bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Relationship of Knee-related Quality of Life With Function, Psychological Factors, Strength, Performance, and Postural Stability After ACL Reconstruction: A Cross-Sectional Study
Authors: Tavares Maria Larissa Azevedo , Lima Pedro Olavo de Paula , Albano Thamyla Rocha , Rodrigues Carlos Augusto Silva , Almeida Gabriel Peixoto Leão 
Published: September 2022

Background: Patients after anterior cruciate ligament reconstruction (ACLR) have decreased health-related quality of life (QoL) compared with healthy control participants. Few studies have verified the predictors of QoL using Quality of Life Outcome Measure Questionnaire for Chronic Anterior Cruciate Ligament Deficiency (ACL-QoL), and no study has verified the relationship of psychological factors and knee function with ACL-QoL in patients after ACLR. Hypothesis: Knee functional status, muscle strength, performance in hop tests, postural stability, and psychological factors would be the predictors of QoL after ACLR. Study Design: Cross-sectional study. Level of Evidence: Level 4. Methods: A total of 131 participants who had undergone ACLR at least 6 months previously were evaluated. QoL was assessed using ACL-QoL; knee functional status, using International Knee Documentation Committee Subjective Knee (IKDC) and global rating scale (GRS); psychological readiness, using Anterior Cruciate Ligament Return to Sport after Injury Scale (ACL-RSI); kinesiophobia, using Tampa Scale for Kinesiophobia (TSK-17); knee strength, using isokinetic dynamometer; performance, using single-leg hop tests; and postural stability, using Biodex Balance System. Pearson’s linear correlation and stepwise hierarchical multiple linear regression analyses were performed to verify the predictors of QoL. Results: ACL-QoL showed a moderate correlation with IKDC ( r = 0.69), GRS ( r = 0.55), ACL-RSI ( r = 0.50), and TSK-17 ( r = -0.49). ACL-QoL presented none to low correlations with the variables of muscle strength, postural stability, and performance in hop tests. The variables related to the knee functional status and psychological factors (IKDC, GRS, ACL-RSI, and TSK-17) were found to be the predictors of QoL ( R2 = 0.56; P = 0.01). Conclusion: Knee functional status, psychological readiness, and kinesiophobia were the predictors of knee-related QoL in patients after ACLR. Clinical Relevance: These results can assist clinicians in the therapeutic monitoring of the factors that may interfere with QoL in patients after ACLR.
Management Strategy of Intracranial Complications of Sinusitis: Our Experience and Review of the Literature
Authors: Hallak Bassel , Bouayed Salim , Ghika Joseph André , Teiga Pedro S. , Alvarez Vincent 
Published: September 2022

Objective Sinusitis or rhinosinusitis is a very common disease worldwide, and in some cases, it leads to intracranial complications (ICS). These are more common in immunocompromised patients or with underlying comorbidities, but even healthy individuals, can be affected. Nowadays, ICS have become less common thanks to improved antibiotic therapies, radiological diagnostic methods, surgical techniques and skills. Nonetheless, they can still cause significant morbidity and mortality. For this reason, management of these complications requires a multidisciplinary approach to plan and customize treatment options. This paper presents our strategy in the management of a series of intracranial complications induced by acute sinusitis and compares our experience and outcomes with the literature. Study design Single institute experience, retrospective analysis of cases series and literature review. Methods Adult and child patients who were treated for ICS in the Department of Otorhinolaryngology at Sion Hospital, in Switzerland from 2016 to 2020 were included. Their symptoms, medical history, clinical and radiological findings, treatment, and outcome were documented. Results Eight patients (6 males- 2 females) aged from 14 to 88 y.o., were enrolled. None had any previous history of chronic, or recurrent sinusitis. Moreover, very few presented specific rhinological symptoms, but with neurological or other symptoms. Computed tomography (CT) and Magnetic Resonance Imaging (MRI) were used to confirm the diagnosis of all ICS. All types of known intracranial complications were observed in our cohort with a wide range of extension and severity of sinusitis. A multidisciplinary approach with individual treatments was tailored to each patient. Outcomes were favorable in almost all patients with neither recurrence, nor neurological sequels being observed in the follow-up. Only one patient was lost due to fatal complications of advanced lung cancer. Conclusion ICS remain a challenging clinical problem due to substantial associated morbidity and mortality. The incidence of these complications is relatively low. Therapeutical management guidelines are lacking. Early detection and multidisciplinary approach are key to successful treatment.
Theoretical accuracy for indirect predictions based on SNP effects from single-step GBLUP
Authors: Garcia Andre , Aguilar Ignacio , Legarra Andres , Tsuruta Shogo , Misztal Ignacy , Lourenco Daniela 
Published: September 2022

