bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Neural Signature of Psychological Interventions in Persons With Cancer: A Scoping Review
Authors: Rossini Pierre Gilbert , Ostacoli Luca , Pagani Marco , Malandrone Francesca , Oliva Francesco , Cominu Luca , Annetta Maria Chiara , Carletto Sara 
Published: May 2022

Objective: People diagnosed with cancer have to deal with the debilitating psychological implications of this disease. Although the clinical efficacy of psychological interventions is well documented, relatively little has been written on the neural correlates of these treatments in the context of oncology. The present work is the first to provide an overall perspective of the existing literature on this topic. It also considers the potential directions for future research. Methods: This scoping review was carried out across 5 databases (EMBASE, PsycINFO, OVID MEDLINE, CINAHL, COCHRANE CENTRAL), from conception dates until 3 December 2021. Results: From an initial set of 4172 records, 13 papers were selected for this review. They consisted of 9 randomized controlled studies (RCTs), 1 quasi-experiment, 2 single case studies, and 1 secondary quantitative analysis. The studies were also heterogeneous in terms of the patient and control populations, psychological interventions, and neuroimaging methodologies used. The findings from these few studies suggest that psychological interventions in oncology patients may modulate both cortical and subcortical brain activity, consistent with the brain areas involved in distress reactions in general and to cancer specifically. The implications of this scoping review in terms of future research are also discussed. Conclusions: The literature on the neural correlates of psychological interventions in cancer patients is very limited, and thus requires further exploration. The provision of psychological interventions offers cancer patients a more integrated approach to care, which may in turn help preserve both the physical and the psychological wellbeing of individuals with cancer.
Global outflow angle influences silent ischemic events in coil embolization for unruptured distal anterior cerebral artery aneurysms
Authors: Suzuki Ryotaro , Takigawa Tomoji , Nagaishi Masaya , Hyodo Akio , Suzuki Kensuke 
Published: May 2022

Background Distal anterior cerebral artery (DACA) aneurysms are rare, and endovascular treatment of these aneurysms is challenging. Thromboembolic events, including silent ischemic events, are one of the most important complications of coil embolization for cerebral aneurysms. The treatment outcomes and predictors of silent ischemic events in coil embolization for unruptured DACA aneurysms were investigated, focusing on the morphological characteristics of aneurysms, especially the inflow angle (IA) and global outflow angle (GOA). Methods A total of 12 patients with 12 unruptured DACA aneurysms, treated with coil embolization at our institute, were retrospectively investigated. Predictors for silent ischemic events were evaluated by comparing diffusion-weighted imaging (DWI)-positive and DWI-negative patients. Results Silent ischemic events detected on DWI were observed in eight aneurysms (66.7%). Comparison of the morphological characteristics of aneurysms between the two groups showed a significantly smaller GOA in the DWI-positive group than in the DWI-negative group (172.6 ± 17.7° vs. 216.8 ± 16.8°, P < 0.01). A multivariate analysis showed that GOA <195° was a significant predictor of silent ischemic events ( P = 0.04; odds ratio: 23.62; 95% confidence interval: 1.11–490.39). Conclusion A small GOA was a significant predictor of silent ischemic events after coil embolization for unruptured DACA aneurysms. While some patients can be treated safely with minimally invasive coil embolization, it is necessary to consider surgical clipping in patients at high risk of thromboembolic events with coil embolization.
Factors Associated With Nonunion and Infection Following Ankle Arthrodesis Using a Large Claims Database: Who Has Elevated Risk?
Authors: Wong Liam H. , Chrea Bopha , Meeker James E. , Yoo Jung U. , Atwater Lara C. 
Published: May 2022

