bluuebunny/crossref_metadata_2025_split huggingface dataset:
Energy‐based graph convolutional networks for scoring protein docking models
Authors: Cao Yue , Shen Yang 
Published: March 2020

AbstractStructural information about protein‐protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational alternative for such information. However, ranking near‐native docked models high among a large number of candidates, often known as the scoring problem, remains a critical challenge. Moreover, estimating model quality, also known as the quality assessment problem, is rarely addressed in protein docking. In this study, the two challenging problems in protein docking are regarded as relative and absolute scoring, respectively, and addressed in one physics‐inspired deep learning framework. We represent protein and complex structures as intra‐ and inter‐molecular residue contact graphs with atom‐resolution node and edge features. And we propose a novel graph convolutional kernel that aggregates interacting nodes’ features through edges so that generalized interaction energies can be learned directly from 3D data. The resulting energy‐based graph convolutional networks (EGCN) with multihead attention are trained to predict intra‐ and inter‐molecular energies, binding affinities, and quality measures (interface RMSD) for encounter complexes. Compared to a state‐of‐the‐art scoring function for model ranking, EGCN significantly improves ranking for a critical assessment of predicted interactions (CAPRI) test set involving homology docking; and is comparable or slightly better for Score_set, a CAPRI benchmark set generated by diverse community‐wide docking protocols not known to training data. For Score_set quality assessment, EGCN shows about 27% improvement to our previous efforts. Directly learning from 3D structure data in graph representation, EGCN represents the first successful development of graph convolutional networks for protein docking.
An estimate on in‐construction differential settlement of super high‐rise frame core–tube buildings
Authors: He Zheng , Lu Yi , Liu Fengning , Pan Feng , He Shuaishuai 
Published: March 2020

SUMMARYTo physically identify the mechanisms behind the development of in‐construction settlement of super high‐rise frame core–tube buildings, a simplified approach is developed by the full understanding about the typical structural layouts, specific construction feature, and load transfer path of those buildings as well as time‐dependent effects. With the reference to several typical structural layouts, a simplified one‐bay multistory model is developed that consists of two overall vertical components and horizontal components representing the exterior columns, core tubes, and beams (or mega trusses), respectively, in those super high‐rise buildings. Based on this model, a simplified approach with a so‐called “global–local” strategy is proposed to account for the difference in the settlement of the corner columns and side columns. The leading construction and final screwing at the rigid connections between beams (or trusses) and exterior columns, which are commonly implemented during the construction of those buildings, are seriously addressed in the simplified approach, as well as strengthened floors and time‐dependent effects. The applicability and accuracy of the proposed approach is demonstrated by a 128‐story 606‐m‐level super high‐rise frame core–tube building. The proposed simplified approach can be helpful for the development of preliminary construction schemes and the control strategy for differential settlement.
Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue
Authors: Caputo Tiziana , Tran Van Du T. , Bararpour Nasim , Winkler Carine , Aguileta Gabriela , Trang Khanh Bao , Giordano Attianese Greta M. P. , Wilson Anne , Thomas Aurelien , Pagni Marco , Guex Nicolas , Desvergne Béatrice , Gilardi Federica 
Published: March 2020

AbstractChronic inflammation that affects primarily metabolic organs, such as white adipose tissue (WAT), is considered as a major cause of human obesity-associated co-morbidities. However, the molecular mechanisms initiating this inflammation in WAT are poorly understood. By combining transcriptomics, ChIP-seq and modeling approaches, we studied the global early and late responses to a high-fat diet (HFD) in visceral (vWAT) and subcutaneous (scWAT) AT, the first being more prone to obesity-induced inflammation. HFD rapidly triggers proliferation of adipocyte precursors within vWAT. However, concomitant antiadipogenic signals limit vWAT hyperplastic expansion by interfering with the differentiation of proliferating adipocyte precursors. Conversely, in scWAT, residing beige adipocytes lose their oxidizing properties and allow storage of excessive fatty acids. This phase is followed by tissue hyperplastic growth and increased angiogenic signals, which further enable scWAT expansion without generating inflammation. Our data indicate that scWAT and vWAT differential ability to modulate adipocyte number and differentiation in response to obesogenic stimuli has a crucial impact on the different susceptibility to obesity-related inflammation of these adipose tissue depots.
BRAID GROUP ACTION AND ROOT VECTORS FOR THE q-ONSAGER ALGEBRA
Authors: BASEILHAC PASCAL , KOLB STEFAN 
Published: March 2020

