bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk assessment in aortic aneurysm repair by medical specialists versus the American College of Surgeons National Surgical Quality Improvement Program risk calculator outcomes
Authors: van Schaik Jan , Hers Tessa M , van Rijswijk Carla SP , Schooneveldt Maaike S , Putter Hein , Eefting Daniël , van der Vorst Joost R 
Published: April 2021

Objective The aim of this online clinical vignette-based survey study was to compare risk assessments by vascular surgeons, anaesthesiologists and interventional radiologists involved in treating patients with aortic aneurysms in the Netherlands with the NSQIP risk calculator outcomes. Methods Participants, recruited using purposive sampling, provided their estimation of the likelihood of postoperative complications and events following aortic surgery in five fictional cases. These cases were subsequently scored using the NSQIP calculator. The risk assessments were statistically analysed using the ANOVA and student t-test. Results All participating specialists i.e. twelve vascular surgeons, ten interventional radiologists and ten anaesthesiologists completed the survey. In the vast majority of outcomes and vignettes, no significant differences were found between various specialists, whereas significant differences were found between the NSQIP risk calculator outcomes and the combined risk assessments of the specialists. Overall, specialist risk assessments differ from the NSQIP, but neither particularly higher nor lower compared to the risk calculator. Conclusions Risk assessment by vascular surgeons, anaesthesiologists and interventional radiologists differs significantly with NSQIP risk calculator outcomes, within the framework of both endovascular and open aortic aneurysm repair. Based on these results, implementing the NSQIP risk calculator in preoperative workup could be of added value in both patient planning as well as adequately informing patients for obtaining consent.
Stress, Resilience, and Coping of Healthcare Workers during the COVID-19 Pandemic
Authors: Croghan Ivana T. , Chesak Sherry S. , Adusumalli Jayanth , Fischer Karen M. , Beck Elizabeth W. , Patel Shruti R. , Ghosh Karthik , Schroeder Darrell R. , Bhagra Anjali 
Published: April 2021

Objective To estimate the health care workers (HCWs) self-reported stress, resilience, and coping during the COVID-19 pandemic, and to determine inter-professional differences. Participants and Methods An email survey was sent to 474 HCW at a Midwestern HealthCare facility between April 9, 2020 and April 30, 2020. A total of 311 (65.6%) responses were received by May 31, 2020. The survey utilized 3 validated instruments: Perceived Stress Scale (PSS), Brief Resilience Scale (BRS), Brief Resilience Coping Scale (BRCS). Results Of the 311 responses, 302 were evaluated: 97 from nonmedical staff with patient contact (NMPC); 86 from nonmedical staff with no patient contact (NMNPC); 62 from medical doctors (MD), physician assistants (PA) and nurse practitioners (NP); and 57 from nurses. Significant differences were noted across job categories for stress and resilience, with nurses reporting highest PSS scores (effect estimates: −2.72, P = .009 for NMNPC; −2.50, P = .015 for NMPC; −3.21, P = .006 for MD/NP/PA respectively), and MD/NP/PA group with highest BRS scores: nurses (−0.31, P = .02); NMPC (−0.3333, P = .01); and NMNPC (−0.2828, P = .02). Younger personnel had higher stress (−1.59 per decade of age, P < .01) and more resilience (0.11 per decade of age, P = .002). Conclusion These self-reported data indicate that MD/NP/PA had the highest resilience scores and the nurses had highest stress levels. Efforts are warranted to include all HCWs in systematic stress mitigating interventions with particular attention to understand specific factors contributing to stress for the nursing team.
The Relationship Between Posterior Communicating Artery Formation and Vertebral Artery Flow Parameters
Authors: Yeniçeri İbrahim Önder , Bek Vedat Semai , Çullu Neşat , Kutlu Gülnihal 
Published: April 2021

