bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying disulfidptosis subtypes in hepatocellular carcinoma through machine learning and preliminary exploration of its connection with immunotherapy
Authors: Chen Guanjun , Zhang Ganghua , Zhu Yuxing , Wu Anshan , Fang Jianing , Yin Zhijing , Chen Haotian , Cao Ke 
Published: June 2024

Abstract
Background
Hepatocellular carcinoma (HCC) is a highly prevalent and deadly cancer, with limited treatment options for advanced-stage patients. Disulfidptosis is a recently identified mechanism of programmed cell death that occurs in SLC7A11 high-expressing cells due to glucose starvation-induced disintegration of the cellular disulfide skeleton. We aimed to explore the potential of disulfidptosis, as a prognostic and therapeutic marker in HCC.

Methods
We classified HCC patients into two disulfidptosis subtypes (C1 and C2) based on the transcriptional profiles of 31 disulfrgs using a non-negative matrix factorization (NMF) algorithm. Further, five genes (NEIL3, MMP1, STC2, ADH4 and CFHR3) were screened by Cox regression analysis and machine learning algorithm to construct a disulfidptosis scoring system (disulfS). Cell proliferation assay, F-actin staining and PBMC co-culture model were used to validate that disulfidptosis occurs in HCC and correlates with immunotherapy response.

Results
Our results suggests that the low disulfidptosis subtype (C2) demonstrated better overall survival (OS) and progression-free survival (PFS) prognosis, along with lower levels of immunosuppressive cell infiltration and activation of the glycine/serine/threonine metabolic pathway. Additionally, the low disulfidptosis group showed better responses to immunotherapy and potential antagonism with sorafenib treatment. As a total survival risk factor, disulfS demonstrated high predictive efficacy in multiple validation cohorts. We demonstrated the presence of disulfidptosis in HCC cells and its possible relevance to immunotherapeutic sensitization.

Conclusion
The present study indicates that novel biomarkers related to disulfidptosis may serve as useful clinical diagnostic indicators for liver cancer, enabling the prediction of prognosis and identification of potential treatment targets.

Graphical Abstract
Cytological diagnosis of patients with embryonal rhabdomyosarcoma of the cervix: case report and literature review
Authors: Wei Xiaoxia , Li Lei 
Published: June 2024

AbstractCervical embryonal rhabdomyosarcoma(ERMS) is a rare malignancy. To date, no cases of ERMS diagnosed by cervical cytology have been reported. In this study, we report a case of cervical ERMS identified by a liquid-based cytology test and cell blocks in a 46-year-old postmenopausal woman. We describe the cytological features of ERMS, with the aim of helping cytopathologists recognize this rare cervical tumor.
From cells to power cells: harnessing bacterial electron transport for microbial fuel cells (MFCs)
Authors: Garimella Sri Sathya Sandilya , Rachakonda Sai Vennela , Pratapa Sai Sowmya , Mannem Gnana Divya , Mahidhara Ganesh 
Published: June 2024

AbstractMicrobial fuel cells (MFCs), which use bacterial electron transport mechanisms to generate energy, have become a viable technology for renewable energy production. This review investigates the evolutionary and functional connections between bacterial energy transduction mechanisms and mitochondrial electron transport chains, building on the endosymbiont theory of eukaryotic cell evolution. The conserved features and similarities between prokaryotic and eukaryotic electron transport pathways were elucidated, highlighting their common origins and roles in cellular bioenergetics. This discussion explores the essential mechanisms governing the movement of electrons and ions across biological membranes, crucial for generating energy and maintaining electrochemical gradients in bacteria and mitochondria. Capitalizing on these insights, we explore the applications of electrogenic bacteria in MFCs for renewable electricity generation. Optimal conditions for enhancing bacterial electron transfer to electrode surfaces are identified, paving the way for improved MFC performance. Potential large-scale implementations of MFCs in wastewater treatment, biosensing, and bioremediation of contaminated environments are discussed, underscoring their versatility and environmental benefits. The importance of investigating bioenergetic mechanisms at both the cellular and molecular scales of fully harnessing the capabilities of microbial energy conversion systems is highlighted in this review. By bridging the gap between fundamental cellular processes and sustainable technologies, we aim to advance renewable energy solutions that harness the remarkable capabilities of electrogenic microorganisms.
Investigation of the anatomic risk factors in acute anterior cruciate ligament ruptures to develop ramp lesions of the medial meniscus by quantitative MRI
Authors: Tang Ziyi , Luo Yuxi , Liu Dan , Zhou Suying , Xu Zhangyan , Zhu Tongxin , Yang HaiTao 
Published: June 2024

Abstract
Objective
To investigate the anatomic risk factors of knee in patients with acute non-contact anterior cruciate ligament (aACL) ruptures to develop ramp lesions.