Background: Complications such as nonunion and infection following ankle arthrodesis can lead to increased patient morbidity and financial burden from repeat operations. Improved knowledge of risk factors can improve patient selection and inform post–ankle arthrodesis surveillance protocols. Methods: This is a large retrospective, database study with structured query of a national insurance claims database (PearlDiver Technologies) for patients treated with ankle arthrodesis from 2015 to 2019 as identified by International Classification of Diseases, Tenth Revision ( ICD-10), codes. Patients with any operation 1 year prior to or following ankle arthrodesis were excluded from analysis to prevent attributing complications to another operation. Likelihoods of nonunion and infection within 1 year and 3 years following ankle arthrodesis were analyzed using Kaplan-Meier estimations. Patient characteristics associated with the identified complications following ankle arthrodesis were analyzed using multivariable logistic regression analyses. Results: Our query yielded 2463 patients in the 5-year period who underwent ankle arthrodesis. Nonunion occurred in 11% (95% CI 10-12) of patients within 1 year of ankle arthrodesis and 16% (95% CI 14-17) of patients within 3 years. Infection occurred in 3.9% (95% CI 3.1-4.7) of patients within 1 year of ankle arthrodesis and in 6.2% (95% CI 5.1-7.2) of patients within 3 years. Obese patients increased odds of nonunion on multivariable analysis (OR 1.6, 95% CI 1.3-2.0; P < .001). On multivariable analysis, diabetes (OR 1.7, 95% CI 1.2-2.6; P = .010) and each 1-unit increase in Elixhauser Comorbidity Index scores (OR 1.1, 95% CI 1.1-1.2; P < .001) contributed to increased odds of infection after ankle arthrodesis. Conclusion: Nonunion and infection following ankle arthrodesis have a 3-year probability of 16% and 6%, respectively. More than one-quarter of patients with nonunion following ankle arthrodesis experience a delay in diagnosis beyond 1 year. The risk of post–ankle arthrodesis nonunion is highest in patients with obesity; the risk of post–ankle arthrodesis infection is highest in patients with diabetes or an elevated Elixhauser Comorbidity Index score. Level of Evidence: Level III, prognostic study.
Genetic support of a causal relationship between iron status and atrial fibrillation: a Mendelian randomization study
Authors: Wang Tianyi , Cheng Jun , Wang Yanggan 
Published: May 2022

Abstract
Background
Atrial fibrillation is the most common arrhythmia disease. Animal and observational studies have found a link between iron status and atrial fibrillation. However, the causal relationship between iron status and AF remains unclear. The purpose of this investigation was to use Mendelian randomization (MR) analysis, which has been widely applied to estimate the causal effect, to reveal whether systemic iron status was causally related to atrial fibrillation.

Methods
Single nucleotide polymorphisms (SNPs) strongly associated (P < 5 × 10−8) with four biomarkers of systemic iron status were obtained from a genome-wide association study involving 48,972 subjects conducted by the Genetics of Iron Status consortium. Summary-level data for the genetic associations with atrial fibrillation were acquired from the AFGen (Atrial Fibrillation Genetics) consortium study (including 65,446 atrial fibrillation cases and 522,744 controls). We used a two-sample MR analysis to obtain a causal estimate and further verified credibility through sensitivity analysis.

Results
Genetically instrumented serum iron [OR 1.09; 95% confidence interval (CI) 1.02–1.16; p = 0.01], ferritin [OR 1.16; 95% CI 1.02–1.33; p = 0.02], and transferrin saturation [OR 1.05; 95% CI 1.01–1.11; p = 0.01] had positive effects on atrial fibrillation. Genetically instrumented transferrin levels [OR 0.90; 95% CI 0.86–0.97; p = 0.006] were inversely correlated with atrial fibrillation.

Conclusion
In conclusion, our results strongly elucidated a causal link between genetically determined higher iron status and increased risk of atrial fibrillation. This provided new ideas for the clinical prevention and treatment of atrial fibrillation.
A tensor-based bi-random walks model for protein function prediction
Authors: Hu Sai , Zhang Zhihong , Xiong Huijun , Jiang Meiping , Luo Yingchun , Yan Wei , Zhao Bihai 
Published: May 2022

AbstractBackgroundThe accurate characterization of protein functions is critical to understanding life at the molecular level and has a huge impact on biomedicine and pharmaceuticals. Computationally predicting protein function has been studied in the past decades. Plagued by noise and errors in protein–protein interaction (PPI) networks, researchers have undertaken to focus on the fusion of multi-omics data in recent years. A data model that appropriately integrates network topologies with biological data and preserves their intrinsic characteristics is still a bottleneck and an aspirational goal for protein function prediction.ResultsIn this paper, we propose the RWRT (Random Walks with Restart on Tensor) method to accomplish protein function prediction by applying bi-random walks on the tensor. RWRT firstly constructs a functional similarity tensor by combining protein interaction networks with multi-omics data derived from domain annotation and protein complex information. After this, RWRT extends the bi-random walks algorithm from a two-dimensional matrix to the tensor for scoring functional similarity between proteins. Finally, RWRT filters out possible pretenders based on the concept of cohesiveness coefficient and annotates target proteins with functions of the remaining functional partners. Experimental results indicate that RWRT performs significantly better than the state-of-the-art methods and improves the area under the receiver-operating curve (AUROC) by no less than 18%.ConclusionsThe functional similarity tensor offers us an alternative, in that it is a collection of networks sharing the same nodes; however, the edges belong to different categories or represent interactions of different nature. We demonstrate that the tensor-based random walk model can not only discover more partners with similar functions but also free from the constraints of errors in protein interaction networks effectively. We believe that the performance of function prediction depends greatly on whether we can extract and exploit proper functional similarity information on protein correlations.
A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus
Authors: Chrzastek Klaudia , Tennakoon Chandana , Bialy Dagmara , Freimanis Graham , Flannery John , Shelton Holly 
Published: May 2022

Abstract
Background
Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions.

