bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of reconstructive techniques in breast cancer using BCCT. core software
Authors: Kurt Sevgi , İlgün Ahmet Serkan , Özkurt Enver , Soybir Gürsel , Alço Gül , Ünal Çağlar , Çelebi Filiz Elbüken , Duymaz Tomris , Tapan Tuğba Kayan , Ak Naziye , Ordu Çetin , Özmen Vahit 
Published: March 2024

Abstract
Background
Surgery remains a priority for breast cancer treatment. This study aimed to compare the cosmetic outcomes of oncoplastic patients who had undergone breast-conserving surgery, mini-LDF (latissimus dorsi flap), and immediate implant reconstruction using both the Japanese scale and the BCCT.core (The Breast Cancer Conservative Treatment cosmetic results software) program and to validate this program.

Patients and methods
Patients who underwent surgery for breast cancer between 1997 and 2021 were retrospectively studied. Patients were divided into three groups: 1-those who had undergone breast-conserving surgery (245 patients, 71.3%), 2-those who had undergone mini-LDF after lumpectomy (38 patients, 11.02%), and 3- those who underwent reconstruction with implants after nipple-sparing mastectomy (61 patients, 17.68%). The patients were called for a follow-up examination, and their photos were taken. The photographs were shown to an independent breast surgeon and a plastic surgeon who was not included in the surgeries, and they were asked to evaluate and rate them according to the Japanese cosmetic evaluation scale. The same images were transferred to the computer and scored using BCCT.core.

Results
The plastic and breast surgeon evaluation results showed no significant difference between the three cosmetic techniques (p = 0.99, 0.98).
The results of BCCT.core software measurements were similar to the results of plastic and breast surgeons (p: 0.43).

Conclusion
Patients are more knowledgeable about cosmetic outcomes and expect more objective data. In this study, we used 3 different cosmetic evaluation scales. We found that these techniques give results that are compatible with each other in terms of evaluating the work done in a more concrete way. For this reason, we recommend the use of such software, which offers objective results in a subjective field such as aesthetics and is very easy to apply.
Immunological profile of lactylation-related genes in Crohn’s disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data
Authors: Wu Jingtong , Lv Yinyin , Hao Pei , Zhang Ziyi , Zheng Yongtian , Chen Ermei , Fan Yanyun 
Published: March 2024

Abstract
Background
Crohn's disease (CD) is a disease characterized by intestinal immune dysfunction, often accompanied by metabolic abnormalities. Disturbances in lactate metabolism have been found in the intestine of patients with CD, but studies on the role of lactate and related Lactylation in the pathogenesis of CD are still unknown.

Methods
We identified the core genes associated with Lactylation by downloading and merging three CD-related datasets (GSE16879, GSE75214, and GSE112366) from the GEO database, and analyzed the functions associated with the hub genes and the correlation between their expression levels and immune infiltration through comprehensive analysis. We explored the Lactylation levels of different immune cells using single-cell data and further analyzed the differences in Lactylation levels between inflammatory and non-inflammatory sites.

Results
We identified six Lactylation-related hub genes that are highly associated with CD. Further analysis revealed that these six hub genes were highly correlated with the level of immune cell infiltration. To further clarify the effect of Lactylation on immune cells, we analyzed single-cell sequencing data of immune cells from inflammatory and non-inflammatory sites in CD patients and found that there were significant differences in the levels of Lactylation between different types of immune cells, and that the levels of Lactylation were significantly higher in immune cells from inflammatory sites.

Conclusions
These results suggest that Lactylation-related genes and their functions are closely associated with changes in inflammatory cells in CD patients.
Cryopreservation of cerebrospinal fluid cells preserves the transcriptional landscape for single-cell analysis
Authors: Kodali Mahesh Chandra , Antone Jerry , Alsop Eric , Jayakumar Rojashree , Parikh Khushi , Chiot Aude , Sanchez-Molina Paula , Ajami Bahareh , Arnold Steven E. , Jensen Kendall , Das Sudeshna , Weinberg Marc S. 
Published: March 2024

