bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cancer multidisciplinary team meetings: impact of logistical challenges on communication and decision-making
Authors: Soukup Tayana , Lamb Benjamin W , Morbi Abigail , Shah Nisha J , Bali Anish , Asher Viren , Gandamihardja Tasha , Giordano Pasquale , Darzi Ara , Sevdalis Nick , Green James S A 
Published: August 2022

Abstract

Background
Multidisciplinary teams (MDTs) are widely used in cancer care. Recent research points to logistical challenges impeding MDT decision-making and dissatisfaction among members. This study sought to identify different types of logistical issues and how they impacted team processes.

Methods
This was a secondary analysis of a cross-sectional observational study. Three cancer MDTs (breast, colorectal, and gynaecological) were recruited from UK hospitals. Validated observational instruments were used to measure decision-making (Metrics of Observational Decision-making, MDT-MODe), communication (Bales' Interaction Process Analysis, Bales' IPA), and case complexity (Measure of Case Discussion Complexity, MeDiC), including logistical challenges (Measure of Case Discussion Complexity, MeDiC), across 822 case discussions from 30 videoed meetings. Descriptive analysis and paired samples t tests were used to identify and compare frequency of different types of logistical challenges, along with partial correlations, controlling for clinical complexity of cases, to understand how such issues related to the MDT decision-making and communication.

Results
A significantly higher frequency of administrative and process issues (affecting 30 per cent of cases) was seen compared with the frequency of equipment issues (affecting 5 per cent of cases; P &lt; 0.001) and the frequency of the attendance issues (affecting 16 per cent of cases; P &lt; 0.001). The frequency of the attendance issues was significantly higher than the frequency of equipment issues (P &lt; 0.001). Partial correlation analysis revealed that administrative and process issues, including attendance, were negatively correlated with quality of information (r = −0.15, P &lt; 0.001; r = −0.11, P &lt; 0.001), and equipment issues with the quality of contribution to meeting discussion (r = −0.14, P &lt; 0.001). More questioning and answering by MDT members was evident with the administrative and process issues (r = 0.21, P &lt; 0.001; r = 0.19, P &lt; 0.001). Some differences were observed in teams' socioemotional reactions to the administrative and process issues with the gynaecological MDT showing positive correlation with positive socioemotional reactions (r = 0.20, P &lt; 0.001), and the breast cancer MDT with negative socioemotional reactions (r = 0.17, P &lt; 0.001).

Conclusion
Administrative and process issues were the most frequent logistical challenges for the studied teams. Where diagnostic results were unavailable, and inadequate patient details provided, the quality of decision-making was reduced.
Exposure theory for learning complex networks with random walks
Authors: Klishin Andrei A , Bassett Dani S 
Published: August 2022

AbstractRandom walks are a common model for the exploration and discovery of complex networks. While numerous algorithms have been proposed to map out an unknown network, a complementary question arises: in a known network, which nodes and edges are most likely to be discovered by a random walker in finite time? Here, we introduce exposure theory, a statistical mechanics framework that predicts the learning of nodes and edges across several types of networks, including weighted and temporal, and show that edge learning follows a universal trajectory. While the learning of individual nodes and edges is noisy, exposure theory produces a highly accurate prediction of aggregate exploration statistics.
SLOAD: a comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis
Authors: Guo Li , Dou Yuyang , Xia Daoliang , Yin Zibo , Xiang Yangyang , Luo Lulu , Zhang Yuting , Wang Jun , Liang Tingming 
Published: August 2022

Abstract
Synthetic lethality has been widely concerned because of its potential role in cancer treatment, which can be harnessed to selectively kill cancer cells via identifying inactive genes in a specific cancer type and further targeting the corresponding synthetic lethal partners. Herein, to obtain cancer-specific synthetic lethal interactions, we aimed to predict genetic interactions via a pan-cancer analysis from multiple molecular levels using random forest and then develop a user-friendly database. First, based on collected public gene pairs with synthetic lethal interactions, candidate gene pairs were analyzed via integrating multi-omics data, mainly including DNA mutation, copy number variation, methylation and mRNA expression data. Then, integrated features were used to predict cancer-specific synthetic lethal interactions using random forest. Finally, SLOAD (http://www.tmliang.cn/SLOAD) was constructed via integrating these findings, which was a user-friendly database for data searching, browsing, downloading and analyzing. These results can provide candidate cancer-specific synthetic lethal interactions, which will contribute to drug designing in cancer treatment that can promote therapy strategies based on the principle of synthetic lethality.
Database URL http://www.tmliang.cn/SLOAD/
Cost effectiveness of population screening vs. no screening for cardiovascular disease: the Danish Cardiovascular Screening trial (DANCAVAS)
Authors: Søgaard Rikke , Diederichsen Axel Cosmus Pyndt , Rasmussen Lars M , Lambrechtsen Jess , Steffensen Flemming H , Frost Lars , Egstrup Kenneth , Urbonaviciene Grazina , Busk Martin , Lindholt Jes S 
Published: August 2022

