bluuebunny/crossref_metadata_2025_split huggingface dataset:
The neurosurgical outpatient clinic: comparison between accesses in public and private activities
Authors: Menegatti Marta , Del Villano Nunzia , Scerrati Alba , Travaglini Francesco , Ricciardi Luca , Lofrese Giorgio , Cavallo Michele Alessandro , De Bonis Pasquale 
Published: January 2024

Abstract
Background
Neurosurgical clinic assesses presence and extent of pathologies of central and peripheral nervous system or disorders affecting the spine, to identify most effective treatment and possible recourse to surgery. The aim of the study is to evaluate the appropriateness of request for a neurosurgical consult both in private and in public outpatient clinics.

Materials and methods
We collected and analyzed all the reports of outpatient visits of public and private clinic over a period between January and December 2018.

Results
There were 0.62% real urgent visits in the public sector and 1.19% in the private sector (p = 0.05). Peripheral pathologies represented 12.53% and 6.21% of pathologies evaluated in public and private sector respectively (p < 0.00001). In addition, 15.76% of visits in public lead to surgery, while they represented 11.45% in private (p = 0.0003).

Conclusions
No study is available comparing accesses of patients in neurosurgical outpatient clinics. In public clinic, visits are booked as urgent on the prescription of the general practitioner: in reality, only 5% of these visits were really confirmed as urgent by the specialist. Peripheral pathologies are more frequent in public clinic, while cranial pathologies are more frequent in private one. Patients with cranial pathologies prefer to choose their surgeon by accessing private clinic.
Preliminary study of the effect of gut microbiota on the development of prostatitis
Authors: Shen Cheng , Chen Zhan , Zhang Wei , Chen Xinfeng , Zheng Bing , Shi Chunmei 
Published: January 2024

Abstract
Background
Dysbacteriosis of intestinal tract may cause systemic inflammation, making distant anatomical locations more susceptible to illness. Recent research has demonstrated that the microbiome can affect both prostatitis and the inflammation of the prostate that is linked to prostate cancer. It is still unclear, though, whether this relationship indicates causation. We conducted a Mendelian randomization investigation on two samples to fully uncover gut microbiota’s potential genetic causal role in prostatitis.

Method
Prostatitis (1859 prostatitis cases and 72,799 controls) was utilized as the outcome, while SNPs highly linked with 196 microbial taxa (18 340 people) were chosen as instrumental factors. Random effects, inverse variance weighting, weighted medians, and MR-Egger were used to analyze causal effects. The Cochran’s Q test, funnel plot, leave-one-out analysis, and MR-Egger intercept test were all used in the sensitivity analysis.

Results
A causal effect in lowering the incidence of prostatitis is anticipated for five gut microorganisms (Methanobacteria, Methanobacteriaceae, Erysipelatoclostridium, Parasutterella, and Slackia; P < 0.05). Four gut bacteria, including Faecalibacterium, LachnospiraceaeUCG004, Sutterella, and Gastranaerophilales, are predicted to play a causal role in increasing the risk of prostatitis (P < 0.05). There were no discernible estimates of pleiotropy or heterogeneity.

Conclusion
Our investigation established the genetic links between nine gut microorganisms and prostatitis, which may offer fresh perspectives and a theoretical framework for the future prevention and management of prostatitis.
Blood FOLR3 methylation dysregulations and heterogeneity in non-small lung cancer highlight its strong associations with lung squamous carcinoma
Authors: Qu Yunhui , Zhang Xiuzhi , Qiao Rong , Di Feifei , Song Yakang , Wang Jun , Ji Longtao , Zhang Jie , Gu Wanjian , Fang Yifei , Han Baohui , Yang Rongxi , Dai Liping , Ouyang Songyun 
Published: January 2024

Abstract
Background
Non-small cell lung cancer (NSCLC) accounts for the vast majority of lung cancers. Early detection is crucial to reduce lung cancer-related mortality. Aberrant DNA methylation occurs early during carcinogenesis and can be detected in blood. It is essential to investigate the dysregulated blood methylation markers for early diagnosis of NSCLC.

