bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient and enhanced sampling of drug‐like chemical space for virtual screening and molecular design using modern machine learning methods
Authors: Goel Manan , Aggarwal Rishal , Sridharan Bhuvanesh , Pal Pradeep Kumar , Priyakumar U. Deva 
Published: September 2022

AbstractDrug design involves the process of identifying and designing novel molecules that have desirable properties and bind well to a given target receptor. Typically, such molecules are identified by screening large chemical libraries for desirable physicochemical properties and binding strength with the target protein. This traditional approach, however, has severe limitations as exhaustively screening every molecule in known chemical libraries is computationally infeasible. Furthermore, currently available molecular libraries are only a minuscule part of the entire set of possible drug‐like molecular structures (drug‐like chemical space). In this review, we discuss how the former limitation is addressed by modeling virtual screening as a search space problem and how these endeavors utilize machine learning to reduce the number of required computational experiments to identify top candidates. We follow that up by discussing generative methods that attempt to approximate the entire drug‐like chemical space providing us a path to explore beyond the known drug‐like chemical space. We place special emphasis on generative models that learn the marginal distributions conditioned on specific properties or receptor structures for efficient sampling of molecules. Through this review, we aim to highlight modern machine learning based methods that try to efficiently enhance our sampling capability beyond conventional screening methods which, in turn, would benefit drug design significantly. Therefore, we also encourage further methods of development that work on such important aspects of drug design.This article is categorized under:
Data Science > Chemoinformatics
Data Science > Artificial Intelligence/Machine Learning
Data Science > Computer Algorithms and Programming
Semi‐analytical solution of solute dispersion model in semi‐infinite media
Authors: Taghvaei Poorya , Pourshahbaz Hanif , Pu Jaan H. , Pandey Manish , Pourshahbaz Vahid , Abbasi Saeed , Tofangdar Nafiseh 
Published: September 2022

AbstractThe advection–dispersion equation (ADE) is one of the most widely used methods for estimating natural stream pollution at different locations and times. In this paper, variational iteration method (VIM) is utilized to obtain a semi‐analytical solution for 1D ADE in a temporally dependent solute dispersion within uniformsteady flow. Through a computational validation, the effect of different parameters such as uniform flow velocity and dispersion coefficient on the solute concentration values has been investigated. Results show that the change in velocity has a strong effect on fluid density variation. However, when the diffusion coefficient has been increased, the change in flow and velocity behaviors is negligible. To verify the proposed semianalytical solution, the results were compared to analytical solutions and errors were found to be <0.7% in all simulations.
Hybrid Immediacy: Designing with Artificial Neural Networks Through Physical Concept Modelling
Authors: Bank Mathias , Sandor Viktoria , Kraft Robby , Antholzer Stephan , Berger Martin , Fabini Tilman , Kovacs Balint , Hell Tobias , Rutzinger Stefan , Schinegger Kristina 
Published: September 2022

AbstractIn digital design practice, the connection and feedback between physical and digital modelling is receiving increasing attention and is seen as a source of creativity and design innovation. The authors present a workflow that supports real-time design collaboration between human and machine intelligence through physical model building. The proposed framework is investigated through a case study, where we test the direct connectivity of physical and digital modelling environments with the integration of artificial neural networks. By combining 3D capturing tools and machine learning algorithms, the research creates an instant feedback loop between human and machine, introducing a hybrid immediacy that puts physical model building back at the centre of the digitally focused design process. By fusing physical models and digital workflows, the research aims to create interactivity between data, material and designer already at the early stage of the design.
New benchmark scenarios of electroweak baryogenesis in aligned two Higgs double models
Authors: Enomoto Kazuki , Kanemura Shinya , Mura Yushi 
Published: September 2022

Abstract
We discuss electroweak baryogenesis in aligned two Higgs doublet models. It is known that in this model the severe constraint from the experimental results for the electron electric dipole moment can be avoided by destructive interference among CP-violating effects in the Higgs sector. In our previous work, we showed that the observed baryon number in the Universe can be explained without contradicting current available data in a specific scenario in the same model. We here first discuss details of the evaluation of baryon number based on the WKB method taking into account all order of the wall velocity. We then investigate parameter spaces which are allowed under the current available data from collider, flavor and electric dipole moment experiments simultaneously. We find several benchmark scenarios which can explain baryon asymmetry of the Universe. We also discuss how we can test these benchmark scenarios at future collider experiments, various flavor experiments and gravitational wave observations.
Fine-tuned vs. natural supersymmetry: what does the string landscape predict?
Authors: Baer Howard , Barger Vernon , Martinez Dakotah , Salam Shadman 
Published: September 2022