Abstract

Aims
A recent trial has shown that screening of men for cardiovascular disease (CVD) may reduce all-cause mortality. This study assesses the cost effectiveness of such screening vs. no screening from the perspective of European healthcare systems.

Methods and results
Randomized controlled trial-based cost-effectiveness evaluation with a mean 5.7 years of follow-up. Screening was based on low-dose computed tomography to detect coronary artery calcification and aortic/iliac aneurysms, limb blood pressure measurement to detect peripheral artery disease and hypertension, telemetric assessment of the heart rhythm to detect atrial fibrillation, and measurements of the cholesterol and HgbA1c levels. Censoring-adjusted incremental costs, life years (LY), and quality-adjusted LY (QALY) were estimated and used for cost-effectiveness analysis. The incremental cost of screening for the entire health care sector was €207 [95% confidence interval (CI) −24; 438, P = 0.078] per invitee for which gains of 0.019 LY (95% CI −0.007; 0.045, P = 0.145) and 0.023 QALY (95% CI −0.001; 0.046, P = 0.051) were achieved. The corresponding incremental cost-effectiveness ratios were of €10 812 per LY and €9075 per QALY, which would be cost effective at probabilities of 0.73 and 0.83 for a willingness to pay of €20 000. Assessment of population heterogeneity showed that cost effectiveness could be more attractive for younger men without CVD at baseline.

Conclusions
Comprehensive screening for CVD is overall cost effective at conventional thresholds for willingness to pay and also competitive to the cost effectiveness of common cancer screening programmes. The screening target group, however, needs to be settled.
Vegetation drives the response of the active fraction of the rhizosphere microbial communities to soil warming in Antarctic vascular plants
Authors: Parada-Pozo Génesis , Bravo León A , Sáez Patricia L , Cavieres Lohengrin A , Reyes-Díaz Marjorie , Abades Sebastián , Alfaro Fernando D , De la Iglesia Rodrigo , Trefault Nicole 
Published: August 2022

Abstract
In the Antarctic Peninsula, increases in mean annual temperature are associated with the coverage and population density of the two Antarctic vascular plant species—Deschampsia antarctica and Colobanthus quitensis—potentially modifying critical soil processes. In this study, we characterized the diversity and community composition of active microorganisms inhabiting the vascular plant rhizosphere in two sites with contrasting vegetation cover in King George Island, Western Antarctic Peninsula. We assessed the interplay between soil physicochemical properties and microbial diversity and composition, evaluating the effect of an in situ experimental warming on the microbial communities of the rhizosphere from D. antarctica and C. quitensis. Bacteria and Eukarya showed different responses to warming in both sites, and the effect was more noticeable in microbial eukaryotes from the low vegetation site. Furthermore, important changes were found in the relative abundance of Tepidisphaerales (Bacteria) and Ciliophora (Eukarya) between warming and control treatments. Our results showed that rhizosphere eukaryal communities are more sensitive to in situ warming than bacterial communities. Overall, our results indicate that vegetation drives the response of the active fraction of the microbial communities from the rhizosphere of Antarctic vascular plants to soil warming.
Identification of upregulated genes in Tricholoma matsutake mycorrhiza
Authors: Sakamoto Yuichi , Sato Shiho , Takizawa Miyuki , Narimatsu Maki 
Published: August 2022

