bluuebunny/crossref_metadata_2025_split huggingface dataset:
Random control selection for conducting high‐throughput adverse drug events screening using large‐scale longitudinal health data
Authors: Chiang Chien‐Wei , Zhang Pengyue , Donneyong Macarius , Chen You , Su Yu , Li Lang 
Published: July 2021

AbstractCase‐control design based high‐throughput pharmacoinformatics study using large‐scale longitudinal health data is able to detect new adverse drug event (ADEs) signals. Existing control selection approaches for case‐control design included the dynamic/super control selection approach. The dynamic/super control selection approach requires all individuals to be evaluated at all ADE case index dates, as the individuals’ eligibilities as control depend on ADE/enrollment history. Thus, using large‐scale longitudinal health data, the dynamic/super control selection approach requires extraordinarily high computational time. We proposed a random control selection approach in which ADE case index dates were matched by randomly generated control index dates. The random control selection approach does not depend on ADE/enrollment history. It is able to significantly reduce computational time to prepare case‐control data sets, as it requires all individuals to be evaluated only once. We compared the performance metrics of all control selection approaches using two large‐scale longitudinal health data and a drug‐ADE gold standard including 399 drug‐ADE pairs. The F‐scores for the random control selection approach were between 0.586 and 0.600 compared to between 0.545 and 0.562 for dynamic/super control selection approaches. The random control selection approach was ~ 1000 times faster than dynamic/super control selection approach on preparing case‐control data sets. With large‐scale longitudinal health data, a case‐control design‐based pharmacoinformatics study using random control selection is able to generate comparable ADE signals than the existing control selection approaches. The random control selection approach also significantly reduces computational time to prepare the case‐control data sets.
Engineering Bioactive Scaffolds for Skin Regeneration
Authors: Hosseini Motaharesadat , Shafiee Abbas 
Published: July 2021

AbstractLarge skin wounds pose a major clinical challenge. Scarcity of donor site and postsurgical scarring contribute to the incomplete or partial loss of function and aesthetic concerns in skin wound patients. Currently, a wide variety of skin grafts are being applied in clinical settings. Scaffolds are used to overcome the issues related to the misaligned architecture of the repaired skin tissues. The current review summarizes the contribution of biomaterials to wound healing and skin regeneration and addresses the existing limitations in skin grafting. Then, the clinically approved biologic and synthetic skin substitutes are extensively reviewed. Next, the techniques for modification of skin grafts aiming for enhanced tissue regeneration are outlined, and a summary of different growth factor delivery systems using biomaterials is presented. Considering the significant progress in biomaterial science and manufacturing technologies, the idea of biomaterial‐based skin grafts with the ability for scarless wound healing and reconstructing full skin organ is more achievable than ever.
Insight into the isomerization mechanism of retinal proteins from hybrid quantum mechanics/molecular mechanics simulations
Authors: Sen Saumik , Kar Rajiv K. , Borin Veniamin A. , Schapiro Igor 
Published: July 2021

AbstractThe photoisomerization of retinal is a unifying primary event in the rhodopsin protein family. In vertebrate rhodopsins it is the first step in the vision process, while in the microbial rhodopsins it activates the transport of ions across the cell‐membrane. This reaction is highly optimized in the protein, which is ultrafast, selective, and efficient. A great effort was directed to elucidate the mechanism due to the overall complexity of the process inside the protein. The classical one‐bond‐flip is too demanding in space for the confined protein cavity. Therefore, various space saving mechanisms based on the rotation of multiple double bonds have been proposed. The hybrid quantum mechanics/molecular mechanics (QM/MM) method played an important role in the elucidation of the mechanism inside the tight protein environment. It allows to take the entire protein into account while describing the ground and excited states of retinal. The predicted mechanisms include full isomerization of two or three double bonds, a simultaneous isomerization of a single and a double bond as well as the partial rotation of bonds adjacent to the central isomerization. This review summarizes mechanistic studies in the literature and compares them.This article is categorized under:
Structure and Mechanism > Computational Biochemistry and Biophysics
Electronic Structure Theory > Combined QM/MM Methods
Software > Molecular Modeling
Partition functions of Chern-Simons theory on handlebodies by radial quantization
Authors: Porrati Massimo , Yu Cedric 
Published: July 2021

Abstract
We use radial quantization to compute Chern-Simons partition functions on handlebodies of arbitrary genus. The partition function is given by a particular transition amplitude between two states which are defined on the Riemann surfaces that define the (singular) foliation of the handlebody. The final state is a coherent state while on the initial state the holonomy operator has zero eigenvalue. The latter choice encodes the constraint that the gauge fields must be regular everywhere inside the handlebody. By requiring that the only singularities of the gauge field inside the handlebody must be compatible with Wilson loop insertions, we find that the Wilson loop shifts the holonomy of the initial state. Together with an appropriate choice of normalization, this procedure selects a unique state in the Hilbert space obtained from a Kähler quantization of the theory on the constant-radius Riemann surfaces. Radial quantization allows us to find the partition functions of Abelian Chern-Simons theories for handlebodies of arbitrary genus. For non-Abelian compact gauge groups, we show that our method reproduces the known partition function at genus one.
How many angels can dance on the head of a pin? Understanding ‘alien’ thought
Authors: Lushetich Natasha 
Published: July 2021