AbstractCerebrospinal fluid (CSF) matrix biomarkers have become increasingly valuable surrogate markers of neuropsychiatric diseases in research and clinical practice. In contrast, CSF cells have been rarely investigated due to their relative scarcity and fragility, and lack of common collection and cryopreservation protocols, with limited exceptions for neurooncology and primary immune-based diseases like multiple sclerosis. The advent of a microfluidics-based multi-omics approach to studying individual cells has allowed for the study of cellular phenotyping, intracellular dynamics, and intercellular relationships that provide multidimensionality unable to be obtained through acellular fluid-phase analyses. Challenges to cell-based research include site-to-site differences in handling, storage, and thawing methods, which can lead to inaccuracy and inter-assay variability. In the present study, we performed single-cell RNA sequencing (10x Genomics) on fresh or previously cryopreserved human CSF samples from three alternative cryopreservation methods: Fetal Bovine Serum with Dimethyl sulfoxide (FBS/DMSO), FBS/DMSO after a DNase step (a step often included in epigenetic studies), and cryopreservation using commercially available Recovery© media. In comparing relative differences between fresh and cryopreserved samples, we found little effect of the cryopreservation method on being able to resolve donor-linked cell type proportions, markers of cellular stress, and overall gene expression at the single-cell level, whereas donor-specific differences were readily discernable. We further demonstrate the compatibility of fresh and cryopreserved CSF immune cell sequencing using biologically relevant sexually dimorphic gene expression differences by donor. Our findings support the utility and interchangeability of FBS/DMSO and Recovery cryopreservation with fresh sample analysis, providing a methodological grounding that will enable researchers to further expand our understanding of the CSF immune cell contributions to neurological and psychiatric disease.
Inflammation-induced TRPV4 channels exacerbate blood–brain barrier dysfunction in multiple sclerosis
Authors: Hansen Cathrin E. , Kamermans Alwin , Mol Kevin , Berve Kristina , Rodriguez-Mogeda Carla , Fung Wing Ka , van het Hof Bert , Fontijn Ruud D. , van der Pol Susanne M. A. , Michalick Laura , Kuebler Wolfgang M. , Kenkhuis Boyd , van Roon-Mom Willeke , Liedtke Wolfgang , Engelhardt Britta , Kooij Gijs , Witte Maarten E. , de Vries Helga E. 
Published: March 2024

Abstract
Background
Blood–brain barrier (BBB) dysfunction and immune cell migration into the central nervous system (CNS) are pathogenic drivers of multiple sclerosis (MS). Ways to reinstate BBB function and subsequently limit neuroinflammation present promising strategies to restrict disease progression. However, to date, the molecular players directing BBB impairment in MS remain poorly understood. One suggested candidate to impact BBB function is the transient receptor potential vanilloid-type 4 ion channel (TRPV4), but its specific role in MS pathogenesis remains unclear. Here, we investigated the role of TRPV4 in BBB dysfunction in MS.

Main text
In human post-mortem MS brain tissue, we observed a region-specific increase in endothelial TRPV4 expression around mixed active/inactive lesions, which coincided with perivascular microglia enrichment in the same area. Using in vitro models, we identified that microglia-derived tumor necrosis factor-α (TNFα) induced brain endothelial TRPV4 expression. Also, we found that TRPV4 levels influenced brain endothelial barrier formation via expression of the brain endothelial tight junction molecule claudin-5. In contrast, during an inflammatory insult, TRPV4 promoted a pathological endothelial molecular signature, as evidenced by enhanced expression of inflammatory mediators and cell adhesion molecules. Moreover, TRPV4 activity mediated T cell extravasation across the brain endothelium.

Conclusion
Collectively, our findings suggest a novel role for endothelial TRPV4 in MS, in which enhanced expression contributes to MS pathogenesis by driving BBB dysfunction and immune cell migration.
Predictive factors of thoracic aortic calcification in patients candidate for cardiac surgery
Authors: Bagheri Amin , Shirani Shapour , Jalali Arash , Salehbeigi Shahrzad , Bagheri Jamshid 
Published: March 2024

Abstract
Background
The presence of the severe thoracic aortic calcification (TAC) in cardiac surgery patients is associated with adverse post-operative outcome. However, the relationship between cardiovascular risk factors and aortic plaque burden remains unknown. The objective of this study was to determine the predictive factors of TAC in patients candidate for cardiac surgery.

Methods
Patients who underwent thoracic CT scan prior to cardiac surgery between August 2020 to April 2021 were included. Of 556 patients, 209 (36.7%) had a thoracic aortic calcium score (TACS) ≥ 400 mm [3] and were compare with the remaining patients. Predictors of severe TAC were assessed through stepwise multivariable logistic regression analysis.

