bluuebunny/crossref_metadata_2025_split huggingface dataset:
68Ga-PSMA-11 PET Identified Tumor Recurrence in Prostatectomy Bed With Rising PSA of 0.9 ng/mL but Negative on MRI and 18F-Fluciclovine PET Scan
Authors: Xu Guofan , Lu Yang 
Published: January 2022

Abstract
A 63-year-old man with prostate cancer was treated with prostatectomy who had postoperative PSA of 0.6 ng/mL. A pelvic MRI, whole body bone scan, CT chest and abdomen exams did not show any residual or metastatic prostate disease. His PSA increased to 0.9 ng/mL in two months. A fluciclovine PET did not show any tracer avid metastatic or recurrent disease. A 0.7 cm non-fluciclovine-avid nodule at the left prostatectomy bed was considered benign. A 68Ga-PSMA-11 PET one month later showed avid radiotracer uptake within this nodule. The patient received androgen deprivation treatment after PSMA PET/CT and responded well.
18F-PSMA-11 PET/MRI in Prostate Adenocarcinoma With Mucinous Features
Authors: Zhao Qian , Yang Bo , Dong Aisheng , Zuo Changjing 
Published: January 2022

Abstract
Primary mucinous tumors involving the prostate gland are rare. We describe MRI and 18F-PSMA-11 PET/MRI findings in a case of prostate adenocarcinoma with mucinous features. The prostate tumor showed inhomogeneous hyperintensity on T2-weighted images due to high extracellular mucin content and inhomogeneous 18F-PSMA-11 uptake with SUVmax of 12.5. This case indicates PSMA PET imaging may be helpful for detection of this uncommon variant of prostate adenocarcinoma.
Lesion-Based Radiomics Signature in Pretherapy 18F-FDG PET Predicts Treatment Response to Ibrutinib in Lymphoma
Authors: Jimenez Jorge E. , Dai Dong , Xu Guofan , Zhao Ruiyang , Li Tengfei , Pan Tinsu , Wang Linghua , Lin Yingyan , Wang Zhangyang , Jaffray David , Hazle John D. , Macapinlac Homer A. , Wu Jia , Lu Yang 
Published: January 2022

Purpose
The aim of this study was to develop a pretherapy PET/CT-based prediction model for treatment response to ibrutinib in lymphoma patients.

Patients and Methods
One hundred sixty-nine lymphoma patients with 2441 lesions were studied retrospectively. All eligible lymphomas on pretherapy 18F-FDG PET images were contoured and segmented for radiomic analysis. Lesion- and patient-based responsiveness to ibrutinib was determined retrospectively using the Lugano classification. PET radiomic features were extracted. A radiomic model was built to predict ibrutinib response. The prognostic significance of the radiomic model was evaluated independently in a test cohort and compared with conventional PET metrics: SUVmax, metabolic tumor volume, and total lesion glycolysis.

Results
The radiomic model had an area under the receiver operating characteristic curve (ROC AUC) of 0.860 (sensitivity, 92.9%, specificity, 81.4%; P < 0.001) for predicting response to ibrutinib, outperforming the SUVmax (ROC AUC, 0.519; P = 0.823), metabolic tumor volume (ROC AUC, 0.579; P = 0.412), total lesion glycolysis (ROC AUC, 0.576; P = 0.199), and a composite model built using all 3 (ROC AUC, 0.562; P = 0.046). The radiomic model increased the probability of accurately predicting ibrutinib-responsive lesions from 84.8% (pretest) to 96.5% (posttest). At the patient level, the model's performance (ROC AUC = 0.811; P = 0.007) was superior to that of conventional PET metrics. Furthermore, the radiomic model showed robustness when validated in treatment subgroups: first (ROC AUC, 0.916; P < 0.001) versus second or greater (ROC AUC, 0.842; P < 0.001) line of defense and single treatment (ROC AUC, 0.931; P < 0.001) versus multiple treatments (ROC AUC, 0.824; P < 0.001).

