bluuebunny/crossref_metadata_2025_split huggingface dataset:
A practical approach to the diagnosis and management of malignant pleural effusions in resource-constrained settings
Authors: Shaw Jane A. , Louw Elizabeth H. , Koegelenberg Coenraad F.N. 
Published: December 2023

No pleural intervention in a patient with confirmed malignant pleural effusion (MPE) prolongs life, but even the recommended interventions for diagnosis and palliation can be costly and therefore unavailable in large parts of the world. However, there is good evidence to guide clinicians working in low- and middle-income countries on the most cost-effective and clinically effective strategies for the diagnosis and management of MPE. Transthoracic ultrasound-guided closed pleural biopsy is a safe method of pleural biopsy with a diagnostic yield approaching that of thoracoscopy. With the use of pleural fluid cytology and ultrasound-guided biopsy, ≥90% of cases can be diagnosed. Cases with an associated mass lesion are best suited to an ultrasound-guided fine needle aspiration with/without core needle biopsy. Those with diffuse pleural thickening and/or nodularity should have an Abrams needle (<1 cm thickening) or core needle (≥1 cm thickening) biopsy of the area of interest. Those with insignificant pleural thickening should have an ultrasound-guided Abrams needle biopsy close to the diaphragm. The goals of management are to alleviate dyspnoea, prevent re-accumulation of the pleural effusion and minimise re-admissions to hospital. As the most cost-effective strategy, we suggest early use of indwelling pleural catheters with daily drainage for 14 days, followed by talc pleurodesis if the lung expands. The insertion of an intercostal drain with talc slurry is an alternative strategy which is noninferior to thoracoscopy with talc poudrage.Educational aimsTo provide clinicians practising in resource-constrained settings with a practical evidence-based approach to the diagnosis and management of malignant pleural effusions.To explain how to perform an ultrasound-guided closed pleural biopsy.To explain the cost-effective use of indwelling pleural catheters.
TIM-3 regulates the proliferation by BDNF-mediated PI3K/AKT axis in the process of endometriosis
Authors: Tian Wei , Liu Min , Liu Yuqiu , Lv Qingfeng , Cheng HuaFeng , Gu Yanling , Li Mingjiang 
Published: December 2023

Abstract
Background
T cell immunoglobulin and mucin domain-containing molecule-3 (TIM-3) initially discovered on the surface of Th1 cells, negatively regulates immune responses and mediates apoptosis of Th1 cells. An increasing number of studies have since shown that TIM-3 is crucial in the genesis and development of immune diseases, cancers, and chronic infectious illnesses. However, the effect of TIM-3 on endometriosis is still unknown.

Methods
Quantitative real-time polymerase chain reaction, western blotting, and immunohistochemistry were used to measure TIM-3 levels in endometriosis. Cell Counting Kit-8, 5-ethynyl-2’-deoxyuridine, colony-forming, Transwell® migration, Matrigel® invasion, and flow cytometry assays were used to explore the function of TIM-3 in vitro, and xenograft experiments in nude mice were used to assess its role in vivo. According to the RNA seq, brain-derived neurotrophic factor (BDNF) was screened. The involvement of specific proliferation-related signaling molecules was determined by transfecting a plasmid and adding an inhibitor in vivo and in vitro.

Results
TIM-3 mRNA and protein expression levels were significantly higher in eutopic and ectopic endometrial tissues than in normal endometrial tissues. By examining the effects of TIM-3 overexpression and knockdown on cell proliferation, migration, and invasion in vitro, and lesions formation in vivo, we found that the expression of TIM-3 was positively correlated with cell proliferation and clone formation in vitro, as well as lesions growth in nude mice. By adding the phosphatidylinositol 3 kinase/protein kinase B(PI3K/AKT) pathway inhibitor LY294002 and knocking down PI3K, we further verified that TIM-3 promotes proliferation in vivo and in vitro via the PI3K pathway. By transfecting the plasmid into ESC cells and gave inhibitors to endometriotic rats models, we tested that TIM-3 regulates the proliferation by BDNF-mediated PI3K/AKT axis.

