bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiological and clinical characteristics of psittacosis among cases with complicated or atypical pulmonary infection using metagenomic next-generation sequencing: a multi-center observational study in China
Authors: Huang Weifeng , Wang Fengge , Cai Qingqing , Xu Huiliang , Hong Dengwei , Wu Han , Zhou Lu , Hu Linjie , Lu Yihan 
Published: September 2023

Abstract
Background
Chlamydia psittaci (C. psittaci) causes parrot fever in humans. Development of metagenomic next-generation sequencing (mNGS) enables the identification of C. psittaci.

Methods
This study aimed to determine the epidemiological and clinical characteristics of parrot fever cases in China. A multi-center observational study was conducted in 44 tertiary and secondary hospitals across 14 provinces and municipalities between April 2019 and October 2021.

Results
A total of 4545 patients with complicated or atypical pulmonary infection were included in the study, among which the prevalence of C. psittaci was determined to be 2.1% using mNGS. The prevalence of C. psittaci was further determined across demographic groups and types of specimens. It was significantly higher in patients with senior age (2.6% in those > 50 years), winter-spring (3.6%; particularly in December, January, and February), and southwestern (3.4%) and central and southern China (2.7%) (each P < 0.001). Moreover, the prevalence was the highest in bronchoalveolar lavage fluid (BALF) (2.9%), compared with sputum (1.1%) and peripheral blood specimens (0.9%). Additionally, co-infection of principal microorganisms was compared. Certain microorganisms were more likely to co-infect in parrot fever cases, such as Candida albicans in BALF (26.7%) and peripheral blood (6.3%), compared with non-parrot fever cases (19.7% and 1.3%); however, they did not significantly differ (each P > 0.05).

Conclusion
Parrot fever remains low in patients with complicated or atypical pulmonary infection. It is likely to occur in winter-spring and southwestern region in China. BALF may be the optimal specimen in the application of mNGS. Co-infection of multiple microorganisms should be further considered.
Emergence of carbapenem-resistant enterobacterales co-harboring blaOXA−78 and blaOXA−58 from India
Authors: Das Bhaskar Jyoti , Singha K. Melson , Wangkheimayum Jayalaxmi , Chanda Debadatta Dhar , Bhattacharjee Amitabha 
Published: September 2023

Abstract
Background
Carbapenem-Resistant Enterobacterales (CRE) has been categorized as pathogens of critical priority by World Health organization (WHO) as they pose significant threat to global public health. Carbapenemase production considered as the principal resistance mechanism against carbapenems and with the recent surge and expansion of carbapenemases and its variants among clinically significant bacteria in India, the present study reports expansion blaOXA−78 and blaOXA−58 of in CRE of clinical origin.

Methods
Bacterial isolates were collected from a tertiary referral hospital and identified through VITEK® 2 Compact automated System (Biomerieux, France). Rapidec® Carba NP (Biomerieux, France) was used to investigate carbapenemase production followed by antibiotic susceptibility testing through Kirby-Bauer Disc Diffusion method and agar dilution method. Class D carbapenemase genes were targeted through PCR assay followed by investigation of horizontal transmission of blaOXA−58 and blaOXA−78. Whole genome sequencing was carried out using Illumina platform to investigate the genetic context of blaOXA−58 and blaOXA−78 genes and further characterization of the CRE isolates.

Results
The carbapenem-resistant Escherichia coli (BJD_EC456) and Serratia marcescens (BJD_SM81) received during the study from the tertiary referral hospital were isolated from sputum and blood samples respectively. PCR assay followed by whole genome sequencing revealed that the isolates co-harbor blaOXA−58 and blaOXA−78, a variant of blaOXA−51. Horizontal transfer of blaOXA−58 and blaOXA−78 genes were unsuccessful as these genes were located on the chromosome of the study isolates. Transposon Tn6080 was linked to blaOXA−78 in the upstream region while the insertion sequences ISAba26 and ISCfr1 were identified in the upstream and downstream region of blaOXA−58 gene respectively. In addition, both the isolates were co-harboring multiple antibiotic resistance genes conferring clinical resistance towards beta-lactams, aminoglycosides, fluroquinolones, sulphonamides, tetracyclines. BJD_EC180 belonged to ST2437 while BJD_SM81 was of an unknown sequence type. The nucleotide sequences of blaOXA−78 (OQ533021) and blaOXA−58 (OQ533022) have been deposited in GenBank.

