occurs with the seasonal dryness characteristic of most west coast climate systems, for example, in the Pacific coast of North and South America, the southwestern African coast, and southern coastal Europe. Understanding coastal fog formation and effects has consequences for many disciplines, including the physical (e.g., atmospheric science, oceanography), biological (e.g., biogeography, ecophysiology), and socio-ecological realms (e.g., Indigenous cultural knowledge, public safety, economics). Although research practices differ across disciplines, they share many of the challenges needed to advance fog science. For example, coastal fog remains difficult to reliably monitor when, where, and why it occurs, which adds difficulty to understanding fog’s effects on all facets of the integrated coastal system. These shared challenges provide ripe opportunities for interdisciplinary collaboration, a template with past success in advancing fog-related science that can continue to have success in the future. In this perspectives review, we summarize the current status and frontiers of fog-related science from multiple disciplines, leveraging examples primarily drawn from the Pacific Northwest coastal region of the United States to show how interdisciplinary collaboration is needed to continue to advance our collective understanding of coastal fog formation and effects on west coast environments.
De novo SCN1A missense variant in a patient with Parkinson’s disease
Authors: Alluqmani Majed , Alayoubi Abdulfatah M. , Hashmi Jamil A. , Basit Sulman
Published: November 2024

Background

Variants in a gene encoding sodium voltage-gated channel alpha subunit 1 (SCN1A) are known to cause a broad clinical spectrum of epilepsy and associated features, including Dravet syndrome (MIM 607208), non-Dravet developmental and epileptic encephalopathy (MIM 619317), familial febrile seizures (MIM 604403), familial hemiplegic migraine (MIM 609634), and generalized epilepsy with febrile seizures (MIM 604403).

Methods

In this study, we examined a patient with Parkinson’s disease (PD) without any clinical manifestations of epilepsy and associated features. Genomic nucleic acid was extracted, and a complete coding sequence of the human genome (whole-exome sequencing) was sequenced. Moreover, Sanger sequencing of variants of interest was performed to validate the exome-discovered variants.

Results

We identified a heterozygous pathogenic missense mutation (c.1498C>T; p.Arg500Trp) in the SCN1A gene in the patient using the whole-exome sequencing approach. The onset of PD features in our patient occurred at the age of 30 years. Biochemical investigations were carried out to rule out any secondary cause of the disease, including Wilson's disease or another metabolic disorder. MRI of the brain and spinal images were unremarkable. Moreover, a dramatic response to carbidopa–levodopa treatment was also observed in the patient.

Conclusion

Our results suggest that the pathogenic variant in SCN1A may lead to PD features without epilepsy.
NET-EN treatment leads to delayed HSV-2 infection, enhanced mucin and T cell functions in the female genital tract when compared to DMPA in a preclinical mouse model
Authors: Mian M. Firoz , Pa Sidney , Rahman Nuzhat , Gillgrass Amy , Kaushic Charu
Published: November 2024

Depot-medroxyprogesterone acetate (DMPA) and Norethisterone Enanthate (NET-EN) are progestin-only injectable contraceptives widely used by women in sub-Sharan Africa, where incidence of HIV-1 and HSV-2 infection remains high. Studies indicate that DMPA usage can increase the risk of HSV-2 infection, but limited data indicate no increased risk with use of NET-EN. We therefore investigated the effects of NET-EN and DMPA on susceptibility to vaginal HSV-2 infection in ovariectomized (OVX) mice and effects on immune responses, particularly in the vaginal tract (VT). OVX mice, when treated with NET-EN and infected intravaginally, had delayed genital pathology, decreased viral shedding, and extended survival compared to DMPA- or untreated OVX mice. CD4+ T cells isolated from VT showed no significant change in frequency with either contraceptive. However, DMPA significantly decreased the total number of VT CD4+ and CD8+ T cells and the number of IFN-γ producing CD4 and CD8 T cells and increased the percentage of CD4 and CD8 T cells producing TNF-α compared to untreated mice. In contrast, NET-EN significantly enhanced percentages of CD8+ T cells compared to DMPA treated mice, and frequencies of IFN-γ+ CD4 and CD8 T cells in the VT compared to untreated mice. Comparative analysis of splenic lymphocytes indicated that DMPA treatment resulted in reduction of CD4+ T cell frequency, but enhanced TNF-α+ CD4 T cells compared to untreated mice. NET-EN enhanced the frequency of CD8 T cells, as well as IFN-γ+ and TNF-α+ CD4, and IFN-γ+ CD8 T cells in the spleen compared to untreated mice. Importantly, we found DMPA treatment that significantly reduced mucin production, whereas NET-EN enhanced expression of cell-associated mucin in VT. High levels of mucin in NET-EN mice were associated with lower levels of HSV-2 virus detected in the vaginal tract. This study provides the first evidence that NET-EN treatment can delay HSV-2 infection compared to DMPA.
Hemophagocytic lymphohistiocytosis caused by multiple infections during primary chemotherapy for pediatric acute lymphoblastic leukemia: a case report
Authors: Ao Yaning , Huang Yusheng , Zhou Xiaobo , Li Jiawen , Zhang Qing , Wu Sujun , Fu Ying , Zhang Jinfeng
Published: November 2024