Abstract
A vast array of (metastable) vacuum solutions arise from string compactifications, each leading to different 4-d laws of physics. The space of these solutions, known as the string landscape, allows for an environmental solution to the cosmological constant problem. We examine the possibility of an environmental solution to the gauge hierarchy problem. We argue that the landscape favors softly broken supersymmetric models over particle physics models containing quadratic divergences, such as the Standard Model. We present a scheme for computing relative probabilities for supersymmetric models to emerge from the landscape. The probabilities are related to the likelihood that the derived value of the weak scale lies within the Agrawal et al. (ABDS) allowed window of values leading to atoms as we know them. This then favors natural SUSY models over unnatural (SUSY and other) models via a computable probability measure.
Two-loop scattering amplitude for heavy-quark pair production through light-quark annihilation in QCD
Authors: Mandal Manoj K. , Mastrolia Pierpaolo , Ronca Jonathan , Torres Bobadilla William J. 
Published: September 2022

Abstract
We present the first full analytic evaluation of the scattering amplitude for the process qq → $$ Q\overline{Q} $$
Q

Q
¯

up-to two loops in Quantum Chromodynamics, for a massless (q) and a massive (Q) quark flavour. The interference terms of the one- and two-loop amplitudes with the Born amplitude, decomposed in terms of gauge invariant form factors depending on the colour and flavour structure, are analytically calculated by keeping complete dependence on the squared center-of-mass energy, the squared momentum transfer, and the heavy-quark mass. The results are expressed as Laurent series around four space-time dimensions, with coefficients given in terms of generalised polylogarithms and transcendental constants up-to weight four. Our results validate the known, purely numerical calculations of the squared amplitude, and extend the analytic knowledge, previously limited to a subset of form factors, to their whole set, coming from both planar and non-planar diagrams, up-to the second order corrections in the strong coupling constant.
New AdS3/CFT2 pairs in massive IIA with (0, 4) and (4, 4) supersymmetries
Authors: Lozano Yolanda , Macpherson Niall T. , Petri Nicolò , Risco Cristian 
Published: September 2022

Abstract
We construct a new class of AdS3 × S3 × M4 solutions of massive Type IIA supergravity with (0, 4) supersymmetries and SU(3) structure. We study in detail two subclasses of these solutions. The first subclass is when M4 = S2× Σ2, with Σ2 a 2d Riemann surface, and the geometry is foliated over the Σ2. We interpret these solutions as duals to surface defect CFTs within the 6d (1, 0) CFTs dual to the AdS7 × S2 × I solutions of massive IIA supergravity. The second subclass is when M4 = 𝕋3 × I and the geometry is foliated over the interval. In this case supersymmetry is enhanced to (4, 4) in the massless limit, and the solutions are the sought-for holographic duals of (4, 4) CFTs living in two dimensional D2-NS5-D4 Hanany-Witten brane set-ups. In turn, in the massive case the solutions find an interpretation as D2-D4 branes embedded in Type I’ string theory. We construct explicit quiver gauge theories from the different brane set-ups that flow in the IR to the 2d dual CFTs dual to the solutions. We check the validity of our proposals with the matching between the field theory and holographic central charges.
Antipodal symmetry of two-loop MHV amplitudes
Authors: Liu Yu-Ting 
Published: September 2022

Abstract
I present a conjecture that all two-loop MHV amplitudes in planar $$ \mathcal{N} $$
N
= 4 super-Yang-Mills theory possess an antipodal symmetry when evaluated on parity-even kinematics. The symmetry acts as a change of basis on the symbol letters, followed by the antipode operation associated with the Hopf algebra structure of multiple polylogarithms. At the symbol level, I provide the symmetry map explicitly for amplitudes with up to eight external particles, and also provide evidence at all multiplicities. Intriguingly, the map acts as an isomorphism on the normal fans of the Newton polytopes of the symbol letters. The conjectured symmetry is one of the rare known cases where the antipode map shows up in physically important examples.
Catalan Generating Functions for Generators of Uni-parametric Families of Operators
Authors: Mahillo Alejandro , Miana Pedro J. 
Published: September 2022