Conclusion
TIM-3 can promote the proliferation of endometriosis by BDNF-mediated PI3K/AKT axis in vivo and in vitro, which may provide a new therapeutic target for the treatment of endometriosis.
GPDRP: a multimodal framework for drug response prediction with graph transformer
Authors: Yang Yingke , Li Peiluan 
Published: December 2023

Abstract
Background
In the field of computational personalized medicine, drug response prediction (DRP) is a critical issue. However, existing studies often characterize drugs as strings, a representation that does not align with the natural description of molecules. Additionally, they ignore gene pathway-specific combinatorial implication.

Results
In this study, we propose drug Graph and gene Pathway based Drug response prediction method (GPDRP), a new multimodal deep learning model for predicting drug responses based on drug molecular graphs and gene pathway activity. In GPDRP, drugs are represented by molecular graphs, while cell lines are described by gene pathway activity scores. The model separately learns these two types of data using Graph Neural Networks (GNN) with Graph Transformers and deep neural networks. Predictions are subsequently made through fully connected layers.

Conclusions
Our results indicate that Graph Transformer-based model delivers superior performance. We apply GPDRP on hundreds of cancer cell lines’ bulk RNA-sequencing data, and it outperforms some recently published models. Furthermore, the generalizability and applicability of GPDRP are demonstrated through its predictions on unknown drug-cell line pairs and xenografts. This underscores the interpretability achieved by incorporating gene pathways.
Pair bonding and disruption impact lung transcriptome in monogamous Peromyscus californicus
Authors: Naderi A. , Liles K. , Burns T. , Chavez B. , Huynh-Dam K-T. , Kiaris H. 
Published: December 2023

AbstractSocial interactions affect physiological and pathological processes, yet their direct impact in peripheral tissues remains elusive. Recently we showed that disruption of pair bonds in monogamous Peromyscus californicus promotes lung tumorigenesis, pointing to a direct effect of bonding status in the periphery (Naderi et al., 2021). Here we show that lung transcriptomes of tumor-free Peromyscus are altered in a manner that depends on pair bonding and superseding the impact of genetic relevance between siblings. Pathways affected involve response to hypoxia and heart development. These effects are consistent with the profile of the serum proteome of bonded and bond-disrupted Peromyscus and were extended to lung cancer cells cultured in vitro, with sera from animals that differ in bonding experiences. In this setting, the species’ origin of serum (deer mouse vs FBS) is the most potent discriminator of RNA expression profiles, followed by bonding status. By analyzing the transcriptomes of lung cancer cells exposed to deer mouse sera, an expression signature was developed that discriminates cells according to the history of social interactions and possesses prognostic significance when applied to primary human lung cancers. The results suggest that present and past social experiences modulate the expression profile of peripheral tissues such as the lungs, in a manner that impacts physiological processes and may affect disease outcomes. Furthermore, they show that besides the direct effects of the hormones that regulate bonding behavior, physiological changes influencing oxygen metabolism may contribute to the adverse effects of bond disruption.
Evaluation of noninvasive biospecimens for transcriptome studies
Authors: Martorella Molly , Kasela Silva , Garcia-Flores Renee , Gokden Alper , Castel Stephane E. , Lappalainen Tuuli 
Published: December 2023

AbstractTranscriptome studies disentangle functional mechanisms of gene expression regulation and may elucidate the underlying biology of disease processes. However, the types of tissues currently collected typically assay a single post-mortem timepoint or are limited to investigating cell types found in blood. Noninvasive tissues may improve disease-relevant discovery by enabling more complex longitudinal study designs, by capturing different and potentially more applicable cell types, and by increasing sample sizes due to reduced collection costs and possible higher enrollment from vulnerable populations. Here, we develop methods for sampling noninvasive biospecimens, investigate their performance across commercial and in-house library preparations, characterize their biology, and assess the feasibility of using noninvasive tissues in a multitude of transcriptomic applications. We collected buccal swabs, hair follicles, saliva, and urine cell pellets from 19 individuals over three to four timepoints, for a total of 300 unique biological samples, which we then prepared with replicates across three library preparations, for a final tally of 472 transcriptomes. Of the four tissues we studied, we found hair follicles and urine cell pellets to be most promising due to the consistency of sample quality, the cell types and expression profiles we observed, and their performance in disease-relevant applications. This is the first study to thoroughly delineate biological and technical features of noninvasive samples and demonstrate their use in a wide array of transcriptomic and clinical analyses. We anticipate future use of these biospecimens will facilitate discovery and development of clinical applications.
Reduction of UreB and CagA expression level by siRNA construct in Helicobacter pylori strain SS1
Authors: Motamedi Hamid , Abiri Ramin , Salari Farhad , Jalili Cyrus , Alvandi Amirhoushang 
Published: December 2023