Hemophagocytic lymphohistiocytosis (HLH) is a life-threatening hyperinflammatory disorder that occurs as a consequence of immune dysregulation. HLH can be primary (familial or non-familial) or secondary to infection, autoimmune disease or malignancy. Malignancy-associated HLH is often accompanied by hematologic and lymphoid neoplasms. This report describes the case of a 3-year-old girl with an initial diagnosis of acute lymphoblastic leukemia who subsequently developed HLH during primary chemotherapy. She was admitted with a pulmonary infection, and initial blood tests showed thrombocytopenia and anemia. Whole-exome sequencing of gene and whole transcriptome RNA sequencing data indicated mutations of UNC13D. The hospital course was complicated by multiple infections, altered mental status and acute respiratory distress syndrome. HLH secondary to multiple infections that achieved remission following targeted therapy with ruxolitinib, in conjunction with corticosteroids and other complementary treatments. This report provides a synopsis of the diagnostic and treatment procedures implemented in this case.
A review on the novel biomarkers of systemic lupus erythematosus discovered via metabolomic profiling
Authors: Liu Yinghong , Yang Xiaojuan
Published: November 2024

Systemic lupus erythematosus (SLE) is a multifaceted autoimmune disease affecting various body organs and systems. The diagnosis of SLE and its complications is based on evident clinical symptoms, serological marker levels, and pathological findings. Some serological markers have a low sensitivity and specificity, and biopsy procedures are invasive in nature. Hence, metabolomics has emerged as a valuable tool for SLE screening and categorization. Its application has contributed significantly to identifying SLE pathogenesis, improving clinical diagnosis, and developing treatment approaches. This review provides an overview of the utilization of metabolomics in the study of SLE, focusing on advancements in understanding the disease’s pathogenesis, aiding in diagnosis, and monitoring treatment efficacy.
Clinical characteristics and antibody response to Omicron variants among solid carcinoma patients in China on the 2022.12–2023.4 wave of the COVID-19 pandemic
Authors: Dai Rongrong , Peng Weiyu , Xu Nani , Qin Pan , Ding Linling , Hua Qianhui , Jiang Jianmin , He Fang , Zhang Hangjie
Published: November 2024

Background

China experienced a surge of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants after adjusting its zero-coronavirus disease 2019 (COVID-19) policy. Although infections with Omicron variants are generally less severe than infections with previous SARS-CoV-2 variants, the clinical characteristics, persistent symptoms, and antibody responses in solid carcinoma patients (SCPs) with COVID-19 during the Omicron wave are unclear.

Methods

We conducted a cross-sectional study in April 2023, recruiting healthy controls (HCs) from the community and SCPs from Zhejiang Provincial People’s Hospital. Serum samples were collected, and a questionnaire was used to assess SARS-CoV-2 infection status, including demographic characteristics, clinical manifestations, and “long COVID” symptoms. Humoral immune responses were analyzed by enzyme-linked immunosorbent assays (ELISAs) targeting immunoglobulin G (IgG) antibodies against the receptor-binding domain (RBD; Omicron BA.4/5) protein and cell culture-based neutralization assays against Omicron variants (BA.4/5, BF.7, XBB.1.5, and EG.5).

Results

In total, 298 SCPs and 258 HCs were enrolled. Self-reported COVID-19 case rates were significantly lower in SCPs than in HCs (78.5% vs. 93.8%, P<0.001). Common COVID-19 symptoms were similar between the two groups, primarily comprising general (92.6% vs. 84.9%) and respiratory symptoms (51.9% vs. 48.2%) after acute infection. There was no significant difference in persistent symptoms at 1–3 months post-infection (P=0.353); fatigue was the most common symptom (45.0% vs. 44.8%). SCPs exhibited lower anti-RBD-IgG titers compared with HCs (1.061 vs. 1.978, P=0.001). The 50% pseudovirus neutralization titer (pVNT50) values for prevalent Omicron strains (BA.4/5 and BF.7) were lower in SCPs than in HCs (621.0 [288.8, 1333.0] vs. 894.1 [458.5, 1637.0] and 529.6 [215.3, 1264.5] vs. 463.1 [185.2, 914.0], respectively). Levels of antibodies against subsequent variants (XBB.1.5 and EG.5) also were reduced. There were no significant differences among carcinoma types in the levels of antibodies against Omicron variants. However, SCPs who received the SARS-CoV-2 vaccine or had COVID-19 during the Omicron wave displayed higher antibody levels.

Conclusions

This study elucidated the clinical and immunological characteristics of SCPs during the Omicron wave in China after the shift away from a zero-COVID-19 policy. Our findings provide insights regarding factors that influence COVID-19 symptoms and antibody levels in this population.
Impairment of regulatory T cell stability in axial spondyloarthritis: role of EZH2 and pSTAT5
Authors: Mebrek Majda Lyna , Abaab Tessnime , Lemeiter Delphine , Breckler Magali , Hervé Roxane , Petit Mylène , Clavel Gaëlle , Sigaux Johanna , Boissier Marie-Christophe , Semerano Luca , Biton Jérôme , Bessis Natacha
Published: November 2024

Background and objectives

Axial spondyloarthritis (axSpA) is a chronic inflammatory disease involving the spine, peripheral joints, and entheses. Functional impairment of regulatory T cells (Treg) is linked to inflammatory diseases, but limited data is available regarding Treg involvement in axSpA. Treg stability refers to their ability to maintain their functions and characteristics in pro-inflammatory environments. EZH2 and phosphorylated STAT5 (pSTAT5) play a critical role in maintaining Treg stability. We aimed to characterize Treg stability in patients with axSpA.

