bluuebunny/crossref_metadata_2025_split huggingface dataset:
OmicsOne: associate omics data with phenotypes in one-click
Authors: Zhang Hui , Ao Minghui , Boja Arianna , Schnaubelt Michael , Hu Yingwei 
Published: December 2021

AbstractBackgroundThe rapid advancements of high throughput “omics” technologies have brought a massive amount of data to process during and after experiments. Multi-omic analysis facilitates a deeper interrogation of a dataset and the discovery of interesting genes, proteins, lipids, glycans, metabolites, or pathways related to the corresponding phenotypes in a study. Many individual software tools have been developed for data analysis and visualization. However, it still lacks an efficient way to investigate the phenotypes with multiple omics data. Here, we present OmicsOne as an interactive web-based framework for rapid phenotype association analysis of multi-omic data by integrating quality control, statistical analysis, and interactive data visualization on ‘one-click’.Materials and methodsOmicsOne was applied on the previously published proteomic and glycoproteomic data sets of high-grade serous ovarian carcinoma (HGSOC) and the published proteome data set of lung squamous cell carcinoma (LSCC) to confirm its performance. The data was analyzed through six main functional modules implemented in OmicsOne: (1) phenotype profiling, (2) data preprocessing and quality control, (3) knowledge annotation, (4) phenotype associated features discovery, (5) correlation and regression model analysis for phenotype association analysis on individual features, and (6) enrichment analysis for phenotype association analysis on interested feature sets.ResultsWe developed an integrated software solution, OmicsOne, for the phenotype association analysis on multi-omics data sets. The application of OmicsOne on the public data set of ovarian cancer data showed that the software could confirm the previous observations consistently and discover new evidence for HNRNPU and a glycopeptide of HYOU1 as potential biomarkers for HGSOC data sets. The performance of OmicsOne was further demonstrated in the Tumor and NAT comparison study on the proteome data set of LSCC.ConclusionsOmicsOne can effectively simplify data analysis and reveal the significant associations between phenotypes and potential biomarkers, including genes, proteins, and glycopeptides, in minutes to assist users to understand aberrant biological processes.
Prophylactic role of ciprofloxacin and ceftriaxone in prostate biopsy-related infection: randomized comparative study of bacterial spectrum and antibiotic sensitivities
Authors: Odo Chinonso , Afogu Emmanuel Nwali , Odoemene Charles Azuwuike , Obi Anselm Okwudili , Mbaeri Timothy Uzoma , Obiesie Emmanuel Ahuizechukwu , Okeke Chike John , Nnadozie Ugochukwu Uzodimma , Ulebe Augustine Obasi 
Published: December 2021

AbstractBackgroundThe mainstay for the diagnosis of prostate cancer is transrectal ultrasound-guided prostate biopsy.However, prostate biopsy is associated with a significant risk of complications including urinary tract infection. This study aims to compare the bacterial profile and antibiotic susceptibility pattern in urinary tract infection after prostate biopsy between patients on 2 different antimicrobial prophylactic regimens.MethodsThis was a comparative cross-sectional study done at the urology unit of our institution, over 13 months. Fifty-six patients who met the inclusion criteria made up the study population and were randomly assigned to two groups. Those in group 1 (28) received intravenous ciprofloxacin (Juhel) 400 mg at induction of anesthesia, while those in group 2 (28) received intravenous ceftriaxone (Rocephin) 1 g at induction of anesthesia. All patients received bisacodyl (dulcolax) rectal suppositories 20 mg nocte starting 2 nights before the procedure as well as intravenous metronidazole (Juhel) at induction of anesthesia. Urine samples were taken for urine culture and sensitivity three days after biopsy. Isolated organisms and their antibiotics sensitivities were documented. Statistical analysis was done using SPSS version 21.0 with the level of significance set atP < 0.05.ResultsIn group 1 the prevalence of urinary tract infection was 61%.Escherichia coliwas isolated in 11(64.71%) cases,Klebsiella speciesin 3(17.65%),staphylococcus aureusin 1(5.88%), Proteus speciesin 1(5.88%), and non-hemolyticstreptococcus speciesin 1(5.88%). In this group, all isolated bacterial organisms were resistant to ciprofloxacin. In group 2 the prevalence of urinary tract infection was 43%.Klebsiella sppwas isolated in 6(50%) cases,Pseudomonas aeruginosain 3(25%),E. coliin 2(16.67%), Staphylococcusin 1(8.33%). In group 2 all isolated bacterial organisms were resistant to ceftriaxone.ConclusionCiprofloxacin and ceftriaxone are both associated with a high rate of urinary tract infection when used as prophylaxis for prostate biopsy. The bacterial etiology of prostate biopsy-related urinary tract infection is dependent on the prophylactic antibiotics used. Based on the high rate of urinary tract infection associated with the use of either ciprofloxacin or ceftriaxone, we recommend a combination of both drugs as prophylaxis for prostate biopsy.
Impact of surgical intervention on progression to end-stage renal disease in patients with posterior urethral valve
Authors: Velhal Rishikesh , Jain Aadhar , Nayan Anveshi , Patwardhan Sujata , Patil Bhushan 
Published: December 2021

Abstract
Background
Posterior urethral valve patients present with varied presentations at any age of life and have significant associated morbidity and require long-term follow-up and care.