Abstract
Background
Although single-step GBLUP (ssGBLUP) is an animal model, SNP effects can be backsolved from genomic estimated breeding values (GEBV). Predicted SNP effects allow to compute indirect prediction (IP) per individual as the sum of the SNP effects multiplied by its gene content, which is helpful when the number of genotyped animals is large, for genotyped animals not in the official evaluations, and when interim evaluations are needed. Typically, IP are obtained for new batches of genotyped individuals, all of them young and without phenotypes. Individual (theoretical) accuracies for IP are rarely reported, but they are nevertheless of interest. Our first objective was to present equations to compute individual accuracy of IP, based on prediction error covariance (PEC) of SNP effects, and in turn, are obtained from PEC of GEBV in ssGBLUP. The second objective was to test the algorithm for proven and young (APY) in PEC computations. With large datasets, it is impossible to handle the full PEC matrix, thus the third objective was to examine the minimum number of genotyped animals needed in PEC computations to achieve IP accuracies that are equivalent to GEBV accuracies.

Results
Correlations between GEBV and IP for the validation animals using SNP effects from ssGBLUP evaluations were ≥ 0.99. When all available genotyped animals were used for PEC computations, correlations between GEBV and IP accuracy were ≥ 0.99. In addition, IP accuracies were compatible with GEBV accuracies either with direct inversion of the genomic relationship matrix (G) or using the algorithm for proven and young (APY) to obtain the inverse of G. As the number of genotyped animals included in the PEC computations decreased from around 55,000 to 15,000, correlations were still ≥ 0.96, but IP accuracies were biased downwards.

Conclusions
Theoretical accuracy of indirect prediction can be successfully obtained by computing SNP PEC out of GEBV PEC from ssGBLUP equations using direct or APY G inverse. It is possible to reduce the number of genotyped animals in PEC computations, but accuracies may be underestimated. Further research is needed to approximate SNP PEC from ssGBLUP to limit the computational requirements with many genotyped animals.
LncRNA RPL34-AS1 suppresses the proliferation, migration and invasion of esophageal squamous cell carcinoma via targeting miR-575/ACAA2 axis
Authors: Zhang Hu , Pan Enchun , Zhang Ying , Zhao Chao , Liu Qiwei , Pu Yuepu , Yin Lihong 
Published: September 2022

Abstract
Background
Long noncoding RNAs (lncRNAs) are abnormally expressed in a broad type of cancers and play significant roles that regulate tumor development and metastasis. However, the pathological roles of lncRNAs in esophageal squamous cell carcinoma (ESCC) remain largely unknown. Here we aimed to investigate the role and regulatory mechanism of the novel lncRNA RPL34-AS1 in the development and progression of ESCC.

Methods
The expression level of RPL34-AS1 in ESCC tissues and cell lines was determined by RT-qPCR. Functional experiments in vitro and in vivo were employed to explore the effects of RPL34-AS1 on tumor growth in ESCC cells. Mechanistically, fluorescence in situ hybridization (FISH), bioinformatics analyses, luciferase reporter assay, RNA immunoprecipitation (RIP) assay and western blot assays were used to detect the regulatory relationship between RPL34-AS1, miR-575 and ACAA2.

Results
RPL34-AS1 was significantly down-regulated in ESCC tissues and cells, which was negatively correlated with overall survival in ESCC patients. Functionally, upregulation of RPL34-AS1 dramatically suppressed ESCC cell proliferation, colony formation, invasion and migration in vitro, whereas knockdown of RPL34-AS1 elicited the opposite function. Consistently, overexpression of RPL34-AS1 inhibited tumor growth in vivo. Mechanistically, RPL34-AS1 acted as a competing endogenous RNA (ceRNA) of miR-575 to relieve the repressive effect of miR-575 on its target ACAA2, then suppressed the tumorigenesis of ESCC.