Methods

Peripheral blood mononuclear cells (PBMCs) from axSpA patients, either naïve from targeted therapy or treated by TNF inhibitors (TNFi), and from healthy donors (HD), were freshly isolated. Expression of stability (EZH2, pSTAT5) and suppressive (TNFR2 and CD39) markers by Treg was analyzed by flow cytometry.

Results

EZH2 expression by Treg was decreased in axSpA patients as compared to HD (p<0.01). Mechanistic study showed that inhibition of EZH2 attenuated Treg differentiation and suppressive phenotype in vitro. EZH2 was predominantly expressed by highly suppressive TNFR2+ and CD39+ Treg. Additionally, axSpA patients also exhibited a reduced frequency of pSTAT5+ Treg compared to HD (p<0.05), and pSTAT5+ Treg frequency increased at 3 months of TNFi treatment compared to baseline (p<0.05). This last result suggested a restoration of Treg stability upon TNFi treatment.

Conclusion

By highlighting a deficient expression of EZH2 and pSTAT5 by Treg, we revealed an impaired Treg stability in axSpA. Deciphering the pathways influenced by these molecules is necessary to assess the potential therapeutic benefits of restoring Treg stability in axSpA.
Case report: Rapid clinical improvement of anti-HMGCR immune-mediated necrotizing myopathy treated with efgartigimod
Authors: Zeng Quantao , Chen Kai , Zeng Li , Xu Lixia , Tan Song
Published: November 2024

Immune-mediated necrotizing myopathy (IMNM) with anti-HMGCR antibody positivity is characterized by proximal extremity weakness, increased creatine kinase, and extensive muscle edema. There is an urgent need to find more appropriate treatment options for anti-HMGCR IMNM patients who do not respond well to conventional therapy in the acute phase. With the advent of targeted biologics, new treatment options are available. We report on a 66-year-old anti-HMGCR IMNM patient who initially presented with a 1-month history of progressive proximal extremity weakness and dysphagia with markedly elevated creatine kinase. The patient did not respond to conventional high-dose glucocorticoid and intravenous immunoglobulin therapy, and his symptoms rapidly deteriorated over the 2 weeks after this treatment, with worsening limb weakness that prevented walking, marked proximal muscle atrophy, and weight loss. After one cycle (four infusions) of efgartigimod, the patient’s symptoms improved markedly and he has since (for several months) remained in a good clinical state.
Take good care of your fish: fish re-identification with synchronized multi-view camera system
Authors: Fan Suzhen , Song Chengyang , Feng Haiyang , Yu Zhibin
Published: November 2024

Introduction

Fish re-identification (re-ID) is of great significance for fish monitoring and can contribute to aquaculture and fish breeding. Synchronizing information from different cameras is beneficial for optimizing re-ID performance.

Methods

We constructed the first underwater fish re-identification benchmark dataset (FS48) under three camera conditions. FS48 encompasses 48 different fish identities, 10,300 frames, and 39,088 bounding boxes, covering various lighting conditions and background environments. Additionally, we developed the first robust and accurate fish re-identification baseline, FSNet, which fuses information from three camera positions by extracting features from synchronized video frames of each position and combining the synchronized information.

Results

The experimental results show that FS48 is universal and of high quality. FSNet has an effective network design and demonstrates good performance, achieving better re-identification performance by combining information from three positions, helping improve overall re-test accuracy, and evaluating the effectiveness of re-identification among detectors.

Discussion

Our dataset will be released upon acceptance of this paper, which is expected to further promote the development of underwater fish re-identification.
Application of the electrical impedance method to steel/steel EHD point contacts
Authors: Maruyama Taisuke , Kosugi Daichi , Iwase Shunsuke , Maeda Masayuki , Nakano Ken , Momozono Satoshi
Published: November 2024

The authors have previously developed the electrical impedance method which simultaneously measure the thickness and breakdown ratio of oil films in EHD (elastohydrodynamic) contacts. Furthermore, using a ball-on-disc-type apparatus, the authors have also confirmed that the accuracy of oil film measurement by the developed method is comparable to that of optical interferometry (i.e., glass-steel contacts). In this study, we discussed the experimental results obtained by applying the electrical impedance method to steel-steel contacts using a steel disc instead of a glass disc. It was found that under the mixed lubrication regime where wear occurs, the oil film thickness obtained by this method is calculated to be significantly thicker than the theoretical value. This can be attributed to the increase in the apparent dielectric constant of the lubricant due to wear particles in the lubricant.
Procedure of developing more energy efficient and electrified hydraulic systems for loader cranes
Authors: Rankka Amy , Dell’Amico Alessandro
Published: November 2024