Methods
A total of 202 subjects were retrospectively divided into three groups: (1) aACL ruptures combined with ramp lesions group (n = 76); (2) isolated ACL ruptures group (n = 56) and (3) normal controls group (n = 70). Quantitative morphological parameters on MRI were measured including: diameter of medial femoral condyle (MFC), anterior-posterior length and depth of medial tibial plateau (MTP AP length and depth), lateral posterior tibial slope (LPTS) and medial posterior tibial slope (MTPS), asymmetry of LPTS and MPTS (LMPTS), lateral meniscal slope (LMS), and medial meniscal slope (MMS).

Results
The MTP AP length, MTP AP length/MFC diameter ratio, MTP depth, LPTS and the asymmetry of LMPTS showed significant differences among the three groups (p < 0.001). The risk factors associated with the ramp lesions including a longer MTP AP length (OR 1.17, 95% CI 1.00–1.44, p = 0.044), increased MTP depth (OR 1.91, 95% CI 1.22–3.00, p = 0.005) and lager ratio (OR 1.11, 95% CI 1.01–1.22, p = 0.036). The highest AUC was the MTP AP length/MFC diameter ratio (0.74; 95% CI, 0.66–0.82). The combination model increased higher accuracy (0.80; 95% CI, 0.72–0.88).

Conclusion
Several bony anatomic characteristics of the knee, especially the morphology of medial tibia plateau, are additional risk factors for aACL ruptures to develop ramp lesions.

Critical relevance statement
Predictive anatomic risk factors of the knee for patients with acute non-contact anterior cruciate ligament (aACL) ruptures to develop ramp lesions, especially the morphology of medial tibia plateau, are detectable by MRI.

Key Points

Ramp lesion development can complicate aACL ruptures and requires specific treatment.

Longer AP length and increased MTP depth are risk factors for concurrent ramp lesions.

Identification of ramp lesions allows for the most appropriate treatment.

Graphical Abstract
PrEP facilitators and barriers in substance use bridge clinics for women who engage in sex work and who use drugs
Authors: Harris Miriam TH , Weinberger Emma , O’Brien Christine , Althoff Mary , Paltrow-Krulwich Samantha , Taylor Jessica L. , Judge Abigail , Samet Jeffrey H. , Walley Alexander Y. , Gunn Christine M. 
Published: June 2024

Abstract
Background
Women who engage in sex work and use drugs (WSWUD) experience disproportionate HIV risks. Substance use treatment bridge clinics offer an opportunity to increase HIV pre-exposure prophylaxis (PrEP) delivery to WSWUD, but research on best practices is lacking. Therefore, we explored facilitators and barriers to PrEP across the PrEP care continuum in these settings.

Methods
Bridge clinic and affiliated harm reduction health service providers and WSWUD from Boston were recruited using passive and active outreach between December 2021 and August 2022. Participants were invited to take part in semi-structured phone or in-person interviews to explore HIV prevention and PrEP care experiences overall and within bridge clinic settings. Deductive codes were developed based on HIV risk environment frameworks and the Information-Motivation-Behavioral Skills model and inductive codes were added based on transcript review. Grounded content analysis was used to generate themes organized around the PrEP care continuum.

Results
The sample included 14 providers and 25 WSWUD. Most WSWUD were aware of PrEP and more than half had initiated PrEP at some point. However, most who initiated PrEP did not report success with daily oral adherence. Providers and WSWUD described facilitators and barriers to PrEP across the steps of the care continuum: Awareness, uptake, adherence, and retention. Facilitators for WSWUD included non-stigmatizing communication with providers, rapid wraparound substance use treatment and HIV services, having a PrEP routine, and service structures to support PrEP adherence. Barriers included low HIV risk perceptions and competing drug use and survival priorities. Provider facilitators included clinical note templates prompting HIV risk assessments and training. Barriers included discomfort discussing sex work risks, competing clinical priorities, and a lack of PrEP adherence infrastructure.