Methods
NSCLC-associated methylation gene folate receptor gamma (FOLR3) was selected from an Illumina 850K array analysis of peripheral blood samples. Mass spectrometry was used for validation in two independent case–control studies (validation I: n = 2548; validation II: n = 3866). Patients with lung squamous carcinoma (LUSC) or lung adenocarcinoma (LUAD), normal controls (NCs) and benign pulmonary nodule (BPN) cases were included. FOLR3 methylations were compared among different populations. Their associations with NSCLC clinical features were investigated. Receiver operating characteristic analyses, Kruskal–Wallis test, Wilcoxon test, logistics regression analysis and nomogram analysis were performed.

Results
Two CpG sites (CpG_1 and CpG_2) of FOLR3 was significantly lower methylated in NSCLC patients than NCs in the discovery round. In the two validations, both LUSC and LUAD patients presented significant FOLR3 hypomethylations. LUSC patients were highlighted to have significantly lower methylation levels of CpG_1 and CpG_2 than BPN cases and LUAD patients. Both in the two validations, CpG_1 methylation and CpG_2 methylation could discriminate LUSC from NCs well, with areas under the curve (AUCs) of 0.818 and 0.832 in validation I, and 0.789 and 0.780 in validation II. They could also differentiate LUAD from NCs, but with lower efficiency. CpG_1 and CpG_2 methylations could also discriminate LUSC from BPNs well individually in the two validations. With the combined dataset of two validations, the independent associations of age, gender, and FOLR3 methylation with LUSC and LUAD risk were shown and the age-gender-CpG_1 signature could discriminate LUSC and LUAD from NCs and BPNs, with higher efficiency for LUSC.

Conclusions
Blood-based FOLR3 hypomethylation was shown in LUSC and LUAD. FOLR3 methylation heterogeneity between LUSC and LUAD highlighted its stronger associations with LUSC. FOLR3 methylation and the age-gender-CpG_1 signature might be novel diagnostic markers for the early detection of NSCLC, especially for LUSC.
Single-cell N6-methyladenosine-related genes function within the tumor microenvironment to affect the prognosis and treatment sensitivity in patients with gastric cancer
Authors: Wang Zehua , Chen Chen , Shu Jiao , Ai Jiaoyu , Liu Yihan , Cao Haoyue , Jia Yongxu , Qin Yanru 
Published: January 2024

Abstract
Background
Gastric cancer (GC) ranks fifth for morbidity and third for mortality worldwide. The N6-methyladenosine (m6A) mRNA methylation is crucial in cancer biology and progression. However, the relationship between m6A methylation and gastric tumor microenvironment (TME) remains to be elucidated.

Methods
We combined single-cell and bulk transcriptome analyses to explore the roles of m6A-related genes (MRG) in gastric TME.

Results
Nine TME cell subtypes were identified from 23 samples. Fibroblasts were further grouped into four subclusters according to different cell markers. M6A-mediated fibroblasts may guide extensive intracellular communications in the gastric TME. The m6A-related genes score (MRGs) was output based on six differentially expressed single-cell m6A-related genes (SCMRDEGs), including GHRL, COL4A1, CAV1, GJA1, TIMP1, and IGFBP3. The protein expression level was assessed by immunohistochemistry. We identified the prognostic value of MRGs and constructed a nomogram model to predict GC patients’ overall survival. MRGs may affect treatment sensitivity in GC patients.

Conclusion
Our study visualized the cellular heterogeneity of TME at the single-cell level, revealed the association between m6A mRNA modification and intracellular communication, clarified MRGs as an independent risk factor of prognosis, and provided a reference for follow-up treatment.
Validation of the psychosocial consequences of screening in lung cancer questionnaire in the international lung screen trial Australian cohort
Authors: Bonney Asha , Brodersen John , Siersma Volkert , See Katharine , Marshall Henry M. , Steinfort Daniel , Irving Louis , Lin Linda , Li Jiashi , Pang Siyuan , Fogarty Paul , Brims Fraser , McWilliams Annette , Stone Emily , Lam Stephen , Fong Kwun M. , Manser Renee 
Published: January 2024

Abstract
Background
Evaluation of psychosocial consequences of lung cancer screening with LDCT in high-risk populations has generally been performed using generic psychometric instruments. Such generic instruments have low coverage and low power to detect screening impacts. This study aims to validate an established lung cancer screening-specific questionnaire, Consequences Of Screening Lung Cancer (COS-LC), in Australian-English and describe early results from the baseline LDCT round of the International Lung Screen Trial (ILST).

