bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of multiparametric magnetic resonance imaging and targeted biopsy in the detection of clinically significant prostate cancer in patients with abnormal digital rectal examination
Authors: Giannarini Gianluca , Ficarra Vincenzo , Rossanese Marta , Buttitta Alessandro , Alibrandi Angela , Anastasi Giuseppina , Blandino Alfredo , Ieni Antonio , Martini Maurizio 
Published: April 2023

Abstract
Background Few studies examined the role of prostate MRI in patients with abnormal digital rectal examination (DRE) and/or PSA > 10 ng/ml. In a cohort of non-screened patients with abnormal DRE, we investigated the rate of avoidable prostate biopsies and potentially missed clinically significant prostate cancer (csPCa) with negative MRI, and the concordance between targeted biopsy (TBx) and systematic biopsy (SBx) in detecting csPCa with positive MRI.Methods We retrospectively examined 199 biopsy-naïve patients with abnormal DRE who underwent prostate MRI before transperineal biopsy. Prostate Imaging - Reporting And Data System (PI-RADS) v2.1 ≥ 3 category of the index lesion defined a positive MRI. Combined TBx/SBx and SBX alone was performed for positive and negative MRI, respectively. An International Society of Urogenital Pathology Grade Group ≥2 defined csPCa. We calculated csPCa detection rate of TBx, SBx and combined TBx/SBx. The Cohen kappa statistic was used to measure the concordance between TBx and SBx.Results Ninety-one (45.7%) csPCa cases were detected. MRI was positive in 153 (76.9%) patients. In the 46 patients with negative MRI, SBx detected 5 (10.9%) csPCa cases. Prostate biopsy could, thus, be avoided in 41/199 (20.6%) patients at the cost of missing 5/91 (5.5%) csPCa cases. The concordance between TBx and SBx in detecting csPCa with positive mpMRI was substantial (k 0.70). Specifically, 6/86 (6.9%) csPCa cases were detected with TBx, and 17/86 (19.7%) with SBx alone. Concordance was almost perfect (k 0.82) in patients with PSA > 10 ng/ml. Only 4/38 (10.5%) csPCa cases were missed by TBx, and only 1 (2.6%) csPCa case was identified by TBx alone.Conclusion MRI in patients with abnormal DRE could avoid roughly 21% of unnecessary biopsies at the cost of missing approximately 6% of csPCa cases. Moreover, MRI and TBx complemented SBx in detecting csPCa in the subgroup with PSA > 10 ng/ml.
Comparison of the fracture strength of single unit metal ceramic and monolithic zirconium restorations in the molar region: A systematic review and meta-analysis
Authors: İŞİSAĞ Özer , PEKTAŞ Nur 
Published: April 2023

Abstract

Background: Despite the increasing popularity of monolithic zirconia restorations (MZ), metal ceramic restorations (MC) are still considered the gold standard in the posterior region. The aim of this systematic review and meta-analysis was to compare the fracture strengths of single unit MC and MZ in the molar region.
Methods: This review was structured based on the Preferred Reporting Items for Systematic Reviews and Meta- Analyses (PRISMA 2020). Literature search was conducted in PubMed and Web of Science databases until November 18, 2022. In vitro studies that evaluated the fracture strength of MC and MZ were included. Statistical analyzes were performed with CMA (Comprehensive Meta-Analysis) program, with a significance level of 0.05.
Results:Five of 753 studies were selected. Fracture strengths of MZ and MC did not show a statistically significant difference both tooth (95% CI:-1.589: 2.118, p=0.779, z= 0.280) and implant (95% CI: -2.215: 2.191, p=0.992 z= -0.010) supported restorations. However in tooth supported restorations a significant difference was found in the subgroup analysis considering different abutment materials (P<0.001) and aging treatments (P<0.001). Additionally in implant supported restorations a significant difference was found in subgroup analysis considering different cements (p=0.001) and load speeds (p=0.001).
Conclusion:Within the limitations this present study, fracture strengths of MZ and MC did not show a significant difference in implant or tooth supported single unit restorations at posterior region.
Clinical relevance: MZ may be an alternative to MC in posterior single restorations. Present results should be interpreted with caution, as included studies were in vitro.
Detection of Cardiovascular Disease Using Gut Microbiota Data
Authors: Duyar Can , Senica Simone Oliver , Kalkan Habil 
Published: April 2023