Conclusions
We developed and validated a pretherapy PET-based radiomic model to predict response to treatment with ibrutinib in a diverse cohort of lymphoma patients.
Complications of Percutaneous Kidney Allograft Biopsy: Systematic Review and Meta-analysis
Authors: Ho Quan Yao , Lim Cynthia Ciwei , Tan Hui Zhuan , Sultana Rehena , Kee Terence , Htay Htay 
Published: January 2022

Background.
Kidney biopsy is important to guide the management of allograft dysfunction but has a risk of complications. This review aimed to determine the incidence and risk factors of complications after kidney allograft biopsy.

Methods.
This is a systematic review and meta-analysis of randomized controlled trials, cohort studies, or case-control studies indexed on PubMed, Embase, Cochrane Central Register of Controlled Trials, World Health Organization International Clinical Trials Registry, and ClinicalTrials.gov, limited to the English language, from January 2000 to December 2020, including adult and pediatric kidney allograft biopsies. Primary outcomes were gross hematuria, bleeding requiring transfusion, and major complications (requiring interventions such as blood transfusion or surgical or radiological interventions).

Results.
The review included 72 studies (40 082 biopsies). The quality of included studies was suboptimal. Pooled rates of gross hematuria, bleeding requiring transfusion, and major complications were 3.18% [95% confidence interval (95% CI), 2.31-4.19], 0.31% (95% CI, 0.15-0.52) and 0.89% (95% CI, 0.61-1.22), respectively. Gross hematuria rates were lower in high-income compared with middle-income countries (2.59% versus 6.44%, P < 0.01) and biopsies performed by radiology as compared with nephrology departments (1.25% versus 3.71%, P < 0.01). Blood transfusion rates were lower in pediatrics than adults (0.0% versus 0.65%, P < 0.01). Major complications were lower in biopsies performed by specialists as compared with trainees (0.02% versus 3.64%, P < 0.01). Graft loss and mortality were extremely rare. Limitations included missing data, few randomized controlled trials, and possible publication bias.

Conclusions.
The risk of complications after kidney allograft biopsy was low. Given the low quality of included studies, risk factors for complications should be further examined in future studies.
Visually induced dizziness
Authors: Steenerson Kristen K. , Hoskin Justin , Fife Terry D. 
Published: January 2022

Purpose of review
Visually induced dizziness (VID) is a common phenomenon in vestibular disorders of both peripheral and central causes. This article provides a review of the most updated understandings of definition, pathophysiology, and treatment options.

Recent findings
The pathophysiology is complex and its severity or persistence may be related both to the underlying cause and heritable factors. Environmental and psychological factors may influence the degree of impact of VID on daily life function. Treatment is mostly empiric at this point but includes pharmacologic, desensitization, cognitive behavioral therapies, visual rehabilitation, and treatment of the underlying cause whenever present. Additional research is needed to clarify the best management of this vestibular symptom as well as some of the other conditions with which it is commonly associated.

Summary
VID is a fairly common vestibular syndrome constitutng spatial disorientation without illusory motion. As it is seen in both peripheral and central vestibular disorders, it should be considered a syndrome or constellation of symptoms rather than a discrete disorder. In some cases, it may be the presenting symptom with no other clear disorder linked to it.
Investigation of the Effects of N-Linked Glycans on the Stability of the Spike Protein in SARS-CoV-2 by Molecular Dynamics Simulations
Authors: Tekin E.Deniz 
Published: January 2022

AbstractWe perform all-atom molecular dynamics simulations to study the effects of the N-linked glycans on the stability of the spike glycoprotein in SARS-CoV-2. After a 100 ns of simulation on the spike proteins without and with the N-linked glycans, we found that the presence of glycans increases the local stability in their vicinity; even though their effect on the full structure is negligible.Graphical Abstract
Practical and Thermodynamic Constraints on Electromicrobially-Accelerated CO2 Mineralization
Authors: Marecos Sabrina , Brigham Rae , Dressel Anastacia , Gaul Larissa , Li Linda , Satish Krishnathreya , Tjokorda Indira , Zheng Jian , Schmitz Alexa M. , Barstow Buz 
Published: January 2022