Results
The patients with TACS ≥ 400 had a higher mean age (67.3 ± 7.1 vs. 55.7 ± 10.6; p < 0.001) with a higher frequency of diabetes mellitus (40.7% vs. 30.8%; p = 0.018), dyslipidemia (49.8% vs. 38.6%; p = 0.010), hypertension (60.8% vs. 44.7%; p < 0.001), opium addiction (18.2% vs. 11.2%; p = 0.023), peripheral vascular disease (PVD) (7.7% vs. 2.3%; p = 0.005) as compared with TACS < 400. The multiple determinants of TAC were PVD (OR = 2.86) followed by opium addiction, diabetes and age.

Conclusions
Thoracic CT scan prior to cardiac surgery for patients with older age, diabetes, opium addiction and PVD is recommended. Our study could serve as a foundation for future research endeavors aimed at establishing a risk score for TAC.
Breath metabolomics for diagnosis of acute respiratory distress syndrome
Authors: Zhang Shiqi , Hagens Laura A. , Heijnen Nanon F. L. , Smit Marry R. , Brinkman Paul , Fenn Dominic , van der Poll Tom , Schultz Marcus J. , Bergmans Dennis C. J. J. , Schnabel Ronny M. , Bos Lieuwe D. J. ,   for the DARTS Consortium, Bos Lieuwe D. J. , Hagens Laura A. , Schultz Marcus J. , Smit Marry R. , Bergmans Dennis C. J. J. , Heijnen Nanon F. L. , Schnabel Ronny M. , Geven Inge , Nijsen Tamara M. E. , Verschueren Alwin R. M. 
Published: March 2024

Abstract
Background
Acute respiratory distress syndrome (ARDS) poses challenges in early identification. Exhaled breath contains metabolites reflective of pulmonary inflammation.

Aim
To evaluate the diagnostic accuracy of breath metabolites for ARDS in invasively ventilated intensive care unit (ICU) patients.

Methods
This two-center observational study included critically ill patients receiving invasive ventilation. Gas chromatography and mass spectrometry (GC–MS) was used to quantify the exhaled metabolites. The Berlin definition of ARDS was assessed by three experts to categorize all patients into “certain ARDS”, “certain no ARDS” and “uncertain ARDS” groups. The patients with “certain” labels from one hospital formed the derivation cohort used to train a classifier built based on the five most significant breath metabolites. The diagnostic accuracy of the classifier was assessed in all patients from the second hospital and combined with the lung injury prediction score (LIPS).

Results
A total of 499 patients were included in this study. Three hundred fifty-seven patients were included in the derivation cohort (60 with certain ARDS; 17%), and 142 patients in the validation cohort (47 with certain ARDS; 33%). The metabolites 1-methylpyrrole, 1,3,5-trifluorobenzene, methoxyacetic acid, 2-methylfuran and 2-methyl-1-propanol were included in the classifier. The classifier had an area under the receiver operating characteristics curve (AUROCC) of 0.71 (CI 0.63–0.78) in the derivation cohort and 0.63 (CI 0.52–0.74) in the validation cohort. Combining the breath test with the LIPS does not significantly enhance the diagnostic performance.

Conclusion
An exhaled breath metabolomics-based classifier has moderate diagnostic accuracy for ARDS but was not sufficiently accurate for clinical use, even after combination with a clinical prediction score.
Comparing silver and gold nanoislands’ surface plasmon resonance for bisacodyl and its metabolite quantification in human plasma
Authors: Kelani Khadiga M. , Ibrahim Maha M. , Ramadan Nesreen K. , Elzanfaly Eman S. , Eid Sherif M. 
Published: March 2024