AbstractInitially coined by Weizenbaum in 1976, ‘alien' thought refers to the radical difference with which ‘thinking machines’ approach the process of thinking. The contemporary paradox of over-determination and indeterminacy—caused largely by algorithmic decision-making in the civic realm—makes these differences both more entangled and more difficult to navigate. In this essay, I trace over-determination to Leibniz and Turing’s axiomatic procedures and to instrumental rationality, and I trace indeterminacy to the mid-twentieth century co-development of computers and neurosciences to advance the following proposition: understanding alien thought requires understanding incomputability, temporal swarming, and inscriptive-significational errance. Understanding these phenomena in turn requires understanding thinking by doing, distributed thinking, and ontological indeterminacy. All are present in machinic operations as well as in the twentieth century experimental artistic practices of artists such as Duchamp, Cage, and Xu. These practices rely on indeterminate procedures and function as diagrammatic machines. A diagrammatic machine is neither abstract nor particular; neither an idea that is determining in the supreme instance, nor an infrastructure that is determining in the last instance, but rather instantiates a real yet to come (Deleuze and Guattari in A thousand plateaus: capitalism and schizophrenia: Trans. Massumi B, University of Minnesota Press, Minneapolis, 1987). In this essay, indeterminate artistic practices are used as an entry into alien thought and its correlates—infinity and complexity—by way of aesthetic analogy.
A multiscale optimisation method for bone growth scaffolds based on triply periodic minimal surfaces
Authors: Lehder E. F. , Ashcroft I. A. , Wildman R. D. , Ruiz-Cantu L. A. , Maskery I. 
Published: July 2021

AbstractTissue engineered bone scaffolds are potential alternatives to bone allografts and autografts. Porous scaffolds based on triply periodic minimal surfaces (TPMS) are good candidates for tissue growth because they offer high surface-to-volume ratio, have tailorable stiffness, and can be easily fabricated by additive manufacturing. However, the range of TPMS scaffold types is extensive, and it is not yet clear which type provides the fastest cell or tissue growth while being sufficiently stiff to act as a bone graft. Nor is there currently an established methodology for TPMS bone scaffold design which can be quickly adopted by medical designers or biologists designing implants. In this study, we examine six TPMS scaffold types for use as tissue growth scaffolds and propose a general methodology to optimise their geometry. At the macro-scale, the optimisation routine ensures a scaffold stiffness within suitable limits for bone, while at the micro-scale it maximises the cell growth rate. The optimisation procedure also ensures the scaffold pores are of sufficient diameter to allow oxygen and nutrient delivery via capillaries. Of the examined TPMS structures, the Lidinoid and Split P cell types provide the greatest cell growth rates and are therefore the best candidates for bone scaffolds.
A multivariate test for detecting fraud based on Benford’s law, with application to music streaming data
Authors: Mumic Nermina , Filzmoser Peter 
Published: July 2021

AbstractBenford’s law became a prevalent concept for fraud and anomaly detection. It examines the frequencies of the leading digits of numbers in a collection of data and states that the leading digit is most often 1, with diminishing frequencies up to 9. In this paper we propose a multivariate approach to test whether the observed frequencies follow the theoretical Benford distribution. Our approach is based on the concept of compositional data, which examines the relative information between the frequencies of the leading digits. As a result, we introduce a multivariate test for Benford distribution. In simulation studies and examples we compare the multivariate test performance to the conventional chi-square and Kolmogorov-Smirnov test, where the multivariate test turns out to be more sensitive in many cases. A diagnostics plot based on relative information allows to reveal and interpret the possible deviations from the Benford distribution.
Automated Vertebral Segmentation and Measurement of Vertebral Compression Ratio Based on Deep Learning in X-Ray Images
Authors: Kim Dong Hyun , Jeong Jin Gyo , Kim Young Jae , Kim Kwang Gi , Jeon Ji Young 
Published: July 2021