Conclusions
The study provides a local epidemiological information regarding carbapenem resistance aided by transposon and insertion sequences associated blaOXA−78 and blaOXA−58 genes associated and warrants continuous monitoring to prevent their further dissemination into carbapenem non-susceptible strains thereby contributing to carbapenem resistance burden which is currently a global concern.
Antileukemic effect of venetoclax and hypomethylating agents via caspase-3/GSDME-mediated pyroptosis
Authors: Ye Fanghua , Zhang Wen , Fan Chenying , Dong Jiajia , Peng Min , Deng Wenjun , Zhang Hui , Yang Liangchun 
Published: September 2023

Abstract
Background
The identifying of B-cell lymphoma 2 (Bcl-2) as a therapeutic target has led to a paradigm shift in acute myeloid leukemia (AML) treatment. Pyroptosis is a novel antitumor therapeutic mechanism due to its cytotoxic and immunogenic effects. The combination of venetoclax and hypomethylating agents (HMAs) has been shown to lead to durable responses and significantly improve prognosis in patients with AML. However, our understanding of the mechanisms underlying this combinatorial activity is evolving.

Methods
We investigated whether the Bcl-2 inhibitor venetoclax induces AML cell pyroptosis and identified pyroptosis effector proteins. Via using western blotting, immunoprecipitation, RNA interference, CCK8 assays, and LDH assays, we explored the mechanism underlying the pyroptotic effect. The relationship between the expression of the pyroptosis effector protein GSDME and AML prognosis was investigated. The effect of GSDME demethylation combined with venetoclax treatment on pyroptosis was investigated and confirmed in mouse models and clinical samples.

Results
Venetoclax induces pyroptosis that is mediated by caspase-3-dependent GSDME cleavage. Mechanistically, venetoclax upregulates caspase-3 and GSDME cleavage by activating the intrinsic apoptotic pathway. GSDME is downregulated in AML by promoter methylation, and low GSDME expression is significantly associated with poor prognosis, based on public databases and patient sample analysis. In vivo and in vitro experiments showed that GSDME overexpression or HMAs-mediated restoration of GSDME expression significantly increased venetoclax-induced pyroptosis in AML.

Conclusion
GSDME-mediated pyroptosis may be a novel aspect of the antileukemic effect of Bcl-2 inhibitors. This finding offers new insights into potential biomarkers and therapeutic strategies, identifying an important mechanism explaining the clinical activity of venetoclax and HMAs in AML.
Diagnostic value of cerebrospinal fluid Neutrophil Gelatinase-Associated Lipocalin for differentiation of bacterial meningitis from tuberculous meningitis or cryptococcal meningitis: a prospective cohort study
Authors: Wang Qi , Lin Qingwen , Wang Haiyan , Tang Minjie , Fan Kengna , Zhang Zeqin , Huang Er , Zhang Weiqing , Wang Fengqing , Ou Qishui , Liu Xiaofeng 
Published: September 2023

AbstractBackgroundThe early differential diagnosis between bacterial meningitis (BM) and tuberculous meningitis (TBM) or cryptococcal meningitis (CM) remains a significant clinical challenge. Neutrophil Gelatinase-Associated Lipocalin (NGAL) has been reported as a novel inflammatory biomarker in the early stages of infection. This study aimed to investigate whether cerebrospinal fluid (CSF) NGAL can serve as a potential biomarker for distinguishing between BM and TBM or CM.MethodsWe prospectively enrolled the patients with suspected CNS infections at admission and divided them into three case groups: BM (n = 67), TBM (n = 55), CM (n = 51), and an age- and sex-matched hospitalized control (HC, n = 58). Detected the CSF NGAL and assessed its diagnostic accuracy in distinguishing between BM and TBM or CM. Additionally, longitudinally measured the CSF NGAL levels in patients with BM to evaluate its potential as a monitoring tool for antibacterial treatment.ResultsThe concentration of CSF NGAL in BM was significantly higher than in TBM, CM, and HC (allP < 0.05), while the serum NGAL did not show significant differences among the three case groups. The ROC analysis demonstrated that CSF NGAL presented a good diagnostic performance with an AUC of 0.834 (0.770–0.886) and at the optimal cutoff value of 74.27 ng/mL with 70.15% sensitivity and 77.36% specificity for discriminating BM with TBM and CM. Additionally, the CSF NGAL in the convalescent period of BM was significantly lower than in the acute period (P < 0.05).ConclusionsCSF NGAL may serve as a potential biomarker for distinguishing between acute BM and TBM or CM. Additionally, it holds clinical significance in monitoring the effectiveness of antibiotic therapy for BM.
Effect of acceptance and commitment therapy for depressive disorders: a meta-analysis
Authors: Zhao Bing , Wang Qian , Wang Liping , Chen Jie , Yin Tongtong , Zhang Jingxuan , Cheng Xiaojing , Hou Ruihua 
Published: September 2023