AbstractIn this paper we study solutions of the quadratic equation$$AY^2-Y+I=0$$AY2-Y+I=0whereAis the generator of a one parameter family of operator ($$C_0$$C0-semigroup or cosine functions) on a Banach spaceXwith growth bound$$w_0 \le \frac{1}{4}$$w0≤14. In the case of$$C_0$$C0-semigroups, we show that a solution, which we call Catalan generating function ofA,C(A), is given by the following Bochner integral,$$\begin{aligned} C(A)x := \int _{0}^\infty c(t) T(t)x \; \mathrm{d}t, \quad x\in X, \end{aligned}$$C(A)x:=∫0∞c(t)T(t)xdt,x∈X,wherecis the Catalan kernel,$$\begin{aligned} c(t) := \frac{1}{2\pi } \int _{\frac{1}{4}}^\infty e^{-\lambda t} \frac{\sqrt{4\lambda -1}}{\lambda } \; \mathrm{d}\lambda , \quad t>0. \end{aligned}$$c(t):=12π∫14∞e-λt4λ-1λdλ,t>0.Similar (and more complicated) results hold for cosine functions. We study algebraic properties of the Catalan kernelcas an element in Banach algebras$$L^1_{\omega }(\mathbb R^+)$$Lω1(R+), endowed with the usual convolution product,$$*$$∗and with the cosine convolution product,$$*_c$$∗c. The Hille–Phillips functional calculus allows to transfer these properties to$$C_0$$C0-semigroups and cosine functions. In particular, we obtain a spectral mapping theorem forC(A). Finally, we present some examples, applications and conjectures to illustrate our results.
SOX9 in organogenesis: shared and unique transcriptional functions
Authors: Ming Zhenhua , Vining Brittany , Bagheri-Fam Stefan , Harley Vincent 
Published: September 2022

AbstractThe transcription factor SOX9 is essential for the development of multiple organs including bone, testis, heart, lung, pancreas, intestine and nervous system. Mutations in the human SOX9 gene led to campomelic dysplasia, a haploinsufficiency disorder with several skeletal malformations frequently accompanied by 46, XY sex reversal. The mechanisms underlying the diverse SOX9 functions during organ development including its post-translational modifications, the availability of binding partners, and tissue-specific accessibility to target gene chromatin. Here we summarize the expression, activities, and downstream target genes of SOX9 in molecular genetic pathways essential for organ development, maintenance, and function. We also provide an insight into understanding the mechanisms that regulate the versatile roles of SOX9 in different organs.
Serum sex hormone-binding globulin is a mediator of the association between intrahepatic lipid content and type 2 diabetes: the Maastricht Study
Authors: Simons Pomme I. H. G. , Valkenburg Olivier , van de Waarenburg Marjo P. H. , van Greevenbroek Marleen M. J. , Kooi M. Eline , Jansen Jacobus F. A. , Schalkwijk Casper G. , Stehouwer Coen D. A. , Brouwers Martijn C. G. J. 
Published: September 2022

Abstract
Aims/hypothesis
Serum sex hormone-binding globulin (SHBG) has been proposed to act as a hepatokine that contributes to the extrahepatic complications observed in non-alcoholic fatty liver disease (NAFLD). However, it remains uncertain whether serum SHBG mediates the association between intrahepatic lipids (IHL) and type 2 diabetes. Therefore, we studied whether, and to what extent, serum SHBG mediates the association between IHL content and type 2 diabetes.

Methods
We used cross-sectional data from the Maastricht Study (n=1554), a population-based cohort study with oversampling of individuals with type 2 diabetes. Type 2 diabetes status was assessed by oral glucose tolerance test, and IHL content was measured using 3T Dixon MRI. Mediation analyses were performed to assess the role of serum SHBG in mediating the association between IHL content and type 2 diabetes.