Abstract
Background
Two important virulence factors, urease and cagA, play an important role in Helicobacter pylori (H. pylori) gastric cancer. Aim of this study was to investigate the expression level and function of ureB and cagA using small interfering RNAs (siRNA).

Methods
SS1 strain of H. pylori was considered as host for natural transformation. siRNA designed for ureB and cagA genes were inserted in pGPU6/GFP/Neo siRNA plasmid vector to evaluate using phenotypic and genotypic approaches. Then, qPCR was performed for determining inhibition rate of ureB and cagA gene expression.

Results
The expression levels of siRNA-ureB and siRNA-cagA in the recombinant strain SS1 were reduced by about 5000 and 1000 fold, respectively, compared to the native H. pylori strain SS1. Also, preliminary evaluation of siRNA-ureB in vitro showed inhibition of urea enzyme activity. These data suggest that siRNA may be a powerful new tool for gene silencing in vitro, and for the development of RNAi-based anti-H. pylori therapies.

Conclusion
Our results show that targeting ureB and cagA genes with siRNA seems to be a new strategy to inhibit urease enzyme activity, reduce inflammation and colonization rate.
Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis
Authors: Mladenov Petko , Wang Xiaohua , Yang Zhaolin , Djilianov Dimitar , Deng Xin 
Published: December 2023

Abstract
Background
Drought is one of the main consequences of global climate change and this problem is expected to intensify in the future. Resurrection plants evolved the ability to withstand the negative impact of long periods of almost complete desiccation and to recover at rewatering. In this respect, many physiological, transcriptomic, proteomic and genomic investigations have been performed in recent years, however, few epigenetic control studies have been performed on these valuable desiccation-tolerant plants so far.

Results
In the present study, for the first time for resurrection plants we provide evidences about the differential chromatin accessibility of Haberlea rhodopensis during desiccation stress by ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing). Based on gene similarity between species, we used the available genome of the closely related resurrection plant Dorcoceras hygrometricum to identify approximately nine hundred transposase hypersensitive sites (THSs) in H. rhodopensis. The majority of them corresponds to proximal and distal regulatory elements of different genes involved in photosynthesis, carbon metabolism, synthesis of secondary metabolites, cell signalling and transcriptional regulation, cell growth, cell wall, stomata conditioning, chaperons, oxidative stress, autophagy and others. Various types of binding motifs recognized by several families of transcription factors have been enriched from the THSs found in different stages of drought. Further, we used the previously published RNA-seq data from H. rhodopensis to evaluate the expression of transcription factors putatively interacting with the enriched motifs, and the potential correlation between the identified THS and the expression of their corresponding genes.

Conclusions
These results provide a blueprint for investigating the epigenetic regulation of desiccation tolerance in resurrection plant H. rhodopensis and comparative genomics between resurrection and non-resurrection species with available genome information.
A core root bacteria contribute to plant growth and anisodine accumulation of Anisodus tanguticus
Authors: Wang Bo , Chen Chen , Xiao Yuanming , Chen Kaiyang , Wang Juan , Wang Lingling , Li Jianan , Kang Zongxiu , Zhou Guoying 
Published: December 2023

Abstract
Background
Although it is well recognized that core root microorganisms contribute to plant health and productivity, little is known about their role to the accumulation of secondary metabolites. The roots of Anisodus tanguticus, a traditional herbal medication utilized by Tibetan medicine, are rich in tropane alkaloids. We collected wild A. tanguticus populations throughout a 1500 km transect on the Qinghai-Tibetan Plateau.