Methods
The performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2–4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing.

Results
The SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of SARS-CoV-2 that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 103 pfu/ml (Ct, 22.4) for whole genome assembly and 101 pfu/ml (Ct, 30) for metagenomics detection.

Conclusions
The SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.
Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach
Authors: Cope Alexander L. , Gilchrist Michael A. 
Published: May 2022

Abstract
Background
Codon usage bias (CUB), the non-uniform usage of synonymous codons, occurs across all domains of life. Adaptive CUB is hypothesized to result from various selective pressures, including selection for efficient ribosome elongation, accurate translation, mRNA secondary structure, and/or protein folding. Given the critical link between protein folding and protein function, numerous studies have analyzed the relationship between codon usage and protein structure. The results from these studies have often been contradictory, likely reflecting the differing methods used for measuring codon usage and the failure to appropriately control for confounding factors, such as differences in amino acid usage between protein structures and changes in the frequency of different structures with gene expression.

Results
Here we take an explicit population genetics approach to quantify codon-specific shifts in natural selection related to protein structure in S. cerevisiae and E. coli. Unlike other metrics of codon usage, our approach explicitly separates the effects of natural selection, scaled by gene expression, and mutation bias while naturally accounting for a region’s amino acid usage. Bayesian model comparisons suggest selection on codon usage varies only slightly between helix, sheet, and coil secondary structures and, similarly, between structured and intrinsically-disordered regions. Similarly, in contrast to prevous findings, we find selection on codon usage only varies slightly at the termini of helices in E. coli. Using simulated data, we show this previous work indicating “non-optimal” codons are enriched at the beginning of helices in S. cerevisiae was due to failure to control for various confounding factors (e.g. amino acid biases, gene expression, etc.), and rather than selection to modulate cotranslational folding.

Conclusions
Our results reveal a weak relationship between codon usage and protein structure, indicating that differences in selection on codon usage between structures are slight. In addition to the magnitude of differences in selection between protein structures being slight, the observed shifts appear to be idiosyncratic and largely codon-specific rather than systematic reversals in the nature of selection. Overall, our work demonstrates the statistical power and benefits of studying selective shifts on codon usage or other genomic features from an explicitly evolutionary approach. Limitations of this approach and future potential research avenues are discussed.
A novel compound heterozygous SPG7 variant is associated with progressive spastic ataxia and persecutory delusions found in Chinese patients: two case reports
Authors: Wang Shan , Wang Yaye , Wu Yue , Zhang Jinru , Zhang Weilin , Li Chang , Song Xueqin 
Published: May 2022

Abstract
Background
Hereditary spastic paraplegia 7 (SPG7) is one of the subtypes of autosomal-recessive hereditary spastic paraplegia, which is a clinically heterogeneous neurodegenerative disorder. SPG7 often displays a complicated phenotype, including optic atrophy, ophthalmoparesis, and impaired emotional communication. In the Chinese population, sporadic cases of SPG7 variant-associated spastic ataxia are rarely reported.

Case presentation
We carefully analysed the clinical features, imaging and genetic tests of two sporadic patients with SPG7, both from the Hebei region of China. One patient presented with progressive bilateral lower limb weakness, spastic-ataxia and no cognitive impairment. Brain MRI revealed mild cerebellar atrophy. Genetic analysis revealed c.1150_1151insCTAC (p.G384Afs*13) frameshift variant and exon1-3 heterozygous deletion. The other patient presented with progressive bilateral lower limb weakness, ataxia, dysarthria and a mild psychosis associated with persecutory delusions, which drew almost no attention, in addition to mild cognitive impairments characterized by a decrease in verbal memory and executive function. Genetic analysis identified two heterozygous variants in the SPG7 gene: c.1150_1151insCTAC (p.G384Afs*13) and c.1496delC (p.Q500Sfs*13).

Conclusions
The c.1496delC (p.Q500Sfs*13) variant in exon 11 has not been reported before. The c.1150_1151insCTAC variant is speculated to be a hotspot variant in the Chinese population. Patients with SPG7 may have cognitive impairments and psychosis, displaying specific characteristics, which should be of concern.
Multinomial network meta-analysis using response rates: relapsed/refractory multiple myeloma treatment rankings differ depending on the choice of outcome
Authors: van Beurden-Tan Chrissy H. Y. , Sonneveld Pieter , Groot Carin A. Uyl-de 
Published: May 2022

Abstract
Background
Due to the fast growing relapsed/refractory multiple myeloma (RRMM) treatment landscape, a comparison of all the available treatments was warranted. For clinical practice it is important to consider both immediate effects such as response quality and prolonged benefits such as progression-free survival (PFS) in a meta-analysis. The objective of this study was to assess the impact of the choice of outcome on the treatment rankings in RRMM.