Conclusion
WSWUD and bridge clinic providers favored integrated HIV prevention and substance use services in harm reduction and bridge clinic settings. Harm reduction and bridge clinic programs played a key role in HIV prevention and PrEP education for WSWUD. Effective behavioral and structural interventions are still needed to improve PrEP adherence for WSWUD.
Single-cell and spatial transcriptomics reveal alterations in trophoblasts at invasion sites and disturbed myometrial immune microenvironment in placenta accreta spectrum disorders
Authors: Ji Kaiyuan , Chen Yunshan , Pan Xiuyu , Chen Lina , Wang Xiaodi , Wen Bolun , Bao Junjie , Zhong Junmin , Lv Zi , Zheng Zheng , Liu Huishu 
Published: June 2024

Abstract
Background
Placenta accreta spectrum disorders (PAS) are a severe complication characterized by abnormal trophoblast invasion into the myometrium. The underlying mechanisms of PAS involve a complex interplay of various cell types and molecular pathways. Despite its significance, both the characteristics and intricate mechanisms of this condition remain poorly understood.

Methods
Spatial transcriptomics (ST) and single-cell RNA sequencing (scRNA-seq), were performed on the tissue samples from four PAS patients, including invasive tissues (ST, n = 3; scRNA-seq, n = 4), non-invasive normal placenta samples (ST, n = 1; scRNA-seq, n = 2). Three healthy term pregnant women provided normal myometrium samples (ST, n = 1; scRNA-seq, n = 2). ST analysis characterized the spatial expression landscape, and scRNA-seq was used to identify specific cellular components in PAS. Immunofluorescence staining was conducted to validate the findings.

Results
ST slices distinctly showed the myometrium in PAS was invaded by three subpopulations of trophoblast cells, extravillous trophoblast cells, cytotrophoblasts, and syncytiotrophoblasts, especially extravillous trophoblast cells. The pathways enriched by genes in trophoblasts, smooth muscle cells (SMC), and immune cells of PAS were mainly associated with immune and inflammation. We identified elevated expression of the angiogenesis-stimulating gene PTK2, alongside the cell proliferation-enhancing gene EGFR, within the trophoblasts of PAS group. Trophoblasts mainly contributed the enhancement of HLA-G and EBI3 signaling, which is crucial in establishing immune escape. Meanwhile, SMC regions in PAS exhibited upregulation of immunomodulatory markers such as CD274, HAVCR2, and IDO1, with CD274 expression experimentally verified to be increased in the invasive SMC areas of the PAS group.

Conclusions
This study provided information of cellular composition and spatial organization in PAS at single-cell and spatial level. The dysregulated expression of genes in PAS revealed a complex interplay between enhanced immune escape in trophoblasts and immune tolerance in SMCs during invasion in PAS. These findings will enhance our understanding of PAS pathogenesis for developing potential therapeutic strategies.
Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities
Authors: Ninck Sabrina , Klaus Thomas , Kochetkova Tatiana V. , Esser Sarah P. , Sewald Leonard , Kaschani Farnusch , Bräsen Christopher , Probst Alexander J. , Kublanov Ilya V. , Siebers Bettina , Kaiser Markus 
Published: June 2024

Abstract
Background
Microbial communities are important drivers of global biogeochemical cycles, xenobiotic detoxification, as well as organic matter decomposition. Their major metabolic role in ecosystem functioning is ensured by a unique set of enzymes, providing a tremendous yet mostly hidden enzymatic potential. Exploring this enzymatic repertoire is therefore not only relevant for a better understanding of how microorganisms function in their natural environment, and thus for ecological research, but further turns microbial communities, in particular from extreme habitats, into a valuable resource for the discovery of novel enzymes with potential applications in biotechnology. Different strategies for their uncovering such as bioprospecting, which relies mainly on metagenomic approaches in combination with sequence-based bioinformatic analyses, have emerged; yet accurate function prediction of their proteomes and deciphering the in vivo activity of an enzyme remains challenging.

Results
Here, we present environmental activity-based protein profiling (eABPP), a multi-omics approach that extends genome-resolved metagenomics with mass spectrometry-based ABPP. This combination allows direct profiling of environmental community samples in their native habitat and the identification of active enzymes based on their function, even without sequence or structural homologies to annotated enzyme families. eABPP thus bridges the gap between environmental genomics, correct function annotation, and in vivo enzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases from eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia.