AbstractGold and silver nanoparticles have witnessed increased scientific interest due to their colourful colloidal solutions and exceptional applications. Comparing the localized surface plasmon resonance (LSPR) of gold and silver nanoparticles is crucial for understanding and optimizing their optical properties. This comparison informs the design of highly sensitive plasmonic sensors, aids in selecting the most suitable nanoparticles for applications like surface-enhanced infrared spectroscopy (SEIRA) and biomedical imaging, and guides the choice between gold and silver nanoparticles based on their catalytic and photothermal properties. Ultimately, the study of LSPR facilitates the tailored use of these nanoparticles in diverse scientific and technological applications. Two SEIRA methods combined with partial least squares regression (PLSR) chemometric tools were developed. This development is based on the synthesis of homogeneous, high-dense deposited metal nanoparticle islands over the surface of glass substrates to be used as lab-on-chip SEIRA sensors for the determination of bisacodyl (BIS) and its active metabolite in plasma. SEM micrographs revealed the formation of metallic islands of colloidal citrate-capped gold and silver nanoparticles of average sizes of 29.7 and 15 nm, respectively. BIS and its active metabolite were placed on the nanoparticles’ coated substrates to be directly measured, then PLSR chemometric modelling was used for the quantitative determinations. Plasmonic citrate-capped gold nanoparticle substrates showed better performance than those prepared using citrate-capped silver nanoparticles in terms of preparation time, enhancement factor, PLSR model prediction, and quantitative results. This study offers a way to determine BIS and its active metabolite in the concentration range 15–240 ng/mL in human plasma using inexpensive disposable glass-coated substrates that can be prepared in 1 h to get results in seconds with good recovery between 98.77 and 100.64%. The sensors provided fast, simple, selective, molecular-specific and inexpensive procedures to determine molecules in their pure form and biological fluid.
Navigating the metabolic maze: anomalies in fatty acid and cholesterol processes in Alzheimer’s astrocytes
Authors: Zhang Xiaoyu , Chen Chuanying , Liu Yi 
Published: March 2024

Abstract Alzheimer’s disease (AD) is the most common cause of dementia, and its underlying mechanisms have been a subject of great interest. The mainstream theory of AD pathology suggests that the disease is primarily associated with tau protein and amyloid-beta (Aβ). However, an increasing body of research has revealed that abnormalities in lipid metabolism may be an important event throughout the pathophysiology of AD. Astrocytes, as important members of the lipid metabolism network in the brain, play a significant role in this event. The study of abnormal lipid metabolism in astrocytes provides a new perspective for understanding the pathogenesis of AD. This review focuses on the abnormal metabolism of fatty acids (FAs) and cholesterol in astrocytes in AD, and discusses it from three perspectives: lipid uptake, intracellular breakdown or synthesis metabolism, and efflux transport. We found that, despite the accumulation of their own fatty acids, astrocytes cannot efficiently uptake fatty acids from neurons, leading to fatty acid accumulation within neurons and resulting in lipotoxicity. In terms of cholesterol metabolism, astrocytes exhibit a decrease in endogenous synthesis due to the accumulation of exogenous cholesterol. Through a thorough investigation of these metabolic abnormalities, we can provide new insights for future therapeutic strategies by literature review to navigate this complex metabolic maze and bring hope to patients with Alzheimer’s disease.
The role of molecular diagnosis in anaphylactic patients with dual or triple-sensitization to Hymenoptera venoms
Authors: Bemanian Mohammad Hassan , Shokouhi Shoormasti Raheleh , Arshi Saba , Jafari Mahsa , Shokri Sima , Fallahpour Morteza , Nabavi Mohammad , Zaremehrjardi Fatemeh 
Published: March 2024

Abstract
Background
The poly-sensitization to Hymenoptera venom makes it difficult to select genuine allergens for immunotherapy and increases patients’ costs. The objective of this study was to determine the culprit allergen in dual or triple-sensitized patients to three Hymenoptera venoms through molecular diagnosis and evaluating the results of incorporating the molecular diagnosis with skin tests.

Methods
Thirty-two patients with anaphylactic reactions and dual or triple-sensitization to Hymenoptera venoms in skin tests entered this study. IgE-sensitization to whole extracts and molecules of Apis mellifera (Api m), Vespula vulgaris (Ves v), and Polistes dominulus (Pol d) was evaluated utilizing ALEX or ImmunoCAP.

Results
Twenty-nine patients (90.6%) were male. IgE-sensitization to at least one of the allergenic molecules related to Apis mellifera, Vespula vulgaris, and Polistes dominulus was seen in 59.4, 53.1, and 21.9%, respectively. Among 32 patients, 14 (43.8) and 8 (25%), were mono-sensitized to Api m and Ves v components in ALEX, respectively. Double sensitization to Hymenoptera was identified in 18.8% of patients in ALEX. Api m 1+/Api m 2−/Api m 10− and Ves v 1+/Ves v 5+ demonstrated the most prevalent sensitizations patterns in our patients.