Results
Our results showed that despite sampling at a distance of 1500 km, the root of A. tanguticus selectively recruits core root bacteria. We obtained 102 root bacterial core OTUs, and although their number only accounted for 2.99% of the total, their relative abundance accounted for 73% of the total. Spearman correlation and random forest analyses revealed that the composition of core root microbiomes was related to anisodine contents, aboveground biomass and nitrogen contents of Anisodus tanguticus. Among them, the main role is played by Rhizobacter, Variovorax, Polaromonas, and Mycobacterium genus that are significantly enriched in roots. Functional prediction by FAPROTAX showed that nitrogen-cycling microorganisms and pathogenic bacteria are strongly associated with anisodine contents, aboveground biomass and nitrogen contents of Anisodus tanguticus.

Conclusions
Our findings show that the root selectively recruits core root bacteria and revealed that the core microbiomes and microbial functions potentially contributed to the anisodine contents, aboveground biomass and nitrogen contents of the plant. This work may increase our understanding of the interactions between microorganisms and plants and improve our ability to manage root microbiota to promote sustainable production of herbal medicines.
Bicarbonate ringer’s solution could improve the intraoperative acid-base equilibrium and reduce hepatocellular enzyme levels after deceased donor liver transplantation: a randomized controlled study
Authors: Li Qingkai , Liu Ying , Wang Yanan , Shan Xin , Liu Chunxiao , Li Zhihua , Cao Jinglin , Dou Jian , Xu Guanjie , Wang Qiujun , Qie Xiaojuan 
Published: December 2023

Abstract
Background
Bicarbonate Ringer’s (BR) solution is a direct liver and kidney metabolism-independent HCO3− buffering system. We hypothesized that BR solution would be more effective in improving acid-base equilibrium and more conducive to better liver function than Acetate Ringer’s (AR) solution in conventional orthotopic liver transplantation (OLT) patients.

Methods
Sixty-nine adult patients underwent OLT. Patients in the bicarbonate and acetate groups received BR solution or AR solution as infused crystalloids and graft washing solution, respectively. The primary outcome was the effect on pH and base excess (BE) levels. The secondary outcome measures were the incidence and volume of intraoperative 5% sodium bicarbonate infusion and laboratory indicates of liver and kidney function.

Results
The pH and absolute BE values changed significantly during the anhepatic phase and immediately after transplanted liver reperfusion in the bicarbonate group compared with the acetate group (all P < 0.05). The incidence and volume of 5% sodium bicarbonate infusion were lower in the bicarbonate group than in the acetate group (all P < 0.05). The aspartate transaminase (AST) level at 7 postoperative days and the creatine level at 30 postoperative days were significantly higher in the acetate group than in the bicarbonate group (all P < 0.05).

Conclusion
Compared with AR solution, BR solution was associated with improved intraoperative acid-base balance and potentially protected early postoperative liver graft function and reduced late-postoperative renal injury.
ABO blood types may affect transient neurological events after surgical revascularization in patients with moyamoya disease: a retrospective single center study
Authors: Qian Mei-Ping , Dong Mei-Rong , Han Ming-Ming , Li Juan , Kang Fang 
Published: December 2023

Abstract
Background
Moyamoya disease (MMD) is a cerebrovascular disease with unknown cause. Patients with MMD disease usually experience transient neurological events (TNEs) after revascularization surgery. This retrospective single-center study was aimed to explore the risk factors of postoperative TNEs after surgical revascularization in patients with MMD.

Methods
We selected 324 patients who underwent surgical revascularization between January 2017 and September 2022 in our center. The perioperative characteristics of the patients were recorded and the outcome was TNEs after surgery. An analysis of risk factors contributing to postoperative TNEs by using logistic regression model.