AbstractWe define two algebra automorphisms Ͳ0 and Ͳ1 of the q-Onsager algebra $$ {\mathcal{B}}_c $$Bc, which provide an analog of G. Lusztig's braid group action for quantum groups. These automorphisms are used to define root vectors which give rise to a PBW basis for $$ {\mathcal{B}}_c $$Bc. We show that the root vectors satisfy q-analogs of Onsager's original commutation relations. The paper is much inspired by I. Damiani's construction and investigation of root vectors for the quantized enveloping algebra of $$ \hat{\mathfrak{s}{\mathfrak{l}}_2} $$sl2̂.
Layout optimization of simplified trusses using mixed integer linear programming with runtime generation of constraints
Authors: Fairclough H. , Gilbert M. 
Published: March 2020

AbstractTraditional truss layout optimization employing the ground structure method will often generate layouts that are too complex to fabricate in practice. To address this, mixed integer linear programming can be used to enforce buildability constraints, leading to simplified truss forms. Limits on the number of joints in the structure and/or the minimum angle between connected members can be imposed, with the joints arising from crossover of pairs of members accounted for. However, in layout optimization, the number of constraints arising from ‘crossover joints’ increases rapidly with problem size, along with computational expense. To address this, crossover constraints are here dynamically generated and added at runtime only as required (so-called lazy constraints); speedups of more than 20 times are observed whilst ensuring that there is no loss of solution quality. Also, results from the layout optimization step are shown to provide a suitable starting point for a non-linear geometry optimization step, enabling results to be obtained that are in agreement with literature solutions. It is also shown that symmetric problems may not have symmetric optimal solutions, and that multiple distinct and equally optimal solutions may be found.
The Achilles tendon Total Rupture Score is a responsive primary outcome measure: an evaluation of the Dutch version including minimally important change
Authors: Dams Olivier C. , Reininga Inge H. F. , Zwerver Johannes , Diercks Ronald L. , van den Akker-Scheek Inge 
Published: March 2020

Abstract
Purpose
Aim of this study was to evaluate the responsiveness of the Dutch version of the Achilles tendon Total Rupture Score (ATRS-NL).

Methods
Patients (N = 47) completed the ATRS-NL at 3 and 6 months after Achilles tendon rupture (ATR). Additionally, they filled out the Euroqol-5D-5L (EQ-5D-5L) and Global Rating of Change Score (GRoC). Effect sizes (ES) and standardized response means (SRM) were calculated. The anchor-based method for determining the minimally important change (MIC) was used. GRoC and improvement on the items mobility and usual activities on the EQ-5D-5L served as external criteria. The scores on these anchors were used to categorize patients’ physical functioning as improved or unchanged between 3 and 6 months after ATR. Receiver operating curve (ROC) analysis was performed, with the calculation of the area under the ROC curve (AUC) and the estimation of MIC values using the optimal cut-off points.

Results
There was a large change (ES: 1.58) and good responsiveness (SRM: 1.19) of the ATRS-NL between 3 and 6 months after ATR. Using ROC analysis, the MIC values ranged from 13.5 to 28.5 for reporting improvement on EQ-5D-5L mobility and GRoC, respectively. The AUC of improvement on mobility and improvement on GRoC were > 0.70.

Conclusion
The ATRS-NL showed good responsiveness in ATR patients between 3 and 6 months after injury. Use of this questionnaire is recommended in clinical follow-up and longitudinal research of ATR patients. MIC values of 13.5 and 28.5 are recommended to consider ATR patients as improved and greatly improved between 3 and 6 months after ATR.