Conclusions
The molecular diagnosis of IgE-sensitization to Hymenoptera venoms can be valuable, especially in patients who show dual or triple-sensitization in skin tests, as the ALEX results revealed mono and double-sensitization to Hymenoptera venoms in 22 and 6 patients, respectively. Regarding the high cost and adverse reactions of venom immunotherapy, especially for two or three venoms, incorporating the molecular diagnosis alongside skin tests for accurate diagnosis of the culprit venom could help decrease costs for patients.
Circ_0070934 promotes MGAT3 expression and inhibits epithelial-mesenchymal transition in bronchial epithelial cells by sponging miR-199a-5p
Authors: Ding Ziqi , Xiao Xinru , Fan Liang , Mao Zhengdao , Sun Chuang , Li Na , Zhang Qian 
Published: March 2024

Abstract
Background
Circular RNA (circRNA) has the potential to serve as a crucial regulator in the progression of bronchial asthma. The objective of this investigation was to elucidate the functional dynamics of the circ_0070934/miR-199a-5p/Mannoside acetylglucosaminyltransferase 3 (MGAT3) axis in the development of asthma.

Methods
Circ_0070934, miR-199a-5p and MGAT3 in peripheral venous blood of 38 asthmatic patients and 43 healthy controls were detected by qRT-PCR, and the expression of MGAT3 protein was examined by ELISA. The GSE148000 dataset was analyzed for differences in MGAT3. The BEAS-2B cells were transfected with circ_0070934 plasmid and small interfering RNA, miR-199a-5p mimics and inhibitors. The apoptosis level was detected by flow cytometry and MGAT3 was detected by qRT-PCR and Western blot. The expression of E-cadherin, N-cadherin, Vimentin was examined by Western blot. Interleukin-4 (IL-4) and IL-13 were used to co-stimulate BEAS-2B cells as an asthmatic airway epithelial cell model. BEAS-2B cells exposed to type 2 cytokines (IL-4 and IL-13) were treated with circ_0070934 plasmid, and the expression of E-cadherin, N-cadherin, and Vimentin was detected by Western blot. The binding relationships were verified using dual-luciferase reporter assay and miRNA pull-down assay.

Results
The expression of circ_0070934 and MGAT3 in peripheral venous blood of asthmatic patients was down-regulated, and the expression of miR-199a-5p was up-regulated. And the expression of MGAT3 was reduced in sputum of asthma patients. Down-regulating the expression of circ_0070934 could promote apoptosis of BEAS-2B cells and increase epithelial-mesenchymal transition (EMT), and this effect can be partially reversed by down-regulating miR-199a-5p. Circ_0070934 could inhibit the process of epithelial mesenchymal transition induced by IL-4 and IL-13 in BEAS-2B cells. In addition, miR-199a-5p could respectively bind to circ_0070934 and MGAT3.

Conclusion
The findings of this study indicate that circ_0070934 may function as a competitive endogenous RNA (ceRNA) of miR-199a-5p, thereby modulating the expression of MGAT3 and impacting the process of EMT in bronchial epithelial cells. These results contribute to the establishment of a theoretical framework for advancing the prevention and treatment strategies for asthma.
Partial facial duplication (diprosopus): a case report and review of the literature
Authors: Salah Fathia Omer , Zewdie Yohannes Girma , Ambachew Semienew , Nour Amal Saleh , Endale Tewodros 
Published: March 2024

Abstract
Background
Diprosopus, or craniofacial duplication, is a rare entity that occurs in approximately 1 in 180,000 to 15 million live births. The degree of duplication varies from complete facial duplication to small facial structure duplication like the nose and eye. The cause of diprosopus is unknown though there are proposed factors.

Case presentation
Our African patient was a term 72 hours old female neonate who was referred to our center with impression of lower facial duplication with two oral cavity that are located side to side separated by large soft tissue, she also had flat nasal bridge with widely separated nostrils and widely spaced eyes. Besides the facial malformation she had multiple episodes of vomiting with aspiration. Her blood tests were normal. Precontract brain computed tomography (CT) scan confirmed partially duplicated mandible and maxilla, two oral cavity separated by large fatty tissue, brain tissue were well formed and the only abnormality was corpus callosum agenesis and interhemispheric lipoma. In her stay at hospital nasogastric tube (NG) tube feed was initiated and started with antibiotics for aspiration pneumonia. After 25th day the neonatal passed away with possible cause of death being respiratory failure.

Conclusion
Craniofacial duplication is a very rare anomaly with only a few cases reported. Most of these patients are stillborn, even if they survive the prognosis is often poor. Early prenatal diagnosis is very important as termination of pregnancy can sometimes be considered an option.