Abstract
Gut microbiota are defined as the microbial population of the intestines. They include various types of bacteria which can influence and predict the existence or onset of some specific diseases. Therefore, it is a common practice in medicine to analyze the gut microbiota for diagnostic purposes by analyzing certain measurable biochemical features associated with the disease under investigation. However, the evaluation of all the data collected from the gut microbiota is a labor-intensive process. Machine learning algorithms may be a helpful tool to identify the hidden patterns in gut microbiota for the detection of disease and other classification problems. In this study, we propose a deep neural model based on 1D-CNN to detect cardiovascular disease using bacterial taxonomy and OTU (Operational Taxonomic Unit) table data. The developed method is compared to classical machine learning algorithms, regression, boosting algorithm and a deep model, TabNet, developed for tabular data and obtained outperforming classification results. The proposed method is robust and well adapted to taxonomy data in tabular form. It can be easily adapted to detect other diseases by using taxonomy data.
Structural features of T-DNA that induce transcriptional gene silencing during agroinfiltration
Authors: Iida Emi , Kuriyama Kazunori , Tabara Midori , Takeda Atsushi , Suzuki Nobuhiro , Moriyama Hiromitsu , Fukuhara Toshiyuki 
Published: April 2023

Abstract

Agrobacterium tumefaciens (Rhizobium radiobacter) is used for the transient expression of foreign genes by the agroinfiltration method, but the introduction of foreign genes often induces transcriptional and/or post-transcriptional gene silencing (TGS and/or PTGS). In this study, we characterized the structural features of T-DNA that induce TGS during agroinfiltration. When A. tumefacienscells harboring an empty T-DNA plasmid containing the cauliflower mosaic virus (CaMV) 35S promoter were infiltrated into the leaves of Nicotiana benthamiana line 16c with a GFP gene over-expressed under the control of the same promoter, no small interfering RNAs (siRNAs) were derived from the GFP sequence. However, siRNAs derived from the CaMV 35S promoter were detected, indicating that TGS against the GFP gene was induced. When the GFP gene was inserted into the T-DNA plasmid, PTGS against the GFP gene was induced whereas TGS against the CaMV 35S promoter was suppressed. In other words, depending on the combination of promoter and coding sequences on T-DNA and the host nuclear genome, either or both TGS and/or PTGS could be induced by agroinfiltration. We also showed the importance of terminator sequences in T-DNA for gene silencing and the possible involvement of three siRNA-producing Dicers in the induction of TGS. These results are valuable for controlling gene expression by agroinfiltration.
Two point mutations in CYP4CE1 promoter contributed to the differential regulation of CYP4CE1 expression by FoxO between susceptible and nitenpyram resistant Nilaparvata lugens
Authors: Zhang Huihui , Lin Xumin , Yang Baojun , Zhang Lingchun , Liu Zewen 
Published: April 2023

Abstract
Four P450s were reported to be important for imidacloprid resistance in Nilaparvata lugens, a major insect pest on rice, which was confirmed in this study in an imidacloprid resistant strain (ImiR). Here we found that only two (CYP4CE1 and CYP6ER1) from these four P450 genes were over-expressed in a nitenpyram resistant strain (NitR) when compared to a susceptible strain SUS. CYP4CE1 RNAi reduced nitenpyram and imidacloprid resistance in NitR and ImiR strains, with a more reduction in nitenpyram resistance. The transcription factor FoxO mediated nitenpyram resistance in NitR and ImiR strains, but it was not differentially expressed among strains. The potential reason for the differential regulation of FoxO on CYP4CE1 expression was mainly from sequence differences in CYP4CE1promoter between susceptible and resistant insects. In six FoxO response elements predicted in CYP4CE1 promoter, the single-nucleotide polymorphisms were frequently detected in over 50% of NitR and ImiR individuals. The luciferase reporter assays showed that two mutations, -650T/G and -2205T/A in two response elements at the position of -648 bp and -2200 bp, mainly contributed to the enhanced regulation on CYP4CE1 expression by FoxO in resistant insects. The frequency was over 69% for both -650T/G and -2205T/A detected in NitR and ImiR individuals, but less than 20% in SUS insects. In conclusion,CYP4CE1 over-expression importantly contributed to nitenpyram resistance in N. lugens, and two mutations in CYP4CE1 promoter of resistant insects led to an enhanced regulation on CYP4CE1 expression by FoxO.
Drug-resistance, treatment outcome and their predictors in pulmonary tuberculosis at Yirgalem General Hospital Multidrug-Resistance Tuberculosis treatment initiation center, Sidama Region, South Ethiopia: a Retrospective cohort study
Authors: Kebede Assefa Hamato , Idris Hassen Mamo 
Published: April 2023