Abstract
Objective
To systematically evaluate the effect of Acceptance and Commitment Therapy (ACT) on depressive disorders.

Methods
The electronic databases of Web of Science Core Collection, Pubmed, EMBASE, Cochrane Library, PsycInfo, CNKI, Wanfang and Weipu were used to select relevant publications. Screening, data extraction, and quality assessment were undertaken following PRISMA guidelines for preferred reporting of systematic reviews and meta-analysis. RevMan5.4 was used for meta-analysis.

Results
11 studies with a total of 962 patients were included. Random-effects model analysis showed that ACT could effectively reduce the level of depressive symptoms in patients with depressive disorders (SMD = − 1.05, 95% CI: − 1.43–− 0.66, P < 0.00001), improve psychological flexibility (MD = 4.84, 95% CI: 2.70–6.97, P < 0.00001), and have good maintenance effect (SMD = − 0.70, 95% CI: − 1.15–− 0.25, P = 0.002). All differences were statistically significant.

Conclusions
ACT not only improves depressive symptoms and psychological flexibility, but also has a good maintenance effect, and it is particularly effective in Chinese patients. Large randomized controlled trials are needed to validate the findings from this meta-analysis.
“The chameleon among diseases” - an explorative view of sarcoidosis and identification of the consequences for affected patients and relatives using qualitative interviews
Authors: Hilker Charlotte , Weis Johanna , Ziehfreund Stefanie , Arkema Elizabeth V. , Biedermann Tilo , Zink Alexander 
Published: September 2023

Abstract
Introduction
Sarcoidosis is a multisystemic disease, with the lungs being the main site of manifestation. Although the exact etiology remains unclear, both genetic and environmental factors are being discussed. Diagnostic evaluation is challenging, and the management of chronic patients and assessment of their needs proves difficult, especially in the absence of targeted therapy. Studies on sarcoidosis patients have shown that quality of life is limited even after clinically measurable parameters have resolved. The question remains how patients and their relatives perceive medical care and the diagnostic process and how these affect their well-being.

Methods
Qualitative, semi-structured interviews were conducted with patients and their relatives between September 2019 and February 2020. Interviews were recorded, transcribed verbatim, and analyzed using qualitative content analysis. Deductive hypotheses were then formed based on categories according to personal aspects, symptoms, diagnostic, daily life activity, therapy, psychological aspects and wishes.

Results
Fourteen patients and five relatives were included. Most patients reported subacute symptoms before the first organ-related episode. A high degree of personal initiative was required from the majority of respondents in both the diagnostic and subsequent therapeutic processes. In addition, respondents reported so-called “doctor-hopping”, a lack of specialists or contacts, and a lack of medical support. The Internet and self-help groups played a fundamental role for patients and relatives in exchanging information with other affected persons and to compensate for an existing information deficit.

Conclusion
The results provide new insights into patients’ and relatives’ perceptions of the sarcoidosis diagnosis and treatment process. Identification of barriers such as a lack of physicians and an information deficit highlights potential targets for strategies to optimize sarcoidosis management.
Transcriptional immunogenomic analysis reveals distinct immunological clusters in paediatric nervous system tumours
Authors: Nabbi Arash , Beck Pengbo , Delaidelli Alberto , Oldridge Derek A. , Sudhaman Sumedha , Zhu Kelsey , Yang S. Y. Cindy , Mulder David T. , Bruce Jeffrey P. , Paulson Joseph N. , Raman Pichai , Zhu Yuankun , Resnick Adam C. , Sorensen Poul H. , Sill Martin , Brabetz Sebastian , Lambo Sander , Malkin David , Johann Pascal D. , Kool Marcel , Jones David T. W. , Pfister Stefan M. , Jäger Natalie , Pugh Trevor J. 
Published: September 2023

Abstract
Background
Cancer immunotherapies including immune checkpoint inhibitors and Chimeric Antigen Receptor (CAR) T-cell therapy have shown variable response rates in paediatric patients highlighting the need to establish robust biomarkers for patient selection. While the tumour microenvironment in adults has been widely studied to delineate determinants of immune response, the immune composition of paediatric solid tumours remains relatively uncharacterized calling for investigations to identify potential immune biomarkers.