AbstractBy the end of the century tens of gigatonnes of CO2 will need to be removed from the atmosphere every year to maintain global temperatures. Natural weathering of ultramafic rocks and subsequent mineralization reactions can convert atmospheric CO2 into ultra-stable carbonates. But, while natural weathering will eventually draw down all excess CO2, this process will need hundreds of thousands of years to do it. The CO2 mineralization process could be accelerated by weathering ultramafic rocks with biodegradable lixiviants like organic acids. But, in this article we show that if these lixiviants are produced from cellulosic biomass, the demand created by CO2 mineralization could monopolize the world’s supply of biomass even if CO2 mineralization performance is high. In this article we demonstrate that electromicrobial production technologies (EMP) that combine renewable electricity and microbial metabolism could produce lixiviants for as little as $200 to $400 per tonne at solar electricity prices achievable within the decade. Furthermore, this allows the lixiviants needed to sequester a tonne of CO2 to be produced for less than $100, even with modest CO2 mineralization performance.
Optimization of capture protocols across species targeting up to 32000 genes and their extension to pooled DNA
Authors: Mariac Cédric , Bethune Kévin , de Aquino Sinara Oliveira , Abdelrahman Mohamed , Barnaud Adeline , Billot Claire , Zekraoui Leila , Couderc Marie , Kané Ndjido , Andrade Alan Carvalho , Marraccini Pierre , Kiwuka Catherine , Albar Laurence , Sabot François , Poncet Valérie , Couvreur Thomas LP , Berthouly-Salazar Cécile , Vigouroux Yves 
Published: January 2022

AbstractPremiseIn-solution based capture is becoming a method of choice for sequencing targeted sequence.Methods and resultsWe assessed and optimized a capture protocol in 20 different species from 6 different plant genus using kits from 20,000 to 200,000 baits targeting from 300 to 32,000 genes. We evaluated both the effectiveness of the capture protocol and the fold enrichment in targeted sequences. We proposed a protocol with multiplexing up to 96 samples in a single hybridization and showed it was an efficient and cost-effective strategy. We also extended the use of capture to pools of 100 samples and proved the efficiency of the method to assess allele frequency. Using a set of various organisms with different genome sizes, we demonstrated a correlation between the percentage of on-target reads vs. the relative size of the targeted sequences.ConclusionAltogether, we proposed methods, strategies, cost-efficient protocols and statistics to better evaluate and more effectively use hybridization capture.
The megabase-scale crossover landscape is independent of sequence divergence
Authors: Lian Qichao , Solier Victor , Walkemeier Birgit , Huettel Bruno , Schneeberger Korbinian , Mercier Raphael 
Published: January 2022

AbstractMeiotic recombination frequency varies along chromosomes and strongly correlates with sequence divergence. However, the causality underlying this correlation is unclear. To untangle the relationship between recombination landscapes and polymorphisms, we characterized the genome-wide recombination landscape in the absence of polymorphisms, usingArabidopsis thalianahomozygous inbred lines in which a few hundred genetic markers were introduced through mutagenesis. We found that megabase-scale recombination landscapes in inbred lines are strikingly similar to the recombination landscapes in hybrids, with the sole exception of heterozygous large rearrangements where recombination is prevented locally. In addition, we found that the megabase-scale recombination landscape can be accurately predicted by chromatin features. Our results show that polymorphisms are not causal for the shape of the megabase-scale recombination landscape, rather, favor alternative models in which recombination and chromatin shape sequence divergence across the genome.
Single-Nucleus Chromatin Accessibility Identifies a Critical Role for TWIST1 in Idiopathic Pulmonary Fibrosis Myofibroblast Activity
Authors: Valenzi Eleanor , Bahudhanapati Harinath , Tan Jiangning , Tabib Tracy , Sullivan Daniel I. , Sembrat John , Fan Li , Chen Kong , Rojas Mauricio , Lafargue Audrey , Felsher Dean W. , Tran Phuoc T. , Kass Daniel J. , Lafyatis Robert 
Published: January 2022