Conclusions
Our results reveal a role for RPL34-AS1 in ESCC tumorigenesis and may provide a strategy for using RPL34-AS1 as a potential biomarker and an effect target for patients with ESCC.
High CENPA expression in papillary renal cell carcinoma tissues is associated with poor prognosis
Authors: Li Junwu , Li Qinke , Yuan Yang , Xie Yiteng , Zhang Yuanfeng , Zhang Ronggui 
Published: September 2022

Abstract
Objective
This work focused on investigating the relation of centromeric protein A (CENPA) gene expression with prognosis of papillary renal cell carcinoma (PRCC).

Methods
We obtained data from PRCC cases in TCGA. Thereafter, CENPA levels between the paired PRCC and matched non-carcinoma samples were analyzed by Wilcoxon rank-sum test, while the relations of clinicopathological characteristics with CENPA level were examined by logistic regression and Wilcoxon rank-sum test. The prognostic value of CENPA was assessed by plotting the receiver operating feature curve (ROC) and calculating the value of area under curve (AUC). In addition, relations between clinicopathological characteristics and PRCC survival were analyzed through Kaplan–Meier (KM) and Cox regression analyses. After dividing the total number of patients into the trial cohort and the validation cohort in a ratio of 7:3, we constructed a nomogram in trial cohort according to multivariate Cox regression results for predicting how CENPA affected patient survival and used the calibration curve to verify its accuracy in both cohorts. We also determined CENPA levels within cancer and matched non-carcinoma samples through immunohistochemistry (IHC). Finally, we utilized functional enrichment for identifying key pathways related to differentially expressed genes (DEGs) between PRCC cases with CENPA up-regulation and down-regulation.

Results
CENPA expression enhanced in PRCC tissues compared with healthy counterparts (P < 0.001). CENPA up-regulation was related to pathological TNM stage and clinical stage (P < 0.05). Meanwhile, the ROC curves indicated that CENPA had a remarkable diagnostic capacity for PRCC, and the expression of CENPA can significantly improve the predictive accuracy of pathological TNM stage and clinical stage for PRCC. As revealed by KM curves, PRCC cases with CENPA up-regulation were associated with poor survival compared with those with CENPA down-regulation (Risk ratio, RR = 3.07, 95% CI: 1.58–5.97, P = 0.001). In the meantime, univariate as well as multivariate analysis showed an independent association of CENPA with overall survival (OS, P < 0.05) and the nomogram demonstrated superior predictive ability in both cohorts. IHC analysis indicated that PRCC cases showed an increased CENPA positive rate compared with controls. As revealed by functional annotations, CENPA was enriched into pathways associated with neuroactive ligand receptor interactions, cytokine receptor interactions, extracellular matrix regulators, extracellular matrix glycoproteins and nuclear matrisome.

Conclusion
CENPA expression increases within PRCC samples, which predicts dismal PRCC survival. CENPA may become a molecular prognostic marker and therapeutic target for PRCC patients.
Oral cleaning habits and the copy number of periodontal bacteria in pregnant women and its correlation with birth outcomes: an epidemiological study in Mibilizi, Rwanda
Authors: Arima Hiroaki , Calliope Akintije Simba , Fukuda Hideki , Nzaramba Theoneste , Mukakarake Marie Goretti , Wada Takayuki , Yorifuji Takashi , Mutesa Leon , Yamamoto Taro 
Published: September 2022

Abstract
Background
Since 1996, many studies have reported that periodontal disease during pregnancy may be a risk factor for preterm birth and low birth weight; however, in Africa, periodontal disease is considered a non-high-priority disease. In addition, there are few dental facilities in rural Rwanda; thus, the oral condition of pregnant women has not been investigated. The objective of this study was to assess the tooth brushing habits of pregnant women in rural Rwanda and evaluate whether periodontal bacteria in the oral cavity of pregnant women are related to birth outcomes or oral cleaning habits.

Methods
A questionnaire survey and saliva collection were conducted for pregnant women in the catchment area population of Mibilizi Hospital located in the western part of Rwanda. Real-time PCR was performed to quantitatively detect total bacteria and 4 species of periodontal bacteria. The relationship of the copy number of each bacterium and birth outcomes or oral cleaning habits was statistically analyzed.

Results
Among the participants, high copy numbers of total bacteria, Tannerella forsythia, and Treponema denticola were correlated with lower birth weight (p = 0.0032, 0.0212, 0.0288, respectively). The sex ratio at birth was higher in women who had high copy numbers of Porphyromonas gingivalis and T. denticola during pregnancy (p = 0.0268, 0.0043). Furthermore, regarding the correlation between oral cleaning habits and the amount of bacteria, the more frequently teeth were brushed, the lower the level of P. gingivalis (p = 0.0061); the more frequently the brush was replaced, the lower the levels of P. gingivalis and T. forsythia (p = 0.0153, 0.0029).