Methods
To inform immunotherapy approaches in paediatric cancers with embryonal origin, we performed an immunogenomic analysis of RNA-seq data from 925 treatment-naïve paediatric nervous system tumours (pedNST) spanning 12 cancer types from three publicly available data sets.

Results
Within pedNST, we uncovered four broad immune clusters: Paediatric Inflamed (10%), Myeloid Predominant (30%), Immune Neutral (43%) and Immune Desert (17%). We validated these clusters using immunohistochemistry, methylation immune inference and segmentation analysis of tissue images. We report shared biology of these immune clusters within and across cancer types, and characterization of specific immune cell frequencies as well as T- and B-cell repertoires. We found no associations between immune infiltration levels and tumour mutational burden, although molecular cancer entities were enriched within specific immune clusters.

Conclusions
Given the heterogeneity of immune infiltration within pedNST, our findings suggest personalized immunogenomic profiling is needed to guide selection of immunotherapeutic strategies.
Efficacy and safety of tart cherry supplementary citrate mixture on gout patients: a prospective, randomized, controlled study
Authors: Wang Can , Sun Wenyan , Dalbeth Nicola , Wang Zhongjun , Wang Xuefeng , Ji Xiaopeng , Xue Xiaomei , Han Lin , Cui Lingling , Li Xinde , Liu Zhen , Ji Aichang , He Yuwei , Sun Mingshu , Li Changgui 
Published: September 2023

Abstract
Background
Low urine pH, which may be mediated by metabolic syndrome (MetS), is common in gout. Tart cherries are shown to improve MetS symptoms and possess anti-inflammatory properties. However, the efficacy of tart cherry supplements on urine pH has yet to be studied.

Objectives
This study aimed to investigate the efficacy and safety of tart cherry supplementary citrate (TaCCi) mixture on urine pH, serum urate (sUA), C-reactive protein (CRP), and gout flares in gout patients initiating urate-lowering therapy (ULT), in comparison to citrate mixture and sodium bicarbonate.

Methods
A prospective, randomized (1:1:1), open-label, parallel-controlled trial was conducted among 282 men with gout and fasting urine pH ≤ 6, who were initiating ULT with febuxostat (initially 20 mg daily, escalating to 40 mg daily if serum urate ≥ 360 μmol/L). Participants were randomized to groups taking either sodium bicarbonate, citrate mixture, or TaCCi mixture. All participants were followed every 4 weeks until week 12. Urine pH and sUA were co-primary outcomes, with various biochemical and clinical secondary endpoints.

Results
Urine pH increased to a similar extent in all three groups. SUA levels declined in all three groups as well, with no significant differences observed between the groups. At week 12, the TaCCi mixture group exhibited a greater reduction in the urine albumin/creatinine ratio (UACR) compared to the other two groups (p < 0.05). Participants taking TaCCi mixture or citrate mixture experienced fewer gout flares than those in the sodium bicarbonate group over the study period (p < 0.05). Additionally, the TaCCi mixture group had a lower CRP level at week 12 relative to the other two groups (p < 0.01). Adverse events were similar across all three groups.

Conclusion
The TaCCi mixture had similar efficacy and safety on urine alkalization and sUA-lowering as the citrate mixture and sodium bicarbonate in patients with gout. However, the TaCCi mixture resulted in greater improvements in UACR and CRP, which suggests that tart cherry supplements may provide additional benefits for renal protection and reduce inflammation in gout, particularly when starting ULT.