AbstractIn idiopathic pulmonary fibrosis (IPF) myofibroblasts are key effectors of fibrosis and architectural distortion by excessive deposition of extracellular matrix and their acquired contractile capacity. Single-cell RNA-sequencing has precisely defined the IPF myofibroblast transcriptome, but identifying critical transcription factor activity by this approach is imprecise. We performed and integrated snATAC-seq and scRNA-seq from human IPF and donor control explants to identify differentially accessible chromatin regions and enriched transcription factor motifs within lung cell populations. TWIST1 and other E-box transcription factor motifs were significantly enriched in IPF myofibroblasts compared to both IPF non-myogenic and control fibroblasts. TWIST1 expression was also selectively upregulated in IPF myofibroblasts. Overexpression of Twist1 in lung COL1A2-expressing fibroblasts in bleomycin-injured mice was associated with increased collagen synthesis. Our studies utilizing human multiomic single-cell analyses combined with in vivo murine disease models confirm a critical regulatory function for TWIST1 in IPF myofibroblast activity in the fibrotic lung. Understanding the global process of opening TWIST1 and other E-box TF motifs that govern myofibroblast differentiation may identify new therapeutic interventions for fibrotic pulmonary diseases.
Evaluation of methods incorporating biological function and GWAS summary statistics to accelerate discovery
Authors: Moore Amy , Marks Jesse , Quach Bryan C. , Guo Yuelong , Bierut Laura J. , Gaddis Nathan C. , Hancock Dana B. , Page Grier P. , Johnson Eric O. 
Published: January 2022

AbstractWhere sufficiently large genome-wide association study (GWAS) samples are not currently available or feasible, methods that leverage increasing knowledge of the biological function of variants may illuminate discoveries without increasing sample size. We comprehensively evaluated 18 functional weighting methods for identifying novel associations. We assessed the performance of these methods using published results from multiple GWAS waves across each of five complex traits. Although no method achieved both high sensitivity and positive predictive value (PPV) for any trait, a subset of methods utilizing pleiotropy and expression quantitative trait loci nominated variants with high PPV (>75%) for multiple traits. Application of functionally weighting methods to enhance GWAS power for locus discovery is unlikely to circumvent the need for larger sample sizes in truly underpowered GWAS, but these results suggest that applying functional weighting to GWAS can accurately nominate additional novel loci from available samples for follow-up studies.
Bioinformatics Analysis of the Potentially Functional circRNA-miRNA-mRNA Network in Breast Cancer
Authors: Erdoğan Cihat , Suer İlknur , Kaya Murat , Kurt Zeyneb , Öztürk Şükrü , Aydın Nizamettin 
Published: January 2022

AbstractObjectiveBreast cancer (BC) is a heterogeneous type of cancer that occurs as a result of distinct molecular alterations in breast tissue. Although there are many new developments in treatment and targeted therapy for BC in recent years, this cancer type is still the most common one among women with high morbidity and mortality. Therefore, new research is still needed for biomarker detection.MethodsGSE101124 and GSE182471 datasets were obtained from Gene Expression Omnibus (GEO) database to evaluate differentially expressed circular RNAs (circRNAs). The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) databases were used to identify the significantly dysregulated microRNAs (miRNAs) and genes considering the Prediction Analysis of Microarray (PAM50) classification. The circRNA-miRNA-gene relationship was investigated using the Cancer Specific CircRNA (v2.0) (CSCD), miRDB, miRWalk and miRTarBase databases. The circRNA–miRNA–mRNA regulatory network was constructed using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) annotation. The protein-protein interaction network was constructed by the STRING 2021 database and visualized by the Cytoscape tool (v3.9.0). Then, raw miRNA data and genes were filtered using some selection criteria according to a specific expression level in PAM50 subgroups. A bottleneck method was utilized to obtain highly interacted hub genes using cytoHubba Cytoscape plugin. The overall survival (OS) and disease-free survival (DFS) analysis were performed for these hub genes, which are detected within the miRNA and circRNA axis in our study.ResultsWe identified three circRNAs, three miRNAs, and eighteen candidate target genes that may play an important role in BC. In addition, it has been determined that these molecules can be useful in the classification of BC, especially in determining the basal-like breast cancer (BLBC) subtype.ConclusionsWe conclude that hsa_circ_0000515/ miR-486-5p/ SDC1 axis may be an important biomarker candidate in distinguishing patients in the BLBC group, especially according to the PAM50 classification of BC.
A Niclosamide-releasing hot-melt extruded catheter prevents Staphylococcus aureus experimental biomaterial-associated infection
Authors: Vazquez-Rodriguez Augusto , Shaqour Bahaa , Guarch-Pérez Clara , Choińska Emilia , Riool Martijn , Verleije Bart , Beyers Koen , Costantini Vivian J.A. , Święszkowski Wojciech , Zaat Sebastian A. J. , Cos Paul , Felici Antonio , Ferrari Livia 
Published: January 2022