Methods
The Danish-version COS-LC was translated to Australian-English using the double panel method and field tested in Australian-ILST participants to examine content validity. A random sample of 200 participants were used to assess construct validity using Rasch item response theory models. Reliability was assessed using classical test theory. The COS-LC was administered to ILST participants at prespecified timepoints including at enrolment, dependent of screening results.

Results
Minor linguistic alterations were made after initial translation of COS-LC to English. The COS-LC demonstrated good content validity and adequate construct validity using psychometric analysis. The four core scales fit the Rasch model, with only minor issues in five non-core scales which resolved with modification. 1129 Australian-ILST participants were included in the analysis, with minimal psychosocial impact observed shortly after baseline LDCT results.

Conclusion
COS-LC is the first lung cancer screening-specific questionnaire to be validated in Australia and has demonstrated excellent psychometric properties. Early results did not demonstrate significant psychosocial impacts of screening. Longer-term follow-up is awaited and will be particularly pertinent given the announcement of an Australian National Lung Cancer Screening Program.

Trial registration
NCT02871856.
Targeting the macrophage immunocheckpoint: a novel insight into solid tumor immunotherapy
Authors: Zhou Bei , Yang Yan , Kang Yan , Hou Jingjing , Yang Yun 
Published: January 2024

AbstractTumor immunotherapy, which targets immune checkpoints, presents a promising strategy for the treatment of various cancer types. However, current clinical data indicate challenges in its application to solid tumors. Recent studies have revealed a significant correlation between the degree of immune response in immunotherapy and the tumor microenvironment, particularly with regard to tumor-infiltrating immune cells. Among these immune cells, macrophages, a critical component, are playing an increasingly vital role in tumor immunotherapy. This review focuses on elucidating the role of macrophages within solid tumors and provides an overview of the progress in immunotherapy approaches centered around modulating macrophage responses through various immune factors.
Non-bone-derived exosomes: a new perspective on regulators of bone homeostasis
Authors: Wang Ping , Shao Wenkai , Li Zilin , Wang Bo , Lv Xiao , Huang Yiyao , Feng Yong 
Published: January 2024

AbstractAccumulating evidence indicates that exosomes help to regulate bone homeostasis. The roles of bone-derived exosomes have been well-described; however, recent studies have shown that some non-bone-derived exosomes have better bone targeting ability than bone-derived exosomes and that their performance as a drug delivery vehicle for regulating bone homeostasis may be better than that of bone-derived exosomes, and the sources of non-bone-derived exosomes are more extensive and can thus be better for clinical needs. Here, we sort non-bone-derived exosomes and describe their composition and biogenesis. Their roles and specific mechanisms in bone homeostasis and bone-related diseases are also discussed. Furthermore, we reveal obstacles to current research and future challenges in the practical application of exosomes, and we provide potential strategies for more effective application of exosomes for the regulation of bone homeostasis and the treatment of bone-related diseases.
Optimize the parameters for the synthesis by the ionic gelation technique, purification, and freeze-drying of chitosan-sodium tripolyphosphate nanoparticles for biomedical purposes
Authors: Gutiérrez-Ruíz Stephany Celeste , Cortes Hernán , González-Torres Maykel , Almarhoon Zainab M. , Gürer Eda Sönmez , Sharifi-Rad Javad , Leyva-Gómez Gerardo 
Published: January 2024

Abstract
Background
Polymeric nanoparticles can be used for wound closure and therapeutic compound delivery, among other biomedical applications. Although there are several nanoparticle obtention methods, it is crucial to know the adequate parameters to achieve better results. Therefore, the objective of this study was to optimize the parameters for the synthesis, purification, and freeze-drying of chitosan nanoparticles. We evaluated the conditions of agitation speed, anion addition time, solution pH, and chitosan and sodium tripolyphosphate concentration.