Abstract
Many plant roots associate with fungi to form mycorrhizae; tree roots especially associate with ectomycorrhizal fungi, such as Tricholoma species. Tricholoma matsutake is an economically important fungus in Asian countries and usually inhabits forests primarily composed of Pinus densiflora (Japanese red pine). In this study, to understand the mycorrhizal association between T. matsutake and P. densiflora, genes specifically expressed in mycorrhiza compared with those expressed in mycelia and fruiting bodies were identified by RNA-seq. This revealed that genes for chromatin, proteasomes, signal transduction, pheromones, cell surface receptors, cytoskeleton, RNA processing and transporters from T. matsutake were highly expressed in mycorrhiza. It also identified 35 mycorrhiza-induced small secreted proteins (MiSSPs) that were highly expressed in mycorrhiza. Meanwhile, genes for proteases, defence-related proteins, cell-wall degradation, signal transduction, pinene synthesis, plant hormones and transporters from P. densiflora were highly expressed in mycorrhiza. These genes may be involved in mycorrhizal formation and maintenance. A MiSSP, 1460819, was highly expressed in mycorrhiza, and this expression was maintained for 24 months. These results provide insight into the mycorrhizal association between T. matsutake and P. densiflora.
The mIAA7 degron improves auxin-mediated degradation inCaenorhabditis elegans
Authors: Sepers Jorian J , Verstappen Noud H M , Vo An A , Ragle James Matthew , Ruijtenberg Suzan , Ward Jordan D , Boxem Mike 
Published: August 2022

AbstractAuxin-inducible degradation is a powerful tool for the targeted degradation of proteins with spatiotemporal control. One limitation of the auxin-inducible degradation system is that not all proteins are degraded efficiently. Here, we demonstrate that an alternative degron sequence, termed mIAA7, improves the efficiency of degradation in Caenorhabditis elegans, as previously reported in human cells. We tested the depletion of a series of proteins with various subcellular localizations in different tissue types and found that the use of the mIAA7 degron resulted in faster depletion kinetics for 5 out of 6 proteins tested. The exception was the nuclear protein HIS-72, which was depleted with similar efficiency as with the conventional AID* degron sequence. The mIAA7 degron also increased the leaky degradation for 2 of the tested proteins. To overcome this problem, we combined the mIAA7 degron with the C. elegans AID2 system, which resulted in complete protein depletion without detectable leaky degradation. Finally, we show that the degradation of ERM-1, a highly stable protein that is challenging to deplete, could be improved further by using multiple mIAA7 degrons. Taken together, the mIAA7 degron further increases the power and applicability of the auxin-inducible degradation system. To facilitate the generation of mIAA7-tagged proteins using CRISPR/Cas9 genome engineering, we generated a toolkit of plasmids for the generation of dsDNA repair templates by PCR.
The Drosophila BEAF insulator protein interacts with the polybromo subunit of the PBAP chromatin remodeling complex
Authors: McKowen J Keller , Avva Satya V S P , Maharjan Mukesh , Duarte Fabiana M , Tome Jacob M , Judd Julius , Wood Jamie L , Negedu Sunday , Dong Yunkai , Lis John T , Hart Craig M 
Published: August 2022

Abstract
The Drosophila Boundary Element-Associated Factor of 32 kDa (BEAF) binds in promoter regions of a few thousand mostly housekeeping genes. BEAF is implicated in both chromatin domain boundary activity and promoter function, although molecular mechanisms remain elusive. Here, we show that BEAF physically interacts with the polybromo subunit (Pbro) of PBAP, a SWI/SNF-class chromatin remodeling complex. BEAF also shows genetic interactions with Pbro and other PBAP subunits. We examine the effect of this interaction on gene expression and chromatin structure using precision run-on sequencing and micrococcal nuclease sequencing after RNAi-mediated knockdown in cultured S2 cells. Our results are consistent with the interaction playing a subtle role in gene activation. Fewer than 5% of BEAF-associated genes were significantly affected after BEAF knockdown. Most were downregulated, accompanied by fill-in of the promoter nucleosome-depleted region and a slight upstream shift of the +1 nucleosome. Pbro knockdown caused downregulation of several hundred genes and showed a correlation with BEAF knockdown but a better correlation with promoter-proximal GAGA factor binding. Micrococcal nuclease sequencing supports that BEAF binds near housekeeping gene promoters while Pbro is more important at regulated genes. Yet there is a similar general but slight reduction of promoter-proximal pausing by RNA polymerase II and increase in nucleosome-depleted region nucleosome occupancy after knockdown of either protein. We discuss the possibility of redundant factors keeping BEAF-associated promoters active and masking the role of interactions between BEAF and the Pbro subunit of PBAP in S2 cells. We identify Facilitates Chromatin Transcription (FACT) and Nucleosome Remodeling Factor (NURF) as candidate redundant factors.
Visceral adipose volume is correlated with surgical tissue fibrosis in Crohn’s disease of the small bowel
Authors: Yuan Gang , He Yao , Cao Qing-Hua , Tang Mi-Mi , Xie Zong-Lin , Qiu Yun , Zeng Zhi-Rong , Peng Sui , Chen Min-Hu 
Published: August 2022

Abstract

Background
This study explored the diagnostic performance of visceral adiposity to predict the degree of intestinal inflammation and fibrosis.