Objectives: It is important to know the range of normal vertebral artery (VA) flow volume. Diminished VA flow volume is associated with vertebrobasilar insufficiency. The study aim was to investigate the relationship between the posterior communicating artery (PCoA) calibration and the VA flow parameters, in patients with no underlying cerebrovascular disease, below 50 years of age. Materials and Methods: The study population consisted of 102 cases below 50 years of age. The basilar artery (BA), internal carotid artery (ICA), and the PCoA calibrations were measured with magnetic resonance angiography. The VA flow parameters (maximum systolic velocity, end-diastolic velocity, mean velocity, VA flow volume, and VA calibration) were measured with duplex sonography. Results: There was no statistically significant difference between these two imaging groups, in terms of VA Vmax, VA flow volumes, VA calibrations, and BA calibrations. However, the mean right ICA and mean left ICA calibrations were significantly higher in group 2 than group 1 ( P < .01). There was no significant correlation between mean PCoA calibration and mean Vmax, mean calibration, and the total flow volume of vertebral arteries. Conclusion: The findings indicate that the VA flow rate may be relatively maintained, regardless of PCoA measurements in this study.
Integrating genomic and infrared spectral data improves the prediction of milk protein composition in dairy cattle
Authors: Baba Toshimi , Pegolo Sara , Mota Lucio F. M. , Peñagaricano Francisco , Bittante Giovanni , Cecchinato Alessio , Morota Gota 
Published: April 2021

AbstractBackgroundOver the past decade, Fourier transform infrared (FTIR) spectroscopy has been used to predict novel milk protein phenotypes. Genomic data might help predict these phenotypes when integrated with milk FTIR spectra. The objective of this study was to investigate prediction accuracy for milk protein phenotypes when heterogeneous on-farm, genomic, and pedigree data were integrated with the spectra. To this end, we used the records of 966 Italian Brown Swiss cows with milk FTIR spectra, on-farm information, medium-density genetic markers, and pedigree data. True and total whey protein, and five casein, and two whey protein traits were analyzed. Multiple kernel learning constructed from spectral and genomic (pedigree) relationship matrices and multilayer BayesB assigning separate priors for FTIR and markers were benchmarked against a baseline partial least squares (PLS) regression. Seven combinations of covariates were considered, and their predictive abilities were evaluated by repeated random sub-sampling and herd cross-validations (CV).ResultsAddition of the on-farm effects such as herd, days in milk, and parity to spectral data improved predictions as compared to those obtained using the spectra alone. Integrating genomics and/or the top three markers with a large effect further enhanced the predictions. Pedigree data also improved prediction, but to a lesser extent than genomic data. Multiple kernel learning and multilayer BayesB increased predictive performance, whereas PLS did not. Overall, multilayer BayesB provided better predictions than multiple kernel learning, and lower prediction performance was observed in herd CV compared to repeated random sub-sampling CV.ConclusionsIntegration of genomic information with milk FTIR spectral can enhance milk protein trait predictions by 25% and 7% on average for repeated random sub-sampling and herd CV, respectively. Multiple kernel learning and multilayer BayesB outperformed PLS when used to integrate heterogeneous data for phenotypic predictions.
Convergence behavior of single-step GBLUP and SNPBLUP for different termination criteria
Authors: Vandenplas Jeremie , Calus Mario P. L. , Eding Herwin , van Pelt Mathijs , Bergsma Rob , Vuik Cornelis 
Published: April 2021

Abstract
Background
The preconditioned conjugate gradient (PCG) method is the current method of choice for iterative solving of genetic evaluations. The relative difference between two successive iterates and the relative residual of the system of equations are usually chosen as a termination criterion for the PCG method in animal breeding. However, our initial analyses showed that these two commonly used termination criteria may report that a PCG method applied to a single-step single nucleotide polymorphism best linear unbiased prediction (ssSNPBLUP) is not converged yet, whereas the solutions are accurate enough for practical use. Therefore, the aim of this study was to propose two termination criteria that have been (partly) developed in other fields, but are new in animal breeding, and to compare their behavior to that of the two termination criteria widely used in animal breeding for the PCG method applied to ssSNPBLUP. The convergence patterns of ssSNPBLUP were also compared to the convergence patterns of single-step genomic BLUP (ssGBLUP).

Results
Building upon previous work, we propose two termination criteria that take the properties of the system of equations into account. These two termination criteria are directly related to the relative error of the iterates with respect to the true solutions. Based on pig and dairy cattle datasets, we show that the preconditioned coefficient matrices of ssSNPBLUP and ssGBLUP have similar properties when using a second-level preconditioner for ssSNPBLUP. Therefore, the PCG method applied to ssSNPBLUP and ssGBLUP converged similarly based on the relative error of the iterates with respect to the true solutions. This similar convergence behavior between ssSNPBLUP and ssGBLUP was observed for both proposed termination criteria. This was, however, not the case for the termination criterion defined as the relative residual when applied to the dairy cattle evaluations.