Results
IHL content was significantly associated with type 2 diabetes in women and men (OR 1.08 [95% CI 1.04, 1.14] and OR 1.12 [95% CI 1.08, 1.17], respectively). Serum SHBG significantly mediated the association between IHL content and type 2 diabetes. The contribution of serum SHBG was higher in women (OR 1.04 [95% CI 1.02, 1.07]; proportion mediated 50.9% [95% CI 26.7, 81.3]) than in men (OR 1.02 [95% CI 1.01, 1.03]; proportion mediated 17.2% [95% CI 9.6, 27.6]). Repeat analyses with proxies of type 2 diabetes and adjustment for covariates did not substantially affect the results.

Conclusions/interpretation
In this large-scale population-based cohort study, serum SHBG was found to be a mediator of the association between IHL content and type 2 diabetes. These findings extend our understanding of the potential mechanisms by which NAFLD is a risk factor for type 2 diabetes, and further elaborate on the role of SHBG as a hepatokine.

Graphical abstract
MILP-based discrete sizing and topology optimization of truss structures: new formulation and benchmarking
Authors: Brütting Jan , Senatore Gennaro , Fivet Corentin 
Published: September 2022

AbstractDiscrete sizing and topology optimization of truss structures subject to stress and displacement constraints has been formulated as a Mixed-Integer Linear Programming (MILP) problem. The computation time to solve a MILP problem to global optimality via a branch-and-cut solver highly depends on the problem size, the choice of design variables, and the quality of optimization constraint formulations. This paper presents a new formulation for discrete sizing and topology optimization of truss structures, which is benchmarked against two well-known existing formulations. Benchmarking is carried out through case studies to evaluate the influence of the number of structural members, candidate cross sections, load cases, and design constraints (e.g., stress and displacement limits) on computational performance. Results show that one of the existing formulations performs significantly worse than all other formulations. In most cases, the new formulation proposed in this work performs best to obtain near-optimal solutions and verify global optimality in the shortest computation time.
Thermal experiments and analysis on adhesive cleaning of work-holding devices by grinding
Authors: Haider Syed Mustafa , Khan Sarmad Ali , Ali Muhammad Asad , Farooq Muhammad Umar , Ishfaq Kashif 
Published: September 2022

AbstractIn the light-activated work-holding devices, hardened adhesive residues on the fixture plate need to be removed to make it available for the subsequent work holding. There are several ways to remove the cured adhesive from the gripper, such as laser-based degradation, and softening and removing with high temperature pressured water wash. These processes are associated with the generation of carbon black, affecting transparency which compromises the efficiency of the light-activated device. A novel peripheral grinding-based cleaning process has been developed to strip the adhesive from the fixture plate. The present research is aimed to analyze the effect of variation in grinding parameters, viz., spindle speed, feed, depth of cut, and the grain size of the grinding wheel on the temperature of the adhesive being ground and cleaning of the adhesive-filled channel. Aggressive values of grinding parameters are selected to achieve the desired removal of adhesive, putting a step towards sustainability. Moreover, a comprehensive investigation of the temperature of the grinding zone and the grinding wheel is made by inspecting the effective cleaning of the cured adhesive-filled channel. Higher values of spindle speed (11.57 m/s) and feed (0.406 mm/rev) resulted in an improved, cleaned surface of the ground adhesive-filled channel. Moreover, the grinding wheel with a more prominent grain size (46/Ø0.35 mm) and porosity was proved to be more effective in the cleaning process by reducing and maintaining the grinding temperature (~52 °C) of the adhesive-filled channel.
On the numerical stability of linear barycentric rational interpolation
Authors: Fuda Chiara , Campagna Rosanna , Hormann Kai 
Published: September 2022

AbstractThe barycentric forms of polynomial and rational interpolation have recently gained popularity, because they can be computed with simple, efficient, and numerically stable algorithms. In this paper, we show more generally that the evaluation of any function that can be expressed as$$r(x)=\sum _{i=0}^n a_i(x) f_i\big /\sum _{j=0}^m b_j(x)$$r(x)=∑i=0nai(x)fi/∑j=0mbj(x)in terms of data values$$f_i$$fiand some functions$$a_i$$aiand$$b_j$$bjfor$$i=0,\ldots ,n$$i=0,…,nand$$j=0,\dots ,m$$j=0,⋯,mwith a simple algorithm that first sums up the terms in the numerator and the denominator, followed by a final division, is forward and backward stable under certain assumptions. This result includes the two barycentric forms of rational interpolation as special cases. Our analysis further reveals that the stability of the second barycentric form depends on the Lebesgue constant associated with the interpolation nodes, which typically grows withn, whereas the stability of the first barycentric form depends on a similar, but different quantity, that can be bounded in terms of the mesh ratio, regardless ofn. We support our theoretical results with numerical experiments.
When running is easier than walking: effects of experience and gait on human obstacle traversal in virtual reality
Authors: Hofmann Florian , Dürr Volker 
Published: September 2022