Abstract
Background: Tuberculosis (TB) is one of the oldest diseases known and the spread of drug-resistant TB poses significant challenges in TB control and eradication program globally, and also the distribution varies geographically worldwide and within the countries. Lack of universal access to rapid diagnostic test, poor infection control and mismanagement of TB at different level increases the spread of DR-TB. The final treatment outcome of patient implicates the level of program implementation in TB control. The current study aimed to assess the proportions of drug-resistance, treatment outcome and their predictors among pulmonary MDR/RR-TB treated patients.
Methods: A six year, 2014 to 2019 retrospective cohort review was conducted for all confirmed pulmonary DR-TB cases admitted at Yirgalem General Hospital treatment initiation center. The records of 228 total MDR/RR-TB cases 32 cases, such as referral cases outside the study area, extra pulmonary tuberculosis and incomplete data were excluded.
Results: Overall, 196 MDR/RR-TB patients included in the study. 184(93.9%) cases were labeled as rifampicin (RIF) mono-drug resistance and 8 (4.1%) cases had resistance to both Isoniazid and Rifampicin (MDR-TB) while 4 (2%) patients were diagnosed for additional resistance for second line drugs (SLDS) at the enrollment. Overall, 131(68.9 %) patients had the recorded treatment success in which 86 (43.9%) patients declared cured while 27(13.8%) declared completed treatment. The trend of successful treatment outcomes fluctuates over the years. The proportion declines from 81.9% in 2014 to 52.4% in 2016. Unsuccessful treatment in cohort was 65(31.1%) of MDR-TB. Of which 18(9.2%) were died during the treatment course while 27(13.8%) and 6(3.1%) were LTFU and treatment failure respectively. multivariate analysis revealed, being above age greater than 26 (AOR: 1.45; 95%CI: 1.044, 2.006), co-morbid disease other than HIV (AOR: 1.71; 95%CI: 0.937, 12.618), baseline positive sputum smear (AOR: 0.54; 95%CI: 0.375, 0.789) were significantly associated with unfavorable treatment outcomes with P-value<0.05.
Conclusion: 2% additional resistance for SLDs is alarming. Treatment success rate was lower than targeted set by World health organization. Factors affecting poor treatment outcome in MDR-TB management needs to be addressed through targeted interventions. Strengthened TB control strategies should in place to reduce further transmission of drug resistance.
Multifractal analysis of local polynomial entropies for recurrence time
Authors: Si Hongying , Peng Dongmei , Liu Lei 
Published: April 2023

Abstract
In this paper, we introduce the local polynomial entropies and mul-tifractal spectra associated with Poincaré recurrences. By using characteristics of a dynamical system we establish an exact formula on multifractal spectrum of local polynomial entropies for recurrence time.
Mathematics Subject Classification (2010). 54H20, 37B20, 37B40.
Transferable deep learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing
Authors: Yu Xiang , Wu You , Shao Wenna , Yan Mengxiao , Wang Yuqin , Li Xiaofei , Gregory Brian , Yang Jun , Wang Hongxia 
Published: April 2023

Abstract

RNA modifications play crucial roles in various biological processes. Current methods for epitranscriptome profiling using nanopore direct RNA sequencing (DRS) are unable to simultaneously identify multiple types of modifications. Here, we developed TandemMod, a transferable deep learning framework capable of detecting multiple types of RNA modifications in single DRS data. To train high-performance TandemMod models, we generated in vitro epitranscriptome (IVET) datasets from plant cDNA libraries, containing thousands of transcripts labeled with various types of RNA modifications. TandemMod trained on IVET datasets displayed high accuracy of prediction, outperforming existing tools. We applied TandemMod to identify RNA modifications in human cell lines and rice grown in different environments, demonstrating its applicability across species and conditions. In summary, we provide an IVET resource with ground-truth labels that can serve as benchmark datasets for DRS-based machine learning methods, and a deep learning framework, TandemMod, for identifying diverse RNA modifications using single DRS data.
Using the ceRNA network to predict the new circRNA-miRNA-mRNA on pathogenesis of systemic lupus erythematosus
Authors: He Juanjuan , Jianwen Liu , Chenmin Wu , Yunfeng Dai , Zhihan Chen , Yanfang Wu 
Published: April 2023