Methods
This was a single-center ambispective cohort study carried out over a period of 2 years. Patient data regarding the symptoms, investigations, interventions, secondary complications were recorded and were followed up regularly during the study till either normalization of their creatinine level which was maintained up to one-year post-fulguration (non-CKD) or progression to end-stage renal disease (ESRD) requiring renal transplant. Various clinical factors were then compared between these groups.

Results
The age of presentation varies from 6 months antenatal period to a maximum of 34 years. Most common symptom was of lower urinary tract obstruction, followed by recurrent febrile UTI. The interval between disease presentation detection and PU valve fulguration ranged from 6 days to more than 5 years, median duration being 1 month. 85.7% patients had hydroureteronephrosis on initial USG. In VCUG, there was no significant difference found between the presence of reflux and poor renal outcome. Age of presentation greater than 2 years was seen in 52% of patients with CKD compared to only 10% patients in non-CKD group (significant, p value 0.02). Among patients who developed CKD, 60% of patients had PU valve fulguration after one month of disease presentation, while in contrast, among the non-CKD group, 80% of patients had it done within one month of disease presentation. (significant, p value 0.03).

Conclusions
Late age of presentation, delayed fulguration with high initial creatinine, and failure of serum creatinine to return to normal after one-month post-fulguration are important risk factors in the progression of the disease to ESRD. Symptomatic improvement after interventions does not correlate with progression to ESRD. The number of interventions also does not predict progression to ESRD. Interventions should be chosen wisely on case to restore near-normal physiology and delay progression to ESRD.
Exercise-induced ruptured renal tumour in a young patient with hereditary leiomyomata-associated renal cell carcinoma (HLRCC): a case report
Authors: Mohamad Sharin Mohamad Fairuz , Pushpanathan Mugialan , Jagwani Arvind Vashdev , Mohd Ghani Khairul Asri , Mohd Zainuddin Saiful Azli , Omar Noorjehan , Hayati Firdaus 
Published: December 2021

Abstract
Background
Hereditary leiomyomatosis-associated renal cell carcinoma (HLRCC) is rare with only 300 families reported to date worldwide. Despite highlighting renal malignancy, it is infamous for its cutaneous and leiomyomatosis component as the more common cause of presentation. This report is to highlight the rare presentation of HLRCC which occurs in a teenager which is unfortunately complicated with exercise-induced renal tumour rupture.

Case presentation
A 22-year-old gentleman presented with severe right lower abdominal pain for 4 days, associated with fever and nausea following a session of strenuous exercise. He has first-degree relatives and second-degree relatives from his maternal side who were genetically tested positive for HLRCC. Clinical examination revealed a tender right lumbar and right iliac fossa region. A computed tomography of the kidneys demonstrated a ruptured right renal tumour with a large right renal subcapsular and contained right retroperitoneal hematoma. An emergency right radical nephrectomy was performed, and he recovered well. The histopathological examination was consistent with HLRCC associated ruptured right renal cell carcinoma.

Conclusion
Identification of this underreported familial malignancy is paramount as the onset of neoplasia occurs much earlier in life. This necessitates screening of family members at a younger age, and the management is followed by life-long surveillance.
Phycoremediation of contaminated water by cadmium (Cd) using two cyanobacterial strains (Trichormus variabilis and Nostoc muscorum)
Authors: El-Hameed Mona M. Abd , Abuarab Mohamed E. , Al-Ansari Nadhir , Mottaleb Shady Abdel , Bakeer Gomaa A. , Gyasi-Agyei Yeboah , Mokhtar Ali 
Published: December 2021

Abstract
Background
Water pollution with heavy metals is a severe dilemma that concerns the whole world related to its risk to natural ecosystems and human health. The main objective was to evaluate the removal efficiency of Cd of various concentrations from contaminated aqueous solution by use of two cyanobacterial strains (Nostoc muscorum and Trichormus variabilis). For this purpose, a specially designed laboratory pilot-scale experiment was conducted using these two cyanobacterial strains on four different initial concentrations of Cd (0, 0.5, 1.0 and 2.0 mg L−1) for 21 days.