Conclusion
Our results showed that the PCG method can converge similarly when applied to ssSNPBLUP and to ssGBLUP. The two proposed termination criteria always depicted these similar convergence behaviors, and we recommend them for comparing convergence properties of different models and for routine evaluations.
Juxtapose: a gene-embedding approach for comparing co-expression networks
Authors: Ovens Katie , Maleki Farhad , Eames B. Frank , McQuillan Ian 
Published: April 2021

Abstract
Background
Gene co-expression networks (GCNs) are not easily comparable due to their complex structure. In this paper, we propose a tool, Juxtapose, together with similarity measures that can be utilized for comparative transcriptomics between a set of organisms. While we focus on its application to comparing co-expression networks across species in evolutionary studies, Juxtapose is also generalizable to co-expression network comparisons across tissues or conditions within the same species.

Methods
A word embedding strategy commonly used in natural language processing was utilized in order to generate gene embeddings based on walks made throughout the GCNs. Juxtapose was evaluated based on its ability to embed the nodes of synthetic structures in the networks consistently while also generating biologically informative results. Evaluation of the techniques proposed in this research utilized RNA-seq datasets from GTEx, a multi-species experiment of prefrontal cortex samples from the Gene Expression Omnibus, as well as synthesized datasets. Biological evaluation was performed using gene set enrichment analysis and known gene relationships in literature.

Results
We show that Juxtapose is capable of globally aligning synthesized networks as well as identifying areas that are conserved in real gene co-expression networks without reliance on external biological information. Furthermore, output from a matching algorithm that uses cosine distance between GCN embeddings is shown to be an informative measure of similarity that reflects the amount of topological similarity between networks.

Conclusions
Juxtapose can be used to align GCNs without relying on known biological similarities and enables post-hoc analyses using biological parameters, such as orthology of genes, or conserved or variable pathways.

Availability
A development version of the software used in this paper is available at https://github.com/klovens/juxtapose
Alvis: a tool for contig and read ALignment VISualisation and chimera detection
Authors: Martin Samuel , Leggett Richard M. 
Published: April 2021

Abstract
Background
The analysis of long reads or the assessment of assembly or target capture data often necessitates running alignments against reference genomes or gene sets. The aligner outputs are often parsed automatically by scripts, but many kinds of analysis can benefit from the understanding that can follow human inspection of individual alignments. Additionally, diagrams are a useful means of communicating assembly results to others.

Results
We developed Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies.

Conclusion
Alvis diagrams facilitate improved understanding of assembly quality, enable read coverage to be visualised and potential errors to be identified. Additionally, we found that splitting chimeric reads using the output provided by Alvis can improve the contiguity of assemblies, while maintaining correctness.
The inhibitory receptor Tim-3 fails to suppress IFN-γ production via the NFAT pathway in NK-cell, unlike that in CD4+ T cells
Authors: Yu Xiaowen , Lang Bin , Chen Xi , Tian Yao , Qian Shi , Zhang Zining , Fu Yajing , Xu Junjie , Han Xiaoxu , Ding Haibo , Jiang Yongjun 
Published: April 2021

Abstract
Background
T cell immunoglobulin and mucin domain-containing-3 (Tim-3) is a negative regulator expressed on T cells, and is also expressed on natural killer (NK) cells. The function of Tim-3 chiefly restricts IFNγ-production in T cells, however, the impact of Tim-3 on NK cell function has not been clearly elucidated.

Results
In this study, we demonstrated down-regulation of Tim-3 expression on NK cells while Tim-3 is upregulated on CD4+ T cells during HIV infection. Functional assays indicated that Tim-3 mediates suppression of CD107a degranulation in NK cells and CD4+ T cells, while it fails to inhibit the production of IFN-γ by NK cells. Analyses of downstream pathways using an antibody to block Tim-3 function demonstrated that Tim-3 can inhibit ERK and NFκB p65 signaling; however, it failed to suppress the NFAT pathway. Further, we found that the NFAT activity in NK cells was much higher than that in CD4+ T cells, indicating that NFAT pathway is important for promotion of IFN-γ production by NK cells.