Conclusions
By reporting enzyme activities within an ecosystem in their native state, we anticipate that eABPP will not only advance current methodological approaches to sequence homology-guided enzyme discovery from environmental ecosystems for subsequent biocatalyst development but also contributes to the ecological investigation of microbial community interactions by dissecting their underlying molecular mechanisms.
Milk protein concentrate supplementation improved appetite, metabolic parameters, adipocytokines, and body composition in dieting women with obesity: a randomized controlled trial
Authors: Elahikhah Mahsa , Haidari Fatemeh , Khalesi Saman , Shahbazian Hajieh , Mohammadshahi Majid , Aghamohammadi Vahideh 
Published: June 2024

Abstract
Background
Dairy consumption is associated with many health benefits. However, to our knowledge, no clinical trials examined the effects of milk protein concentrate (MPC) on metabolic health in overweight and obese adults. This study investigated the effect of supplementation with MPC on glycaemic status, lipid profile, biomarkers of inflammation, and anthropometric measurements in women with obesity under a weight loss diet.

Methods
This is a single-blind, open-labelled, parallel-group, randomized trial. Forty-four healthy women with obesity were randomized into a control (n = 22) or MPC (n = 22) group. Participants in the MPC group were supplemented with 30 g of MPC per day for 8 weeks. Both groups were on a calorie-restricted diet plan with 800 Kcal lower intakes than their needs. Blood samples, dietary intake, and body composition were assessed before and after the intervention.

Results
MPC group had a significantly lower body mass index (P = 0.009), waist circumference (P = 0.013), fat mass (P = 0.021), appetite score (P = 0.002), fasting blood sugar (P < 0.001), insulin (P = 0.027), low-density lipoprotein cholesterol (P = 0.025), and leptin (P = 0.014) levels and higher high-density lipoprotein cholesterol (P = 0.001) and adiponectin (P = 0.032) compared to the control group after supplementation. Lean body mass, total cholesterol, and triglyceride did not differ significantly (P > 0.05).

Conclusion
Daily intake of 30 g of MPC for 8 weeks may improve several anthropometric and metabolic markers in women with obesity under a hypocaloric diet.
Therapy management and outcome of acute hydrocephalus secondary to intraventricular hemorrhage in adults
Authors: Wang Chaoyang , Bai Jianuo , He Qiheng , Jiao Yuming , Zhang Wenqian , Huo Ran , Wang Jie , Xu Hongyuan , Zhao Shaozhi , Wu Zhiyou , Sun Yingfan , Yu Qifeng , Tang Jinyi , Zeng Xianwei , Yang Wuyang , Cao Yong 
Published: June 2024

Abstract
Background
Intraventricular hemorrhage (IVH) refers to bleeding within the brain’s ventricular system, and hydrocephalus is a life-threatening complication of IVH characterized by increased cerebrospinal fluid accumulation in the ventricles resulting in elevated intracranial pressure. IVH poses significant challenges for healthcare providers due to the complexity of the underlying pathophysiology and lack of standardized treatment guidelines. Herein, we performed a systematic review of the treatment strategies for hydrocephalus secondary to IVH.

Methods
This systematic review was prospectively registered with PROSPERO (CRD42023450786). The search was conducted in PubMed, Cochrane Library, and Web of Science on July 15, 2023. We included original studies containing valid information on therapy management and outcome of hydrocephalus secondary to primary, spontaneous, and subarachnoid or intracranial hemorrhage following IVH in adults that were published between 2000 and 2023. Glasgow Outcome Scale (GOS) or modified Ranking Scale (mRS) scores during follow-up were extracted as primary outcomes. The risk of bias was assessed using the Newcastle–Ottawa Scale for Cohort Studies or Cochrane Risk of Bias 2.0 Tool.

Results
Two hundred and seven patients from nine published papers, including two randomized controlled trials, were included in the analysis. The GOS was used in five studies, while the mRS was used in four. Seven interventions were applied, including craniotomy for removal of hematoma, endoscopic removal of hematoma with/without endoscopic third ventriculostomy (ETV), traditional external ventricular drainage (EVD), and various combinations of EVD, lumbar drainage (LD), and intraventricular fibrinolysis (IVF). Endoscopic removal of hematoma was performed in five of nine studies. Traditional EVD had no obvious benefit compared with new management strategies. Three different combinations of EVD, LD, and IVF demonstrated satisfactory outcomes, although more studies are required to confirm their reliability. Removal of hematoma through craniotomy generated reliable result. Generally, endoscopic removal of hematoma with ETV, removal of hematoma through craniotomy, EVD with IVF, and EVD with early continuous LD were useful.