Methods
A multinomial logistic network meta-analysis was conducted to estimate the ranking of sixteen treatments based on both complete and objective response rates (CRR and ORR). Seventeen phase III randomized controlled trials from a previously performed systematic literature review were included. Treatment ranking was based on the surface under the cumulative ranking curve (SUCRA). Sensitivity analysis was conducted.

Results
The ranking of treatments differed when comparing PFS hazard ratios rankings with rankings based on CRR. Pomalidomide, bortezomib and dexamethasone ranked highest, while a substantial lower ranking was observed for the triplet elotuzumab, lenalidomide, dexamethasone. The ranking of treatments did not differ when comparing PFS hazard ratios and ORR. The scenario analyses showed that the results were robust. In all scenarios the top three was dominated by the same triplets. The treatment with the highest probability of having the best PFS and ORR was the triplet daratumumab, lenalidomide plus dexamethasone in the base case.

Conclusion
This analysis shows that depending on the chosen outcome treatment rankings in RRMM may differ. When conducting NMAs, the response rate, a clinically recognized outcome, should therefore be more frequently considered.
Colorectal cancer concurrent gene signature based on coherent patterns between genomic and transcriptional alterations
Authors: Shen Ming-Hung , Huang Chi-Jung , Ho Thien-Fiew , Liu Chih-Yi , Shih Ying-Yih , Huang Ching-Shui , Huang Chi-Cheng 
Published: May 2022

Abstract
Background
The aim of the study was to enhance colorectal cancer prognostication by integrating single nucleotide polymorphism (SNP) and gene expression (GE) microarrays for genomic and transcriptional alteration detection; genes with concurrent gains and losses were used to develop a prognostic signature.

Methods
The discovery dataset comprised 32 Taiwanese colorectal cancer patients, of which 31 were assayed for GE and copy number variations (CNVs) with Illumina Human HT-12 BeadChip v4.0 and Omni 25 BeadChip v1.1. Concurrent gains and losses were declared if coherent manners were observed between GE and SNP arrays. Concurrent genes were also identified in The Cancer Genome Atlas Project (TCGA) as the secondary discovery dataset (n = 345).

Results
The “universal” concurrent genes, which were the combination of z-transformed correlation coefficients, contained 4022 genes. Candidate genes were evaluated within each of the 10 public domain microarray datasets, and 1655 (2000 probe sets) were prognostic in at least one study. Consensus across all datasets was used to build a risk predictive model, while distinct relapse-free/overall survival patterns between defined risk groups were observed among four out of five training datasets. The predictive accuracy of recurrence, metastasis, or death was between 61 and 86% (cross-validation area under the receiver operating characteristic (ROC) curve: 0.548-0.833) from five independent validation studies.

Conclusion
The colorectal cancer concurrent gene signature is prognostic in terms of recurrence, metastasis, or mortality among 1746 patients. Genes with coherent patterns between genomic and transcriptional contexts are more likely to provide prognostication for colorectal cancer.
Unmet health needs and barriers to health care among people experiencing homelessness in San Francisco’s Mission District: a qualitative study
Authors: Thorndike Anna L. , Yetman Hailey E. , Thorndike Anne N. , Jeffrys Mason , Rowe Michael 
Published: May 2022

Abstract
Background
People experiencing homelessness have unique health needs and barriers to medical and behavioral health care (mental health, substance use disorder, and overall well-being) compared to housed people. It remains unclear why many people experiencing homelessness do not access care when community-based homeless health care resources are available at low or no cost. This qualitative study examined perspectives of people experiencing homelessness and staff members at community-based homeless health and service organizations in San Francisco’s Mission District on unmet medical and behavioral health needs and barriers to accessing care.

Methods
We conducted 34 interviews between September and November 2020: 23 with people experiencing homelessness and 11 with staff at community-based homeless health and service organizations in the Mission District. Qualitative interviews were transcribed, coded, and analyzed using the Framework Method on NVivo Qualitative Data Analysis Software.

Results
Both staff and homeless participants reported unmet and common health needs of mental illness, physical injury and disability, food and nutrition insecurity, and substance use disorder. Barriers to care included negative prior health care experiences, competing priorities, and provider turnover. Recommendations for improving services included building more trust with people experiencing homelessness by training clinic staff to treat patients with respect and patience and expanding clinical outreach and health education programs.

Conclusions
People experiencing homelessness face many different health needs and barriers to care, some of which community-based organizations have the ability to address. These findings can help inform future strategies for homeless health care programs to identify and target the specific unmet health needs and barriers to care of people experiencing homelessness in their communities.