Conclusions
This study suggested that improving tooth brushing habits may reduce the risk of periodontal disease among pregnant women in rural Rwanda. It also indicated that the amount of bacteria is associated with various birth outcomes according to the bacterial species. Both access to dental clinics and the oral cleaning habits of pregnant women should be important considerations in efforts to alleviate reproductive-related outcomes in rural Africa.
Transparency and reporting characteristics of COVID-19 randomized controlled trials
Authors: Kapp Philipp , Esmail Laura , Ghosn Lina , Ravaud Philippe , Boutron Isabelle 
Published: September 2022

Abstract
Background
In the context of the COVID-19 pandemic, randomized controlled trials (RCTs) are essential to support clinical decision-making. We aimed (1) to assess and compare the reporting characteristics of RCTs between preprints and peer-reviewed publications and (2) to assess whether reporting improves after the peer review process for all preprints subsequently published in peer-reviewed journals.

Methods
We searched the Cochrane COVID-19 Study Register and L·OVE COVID-19 platform to identify all reports of RCTs assessing pharmacological treatments of COVID-19, up to May 2021. We extracted indicators of transparency (e.g., trial registration, data sharing intentions) and assessed the completeness of reporting (i.e., some important CONSORT items, conflict of interest, ethical approval) using a standardized data extraction form. We also identified paired reports published in preprint and peer-reviewed publications.

Results
We identified 251 trial reports: 121 (48%) were first published in peer-reviewed journals, and 130 (52%) were first published as preprints. Transparency was poor. About half of trials were prospectively registered (n = 140, 56%); 38% (n = 95) made their full protocols available, and 29% (n = 72) provided access to their statistical analysis plan report. A data sharing statement was reported in 68% (n = 170) of the reports of which 91% stated their willingness to share. Completeness of reporting was low: only 32% (n = 81) of trials completely defined the pre-specified primary outcome measures; 57% (n = 143) reported the process of allocation concealment. Overall, 51% (n = 127) adequately reported the results for the primary outcomes while only 14% (n = 36) of trials adequately described harms. Primary outcome(s) reported in trial registries and published reports were inconsistent in 49% (n = 104) of trials; of them, only 15% (n = 16) disclosed outcome switching in the report. There were no major differences between preprints and peer-reviewed publications. Of the 130 RCTs published as preprints, 78 were subsequently published in a peer-reviewed journal. There was no major improvement after the journal peer review process for most items.

Conclusions
Transparency, completeness, and consistency of reporting of COVID-19 clinical trials were insufficient both in preprints and peer-reviewed publications. A comparison of paired reports published in preprint and peer-reviewed publication did not indicate major improvement.
Pancancer landscape analysis of the thymosin family identified TMSB10 as a potential prognostic biomarker and immunotherapy target in glioma
Authors: Xiong Ye , Qi Yanhua , Pan Ziwen , Wang Shaobo , Li Boyan , Feng Bowen , Xue Hao , Zhao Rongrong , Li Gang 
Published: September 2022

Abstract
Background
Thymosin family genes (TMSs), biologically important peptides with diverse intracellular and extracellular functions, have been shown to promote the progression of multiple cancers. However, multiomics characterization of TMSs and their role in human cancer prognosis has not been systematically performed.

Methods
We performed a comprehensive analysis of TMSs and thymosin β10 (TMSB10) using multiomics data from more than 10,000 tumor samples of 33 cancer types from The Cancer Genome Atlas (TCGA). We used single-sample gene set enrichment analysis (ssGSEA) and the gene set variation analysis (GSVA) algorithm to investigate the differences in tumor microenvironment (TME) cell infiltration and functional annotation for individual tumor samples, respectively. The role of TMSB10 in the malignant progression of glioma, the promotion of macrophage infiltration,and immunosuppressive polarization, and the combination drug efficacy were assessed via biological function assays.