Results
N. muscorum was more efficient than T. variabilis for removing Cd (II), with the optimum value of residual Cd of 0.033 mg L−1 achieved by N. muscorum after 21 days with initial concentration of 0.5 mg L−1, translating to removal efficiency of 93.4%, while the residual Cd (II) achieved by T. variabilis under the same conditions was 0.054 mg L−1 (89.13% removal efficiency). Algal growth parameters and photosynthetic pigments were estimated for both cyanobacterial strains throughout the incubation period.

Conclusions
High Cd concentration had a more toxic impact on algal growth. The outcomes of this study will help to produce treated water that could be reused in agrarian activities.
Hindrances in port digitalization? Identifying problems in adoption and implementation
Authors: Brunila Olli-Pekka , Kunnaala-Hyrkki Vappu , Inkinen Tommi 
Published: December 2021

AbstractDigitalization has an impact on all domains of maritime transport and logistics. Ports’ ability to act as a part of digital networks and information chains is vital for its competitiveness. This requires means and prerequisites to integrate with contemporary technology platforms and system architectures. Such readiness should exist in different parallel processes taking place in organizations of port communities. Successful digitalization requires focused technology management ensuring system and data transfer interoperability. The paper addresses problems, obstacles, and hindrances that ports are currently facing in their digitalization efforts. Interoperability and stakeholder interaction is significant, particularly between the port management, municipal ownership, and business operators and vendors. In the contemporary port development, environmental regulations have an effect on the level and effectiveness of digitalization. The future development of port digitalization will be dependent on the port capabilities to adopt and implement reliable and adoptable technologies with clear vision of the future.
Combining heterogeneous subgroups with graph-structured variable selection priors for Cox regression
Authors: Madjar Katrin , Zucknick Manuela , Ickstadt Katja , Rahnenführer Jörg 
Published: December 2021

AbstractBackgroundImportant objectives in cancer research are the prediction of a patient’s risk based on molecular measurements such as gene expression data and the identification of new prognostic biomarkers (e.g. genes). In clinical practice, this is often challenging because patient cohorts are typically small and can be heterogeneous. In classical subgroup analysis, a separate prediction model is fitted using only the data of one specific cohort. However, this can lead to a loss of power when the sample size is small. Simple pooling of all cohorts, on the other hand, can lead to biased results, especially when the cohorts are heterogeneous.ResultsWe propose a new Bayesian approach suitable for continuous molecular measurements and survival outcome that identifies the important predictors and provides a separate risk prediction model for each cohort. It allows sharing information between cohorts to increase power by assuming a graph linking predictors within and across different cohorts. The graph helps to identify pathways of functionally related genes and genes that are simultaneously prognostic in different cohorts.ConclusionsResults demonstrate that our proposed approach is superior to the standard approaches in terms of prediction performance and increased power in variable selection when the sample size is small.
Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis
Authors: Wang Ailan , Chen Wei , Tao Shiheng 
Published: December 2021

Abstract
Background
F-box proteins represent a diverse class of adaptor proteins of the ubiquitin-proteasome system (UPS) that play critical roles in the cell cycle, signal transduction, and immune response by removing or modifying cellular regulators. Among closely related organisms of the Caenorhabditis genus, remarkable divergence in F-box gene copy numbers was caused by sizeable species-specific expansion and contraction. Although F-box gene number expansion plays a vital role in shaping genomic diversity, little is known about molecular evolutionary mechanisms responsible for substantial differences in gene number of F-box genes and their functional diversification in Caenorhabditis. Here, we performed a comprehensive evolution and underlying mechanism analysis of F-box genes in five species of Caenorhabditis genus, including C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei.

Results
Herein, we identified and characterized 594, 192, 377, 39, 1426 F-box homologs encoding putative F-box proteins in the genome of C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei, respectively. Our work suggested that extensive species-specific tandem duplication followed by a small amount of gene loss was the primary mechanism responsible for F-box gene number divergence in Caenorhabditis genus. After F-box gene duplication events occurred, multiple mechanisms have contributed to gene structure divergence, including exon/intron gain/loss, exonization/pseudoexonization, exon/intron boundaries alteration, exon splits, and intron elongation by tandem repeats. Based on high-throughput RNA sequencing data analysis, we proposed that F-box gene functions have diversified by sub-functionalization through highly divergent stage-specific expression patterns in Caenorhabditis species.