This work presents a process for the requirement management and conceptual design phases of hydraulic systems. The aim is to provide a foundation for developing more energy efficient systems for the working hydraulics of construction machines. A framework is developed and applied in a case study of a loader crane. An important part of the framework is to evaluate and compare different designs based on customer usage of the machine. Emphasis has also been put on incorporating the knowledge and experience of both industry and academia. A large number of different designs are evaluated during a concept exploration phase. The design space is then narrowed down to the system design analysis phase. Losses from simultaneous operation are significant, systems with two and four pumps respectively are therefore selected for analysis by demonstrators. In order to reach equal energy performance, two-pump systems need to be more complex, i.e., they require a more sophisticated control and more components, than four-pump systems. When comparing demonstrator results, the conclusion is that for two-pump systems, it is more challenging to reach the theoretical performance, both in terms of energy efficiency and of drivability, than for the less complex systems made possible with four-pumps.
Primary care physicians' attitudes, practices, and perceived barriers toward depression screening in older people in the Kingdom of Bahrain
Authors: Habbash Fatema , Khamis Zainab , Alasfoor Zahra , Mahdi Aayat , Alsharkhat Masooma , Hasan Noor , Al Qari Alaa , Chlif Sadok , Almarabheh Amer , Ben Salah Afif
Published: November 2024

Purpose

This study aimed to explore attitudes, practices, and perceived barriers of primary care physicians (PCPs) toward depression screening in older people.

Methods

This cross-sectional study enrolled PCPs from randomly selected representative primary care centers in Bahrain. A self-administered piloted semi-structured questionnaire was used for data collection.

Results

We enrolled 248 PCPs in the study (82.3% females, and the mean age = 40 ± 8.7 years). More than half of the participants (54.4%) had a positive attitude toward depression screening in older people. However, only 10.9% of the participants reported systematically screening for this condition without using specific tools for screening in 45.5%. The most reported barriers toward this service are short consultation time (95%), the presence of multiple co-morbidities in this age group (90%), and the absence of guidelines or appropriate training in around 30%. Positive attitudes were significantly higher among older PCPs (p = 0.039), family physician consultants (p = 0.008), those with more than 10 years of work experience (p = 0.024), and those who participated in related educational activities (p = 0.007). Under-screening practice is associated with perceived short consultation time (p = 0.002), insufficient continuous medical education (CME) activities attendance in older people's mental health (p = 0.048) as well as having a general physician's title (p = 0.049). Only the PCPs' job title, Adjusted Odds Ratio (OR) = 3.513, 95 C.I [1.225-10.074] and attendance of CME activities, OR = 1.278, 95 C.I [1.098 – 3.192] remained significant when controlled for age and experience.

Conclusion

More training on older people's mental health and provision of screening and management guidelines are priorities to promote older people's mental health in primary care settings.
Successful sequential management of traumatic choledochal leak and stenosis in children using ERCP: a case report and literature review
Authors: Leng Cuo , Zou Yu , Yang Zhoujian , Zhao Xinhua
Published: November 2024

Traumatic Choledochal Leak and Stenosis in Children is a relatively rare bile leakage, and there is no report of endoscopic retrograde cholangiopancreatography [ERCP] bile duct stent treatment in 3 years old, which avoids procedure and biliary tract modifications after the failure of conservative treatment of bile leakage, and solves the previous need for procedure in a minimally invasive or even non-invasive way. At the same time, it can be concluded that identifying the signs of conservative treatment failure is important, and ERCP is superior to CT and MR in diagnosing traumatic biliary leak in young children. Traumatic bile leakage common bile duct inflammatory stenosis, brittle tissue, not suitable for expansion, the choice of 5 Fr to 10 Fr plastic stent sequential treatment is an effective regimen. At the same time, it is necessary to closely monitor the biliary patency after ERCP to understand the long-term postoperative efficacy. Comprehensive evaluation before ERCP and detailed post ERCP monitoring require the participation of pediatricians.
Construction of a disease risk prediction model for postherpetic pruritus by machine learning
Authors: Lin Zheng , Dou Yuan , Ju Ru-yi , Lin Ping , Cao Yi
Published: November 2024

Background

Postherpetic itch (PHI) is an easily overlooked complication of herpes zoster that greatly affects patients' quality of life. Studies have shown that early intervention can reduce the occurrence of itch. The aim of this study was to develop and validate a predictive model through a machine learning approach to identify patients at risk of developing PHI among patients with herpes zoster, making PHI prevention a viable clinical option.

Method

We conducted a retrospective review of 488 hospitalized patients with herpes zoster at The First Affiliated Hospital of Zhejiang Chinese Medical University and classified according to whether they had PHI. Fifty indicators of these participants were collected as potential input features for the model. Features associated with PHI were identified for inclusion in the model using the least absolute shrinkage selection operator (LASSO). Divide all the data into five pieces, and then use each piece as a verification set and the others as a training set for training and verification, this process is repeated 100 times. Five models, logistic regression, random forest (RF), k-nearest neighbor, gradient boosting decision tree and neural network, were built in the training set using machine learning methods, and the performance of these models was evaluated in the test set.

Results

Seven non-zero characteristic variables from the Lasso regression results were selected for inclusion in the model, including age, moderate pain, time to recovery from rash, diabetes, severe pain, rash on the head and face, and basophil ratio. The RF model performs better than other models. On the test set, the AUC of the RF model is 0.84 [(95% confidence interval (CI): 0.80–0.88], an accuracy of 0.78 (95% CI: 0.69–0.86), a precision of 0.61 (95% CI: 0.45–0.77), a recall of 0.73 (95% CI: 0.58–0.89), and a specificity of 0.79 (95% CI: 0.70–0.89).