Conclusions
Thus, our data show that the expression of Tim-3 on NK cells is insufficient to inhibit IFN-γ production. Collectively, our findings demonstrate a potential mechanism of Tim-3 regulation of NK cells and a target for HIV infection immunotherapy.
A multispecies outbreak of carbapenem-resistant bacteria harboring the blaKPC gene in a non-classical transposon element
Authors: Wozniak Aniela , Figueroa Cristian , Moya-Flores Francisco , Guggiana Piero , Castillo Claudia , Rivas Lina , Munita José M. , García Patricia C. 
Published: April 2021

Abstract
Background
Klebsiella pneumoniae is the most frequent KPC-producing bacteria. The blaKPC gene is frequently embedded in Tn4401 transposon, and less frequently in non-Tn4401 elements (NTEKPC) variants I-III. The first case of KPC in the UC-CHRISTUS Clinical Hospital was detected in Pseudomonas aeruginosa. Soon after this event, KPC was detected in 2 additional Pseudomonas aeruginosa, 3 Escherichia coli, 3 Enterobacter cloacae, 3 Klebsiella pneumoniae, and 1 Citrobacter freundii, isolated from 6 different patients. We aimed to elucidate the possible mechanisms of genetic transfer and dissemination of the blaKPC gene among isolates of this multispecies outbreak. A molecular epidemiology analysis of the above mentioned clinical isolates (n = 13) through Multi-Locus Sequence Typing, plasmid analysis, Pulsed-Field Gel-Electrophoresis, and Whole-genome sequencing (WGS) was performed.

Results
High-risk sequence types were found: K. pneumoniae ST11, P. aeruginosa ST654, and E. cloacae ST114. All enterobacterial isolates were not clonal except for 3 E. coli isolated from the same patient. WGS analysis in 6 enterobacterial isolates showed that 4 of them had blaKPC embedded in a novel variant of NTEKPC designated NTEKPC-IIe. Upstream of blaKPC gene there was a 570 pb truncated blaTEM-1 gene followed by an insertion sequence that was 84% similar to ISEc63, a 4473 bp element of the Tn3 family. Downstream the blaKPC gene there was a truncated ISKpn6 gene, and the inverted repeat right sequence of Tn4401. The ISec63-like element together with the blaKPC gene plus Tn4401 remnants were inserted in the Tra operon involved in conjugative transfer of the plasmid. This NTE was carried in a broad host-range IncN plasmid. P. aeruginosa isolates carried blaKPC gene embedded in a typical Tn4401b transposon in a different plasmid, suggesting that there was no plasmid transfer between Enterobacteriaceae and P. aeruginosa as initially hypothesized.

Conclusions
Most enterobacterial isolates had blaKPC embedded in the same NTEKPC-IIe element, suggesting that this multispecies KPC outbreak was due to horizontal gene transfer rather than clonal spread. This poses a greater challenge to infection control measures often directed against containment of clonal spread.
Association between aging-dependent gut microbiome dysbiosis and dry eye severity in C57BL/6 male mouse model: a pilot study
Authors: Yoon Chang Ho , Ryu Jin Suk , Moon Jayoon , Kim Mee Kum 
Published: April 2021

Abstract
Background
While aging is a potent risk factor of dry eye disease, age-related gut dysbiosis is associated with inflammation and chronic geriatric diseases. Emerging evidence have demonstrated that gut dysbiosis contributes to the pathophysiology or exacerbation of ocular diseases including dry eye disease. However, the relationship between aging-related changes in gut microbiota and dry eye disease has not been elucidated. In this pilot study, we investigated the association between aging-dependent microbiome changes and dry eye severity in C57BL/6 male mice.

Results
Eight-week-old (8 W, n = 15), one-year-old (1Y, n = 10), and two-year-old (2Y, n = 8) C57BL/6 male mice were used. Dry eye severity was assessed by corneal staining scores and tear secretion. Bacterial genomic 16 s rRNA from feces was analyzed. Main outcomes were microbiome compositional differences among the groups and their correlation to dry eye severity. In aged mice (1Y and 2Y), corneal staining increased and tear secretion decreased with statistical significance. Gut microbiome α-diversity was not different among the groups. However, β-diversity was significantly different among the groups. In univariate analysis, phylum Firmicutes, Proteobacteria, and Cyanobacteria, Firmicutes/Bacteroidetes ratio, and genus Alistipes, Bacteroides, Prevotella, Paraprevotella, and Helicobacter were significantly related to dry eye severity. After adjustment of age, multivariate analysis revealed phylum Proteobacteria, Firmicutes/Bacteroidetes ratio, and genus Lactobacillus, Alistipes, Prevotella, Paraprevotella, and Helicobacter to be significantly associated with dry eye severity.