Conclusion
EVD is still crucial for the management of IVH and hydrocephalus. Despite a more reliable result from the removal of hematoma through craniotomy, a trend toward endoscopic approach was observed due to a less invasive profile.
Exploring bekasam, an indigenous fermented fish product of Indonesia: original South Sumatra region
Authors: Setiarto R. Haryo Bimo , Herlina Vika Tresnadiana 
Published: June 2024

AbstractFermentation is a traditional method of food preservation that is widely used for improving shelf life, food safety, and sensory and nutritional properties. Fermented fish are an integral part of numerous food cultures and are produced in different parts of the world. Bekasam is an Indonesian traditional fermented fish commonly used as a condiment in Indonesian dishes because of its umami taste. This review tries to elaborate on various aspects of bekasam. The emphasis of this work is related to cultural history, microfunctional properties, manufacturing processes, biochemical and nutritional properties, as well as their health benefits and safety concerns. Moreover, some challenges and directions for future research regarding bekasam are also discussed in this review. Further investigation into fermented fish products is not only crucial for the food industry, but also for human health. Nevertheless, comprehensive in vivo and toxicological investigations are imperative prior to the utilization of fermented fish products that are abundant in bioactive compounds for the purpose of human health benefits.
Amplitude scintillation detection with geodetic GNSS receivers leveraging machine learning decision tree
Authors: Li Wang , Jiang Yiping , Ji Hongyuan , Wei Wenqiang 
Published: June 2024

AbstractThe amplitude scintillation detection is typically achieved by using the scintillation index generated by dedicated and costly ionospheric scintillation monitoring receivers (ISMRs). Considering the large volume of common Global Navigation Satellite System (GNSS) receivers, this paper presents a strategy to accurately identify the ionospheric amplitude scintillation events utilizing the measurements collected with geodetic GNSS receivers. The proposed detection method relies on a pre-trained machine learning decision tree algorithm, leveraging the scintillation index computed from the carrier-to-noise data and elevation angles collected at 1-Hz. The experimental results using real data demonstrate a 99% accuracy in scintillation detection can be achieved. By combining advanced machine learning techniques with geodetic GNSS receivers, this approach is feasible to effectively detect ionospheric scintillation using non-scintillation GNSS receivers.
Correlation between chest DW-MRI and 18F-FDG PET/CT in newly diagnosed non-small cell lung cancer (NSCLC)
Authors: Lotfy Abeer Gamal , Abdou Nora Nabil , Monib Ahmed Mohamed , Hussein Rasha S. 
Published: June 2024

Abstract
Background
PET/CT is currently the gold standard for lung cancer staging, and it is also used to identify distant and nodal metastases. High-resolution MRI can also be used to diagnose and provide morphological details about lung cancer. Standardized uptake value ‘SUV’ calculated from PET/CT gives information about tumor behavior where the SUV reflects metabolic tumor activity. Apparent diffusion coefficient ‘ADC’ calculated from DW-MRI is a quantitative imaging marker aiming to assess tumor cellularity which reflects tumor behavior. The study aimed to correlate ADC assessed by DW-MRI and metabolic activity determined by SUV max in PET/CT in local and nodal staging of newly diagnosed NSCLC.

Results
Our study involved twenty-one patients who were pathologically proven to be NSCLC, 19 males (90.5%) and 2 females (9.5%), with a median age of 61 years (ranging from 37 to 84 years). Among all NSCLC primary mass lesions, we observed a statistically significant inverse correlation between SUV max achieved from PET/CT and ADC max, ADC mean, and ADC min calculated from DW-MR (r = − 0.509 and p = 0.019, r = − 0.472 and p = 0.031 and r = − 0.434 and p = 0.049 for correlation between SUV max of PET/CT and ADC max, ADC mean and ADC min of DW-MR, respectively). Additionally, we observed another statistically significant inverse correlation between SUV max achieved from PET/CT and ADC max, ADC mean, and ADC min calculated from DW-MR in NSCLC mediastinal lymph nodes (r = − 0.699 and p = 0.011, r = − 0.58 and p = 0.048 and r = − 0.629 and p = 0.028 for correlation between SUV max of PET/CT and ADC max, ADC mean and ADC min of DW-MR, respectively).

Conclusions
ADC values calculated from DW-MRI might act as a new prognostic tool owing to its significant inverse correlation with SUV max achieved from PET/CT in NSCLC primary mass lesions as well as mediastinal lymph nodes.