Methods
The patients with Crohn’s disease (CD) who underwent surgical small bowel resection at the First Affiliated Hospital of Sun Yat-sen University (Guangzhou, China) between January 2007 and December 2017 were enrolled. We evaluated the intestinal imaging features of computed tomography enterography (CTE), including mesenteric inflammatory fat stranding, the target sign, mesenteric hypervascularity, bowel wall thickening, lymphadenopathy, stricture diameter, and maximal upstream diameter. We used A.K. software (Artificial Intelligence Kit, version 1.1) to calculate the visceral fat (VF) and subcutaneous fat (SF) volumes at the third lumbar vertebra level. Pathological tissue information was recorded. Diagnostic models were established based on the multivariate regression analysis results, and their effectiveness was evaluated by area under the curve (AUC) and decision curve analyses.

Results
Overall, 48 patients with CD were included in this study. The abdominal VF/SF volume ratio (odds ratio, 1.20; 95% confidence interval, 1.05–1.38; P = 0.009) and the stenosis diameter/upstream intestinal dilatation diameter (ND) ratio (odds ratio, 0.90; 95% confidence interval, 0.82–0.99; P = 0.034) were independent risk factors for the severe fibrosis of the small intestine. The AUC values of the VF/SF ratio, the ND ratio, and their combination were 0.760, 0.673, and 0.804, respectively. The combination of the VS/SF volume ratio and ND ratio achieved the highest net benefit on the decision curve.

Conclusion
The VF volume on CTE can reflect intestinal fibrosis. The combination of the VF/SF volume ratio and ND ratio of CD patients assessed using CTE can help predict severe fibrosis stenosis of the small intestine.
The thermal state of Volgo–Uralia from Bayesian inversion of surface heat flow and temperature
Authors: Ognev Igor , Ebbing Jörg , Lösing Mareen , Nurgaliev Danis 
Published: August 2022

SUMMARY
Volgo–Uralia is the easternmost segment of the East European Craton. It accommodates the Volga–Ural petroleum province where the maturity of source rocks is tightly related to the temperature distribution in the crust. Numerous heat flow and temperature measurements have been reported for this region. However, no consistent geothermal model was presented for the Volgo–Uralian crustal block so far. In this study, we present a novel model of the Volgo–Uralian geothermal field where we aim to reconcile the reported heat flow and temperature data.
The main goal of the study is to explore lateral variations of the unknown thermal parameters within Volgo–Uralia. For this purpose, we applied a Bayesian Markov Chain Monte Carlo approach where we used the known surface heat flow, surface temperature, lithosphere–asthenosphere boundary temperature and thicknesses of the Earth's lithospheric and crustal layers as input and investigated the possible lateral variations of crustal and lithospheric mantle thermal conductivities, crustal heat production and mantle heat flow. We implemented this methodology for a single-layer and multilayer crust and validated the obtained geothermal models with existing subsurface temperature measurements for the region.
The results show that the Volgo–Uralian subcraton is characterized by significant lateral variations of crustal radiogenic heat production (RHP) and mantle heat flow. The variations of crustal and lithospheric mantle thermal conductivities are less pronounced. According to our model, the surface heat flow distribution is controlled mostly by crustal RHP which accounts for more than half of Volgo–Uralian surface heat flow. Validation of the models shows that single-layer and multilayer crustal models give roughly the same fit of measured and modelled temperatures. This implies that a single-layer crust with constant RHP can be considered a sufficient approximation for regional-scale geothermal modelling.
Gradient-constrained model parametrization in 3-D compact full waveform inversion
Authors: Xu Linan , Winner Valérie , Maurer Hansruedi 
Published: August 2022