AbstractBiomaterial-associated infections are a major healthcare challenge as they are responsible for high disease burden in critically ill patients. In this study, we have developed drug-eluting antibacterial catheters to prevent catheter-related infections. Niclosamide (NIC), originally a well-studied antiparasitic drug, was incorporated into the polymeric matrix of thermoplastic polyurethane (TPU) via solvent casting, and catheters were fabricated using hot-melt extrusion technology. The mechanical and physicochemical properties of TPU polymers loaded with NIC were studied. NIC was released in a sustained manner from the catheters and exhibited antibacterial activity against Staphylococcus aureus and Staphylococcus epidermidis in different in vitro models. Moreover, the antibacterial efficacy of NIC-loaded catheters was validated in an in vivo biomaterial-associated infection mouse model using a methicillin-susceptible and methicillin-resistant strain of S. aureus. The released NIC from the produced catheters reduced bacterial colonization of the catheter as well as of the surrounding tissue. A sustained in vivo release of NIC from the catheters for at least 14 days was observed. In summary, the NIC-releasing hot-melt extruded catheters prevented implant colonization and reduced the bacterial colonization of peri-catheter tissue by methicillin sensitive as well as resistant S. aureus in a biomaterial-associated infection mouse model and has good prospects for preclinical development.
FunOrder 2.0 – a fully automated method for the identification of co-evolved genes
Authors: Vignolle Gabriel A. , Mach Robert L. , Mach-Aigner Astrid R. , Derntl Christian 
Published: January 2022

ABSTRACTCoevolution is an important biological process that shapes interacting species or even proteins – may it be physically interacting proteins or consecutive enzymes in a metabolic pathway. The detection of co-evolved proteins will contribute to a better understanding of biological systems. Previously, we developed a semi-automated method, termed FunOrder, for the detection of co-evolved genes from an input gene or protein set. We demonstrated the usability and applicability of FunOrder by identifying essential genes in biosynthetic gene clusters from different ascomycetes. A major drawback of this original method was the need for a manual assessment, which may create a user bias and prevents a high-throughput application. Here we present a fully automated version of this method termed FunOrder 2.0. To fully automatize the method, we used several mathematical indices to determine the optimal number of clusters in the FunOrder output, and a subsequent k-means clustering based on the first three principal components of a principal component analysis of the FunOrder output. Further, we replaced the BLAST with the DIAMOND tool, which enhanced speed and allows the future integration of larger proteome databases. The introduced changes slightly decreased the sensitivity of this method, which is outweighed by enhanced overall speed and specificity. Additionally, the changes lay the foundation for future high-throughput applications of FunOrder 2.0 in different phyla to solve different biological problems.AUTHOR SUMMARYCoevolution is a process which arises between different species or even different proteins that interact with each other. Any change occurring in one partner must be met by a corresponding change in the other partner to maintain the interaction throughout evolution. These interactions may occur in symbiotic relationships or between rivaling species. Within an organism, consecutive enzymes of metabolic pathways are also subjected to coevolution. We developed a fully automated method, FunOrder 2.0, for the detection of co-evolved proteins, which will contribute to a better understanding of protein interactions within an organism. We demonstrate that this method can be used to identify essential genes of the secondary metabolism of fungi, but FunOrder 2.0 may also be used to detect pathogenicity factors or remains of horizontal gene transfer next to many other biological systems that were shaped by coevolution.