Results
Three hundred twelve patients were enrolled, and the incidence of postoperative TNEs was 34% in our study. Males were more likely to suffer from postoperative TNEs (OR = 2.344, p = 0.002). Preoperative ischemic presentation (OR = 1.849, p = 0.048) and intraoperative hypotension (OR = 2.332, p = 0.002) were associated with postoperative TNEs. Compared to patients with blood type O, patients with blood type A (OR = 2.325, p = 0.028), B (OR = 2.239, p = 0.027) and AB (OR = 2.938, p = 0.019) had a significantly higher incidence of postoperative TNEs. A risk prediction model for postoperative TNEs was established, and the established risk prediction area under the receiver operating characteristic curve (ROC) of the model was 0.741.

Conclusions
Males, preoperative ischemic presentation and intraoperative hypotension were associated with postoperative TNEs. We also found a possible link between postoperative TNEs and ABO blood types after surgical revascularization for moyamoya patients.
Ultrasound imaging findings in primary biliary cholangitis
Authors: Zhang Yuan , Hu Xing , Chang Jing , Li Weihua , Huang Chunyang , Zhang Haiping , Shen Jianjun , Shang Ning , Meng Fankun 
Published: December 2023

Abstract
Background
Our study aimed to analyze the characteristics of ultrasound images corresponding to each histological stage of primary biliary cholangitis (PBC).

Methods
We prospectively analyzed 75 confirmed cases of PBC and used liver biopsy as the gold standard to determine the disease stage.

Results
The typical ultrasound images of patients with PBC were characterized by a thickening of the portal vein wall (PVW) and periportal hypoechoic band (PHB) width with increasing histological stages, and significant increases in the left hepatic lobe diameter (LHLD) in stage II (by 64.0%) and stage III (by 69.2%). PHB width (r = 0.857, p < 0.001), PVW thickness (r = 0.488, p < 0.001), and spleen area (r = 0.8774, p < 0.001) were positively correlated with the histological stage. Significant changes were noted in the liver surface, echo texture, and edge between different stages. The areas under the receiver operating characteristic curve of composite indicators were 0.965 for predicting progressive PBC(≥ stage 2), and 0.926 for predicting advanced PBC(≥ stage 3).

Conclusions
The ultrasound imaging characteristics of patients with PBC varied according to the histological staging. LHLD, PVW thickness, and PHB width were significantly correlated with the histological stage. A combination of high- and low-frequency ultrasound imaging can provide relevant cues regarding the degree of PBC progression and important clinical reference values. The application of all the ultrasound image findings as the composite indicators can better predict progressive and advanced PBC, providing important clinical reference values.
Screening and verification of antiviral compounds against HSV-1 using a method based on a plaque inhibition assay
Authors: Yin Yingxian , Li Jiahui , Su Ling , Ou Zhiying , Lv Qingqun , Xiao Misi , Wang Changbing , Zeng Dan , Gu Yiling , Yang Fengxia , Chen Minxia , Feng Shaojuan , Hu Wanming , Bu Fengling , Zhu Bing , Xu Yi 
Published: December 2023

Abstract
Background
Herpes simplex virus type 1 (HSV-1) infection is a common viral disease that mainly causes oral lesions, but can also cause genital lesions in some instances. Current treatments with nucleoside analogs are limited by the emergence of drug resistance. Therefore, novel anti-HSV-1 drugs are urgently needed.

Methods
In this study, we screened a library of 2080 compounds for anti-HSV-1 activity using a plaque formation assay. We selected 11 potential inhibitors of HSV-1 and further evaluated their antiviral effects by plaque reduction assay and real-time polymerase chain reaction (qPCR).

Results
Five compounds, namely ginsenoside Rd, brassinolide, rosamultin, 3’-hydroxy puerarin, and clinafloxacin HCl, showed potent anti-HSV-1 activity and completely suppressed plaque formation at a concentration of 10 µM. Among them, clinafloxacin HCl, a fluoroquinolone antibiotic, exhibited a high selectivity index for HSV-1.

Conclusions
Our findings suggest that these five compounds have potential antiviral properties against HSV-1 and may have different mechanisms of action. Further studies are warranted to elucidate the antiviral mechanisms of these compounds and to explore their therapeutic potential for HSV-1 infection.