Abstract
Background
Circular RNAs (circRNAs) are a new class of endogenous non-coding RNA molecules that do not have a 5'-terminal cap and a 3'-terminal poly (A) tail and form a closed ring structure with covalent bonds. They act as competitive endogenous RNAs (ceRNAs) or microRNAs (miRNAs), which in turn influence and regulate the expression of target genes and mRNA.
It has been established that these circRNA-associated ceRNAs play significant roles in autoimmune illnesses, although it is still unknown how the circRNA-miRNA-mRNA network in systemic lupus erythematosus works.
Methods
In this investigation, the self-test data and the differential expression of circRNA in the GEO database were retrieved, as well as the circRNA in the bone marrow of SLE patients and healthy volunteers. Using the limma package of R program, the differential expression of mRNA and miRNA in the GEO database was discovered. Then miRNA-mRNA pairs and circRNA-miRNA pairs were established using miRcode, miRDB, miRTarbase, and TargetScan. Additionally, circRNA-miRNA-mRNA ceRNA network was built using Cytoscape, and Hub genes were screened using a protein-protein interaction network.
Results
We created 66 up-regulated circRNAs, 164 down-regulated circRNAs, 167 up-regulated mRNAs, 1916 down-regulated mRNAs, 15 up-regulated miRNAs, and 71 down-regulated miRNAs in accordance with the predetermined hypothesis. SLE development is significantly influenced by pathways in malignancies, according to functional and enrichment studies. Significant biomarkers include SIRT and ESR1. Our predictions included hsa miR 22 3p and HSA circ 0000345, two possible miRNAs and circRNAs that may have a major impact on SLE.
Conclusions
Our study discovered novel circRNA miRNAs and mRNAs through ceRNA network analysis that could be employed as potential biomarkers for SLE and as treatment targets for SLE.
The E592K variant of SF3B1 creates unique RNA missplicing and associates with high-risk MDS without ring sideroblasts
Authors: Choi In Young , Ling Jonathan P. , Zhang Jian , Helmenstine Eric , Walter Wencke , Bergman Riley E. , Philippe Céline , Manley James L. , Rouault-Pierre Kevin , Li Bing , Wiseman Daniel H. , Ouseph Madhu , Bernard Elsa , Li Xiao , Haferlach Torsten , Fazal Salman , Jain Tania , Gocke Christopher D. , DeZern Amy E. , Dalton W. Brian 
Published: April 2023

Abstract

Among the most common genetic alterations in the myelodysplastic syndromes (MDS) are mutations in the spliceosome gene SF3B1. Such mutations induce specific RNA missplicing events, directly promote ring sideroblast (RS) formation, generally associate with more favorable prognosis, and serve as a predictive biomarker of response to luspatercept. However, not all SF3B1 mutations are the same, and here we report that the E592K variant of SF3B1 associates with high-risk disease features in MDS, including a lack of RS, increased myeloblasts, a distinct co-mutation pattern, and decreased survival. Moreover, in contrast to canonical SF3B1 mutations, E592K induces a unique RNA missplicing pattern, retains an interaction with the splicing factor SUGP1, and preserves normal RNA splicing of the sideroblastic anemia genes TMEM14C and ABCB7. These data expand our knowledge of the functional diversity of spliceosome mutations, and they suggest that patients with E592K should be approached differently from low-risk, luspatercept-responsive MDS patients with ring sideroblasts and canonical SF3B1 mutations.
Oral Health-Related Quality of Life (OHQoL) in implant-supported rehabilitations: a double-blind longitudinal prospective single-center observational cohort study
Authors: Manfredini Mattia , Pellegrini Matteo , Rigoni Marta , Beretta Mario , Maiorana Carlo , Poli Pier Paolo 
Published: April 2023