Trial registration
This project was registered in ChiCTR (www.chictr.org.cn), with the registration number: ChiCTR2100050749.
Production of highly immunogenic and safe Triton X-100 produced bacterial ghost vaccine against Shigella flexneri 2b serotype
Authors: Abdelfattah Amany , Samir Reham , Amin Heba M. 
Published: September 2023

Abstract
Background
Bacterial ghost cells (BGCs) are cells were drained of their genetic and cytoplasmic components. This work aimed to develop vaccine candidates against the Shigella flexneri (S. flexneri) 2b serotype using the BGCs approach. For the first time, (S. flexneri) 2b serotype BGCs vaccine was prepared by incubation with Triton X-100 (TX100) for only 12 h. Its safety and immunogenicity were compared to another vaccine produced using a previously used surfactant, namely Tween 80 (TW80). Scanning electron microscopy (SEM), cellular DNA, protein contents measurements, and ghost cell re-cultivation were used to confirm the successful generation of the BGCs. Immunogenicity was assessed through mice's intraperitoneal (IP) immunization followed by infection with S. flexneri ATCC 12022. Finally, histopathological examination was carried out.

Results
Viable colony forming units (CFUs) of S. flexneri were counted from stool samples as well as homogenized colon tissues of the non-immunized challenged group. Immunized mice sera showed a significant increase in serum bactericidal activity of both preparations (TX100 = 40% and TW80 = 56%) compared to the non-immunized challenged group (positive control). The IgG levels of the bacterial ghost-vaccinated groups were four and three times greater for the TX100 and TW80 ghost vaccines, respectively, compared to that of the positive control; both bacterial ghost vaccines (BGVs) were safe and effective, according to the results of the safety check tests and histopathological analysis.

Conclusions
When comparing the BGVs prepared using TX100 and TW80 methods, the use of TX100 as a new chemical treating agent for BGC production attained robust results in terms of shorter incubation time with the targeted cells and a strong immune response against S. flexneri 2b serotype ATCC 12022 in the IP challenge test. However, a clinical study is needed to confirm the efficacy and total safety of this novel vaccine.
Pictorial essay: MRI evaluation of endometriosis-associated neoplasms
Authors: Radzynski Louise , Boyer Louis , Kossai Myriam , Mouraire Anne , Montoriol Pierre-François 
Published: September 2023

AbstractEndometriosis is a frequent pathology mostly affecting women of young age. When typical aspects are present, the diagnosis can easily be made at imaging, especially at MRI. Transformation of benign endometriosis to endometriosis-associated neoplasms is rare. The physiopathology is complex and remains controversial. Endometrioid carcinoma and clear cell carcinoma are the main histological subtypes. Our goal was to review the main imaging characteristics that should point to an ovarian or extra-ovarian endometriosis-related tumor, especially at MRI, as it may be relevant prior to surgical management.Key points• Transformation of benign endometriosis to endometriosis-associated neoplasms is rare.• MRI is useful when displaying endometriosis lesions associated to an ovarian tumor.• Subtraction imaging should be used in the evaluation of complex endometriomas.
Sex-biased gene and microRNA expression in the developing mouse brain is associated with neurodevelopmental functions and neurological phenotypes
Authors: Szakats Susanna , McAtamney Alice , Cross Hugh , Wilson Megan J. 
Published: September 2023

Abstract
Background
Sex differences pose a challenge and an opportunity in biomedical research. Understanding how sex chromosomes and hormones affect disease-causing mechanisms will shed light on the mechanisms underlying predominantly idiopathic sex-biased neurodevelopmental disorders such as ADHD, schizophrenia, and autism. Gene expression is a crucial conduit for the influence of sex on developmental processes; therefore, this study focused on sex differences in gene expression and the regulation of gene expression. The increasing interest in microRNAs (miRNAs), small, non-coding RNAs, for their contribution to normal and pathological neurodevelopment prompted us to test how miRNA expression differs between the sexes in the developing brain.

Methods
High-throughput sequencing approaches were used to identify transcripts, including miRNAs, that showed significantly different expression between male and female brains on day 15.5 of development (E15.5).

Results
Robust sex differences were identified for some genes and miRNAs, confirming the influence of biological sex on RNA. Many miRNAs that exhibit the greatest differences between males and females have established roles in neurodevelopment, implying that sex-biased expression may drive sex differences in developmental processes. In addition to highlighting sex differences for individual miRNAs, gene ontology analysis suggested several broad categories in which sex-biased RNAs might act to establish sex differences in the embryonic mouse brain. Finally, mining publicly available SNP data indicated that some sex-biased miRNAs reside near the genomic regions associated with neurodevelopmental disorders.

Conclusions
Together, these findings reinforce the importance of cataloguing sex differences in molecular biology research and highlight genes, miRNAs, and pathways of interest that may be important for sexual differentiation in the mouse and possibly the human brain.