Results
We comprehensively assessed genomic mutations, expression dysregulation, prognosis and immunotherapeutic response across 33 human cancer samples and showed that TMSB10 is specifically overexpressed in almost all types of cancer tissues. Further pan-cancer analysis showed that TMSB10 is closely related to the biological function, immune regulation and prognosis of glioma. Similar results were also found in several public glioma cohorts and our Qilu local cohort. Further integration with other biological experiments revealed the key roles of TMSB10 in the malignant progression of glioma, the promotion of macrophage infiltration and immunosuppressive polarization. We also identified multiple drugs targeting cells with high TMSB10 expression and validated that knockdown of TMSB10 improved the efficacy of selumetinib (a MEK1/2 inhibitor approved by the FDA for the treatment of neurofibromatosis-associated tumors) and anti-PD1 treatment in glioma.

Conclusion
These results indicate that TMSB10 holds promise as a novel prognostic marker and therapeutic target, providing a theoretical basis for the development of more effective and targeted clinical treatment strategies for glioma patients.
MiR-34b/c play a role in early sex differentiation of Amur sturgeon, Acipenser schrenckii
Authors: Zhang Xiujuan , Wu Wenhua , Zhou Jiabin , Li Linmiao , Jiang Haiying , Chen Jinping 
Published: September 2022

Abstract
Background
Sex differentiation can be viewed as a controlled regulatory balance between sex differentiation-related mRNAs and post-transcriptional mechanisms mediated by non-coding RNAs. In mammals, increasing evidence has been reported regarding the importance of gonad-specific microRNAs (miRNAs) in sex differentiation. Although many fishes express a large number of gonadal miRNAs, the effects of these sex-biased miRNAs on sex differentiation in teleost fish remain unknown. Previous studies have shown the exclusive and sexually dimorphic expression of miR-34b/c in the gonads of the Amur sturgeon (Acipenser schrenckii), suggesting its potential role in the sex differentiation process.

Results
Using quantitative real-time PCR (qPCR), we observed that miR-34b/c showed consistent spatiotemporal expression patterns; the expression levels significantly increased during early sex differentiation. Using in situ hybridization, miR-34c was found to be located in the germ cells. In primary germ cells in vitro, the group subjected to overexpression and inhibition of miR-34c showed significantly higher proliferation ability and lower apoptosis, respectively, compared to the corresponding control group. Luciferase reporter assays using the ar-3′UTR-psiCHECK-2 luciferase vector suggested a targeted regulatory interaction between miR-34b/c and the 3′UTR of the androgen receptor (ar) mRNA. Furthermore, miR-34b/c and ar showed negative expression patterns during early sex differentiation. Additionally, a negative feedback regulation pattern was observed between foxl2 expression in the ovaries and amh and sox9 expression in the testes during early sex differentiation.

Conclusions
This study sheds new light on the roles of miR-34b/c in gonad development of Amur sturgeon, and provides the first comprehensive evidence that the gonad-predominant microRNAs may have a major role in sex differentiation in teleost fish.
Traces of JC polyomavirus in papillary thyroid cancer: a comprehensive study in Iran
Authors: Karimi Amir Ali , Tarharoudi Rahil , Kianmehr Zahra , Sakhaee Fatemeh , Jamnani Fatemeh Rahimi , Siadat Seyed Davar , Fateh Abolfazl 
Published: September 2022

Abstract
Background
JC polyomavirus (JCPyV) is known to induce solid tumors such as astrocytomas, glioblastomas, and neuroblastomas in experimental animals, and recent studies have shown that the virus may be correlated with carcinogenesis. This study aimed to evaluate the impact of JCPyV on the progression of papillary thyroid cancer (PTC).

Methods
A total of 1057 samples, including 645 paraffin-embedded PTC biopsy samples (PEBS) and 412 fresh biopsy samples (FBS), and 1057 adjacent non-cancerous samples were evaluated for the presence of JCPyV DNA and RNA.

Results
We observed that 10.8% (114/1057) samples, including 17.5% (72/412) FBS and 6.5% (42/645) PEBS were positive for the JCPyV DNA. Among the JCPyV-positive samples, the mean JCPyV copy number was lower in patients with PEBS (0.3 × 10–4 ± 0.1 × 10–4 copies/cell) compared to FBS (1.8 × 10–1 ± 0.4 × 10–1 copies/cell) and non-PTC normal samples (0.2 × 10–5 ± 0.01 × 10–5 copies/cell), with a statistically significant difference (P < 0.001). The LT-Ag RNA expression was lower in PEBS than in FBS, while no VP1 gene transcript expression was found.

Conclusions
Although our results confirmed the presence of JCPyV in some Iranian patients with PTC, more research is needed to verify these results.