Abstract
Objectives. To evaluate Oral Health-Related Quality of Life (OHRQoL) perceived by the patient before and after implant-prosthetic rehabilitation, to determine the physical and psychological impact that dental implants and related prosthetic rehabilitations could have in partial or edentulous patients. Finally, it was evaluated if demographic and clinical variables could influence the patient's perceived OHRQoL.
Materials and Methods. A double-blind longitudinal prospective single-center observational cohort study was conducted with patients requiring implant-prosthetic rehabilitation to evaluate OHRQoL before (T0), during (T1), and after treatment (T2) with implant-prosthetic rehabilitations. The three scores obtained at T0, T1, and T2, respectively, were compared with the variables patient's sex, age, implants placed in the aesthetic zone versus nonaesthetic zone, number of implants used in the rehabilitation, site of rehabilitation, type of definitive prosthetic rehabilitation, and type of recipient's bone.
Results. A total of 100 patients rehabilitated with 427 implants were enrolled. Statistically significant data emerged regarding the total OHRQoL score, its 7 domains, and VAS score in the 3 times considered and in relation to gender, age, aesthetics, implants number, dental arch, type of prosthesis, and type of surgery.
Conclusions. Implant-prosthetic rehabilitations significantly improve OHRQoL and aesthetics in edentulous or partially edentulous patients. The change in OHRQoL is accompanied by a marked improvement in the patient's aesthetic perception of the new smile similar in all intervals of the study.
Clinical Relevance. OHRQoL could provide the basis for any dental health care program and should be considered an important element in the overall oral health program.
Fast convergence to an approximate solution by message-passing for complex optimizations
Authors: Hayashi Yukio 
Published: April 2023

Abstract
Message-passing (MP) is a powerful tool for finding an approximate solution in optimization. We generalize it in product-sum form, and numerically show the fast convergence. From the linearity of MP in a logarithmic space, it is derived that an equilibrium solution exists in a neighborhood of random initial values. These results will give one of the reason why the convergence is very fast in collective computation based on a common mathematical background.
WITHDRAWN: Cognitive Behavior Therapy for Academic Burnout, Procrastination, Self-Handicapping Behavior, and Test Anxiety among Adolescents: A Randomized Control Trial
Authors: Abbas Qasir , Khurshid Khizra , Rauf Umara , Anwar Nida , Aljhani Sumayah , Ramzan Zoobia , Shahzadi Mafia 
Published: April 2023

Abstract
Objective Emotional instability during adolescence could make them susceptible to developing mental problems, and these problems could enhance in severity when left unresolved. Other life stressors like job competition, peer pressure, and parental unrealistic expectations could further deteriorate their mental health. Therefore, the present study is designed to investigate the impact of cognitive behavioral therapy (CBT) on adolescents to manage procrastination, burnout, self-handicapping behavior, and test anxiety to enhance academic motivation and achievement.Materials and Methods A total of 200 students were enrolled for eligibility assessment, and 129 participants met the eligibility criteria. Participants were divided into two groups, the experimental group, and the waitlist control group. All the students completed their demographics form and screening tool, the eligible participants were given assessment measures at pre-post-assessment stages (8 weeks intervals). We used different assessment measures to assess the outcome i.e. General Procrastination Scale (GPS), Maslach Burnout Inventory-Student Survey (MBI-SS), Self-handicapping Scale (SHS), Test Anxiety Inventory (TAI), and Living up to Parental Expectation Scale (LPES). Repeated measures ANOVA was used to analyze the results.Results The current RCT findings suggest that CBT substantially reduced emotional and behavioral problems and helped the students manage parental unrealistic expectations in the experimental group compared to the waitlist control condition. Further, CBT significantly reduced the degree of procrastination {F (1, 63) = 25.01, p < .000, η2 = .29} academic burnout {F (1, 63) = 11.08, p < .000, η2 = .16}, test anxiety {F(1, 63) = 88.17, p < .000, η2 = .59}, and self-handicapping {F (3, 56) = 10.17, p < .000, η2 = .16} among adolescents. Overall, CBT significantly helped the students to manage parental unrealistic expectations through providing relationship skills and training {F (3,56) = 546.46, p < .001, η2 = .89)}.Condition: It is concluded that CBT is an effective and evidence-based treatment intervention to address emotional disturbance caused by procrastination, burnout, test anxiety, and self-handicapping behavior among adolescents. Furthermore, it is concluded that CBT is also an effective intervention that helped students to manage peer pressure and parental unrealistic expectations.