Conclusions

In this study, five machine learning methods were used to build postherpetic itch risk prediction models by analyzing historical case data, and the optimal model was selected through comparative analysis, with the random forest model being the top performing model.
Case report: Combined transcutaneous spinal cord stimulation and physical therapy on recovery of neurological function after spinal cord infarction
Authors: León Felix , Rojas Carlos , Aliseda María José , del Río Gerardo , Monzalvo Eduardo , Pliego-Carrillo Adriana , Figueroa Jimena , Ibarra Antonio , Lavrov Igor , Cuellar Carlos A.
Published: November 2024

The case of a 37-year-old woman who suffered from spinal cord infarction (SI), resulting in a complete spinal cord injury (AIS A, neurological level T10), and autonomic dysfunction is presented. This study aimed to assess the effect of transcutaneous Spinal Cord Electrical Stimulation (tSCS) on improving motor, sensory, and autonomic function after SI. During the first 8 months, tSCS was applied alone, then, physical therapy (PT) was included in the sessions (tSCS+PT), until completion of 20 months. Compared to baseline, at 20 months, an increase in ISNCSCI motor (50 vs. 57) and sensory scores (light touch, 72 vs. 82; pinprick, 71 vs. 92) were observed. Neurogenic Bladder Symptoms Score (NBSS) changed from 27 at baseline to 17 at 20 months. ISAFSCI scores in sacral autonomic function improved from 0 pts (absent function) to 1 pt. (altered function) indicating better sphincter control. EMG recordings during volitional movements, including overground stepping with 80% of body weight support showed activity in gluteus medialis, tensor fascia latae, sartorius, rectus femoris, biceps femoris, tibialis anterior, and gastrocnemius medialis, indicating a partial reversion of paralysis. RMS analysis indicated higher activity during “tSCS on” compared to “tSCS off” during overground stepping in bilateral rectus femoris (p < 0.001) and gastrocnemius medialis (p < 0.01); and unilateral biceps femoris, and tibialis anterior (p < 0.001). As this is the first report on the use of tSCS in the case of SI, future studies in a case series are warranted.
Successful treatment of refractory palmoplantar pustulosis by upadacitinib: report of 28 patients
Authors: Du Na , Yang Jingyi , Zhang Yiwen , Lv Xinyan , Cao Lei , Min Wei
Published: November 2024

Background

Upadacitinib, a specific JAK1 inhibitor, has minimal effect on other JAK subtypes. It influences the inflammatory process in various ways. Upadacitinib has been approved for conditions such as rheumatoid arthritis, psoriatic arthritis, atopic dermatitis, and ulcerative colitis in various countries. The purpose of this study is to assess the clinical efficacy and safety of upadacitinib in patients with refractory palmoplantar pustulosis who have not responded to conventional treatments (e.g., Acitretin, Tripterygium wilfordii Hook F, cyclosporine, methotrexate).

Methods

We conducted a retrospective collection of clinical data from 28 patients who received upadacitinib treatment at the Department of Dermatology, First Affiliated Hospital of Suzhou University, from July 2022 to December 2023. We evaluated the Palmoplantar Pustulosis Area and Severity Index (PPPASI) scores, Dermatology Life Quality Index (DLQI) scores, and Physician’s Global Assessment (PGA) scores before and after treatment. We also recorded any adverse events during the treatment process.

Results

A total of 28 patients were diagnosed with PPP, including 10 males and 18 females, and 8 patients (3 males and 5 females) were diagnosed with SAPHO syndrome. The mean age was (36.3 ± 10.5) years. After 12 weeks of treatment, PPPASI scores decreased from baseline (13.86 ± 2.76) to (5.56 ± 1.08), with a statistically significant difference (p < 0.05). DLQI scores decreased from (12.55 ± 4.56) to (2.03 ± 1.13), also showing a statistically significant difference (p < 0.05). Additionally, 20 patients achieved a PGA score of 0/1. No severe adverse events were reported during the treatment and follow-up period.

Conclusion

Upadacitinib could be an additional safe and effective treatment for treating refractory palmoplantar pustulosis with a potential benefit on patients’ quality of life. Further studies are needed to assess its short-and long-term efficacy and safety in larger sample sizes in randomized double-blind controlled trials.
Application of large language model combined with retrieval enhanced generation technology in digestive endoscopic nursing
Authors: Fu Zhaoli , Fu Siyuan , Huang Yuan , He Wenfang , Zhong Zhuodan , Guo Yan , Lin Yanfeng
Published: November 2024

Background

Although large language models (LLMs) have demonstrated powerful capabilities in general domains, they may output information in the medical field that could be incorrect, incomplete, or fabricated. They are also unable to answer personalized questions related to departments or individual patient health. Retrieval-augmented generation technology (RAG) can introduce external knowledge bases and utilize the retrieved information to generate answers or text, thereby enhancing prediction accuracy.

Method

We introduced internal departmental data and 17 commonly used gastroenterology guidelines as a knowledge base. Based on RAG, we developed the Endo-chat medical chat application, which can answer patient questions related to gastrointestinal endoscopy. We then included 200 patients undergoing gastrointestinal endoscopy, randomly divided into two groups of 100 each, for a questionnaire survey. A comparative evaluation was conducted between the traditional manual methods and Endo-chat.