Conclusions
Massive species-specific tandem duplications and occasional gene loss drove the rapid evolution of the F-box gene family in Caenorhabditis, leading to complex gene structural variation and diversified functions affecting growth and development within and among Caenorhabditis species. In summary, our findings outline the evolution of F-box genes in the Caenorhabditis genome and lay the foundation for future functional studies.
Longitudinal alterations of the cisternal segment of trigeminal nerve and brain pain-matrix regions in patients with trigeminal neuralgia before and after treatment
Authors: Chen Tai-Yuan , Ko Ching-Chung , Wu Te-Chang , Lin Li-Ching , Shih Yun-Ju , Hung Yi-Chieh , Chou Ming-Chung 
Published: December 2021

Abstract
Background
Trigeminal neuralgia (TN) is the most common type of chronic neuropathic facial pain, but the etiology and pathophysiological mechanisms after treatment are still not well understood. The purpose of this study was to investigate the longitudinal changes of the cisternal segment of the trigeminal nerve and brain pain-related regions in patients with TN before and after treatment using readout segmentation of long variable echo-train (RESOLVE) diffusion tensor imaging (DTI) and transverse relaxation (T2)-weighted sampling perfection with application-optimized contrast at different flip angle evolutions (T2-SPACE).

Methods
Twelve patients with TN and four healthy controls were enrolled in this study. All patients underwent assessment of the visual analog scale (VAS), and acquisition of RESOLVE DTI and T2-SPACE images before and at 1, 6, and 12 months after treatments. Regions-of-interest were placed on the bilateral anterior, middle, and posterior parts of the cisternal segment of the trigeminal nerve, the bilateral root entry zone (REZ), bilateral nuclear zone, and the center of pontocerebellar tracts, respectively. Voxel-based morphometry (VBM) analysis was conducted with T2-SPACE images, and gray matter volumes (GMV) were measured from brain pain-matrix regions.

Results
The results demonstrated that the VAS scores, the axial diffusivity of the middle part of the affected cisternal trigeminal nerve, the fractional anisotropy of the bilateral nuclear zones, and the mean diffusivity of the center of pontocerebellar tract significantly changed over time before and after treatment. The changes of GMV in the pain-matrix regions exhibited similar trends to the VAS before and after treatment.

Conclusion
We conclude that magnetic resonance imaging with RESOLVE DTI and VBM with T2-SPACE images were helpful in the understanding of the pathophysiological mechanisms in patients with TN before and after treatment.
Response to Revisiting: “Prevalence of and factors associated with sarcopenia among multi-ethnic ambulatory older Asians with type 2 diabetes mellitus in a primary care setting”
Authors: Fung Foon Yin , Tan Ngiap Chuan 
Published: December 2021

AbstractTo address and clarify the concerns of fellow researchers of “Revisiting: “Prevalence of and factors associated with sarcopenia among multi-ethnic ambulatory older Asians with type 2 diabetes mellitus in a primary care setting”. While chronic obstructive pulmonary disease may be a contributing factor, it is our study limitation to capture a significant number of patients with chronic obstructive pulmonary disease for analyses. Also, ethnicity is not associated with sarcopenia.
Satisfaction with life among university students from nine countries: Cross-national study during the first wave of COVID-19 pandemic
Authors: Rogowska Aleksandra M. , Ochnik Dominika , Kuśnierz Cezary , Jakubiak Monika , Schütz Astrid , Held Marco J. , Arzenšek Ana , Benatov Joy , Berger Rony , Korchagina Elena V. , Pavlova Iuliia , Blažková Ivana , Konečná Zdeňka , Aslan Imran , Çınar Orhan , Cuero-Acosta Yonni Angel 
Published: December 2021

Abstract
Background
A cross-sectional study was performed to examine life satisfaction differences between university students from nine countries during the first wave of the COVID-19 pandemic. A cross-national comparison of the association between life satisfaction and a set of variables was also conducted.

Methods
Participants in the study were 2349 university students with a mean age of 23 years (M = 23.15, SD = 4.66). There was a predominance of women (69.26%) and individuals studying at the bachelor level (78%). The research was conducted between May and July 2020 in nine countries: Slovenia (n=209), the Czech Republic (Czechia)(n=308), Germany (n=267), Poland (n=301), Ukraine (n=310), Russia (n=285), Turkey (n=310), Israel (n=199), and Colombia (n=153). Participants completed an online survey involving measures of satisfaction with life (SWLS), exposure to COVID-19, perceived negative impact of coronavirus (PNIC) on students' well-being, general self-reported health (GSRH), physical activity (PA), and some demographics (gender, place of residence, level of study). A one-way ANOVA was used to explore cross-national differences in life satisfaction. The χ2 independence test was performed separately in each country to examine associations between life satisfaction and other variables. Bivariate and multivariate logistic regressions were used to identify life satisfaction predictors among a set of demographic and health-related variables in each of the nine countries.

Results
The level of life satisfaction varied between university students from the nine countries. The results for life satisfaction and the other variables differed between countries. Numerous associations were noted between satisfaction with life and several variables, and these showed cross-national differences. Distinct predictors of life satisfaction were observed for each country. However, poor self-rated physical health was a predictor of low life satisfaction independent of the country.

Conclusions
The association between life satisfaction and subjective assessment of physical health seems to be universal, while the other variables are related to cross-cultural differences. Special public health attention should be focused on psychologically supporting people who do not feel healthy.