Level of evidence
II.
The effect of bank branch closures on new firm formation: the Swedish case
Authors: Ho Cynthia Sin Tian , Berggren Björn 
Published: March 2020

AbstractIn this paper, the effect of local bank branch closures on new firm formation in Sweden is analysed using a panel database that captures the geographical locations of all Swedish bank branches in 2007 and 2013.
The previous research has shown that the further a firm is located away from the bank, the higher the monitoring costs will be for the banks. Furthermore, an increase in the distance to the banks will also increase information asymmetry because of the banks’ eroded ability to collect and analyse soft information. Due to the high risks associated with the lack of information and uncertainty, banks might not be as willing to extend credits to a distant firm compared to a nearby firm. Using spatial econometric analysis at a municipal level, it is shown that bank proximity to firms, unemployment rate, industry structures, income growth, change in housing price and percentage of immigrants are vital for new firm formation in Sweden. From the spatial Durbin model with fixed effects, an increase in the weighted distance to the nearest bank branches is shown to affect new firm formation negatively.
Blow-ups and infinitesimal automorphisms of CR-manifolds
Authors: Kruglikov Boris 
Published: March 2020

AbstractFor a real-analytic connected CR-hypersurfaceMof CR-dimension$$n\geqslant 1$$n⩾1having a point of Levi-nondegeneracy the following alternative is demonstrated for its symmetry algebra$$\mathfrak {s}={\mathfrak {s}}(M)$$s=s(M): (i) either$$\dim {\mathfrak {s}}=n^2+4n+3$$dims=n2+4n+3andMis spherical everywhere; (ii) or$$\dim {\mathfrak {s}}\leqslant n^2+2n+2+\delta _{2,n}$$dims⩽n2+2n+2+δ2,nand in the case of equalityMis spherical and has fixed signature of the Levi form in the complement to its Levi-degeneracy locus. A version of this result is proved for the Lie group of global automorphisms ofM. Explicit examples of CR-hypersurfaces and their infinitesimal and global automorphisms realizing the bound in (ii) are constructed. We provide many other models with large symmetry using the technique of blow-up, in particular we realize all maximal parabolic subalgebras of the pseudo-unitary algebras as a symmetry.
A critical review of recent trends, and a future perspective of optical spectroscopy as PAT in biopharmaceutical downstream processing
Authors: Rolinger Laura , Rüdt Matthias , Hubbuch Jürgen 
Published: March 2020

AbstractAs competition in the biopharmaceutical market gets keener due to the market entry of biosimilars, process analytical technologies (PATs) play an important role for process automation and cost reduction. This article will give a general overview and address the recent innovations and applications of spectroscopic methods as PAT tools in the downstream processing of biologics. As data analysis strategies are a crucial part of PAT, the review discusses frequently used data analysis techniques and addresses data fusion methodologies as the combination of several sensors is moving forward in the field. The last chapter will give an outlook on the application of spectroscopic methods in combination with chemometrics and model predictive control (MPC) for downstream processes.
The role of fatal family history and mode of inheritance in prostate cancer for long-term outcomes following radical prostatectomy
Authors: Meissner Valentin H. , Strüh Jamila G. H. , Kron Martina , Liesenfeld Lea A. , Kranz Stephanie , Gschwend Jürgen E. , Herkommer Kathleen 
Published: March 2020

Abstract
Purpose
To determine whether fatal family history (FFH) or mode of inheritance in prostate cancer (PCa) has an impact on long-term outcomes following radical prostatectomy (RP).

Methods
1076 PCa patients after RP with at least one deceased first-degree relative with PCa were included and stratified by FFH (four subgroups: fraternal, paternal, multiple, and none) and by mode of inheritance (two subgroups: male to male, non-male to male). We compared clinicopathological characteristics between subgroups with Fisher’s exact or Chi-square tests. Biochemical recurrence-free survival (BRFS) and cancer-specific survival (CSS) were analyzed using the method of Kaplan and Meier. Simple and multiple Cox regression with backward elimination were performed to select prognostic factors for BRFS and CSS.

Results
Median age at surgery was 63.3 (range 35.9–79.4) years. The overall Kaplan–Meier estimated BRFS rate at 10 and 15 years was 65.6% and 57.0%, respectively. The overall Kaplan–Meier estimated CSS rate at 10 and 15 years was 98.1% and 95.7%, respectively. Neither FFH nor mode of inheritance were factors associated with worse BRFS. However, in multiple Cox regression, paternal FFH was an important prognostic factor for a better CSS (HR 0.19, CI 0.05–0.71, p = 0.014) compared to non-FFH.