Results

Compared to ChatGPT, Endo-chat can accurately and professionally answer relevant questions after matching the knowledge base. In terms of response efficiency, completeness, and patient satisfaction, Endo-chat outperformed manual methods significantly. There was no statistical difference in response accuracy between the two. Patients showed a preference for AI services and expressed support for the introduction of AI. All participating nurses in the survey believed that introducing AI could reduce nursing workload.

Conclusion

In clinical practice, Endo-chat can be used as a highly effective auxiliary tool for digestive endoscopic care.
Sewage-and fertilizer-derived nutrients alter the intensity, diversity, and toxicity of harmful cyanobacterial blooms in eutrophic lakes
Authors: Gobler Christopher J. , Drinkwater Ruth W. , Anthony Alexander , Goleski Jennifer A. , Famularo-Pecora Ann Marie E. , Wallace Marcella Kretz , Straquadine Nora R. W. , Hem Ronojoy
Published: November 2024

Cyanobacterial harmful algal blooms (CHABs) are promoted by excessive nutrient loading and, while fertilizers and sewage are the most prevalent external nutrient sources in most watersheds, the differential effects of these nutrient sources on CHABs are unknown. Here, we tracked CHABs and performed experiments in five distinct lakes across the Northern US including Lake Erie. Fertilizers with ammonium and orthophosphate, membrane (0.2 μm)-filtered sewage (dominated by reduced forms of nitrogen) sand-and membrane-filtered sewage (dominated by nitrate), and an inorganic nutrient solution of ammonium and orthophosphate were used as experimental nutrient sources for CHABs at N-equivalent, environmentally realistic concentrations. Phytoplankton communities were evaluated fluorometrically, microscopically, and via high throughput sequencing of the 16S rRNA gene, and levels of microcystin and the δ15N content of particulate organic nitrogen (δPO15N) were quantified. Fertilizer and both sources of wastewater increased the abundance of cyanobacteria in all experiments across all five lakes (p < 0.05 for all) whereas effects on eukaryotic phytoplankton were limited. Sand-filtered sewage contained less P, organic matter, and ammonium but more nitrate and had a 25% less potent stimulatory effect on cyanobacteria than membrane-filtered sewage, suggesting nitrification may play a role in reducing CHABs. Fertilizer increased microcystin levels and decreased the δPO15N whereas wastewater increased δPO15N (p < 0.05 for all). Microcystis was the genus most consistently promoted by nutrient sources (p < 0.05 in all experiments), followed by Cyanobium (p < 0.05 in 50% of experiments), with increases in Microcystis biomass consistently elicited by membrane-filtered wastewater. Collectively, results demonstrate that differing types of sewage discharge and fertilizers can promote CHAB intensity and toxicity, while concurrently altering CHAB diversity and δPO15N. While membrane-filtered sewage consistently favored Microcystis, the discharge of sewage through sands muted bloom intensity suggesting sand-beds may represent a tool to remove key nutrients and partially mitigate CHABs.
Molecular characterization of wheat dwarf virus isolates from Serbia based on complete genome sequences
Authors: Stanković Ivana , Zečević Katarina , Ristić Danijela , Vučurović Ivan , Krstić Branka
Published: November 2024

Introduction

Wheat dwarf virus (WDV), the species Mastrevirus hordei of the genus Mastrevirus in the family Geminiviridae, is a cereal virus commonly detected in several European, African and Asian countries that causes economic losses.

Methods

In the spring of 2019, a severe outbreak of wheat dwarfing and yellowing was observed in many winter wheat crops across Serbia. A total of 161 samples were tested for the presence of WDV and other common wheat viruses using double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA). To obtain the complete genome of 23 selected isolates, several overlapping segments of the WDV genome were amplified and sequenced. A phylogenetic tree was constructed using the whole genome sequences of the WDV isolates identified in this study and 40 selected sequences from GenBank.

Results and discussion

The results of DAS-ELISA indicated the presence of WDV in all samples collected from 21 sites in all nine districts surveyed. Further molecular characterization based on complete genome sequencing of 23 selected isolates showed that the Serbian WDV isolates had low nucleotide diversity and were closely related to wheat-infecting isolates from Europe, suggesting the presence of wheat-adapted forms of WDV in Serbia. The constructed phylogenetic tree revealed that Serbian isolates grouped in clade E within the wheat-adapted forms. This study provided the first insight into the genetic structure of WDV in Serbia based on its whole genome sequence. Further studies on the vector biology and population dynamics are needed to better understand the factors influencing the emergence and spread of WDV under local agroecological conditions.
Drosophila melanogaster experimental model to test new antimicrobials: a methodological approach
Authors: Vidal Maria , Arch Marta , Fuentes Esther , Cardona Pere-Joan
Published: November 2024

Given the increasing concern about antimicrobial resistance among the microorganisms that cause infections in our society, there is an urgent need for new drug discovery. Currently, this process involves testing many low-quality compounds, resulting from the in vivo testing, on mammal models, which not only wastes time, resources, and money, but also raises ethical questions. In this review, we have discussed the potential of D. melanogaster as an intermediary experimental model in this drug discovery timeline. We have tackled the topic from a methodological perspective, providing recommendations regarding the range of drug concentrations to test based on the mechanism of action of each compound; how to treat D. melanogaster, how to monitor that treatment, and what parameters we should consider when designing a drug screening protocol to maximize the study’s benefits. We also discuss the necessary improvements needed to establish the D. melanogaster model of infection as a standard technique in the drug screening process. Overall, D. melanogaster has been demonstrated to be a manageable model for studying broad-spectrum infection treatment. It allows us to obtain valuable information in a cost-effective manner, which can improve the drug screening process and provide insights into our current major concern. This approach is also in line with the 3R policy in biomedical research, in particular on the replacement and reduce the use of vertebrates in preclinical development.
Role of methanotrophic communities in atmospheric methane oxidation in paddy soils
Authors: Zheng Yan , Cai Yuanfeng , Jia Zhongjun
Published: November 2024