Results
Chitosan nanoparticles presented an average particle size of 172.8 ± 3.937 nm, PDI of 0.166 ± 0.008, and zeta potential of 25.00 ± 0.79 mV, at the concentration of 0.1% sodium tripolyphosphate and chitosan (pH 5.5), with a dripping time of 2 min at 500 rpm. The most representative factor during nanoparticle fabrication was the pH of the chitosan solution, generating significant changes in particle size and polydispersity index. The observed behavior is attributed to the possible excess of sodium tripolyphosphate during synthesis. We added the surfactants poloxamer 188 and polysorbate 80 to evaluate the stability improvement during purification (centrifugation or dialysis). These surfactants decreased coalescence between nanoparticles, especially during purification. The centrifugation increased the zeta potential to 40.8–56.2 mV values, while the dialyzed samples led to smaller particle sizes (152–184 nm). Finally, freeze-drying of the chitosan nanoparticles proceeded using two cryoprotectants, trehalose and sucrose. Both adequately protected the system during the process, and the sugar concentration depended on the purification process.

Conclusions
In Conclusion, we must consider each surfactant's benefits in formulations for selecting the most suitable. Also, it is necessary to do more studies with the molecule to load. At the same time, the use of sucrose and trehalose generates adequate protection against the freeze-drying process, even at a 5% w/v concentration. However, adjusting the percentage concentration by weight must be made to work with the CS-TPP NPs purified by dialysis.
Antibody selection strategies and their impact in predicting clinical malaria based on multi-sera data
Authors: Fonseca André , Spytek Mikolaj , Biecek Przemysław , Cordeiro Clara , Sepúlveda Nuno 
Published: January 2024

Abstract
Background
Nowadays, the chance of discovering the best antibody candidates for predicting clinical malaria has notably increased due to the availability of multi-sera data. The analysis of these data is typically divided into a feature selection phase followed by a predictive one where several models are constructed for predicting the outcome of interest. A key question in the analysis is to determine which antibodies should be included in the predictive stage and whether they should be included in the original or a transformed scale (i.e. binary/dichotomized).

Methods
To answer this question, we developed three approaches for antibody selection in the context of predicting clinical malaria: (i) a basic and simple approach based on selecting antibodies via the nonparametric Mann–Whitney-Wilcoxon test; (ii) an optimal dychotomizationdichotomization approach where each antibody was selected according to the optimal cut-off via maximization of the chi-squared (χ2) statistic for two-way tables; (iii) a hybrid parametric/non-parametric approach that integrates Box-Cox transformation followed by a t-test, together with the use of finite mixture models and the Mann–Whitney-Wilcoxon test as a last resort. We illustrated the application of these three approaches with published serological data of 36 Plasmodium falciparum antigens for predicting clinical malaria in 121 Kenyan children. The predictive analysis was based on a Super Learner where predictions from multiple classifiers including the Random Forest were pooled together.

Results
Our results led to almost similar areas under the Receiver Operating Characteristic curves of 0.72 (95% CI = [0.62, 0.82]), 0.80 (95% CI = [0.71, 0.89]), 0.79 (95% CI = [0.7, 0.88]) for the simple, dichotomization and hybrid approaches, respectively. These approaches were based on 6, 20, and 16 antibodies, respectively.

Conclusions
The three feature selection strategies provided a better predictive performance of the outcome when compared to the previous results relying on Random Forest including all the 36 antibodies (AUC = 0.68, 95% CI = [0.57;0.79]). Given the similar predictive performance, we recommended that the three strategies should be used in conjunction in the same data set and selected according to their complexity.
Gene panel selection for targeted spatial transcriptomics
Authors: Zhang Yida , Petukhov Viktor , Biederstedt Evan , Que Richard , Zhang Kun , Kharchenko Peter V. 
Published: January 2024

AbstractTargeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on the cell types or processes being studied. A limitation of existing gene selection methods is their reliance on scRNA-seq data, ignoring platform effects between technologies. Here we describe gpsFISH, a computational method performing gene selection through optimizing detection of known cell types. By modeling and adjusting for platform effects, gpsFISH outperforms other methods. Furthermore, gpsFISH can incorporate cell type hierarchies and custom gene preferences to accommodate diverse design requirements.
An intricate vagina penetrating injury with a 22 cm cassava stick in situ for 6 months: a case report
Authors: Irumba Charles , Baragaine Justus , Obore Susan , Mwanje Haruna , Nteziyaremye Julius 
Published: January 2024

Abstract
Background
Trauma remains one of the major causes of morbidity and mortality and a threat to attainment of sustainable development goal 11. Genital urinary trauma is reported in about 10% of patients presenting with trauma worldwide, and in about 6.6% of patients in Sub-Saharan Africa. If not careful enough, one may miss the foreign body in the vagina and this may be associated with morbidity, and although rare, mortality.