SUMMARY
Seismic full waveform inversion (FWI) can produce high-resolution subsurface models by using the complete information of the observed data, but its computational cost can be prohibitively large, particularly for realistically sized 3-D problems. Due to its relatively fast convergence rate, it would be beneficial when Gauss–Newton algorithms could be employed for such problems, but the approximate Hessian matrix required for Gauss–Newton schemes would be too large to be kept in computer memory. Therefore, compact FWI (CFWI) was introduced, with which the number of inversion model parameters can be reduced substantially, and thus the amenable properties of Gauss–Newton inversion schemes can be exploited. Here, we extend the CFWI technology to 3-D problems. Since the spatial coverage of sources and receivers is generally sparser in 3-D (compared with 2-D problems), the total number of model parameters can become very large, and adequate model parametrization is particularly important for 3-D problems. Furthermore, we introduce gradient constrained CFWI (GC-CFWI). This is a novel development that allows the number of model parameters to be further reduced significantly. CFWI employs hierarchical model parametrizations that can be, for example, based on spatial Fourier transforms or wavelet transforms. Only those parameters of such a hierarchical parametrization are retained that exhibit a sufficiently high formal resolution. With GC-CFWI, it is further checked which of these parameters are expected to be changed significantly during a single CFWI iteration. Only parameters with a potentially significant adjustment are retained in the inversion parameter space. We have performed numerical experiments to analyse the performance of CFWI and GC-CFWI for 3-D acoustic FWI problems. For that purpose, we have considered a crosshole geometry including four boreholes and a surface deployment of sources and receivers. As parametrizations, we have considered the Fourier-based Hartley transform and the Haar wavelet transform. For both set-ups, the number of inversion model parameters could be reduced to about 20 per cent for the crosshole model and to about 10 per cent for the surface-based acquisition using CFWI. With GC-CFWI, a further reduction of about 50 per cent for both experimental set-ups could be achieved. The different results for the crosshole and surface-based set-ups indicate that an optimal model parametrization is tightly coupled to the experimental layout.
Impact of the COVID-19 pandemic on total, sex- and age-specific all-cause mortality in 20 countries worldwide during 2020: results from the C-MOR project
Authors: Demetriou Christiana A , Achilleos Souzana , Quattrocchi Annalisa , Gabel John , Critselis Elena , Constantinou Constantina , Nicolaou Nicoletta , Ambrosio Giuseppe , Bennett Catherine M , Le Meur Nolwenn , Critchley Julia A , Mortensen Laust Hvas , Rodriguez-Llanes Jose Manuel , Chong Mario , Denissov Gleb , Klepac Petra , Goldsmith Lucy P , Costa Antonio José Leal , Hagen Terje P , Chan Sun Marie , Huang Qian , Pidmurniak Nataliia , Zucker Inbar , Cuthbertson Joseph , Burström Bo , Barron Manuel , Eržen Ivan , Stracci Fabrizio , Calmon Wilson , Martial Cyndy , Verstiuk Olesia , Kaufman Zalman , Tao Wenjing , Kereselidze Maia , Chikhladze Nino , Zimmermann Claudia , Schernhammer Eva , Polemitis Antonis , Charalambous Andreas 
Published: August 2022

Abstract

Background
To understand the impact of the COVID-19 pandemic on mortality, this study investigates overall, sex- and age-specific excess all-cause mortality in 20 countries, during 2020.

Methods
Total, sex- and age-specific weekly all-cause mortality for 2015–2020 was collected from national vital statistics databases. Excess mortality for 2020 was calculated by comparing weekly 2020 observed mortality against expected mortality, estimated from historical data (2015–2019) accounting for seasonality, long- and short-term trends. Crude and age-standardized rates were analysed for total and sex-specific mortality.

Results
Austria, Brazil, Cyprus, England and Wales, France, Georgia, Israel, Italy, Northern Ireland, Peru, Scotland, Slovenia, Sweden, and the USA displayed substantial excess age-standardized mortality of varying duration during 2020, while Australia, Denmark, Estonia, Mauritius, Norway, and Ukraine did not. In sex-specific analyses, excess mortality was higher in males than females, except for Slovenia (higher in females) and Cyprus (similar in both sexes). Lastly, for most countries substantial excess mortality was only detectable (Austria, Cyprus, Israel, and Slovenia) or was higher (Brazil, England and Wales, France, Georgia, Italy, Northern Ireland, Sweden, Peru and the USA) in the oldest age group investigated. Peru demonstrated substantial excess mortality even in the &lt;45 age group.

Conclusions
This study highlights that excess all-cause mortality during 2020 is context dependent, with specific countries, sex- and age-groups being most affected. As the pandemic continues, tracking excess mortality is important to accurately estimate the true toll of COVID-19, while at the same time investigating the effects of changing contexts, different variants, testing, quarantine, and vaccination strategies.