Conclusion
FFH and mode of inheritance do not seem to be prognostic factors of worse long-term outcomes following RP. Rather, a paternal FFH was associated with a better CSS; however, the reasons remain unclear. Nevertheless, patients after RP and FFH could be reassured that their own PCa diagnosis is not associated with a worse long-term outcome.
Components of one-carbon metabolism and renal cell carcinoma: a systematic review and meta-analysis
Authors: Clasen Joanna L. , Heath Alicia K. , Scelo Ghislaine , Muller David C. 
Published: March 2020

Abstract
Purpose
Little is known about the aetiology of renal cell carcinoma (RCC). Components of one-carbon (1C) metabolism, which are required for nucleotide synthesis and methylation reactions, may be related to risk of RCC but existing evidence is inconclusive. We conducted a systematic review and independent exposure-specific meta-analyses of dietary intake and circulating biomarkers of 1C metabolites and RCC risk.

Methods
Medline and Embase databases were searched for observational studies investigating RCC or kidney cancer incidence or mortality in relation to components of 1C metabolism and 12 eligible articles were included in the meta-analyses. We used Bayesian meta-analyses to estimate summary relative risks (RRs) and 95% credible intervals (CrIs) comparing the highest versus lowest categories as well as the between-study heterogeneity.

Results
We did not find convincing evidence of an association between any exposure (riboflavin, vitamin B6, folate, vitamin B12, methionine, homocysteine, choline, or betaine) and RCC risk. However, vitamin B6 biomarker status did have a protective (RR = 0.62) but imprecise (95% CrI 0.39–1.14) effect estimate and folate intake had a notable association as well (RR = 0.85, 95% CrI 0.71–1.01).

Conclusion
There was a lack of precision due largely to the low number of studies. Further investigation is warranted, especially for folate and vitamin B6, which had consistent suggestive evidence of a protective effect for both dietary intake and biomarker status. A unique strength of this review is the use of Bayesian meta-analyses which allowed for robust estimation of between-study heterogeneity.
Carbonic anhydrases CA1 and CA4 function in atmospheric CO2-modulated disease resistance
Authors: Zhou Yeling , Vroegop-Vos Irene A. , Van Dijken Anja J. H. , Van der Does Dieuwertje , Zipfel Cyril , Pieterse Corné M. J. , Van Wees Saskia C. M. 
Published: March 2020

Abstract
Main conclusion
Carbonic anhydrases CA1 and CA4 attenuate plant immunity and can contribute to altered disease resistance levels in response to changing atmospheric CO2 conditions.

Abstract
β-Carbonic anhydrases (CAs) play an important role in CO2 metabolism and plant development, but have also been implicated in plant immunity. Here we show that the bacterial pathogen Pseudomonas syringae and application of the microbe-associated molecular pattern (MAMP) flg22 repress CA1 and CA4 gene expression in Arabidopsis thaliana. Using the CA double-mutant ca1ca4, we provide evidence that CA1 and CA4 play an attenuating role in pathogen- and flg22-triggered immune responses. In line with this, ca1ca4 plants exhibited enhanced resistance against P. syringae, which was accompanied by an increased expression of the defense-related genes FRK1 and ICS1. Under low atmospheric CO2 conditions (150 ppm), when CA activity is typically low, the levels of CA1 transcription and resistance to P. syringae in wild-type Col-0 were similar to those observed in ca1ca4. However, under ambient (400 ppm) and elevated (800 ppm) atmospheric CO2 conditions, CA1 transcription was enhanced and resistance to P. syringae reduced. Together, these results suggest that CA1 and CA4 attenuate plant immunity and that differential CA gene expression in response to changing atmospheric CO2 conditions contribute to altered disease resistance levels.
Stabilized mixed formulation for phase-field computation of deviatoric fracture in elastic and poroelastic materials
Authors: Gavagnin Claudio , Sanavia Lorenzo , De Lorenzis Laura 
Published: March 2020