Case presentation
We report a case of a 7-year-old Black Ugandan that had suffered vagina trauma 6 months prior to presentation at our facility and presented with chronic vagina pus discharge for 6 months. Prior examinations had failed to recognize the foreign body and so did the two abdominal pelvic ultrasound scans. During examination under anesthesia, we were able to locate the cassava stick that had caused penetrating vagina injury and we were able to dislodge it. It was a blunt cassava stick with length of 22 cm and diameter of 2 cm. Although it had gone through the peritoneal cavity, we did not do a laparotomy.

Conclusion
This case emphasizes the need for a thorough vaginal exam including the need to do it under anesthesia with good lighting even when ultrasound scan findings are normal. It presents an opportunity for one to manage penetrating peritoneal injury without a laparotomy in highly selected cases. Gynecologists should be keen as well to rule out child molestation.
Bias-free estimation of the covariance function and the power spectral density from data with missing samples including extended data gaps
Authors: Damaschke Nils , Kühn Volker , Nobach Holger 
Published: January 2024

AbstractNonparametric estimation of the covariance function and the power spectral density of uniformly spaced data from stationary stochastic processes with missing samples is investigated. Several common methods are tested for their systematic and random errors under the condition of variations in the distribution of the missing samples. In addition to random and independent outliers, the influence of longer and hence correlated data gaps on the performance of the various estimators is also investigated. The aim is to construct a bias-free estimation routine for the covariance function and the power spectral density from stationary stochastic processes under the condition of missing samples with an optimum use of the available information in terms of low estimation variance and mean square error, and that independent of the spectral composition of the data gaps. The proposed procedure is a combination of three methods that allow bias-free estimation of the desired statistical functions with efficient use of the available information: weighted averaging over valid samples, derivation of the covariance estimate for the entire data set and restriction of the domain of the covariance function in a post-processing step, and appropriate correction of the covariance estimate after removal of the estimated mean value. The procedures abstain from interpolation of missing samples as well as block subdivision. Spectral estimates are obtained from covariance functions and vice versa using Wiener–Khinchin’s theorem.
Prognostic impact of oral microbiome on survival of malignancies: a systematic review and meta-analysis
Authors: Li Shuluan , Wang Tianyu , Ren Ya , Liu Zhou , Gao Jidong , Guo Zhi 
Published: January 2024

Abstract
Background
Recent studies have shown that there exists a significant correlation between oral microbiome and the occurrence of malignancies. However, the prognostic significance of oral microbiome for cancer patients remains unclear. The purpose of this meta-analysis is to evaluate the impact of oral microbiome on the survival of patients with malignant neoplasms.

Methods
We conducted a thorough literature search of PubMed, Embase, and Cochrane Library databases until September 2022. The hazard ratio (HR) with a corresponding 95% confidence interval (CI) was analyzed using Review Manager 5.4 software for survival outcomes, including overall survival (OS), disease-specific survival (DSS), progression-free survival (PFS), and disease-free survival (DFS).

Results
A total of 15 studies, covering 5191 samples with various types of cancers, were selected based on specified inclusion and exclusion criteria. In both univariate and multivariate analysis, patients with low diversity of the oral microbiome, or those with Fusobacterium-high/positive, or P. gingivalis positive in cancer tissue displayed poorer OS (univariate HR = 1.74; 95% CI 1.15–2.62; P = 0.009; multivariate HR = 1.56; 95% CI 1.07–2.27; P = 0.02), DSS (univariate HR = 2.06; 95% CI 1.50–2.84; P < 0.00001; multivariate HR = 1.80; 95% CI 1.48–2.20; P < 0.00001), and PFS/DFS (univariate HR = 2.00; 95% CI 1.12–3.58; P = 0.002; multivariate HR = 1.78; 95% CI 1.05–3.02; P = 0.003). Subgroup analysis revealed that Fusobacterium positive or high abundance in cancer tissues was associated with poor OS in multivariate analysis but had no statistical differences in PFS or DFS in univariate and multivariate analysis. Additionally, P. gingivalis positive in cancer tissue was also associated with worse OS.

Conclusions
Our meta-analysis suggests that the composition of the oral microbiome may play a significant role in predicting survival outcomes for cancer patients.