Wetland systems are known methane (CH4) sources. However, flooded rice fields are periodically drained. The paddy soils can absorb atmospheric CH4 during the dry seasons due to high-affinity methane-oxidizing bacteria (methanotroph). Atmospheric CH4 uptake can be induced during the low-affinity oxidation of high-concentration CH4 in paddy soils. Multiple interacting factors control atmospheric CH4 uptake in soil ecosystems. Broader biogeographical data are required to refine our understanding of the biotic and abiotic factors related to atmospheric CH4 uptake in paddy soils. Thus, here, we aimed to assess the high-affinity CH4 oxidation activity and explored the community composition of active atmospheric methanotrophs in nine geographically distinct Chinese paddy soils. Our findings demonstrated that high-affinity oxidation of 1.86 parts per million by volume (ppmv) CH4 was quickly induced after 10,000 ppmv high-concentration CH4 consumption by conventional methanotrophs. The ratios of 16S rRNA to rRNA genes (rDNA) for type II methanotrophs were higher than those for type I methanotrophs in all acid-neutral soils (excluding the alkaline soil) with high-affinity CH4 oxidation activity. Both the 16S rRNA:rDNA ratios of type II methanotrophs and the abundance of 13C-labeled type II methanotrophs positively correlated with high-affinity CH4 oxidation activity. Soil abiotic factors can regulate methanotrophic community composition and atmospheric CH4 uptake in paddy soils. High-affinity methane oxidation activity, as well as the abundance of type II methanotroph, negatively correlated with soil pH, while they positively correlated with soil nutrient availability (soil organic carbon, total nitrogen, and ammonium-nitrogen). Our results indicate the importance of type II methanotrophs and abiotic factors in atmospheric CH4 uptake in paddy soils. Our findings offer a broader biogeographical perspective on atmospheric CH4 uptake in paddy soils. This provides evidence that periodically drained paddy fields can serve as the dry-season CH4 sink. This study is anticipated to help in determining and devising greenhouse gas mitigation strategies through effective farm management in paddy fields.
Genome-wide comparative analysis of clinical and environmental strains of the opportunistic pathogen Paracoccus yeei (Alphaproteobacteria)
Authors: Szuplewska Magdalena , Sentkowska Dorota , Lasek Robert , Decewicz Przemysław , Hałucha Mateusz , Funk Łukasz , Chmielowska Cora , Bartosik Dariusz
Published: November 2024

Introduction

Paracoccus yeei is the first species in the genus Paracoccus to be implicated in opportunistic infections in humans. As a result, P. yeei strains provide a valuable model for exploring how bacteria shift from a saprophytic to a pathogenic lifestyle, as well as for investigating the role of horizontally transferred DNA in this transition. In order to gain deeper insights into the unique characteristics of this bacterium and the molecular mechanisms underlying its opportunistic behavior, a comparative physiological and genomic analysis of P. yeei strains was performed.

Results

Complete genomic sequences of 7 P. yeei isolates (both clinical and environmental) were obtained and analyzed. All genomes have a multipartite structure comprising numerous extrachromosomal replicons (59 different ECRs in total), including large chromids of the DnaA-like and RepB families. Within the mobile part of the P. yeei genomes (ECRs and transposable elements, TEs), a novel non-autonomous MITE-type element was identified. Detailed genus-wide comparative genomic analysis permitted the identification of P. yeei-specific genes, including several putative virulence determinants. One of these, the URE gene cluster, determines the ureolytic activity of P. yeei strains—a unique feature among Paracoccus spp. This activity is induced by the inclusion of urea in the growth medium and is dependent on the presence of an intact nikR regulatory gene, which presumably regulates expression of nickel (urease cofactor) transporter genes.

Discussion

This in-depth comparative analysis provides a detailed insight into the structure, composition and properties of P. yeei genomes. Several predicted virulence determinants (including URE gene clusters) were identified within ECRs, indicating an important role for the flexible genome in determining the opportunistic properties of this bacterium.
First report on the physicochemical and proteomic characterization of Proteus mirabilis outer membrane vesicles under urine-mimicking growth conditions: comparative analysis with Escherichia coli
Authors: González María José , Navarro Nicolás , Cruz Erlen , Sánchez Sofía , Morales Javier O. , Zunino Pablo , Robino Luciana , Lima Analía , Scavone Paola
Published: November 2024

Introduction

Uropathogenic bacteria employ multiple strategies to colonize the urinary tract, including biofilm formation, invasion of urothelial cells, and the production of adhesins, toxins, and siderophores. Among the most prevalent pathogens causing urinary tract infections (UTIs) are Uropathogenic Escherichia coli and Proteus mirabilis. A notable feature of Gram-negative bacteria is their ability to produce outer membrane vesicles (OMVs), which play critical roles in bacterial survival, virulence, and host-pathogen interactions, including UTIs.