AbstractIn the numerical approximation of phase-field models of fracture in porous media with the finite element method, the problem of numerical locking may occur. The causes can be traced both to the hydraulic and to the mechanical properties of the material. In this work we present a mixed finite element formulation for phase-field modeling of brittle fracture in elastic solids based on a volumetric-deviatoric energy split and its extension to water saturated porous media. For the latter, two alternative mixed formulations are proposed. To be able to use finite elements with linear interpolation for all the field variables, which violates the Ladyzenskaja–Babuska–Brezzi condition, a stabilization technique based on polynomial pressure projections, proposed and tested by previous authors in fluid mechanics and poromechanics, is introduced. We develop an extension of this stabilization to phase-field mixed models of brittle fracture in porous media. Several numerical examples are illustrated, to show the occurrence of different locking phenomena and to compare the solutions obtained with different unstable, stable and stabilized low order finite elements.
A low-distortion mesh moving method based on fiber-reinforced hyperelasticity and optimized zero-stress state
Authors: Takizawa Kenji , Tezduyar Tayfun E. , Avsar Reha 
Published: March 2020

AbstractIn computation of flow problems with moving boundaries and interfaces, including fluid–structure interaction, moving-mesh methods enable mesh-resolution control near the interface and consequently high-resolution representation of the boundary layers. Good moving-mesh methods require good mesh moving methods. We introduce a low-distortion mesh moving method based on fiber-reinforced hyperelasticity and optimized zero-stress state (ZSS). The method has been developed targeting isogeometric discretization but is also applicable to finite element discretization. With the large-deformation mechanics equations, we can expect to have a unique mesh associated with each step of the boundary or interface motion. With the fibers placed in multiple directions, we stiffen the element in those directions for the purpose of reducing the distortion during the mesh deformation. We optimize the ZSS by seeking orthogonality of the parametric directions, by mesh relaxation, and by making the ZSS time-dependent as needed. We present 2D and 3D test computations with isogeometric discretization. The computations show that the mesh moving method introduced performs well.
TcMEP threshold change is superior to A-train detection when predicting facial nerve outcome in CPA tumour surgery
Authors: Hendriks Tom , Kunst Henricus P. M. , Huppelschoten Maarten , Doorduin Jonne , Ter Laan Mark 
Published: March 2020

Abstract
Object
Surgery of tumours in the cerebellopontine angle (CPA) can lead to loss of facial nerve function. Different methods of intra-operative nerve monitoring (IOM) (including free-running EMG, direct nerve stimulation and transcranial motor evoked potentials (TcMEP)) have been used to predict facial nerve outcome during surgery. Recent research has shown TcMEP threshold increase and the occurrence of A-trains on the EMG to have great potential in doing so. This study compares these two methods and correlates them to House-Brackmann (HB) scores post-op in patients with tumours in the cerebellopontine angle.

Method
Forty-three patients (one was operated twice) with large CPA tumours treated surgically in the Radboud University Medical Center between 2015 and 2019 were included in this study. During surgery, TcMEP threshold increases and A-train activity were measured. Because our treatment paradigm aims at facial nerve preservation (accepting residual tumour), TcMEP threshold increase of over 20 mA or occurrence of A-trains were considered as warning signs and used as a guide for terminating surgery. HB scores were measured post-op, at 6 weeks, 6 months and 1 year after surgery. Spearman’s correlation was calculated between the IOM-values and the HB scores for a homogeneous subgroup of 30 patients with vestibular schwannoma (VS) without neurofibromatosis type II (NF-II) and all patients collectively.

Results
TcMEP threshold was successfully measured in 39 (90.7%) procedures. In the homogeneous VS non-NFII group, we found a statistically significant moderate-to-strong correlation between TcMEP threshold increase and House Brackmann score immediately post-op, at 6 weeks, 6 months and 1 year after surgery (Spearman’s rho of 0.79 (p < 0.001), 0.74 (p < 0.001), 0.64 (p < 0.001) and 0.58 (p = 0.002), respectively). For A-trains, no correlation was found. Similar results were found when including all patients with CPA tumours. A threshold increase of < 20 mA was a predictor of good facial nerve outcome.

Conclusion
These results show that TcMEP threshold increases are strongly correlated to post-operative HB scores, while A-trains are not. This suggests TcMEP threshold increases can be a valuable predictor for facial nerve outcome in patients with large tumours when facial nerve preservation is prioritized over total resection. In this study, we found no use for A-trains to prevent facial nerve deficits.