Conclusions
Our pilot study suggests that aging-dependent changes in microbiome composition are related to severity of dry eye signs in C57BL/6 male mice.
Spikelet movements, anther extrusion and pollen production in wheat cultivars with contrasting tendencies to cleistogamy
Authors: Zajączkowska Urszula , Denisow Bożena , Łotocka Barbara , Dołkin-Lewko Alicja , Rakoczy-Trojanowska Monika 
Published: April 2021

AbstractBackgroundCleistogamic flowers are a main barrier in pollen dispersal for cross-pollination necessary in wheat hybrid breeding. The aim of our study was to gain new knowledge on the biology of wheat flowering, in particular on the differences between the cleisto- and chasmogamic forms which has certainly cognitive significance, but it can also be used in practice when seeking a female and male ideotypes for cross hybridization.ResultsWe characterized the most significant features defining the flowering specificity in two wheat cultivars with contrasting tendency to cleistogamy: Piko (chasmogamous) and Dacanto (cleistogamous). In the field observations we assessed diurnal pattern of anther extrusion and anther extrusion capacity. For the first time we adapted the time lapse method for measuring kinetics of the spikelet movement and 3-D image correlation technique for the non-invasive measurements of potential deformations of the spikelet lemmas. We found that the two cultivars differ in the potential of pollen dispersion for-cross-pollination and in the spikelet kinetics. We also described some anatomical traits that can have potential functional role in floret opening. None of the cultivars showed any symptoms of lemma surface deformation.ConclusionsThe cleistogamic and chasmogamic wheat cultivars differ significantly in the potential for pollen dispersion for cross-pollination, which is mainly related to anther extrusion capacity. Although none of these features differentiated the cultivars clearly, we assume, based on spikelet kinetics and the lack of lemmas surface deformation, that the water transport and turgor of cells is essential for the floret opening and anther extrusion in wheat. The search for parental ideotype should be supported by marker assisted selection, e.g. based of polymorphisms in genes related to aquaporin biosynthesis.
Biochemical predictors of postoperative atrial fibrillation following cardiac surgery
Authors: Turkkolu Sevket T. , Selçuk Emre , Köksal Cengiz 
Published: April 2021

Abstract
Background
New-onset postoperative atrial fibrillation (POAF) is common after cardiac surgery. Early identification of its risk factors during the preoperative period would help in reducing the associated morbidity, mortality, and healthcare costs.

Aim of the study
This study aimed to identify the predictors of POAF following open cardiac surgery, with emphasis on biochemical parameters.

Methods
A total of 1191 patients with no preoperative atrial fibrillation (AF) and undergoing open cardiac surgery for any reason were included in this retrospective study. Data on clinical and biochemical parameters, the occurrence of new-onset AF, and its clinical course were retrieved from the hospital database.

Results
During the early postoperative period 330 patients (27.7%) developed atrial fibrillation, at median third postoperative day (range 1–6 days) and 217 (65.8%) responded to treatment. Multivariate analysis identified the following as the significant independent predictors of any POAF: EF < 60% (Odds ratio (OR), 2.6), valvular intervention (OR, 2.4), liver failure (OR, 2.4), diabetes (OR, 1.6), low hematocrit (OR, 2.1), low thrombocyte (OR, 5.6), low LDL (OR, 1.6), high direct bilirubin (OR, 2.0), low GFR (OR, 1.6), and high CRP (OR, 2.0). Following parameters emerged as significant independent predictors of persistent AF: EF < 60% (OR, 1.9), diabetes (OR, 2.1), COPD (OR, 1.8), previous cardiac surgery (OR, 3.1), valvular intervention (OR, 2.4), low hematocrit (OR, 1.9), low LDL (OR, 2.1), high HbA1c (OR, 2.0), and high CRP (OR, 2.7).

Conclusions
Certain parameters assessed during preoperative physical and laboratory examinations have the potential to be used as markers of POAF.