Methods

In this study, OMVs were isolated and characterized from two clinical strains, E. coli U144 and P. mirabilis 2,921, cultured in both Luria-Bertani broth and artificial urine.

Result and discussion

The OMVs ranged in size from 85 to 260 nm, with the largest vesicles observed in artificial urine. Proteomic analysis allowed the identification of 282 proteins in OMVs from E. coli and 353 proteins from P. mirabilis when cultured LB medium, while 215 were identified from E. coli and 103 from P. mirabilis when cultured in artificial urine. The majority of these proteins originated from the bacterial envelope, while others were linked to motility and adhesion. Notably, the protein composition of OMVs varied depending on the growth medium, and proteins associated with zinc and iron uptake being more prominent in artificial urine, suggesting their importance in the urinary environment. Crucially, this is the first report to characterize P. mirabilis OMVs under different culture conditions, offering novel insights into the role of OMVs in UTI pathogenesis. These findings provide a deeper understanding of the molecular mechanisms by which OMVs contribute to bacterial virulence, establishing the foundation for potential therapeutic interventions targeting OMV-mediated processes in UTIs.
Correlation between oxygenation function and laboratory indicators in COVID-19 patients based on non-enhanced chest CT images and construction of an artificial intelligence prediction model
Authors: Kong Weiheng , Liu Yujia , Li Wang , Yang Keyi , Yu Lixin , Jiao Guangyu
Published: November 2024

Objective

By extracting early chest CT radiomic features of COVID-19 patients, we explored their correlation with laboratory indicators and oxygenation index (PaO2/FiO2), thereby developed an Artificial Intelligence (AI) model based on radiomic features to predict the deterioration of oxygenation function in COVID-19 patients.

Methods

This retrospective study included 384 patients with COVID-19, whose baseline information, laboratory indicators, oxygenation-related parameters, and non-enhanced chest CT images were collected. Utilizing the PaO2/FiO2 stratification proposed by the Berlin criteria, patients were divided into 4 groups, and differences in laboratory indicators among these groups were compared. Radiomic features were extracted, and their correlations with laboratory indicators and the PaO2/FiO2 were analyzed, respectively. Finally, an AI model was developed using the PaO2/FiO2 threshold of less than 200 mmHg as the label, and the model’s performance was assessed using the area under the receiver operating characteristic curve (AUC), sensitivity and specificity. Group datas comparison was analyzed using SPSS software, and radiomic features were extracted using Python-based Pyradiomics.

Results

There were no statistically significant differences in baseline characteristics among the groups. Radiomic features showed differences in all 4 groups, while the differences in laboratory indicators were inconsistent, with some PaO2/FiO2 groups showed differences and others not. Regardless of whether laboratory indicators demonstrated differences across different PaO2/FiO2 groups, they could all be captured by radiomic features. Consequently, we chose radiomic features as variables to establish an AI model based on chest CT radiomic features. On the training set, the model achieved an AUC of 0.8137 (95% CI [0.7631–0.8612]), accuracy of 0.7249, sensitivity of 0.6626 and specificity of 0.8208. On the validation set, the model achieved an AUC of 0.8273 (95% CI [0.7475–0.9005]), accuracy of 0.7739, sensitivity of 0.7429 and specificity of 0.8222.

Conclusion

This study found that the early chest CT radiomic features of COVID-19 patients are strongly associated not only with early laboratory indicators but also with the lowest PaO2/FiO2. Consequently, we developed an AI model based on CT radiomic features to predict deterioration in oxygenation function, which can provide a reliable basis for further clinical management and treatment.
Outward depolarization of the microglia mitochondrial membrane potential following lipopolysaccharide exposure: a novel screening tool for microglia metabolomics
Authors: McGlothen Kendra I. , Hines Rochelle M. , Hines Dustin J.
Published: November 2024

Microglia are non-electrogenic immune cells that respond rapidly to protect the central nervous system (CNS) from infections, injuries, or other forms of damage. Microglia mitochondria are essential for providing the requisite energy resources for immune regulation. While fluctuations in energy metabolism are regulated by mitochondria and are reflected in the mitochondrial membrane potential (ΔΨm), there remains a lack of innovation in microglia-centric tools that capitalize on this. In this study, live imaging of microglia in acute slices from EGFP reporter mice expressing EGFP under the control of the fractalkine receptor (CX3CR1) promoter is combined with loading a fluorescent reporter of ΔΨm. Depolarizations in the ΔΨm were recorded after administering the well-characterized immune stimulant lipopolysaccharide (LPS). Microglia ΔΨm increased in distinctive phases with a relatively steep slope following LPS exposure. Conversely, the ΔΨm of neurons showed minimal regulation, highlighting a distinct microglia ΔΨm response to immune stimuli. Analysis of the depolarization of the microglia ΔΨm in the soma, branches, and endfeet revealed progressive changes in each subcellular domain originating in the soma and progressing outward. The inverse agonist emapunil attenuated the depolarization of the ΔΨm across states in a domain-specific manner. These findings emphasize the contribution of mitochondrial membrane dynamics in regulating microglial responses to immune stimuli. Further, this work advances a novel drug screening strategy for the therapeutic regulation of metabolic activity in inflammatory conditions of the brain.