AbstractHumans readily traverse obstacles irrespective of whether they walk or run, despite strong differences between these gaits. Assuming that the control of human obstacle traversal may be either gait-specific or gait-independent, the present study investigates whether previous experience in an obstacle traversal task transfers between the two gaits, and, if this was the case, whether transfer worked both ways. To this end, we conducted a within-group comparison of kinematic adjustments during human obstacle traversal in both walking and running, with distinct participant groups for the two gait sequences. Participants (n = 12/12 (f/m), avg. 25 yo) were motion captured as they traversed obstacles at walking and running speeds on a treadmill, surrounded by an immersive virtual reality (VR) environment. We find that kinematics recorded in our VR setup are consistent with that obtained in real-world experiments. Comparison of learning curves reveals that participants are able to utilize previous experience and transfer learned adjustments from one gait to another. However, this transfer is not symmetrical, with previous experience during running leading to increased success rate in walking, but not the other way round. From a range of step parameters we identified lacking toe height of the trailing leg as the main cause for this asymmetry.
Impact of coronary bifurcation angle on computed tomography derived fractional flow reserve in coronary vessels with no apparent coronary artery disease
Authors: Tsugu Toshimitsu , Tanaka Kaoru , Nagatomo Yuji , Belsack Dries , Devos Hannes , Buls Nico , Cosyns Bernard , Argacha Jean-François , De Maeseneer Michel , De Mey Johan 
Published: September 2022

Abstract
Objectives
Computed tomography (CT) derived fractional flow reserve (FFRCT) decreases from the proximal to the distal part due to a variety of factors. The energy loss due to the bifurcation angle may potentially contribute to a progressive decline in FFRCT. However, the association of the bifurcation angle with FFRCT is still not entirely understood. This study aimed to investigate the impact of various bifurcation angles on FFRCT decline below the clinically crucial relevance of 0.80 in vessels with no apparent coronary artery disease (CAD).

Methods
A total of 83 patients who underwent both CT angiography including FFRCT and invasive coronary angiography, exhibiting no apparent CAD were evaluated. ΔFFRCT was defined as the change in FFRCT from the proximal to the distal in the left anterior descending artery (LAD) and left circumflex artery (LCX). The bifurcation angle was calculated from three-dimensional volume rendered images. Vessel morphology and plaque characteristics were also assessed.

Results
ΔFFRCT significantly correlated with the bifurcation angle (LAD angle, r = 0.35, p = 0.001; LCX angle, r = 0.26, p = 0.02) and vessel length (LAD angle, r = 0.30, p = 0.005; LCX angle, r = 0.49, p < 0.0001). In LAD, vessel length was the strongest predictor for distal FFRCT of ≤ 0.80 (β-coefficient = 0.55, p = 0.0003), immediately followed by the bifurcation angle (β-coefficient = 0.24, p = 0.02). The bifurcation angle was a good predictor for a distal FFRCT ≤ 0.80 (LAD angle, cut-off 31.0°, AUC 0.70, sensitivity 74%, specificity 68%; LCX angle, cut-off 52.6°, AUC 0.86, sensitivity 88%, specificity 85%).

Conclusions
In vessels with no apparent CAD, vessel length was the most influential factor on FFRCT, directly followed by the bifurcation angle.

Key Points
• Both LAD and LCX bifurcation angles are factors influencing FFRCT.
• Bifurcation angle is one of the predictors of a distal FFRCTof ≤ 0.80 and an optimal cut-off value of 31.0° for the LAD and 52.6° for the LCX.
• Bifurcation angle should be taken into consideration when interpreting numerical values of FFRCT.