AbstractVertebral compression fracture is a deformity of vertebral bodies found on lateral spine images. To diagnose vertebral compression fracture, accurate measurement of vertebral compression ratio is required. Therefore, rapid and accurate segmentation of vertebra is important for measuring the vertebral compression ratio. In this study, we used 339 data of lateral thoracic and lumbar vertebra images for training and testing a deep learning model for segmentation. The result of segmentation by the model was compared with the manual measurement, which is performed by a specialist. As a result, the average sensitivity of the dataset was 0.937, specificity was 0.995, accuracy was 0.992, and dice similarity coefficient was 0.929, area under the curve of receiver operating characteristic curve was 0.987, and the precision recall curve was 0.916. The result of correlation analysis shows no statistical difference between the manually measured vertebral compression ratio and the vertebral compression ratio using the data segmented by the model in which the correlation coefficient was 0.929. In addition, the Bland–Altman plot shows good equivalence in which VCR values are in the area within average ± 1.96. In conclusion, vertebra segmentation based on deep learning is expected to be helpful for the measurement of vertebral compression ratio.
Climate change is creating a mismatch between protected areas and suitable habitats for frogs and birds in Puerto Rico
Authors: Campos-Cerqueira Marconi , Terando Adam J. , Murray Brent A. , Collazo Jaime A. , Aide T. Mitchell 
Published: July 2021

AbstractClimate change is altering the spatial distribution of many species around the world. In response, we need to identify and protect suitable areas for a large proportion of the fauna so that they persist through time. This exercise must also evaluate the ability of existing protected areas to provide safe havens for species in the context of climate change. Here, we combined passive acoustic monitoring, semi-automatic species identification models, and species distribution models of 21 bird and frog species based on past (1980–1989), present (2005–2014), and future (2040–2060) climate scenarios to determine how species distributions relate to the current distribution of protected areas in Puerto Rico. Species detection/non-detection data were acquired across ~ 700 sampling sites. We developed always-suitable maps that characterized suitable habitats in all three time periods for each species and overlaid these maps to identify regions with high species co-occurrence. These distributions were then compared with the distribution of existing protected areas. We show that Puerto Rico is projected to become dryer by 2040–2060, and precipitation in the warmest quarter was among the most important variables affecting bird and frog distributions. A large portion of always-suitable areas (ASA) is outside of protected areas (> 80%), and the percent of protected areas that overlaps with always-suitable areas is larger for bird (75%) than frog (39%) species. Our results indicate that present protected areas will not suffice to safeguard bird and frog species under climate change; however, the establishment of larger protected areas, buffer zones, and connectivity between protected areas may allow species to find suitable niches to withstand environmental changes.
A Feasibility Study for Determining the Sensible Heat Flux to and from Small Green Roofs
Authors: Wollschläger Niels , Schlink Uwe , Raabe Armin 
Published: July 2021

AbstractEddy covariance is an established technique for registering sensible heat fluxes. However, this method is less adequate for smaller surfaces that cannot match the associated footprint. As an alternative technique, a recently constructed acoustic anemometer (Ly-ATOM) is tested, which operates horizontally at an extension of circa 1 m and a data-acquisition frequency of 1 Hz. The Ly-ATOM device reproduces both the acoustic virtual temperature and the horizontal wind components registered by a three-dimensional sonic anemometer. As this Ly-ATOM device can be applied much closer to the ground compared with a sonic anemometer, the size of the related source area is significantly reduced (by a factor of 25). Two methods are used to retrieve the sensible heat flux from variance characteristics of temperature and the horizontal wind components recorded by the Ly-ATOM device: combining the flux-variance-similarity and alternative-flux-variance methods for use in unstable and stable stratification, respectively, yields good results for the sonic measurements. Therefore, these methods can be applied to the Ly-ATOM device as well. In investigating the sensitivity to detect modified surface characteristics, specifically increased evapotranspiration and decreased surface albedo, the Ly-ATOM device proves to be superior to the sonic anemometer which is more vertically removed from the surface of interest.
Investigating microcrystalline cellulose crystallinity using Raman spectroscopy
Authors: Queiroz Ana Luiza P. , Kerins Brian M. , Yadav Jayprakash , Farag Fatma , Faisal Waleed , Crowley Mary Ellen , Lawrence Simon E. , Moynihan Humphrey A. , Healy Anne-Marie , Vucen Sonja , Crean Abina M. 
Published: July 2021

AbstractMicrocrystalline cellulose (MCC) is a semi-crystalline material with inherent variable crystallinity due to raw material source and variable manufacturing conditions. MCC crystallinity variability can result in downstream process variability. The aim of this study was to develop models to determine MCC crystallinity index (%CI) from Raman spectra of 30 commercial batches using Raman probes with spot sizes of 100 µm (MR probe) and 6 mm (PhAT probe). A principal component analysis model separated Raman spectra of the same samples captured using the different probes. The %CI was determined using a previously reported univariate model based on the ratio of the peaks at 380 and 1096 cm−1. The univariate model was adjusted for each probe. The %CI was also predicted from spectral data from each probe using partial least squares regression models (where Raman spectra and univariate %CI were the dependent and independent variables, respectively). Both models showed adequate predictive power. For these models a general reference amorphous spectrum was proposed for each instrument. The development of the PLS model substantially reduced the analysis time as it eliminates the need for spectral deconvolution. A web application containing all the models was developed.
Graphic abstract
The impact of macroeconomic and structural factors on the unemployment of young women and men
Authors: Bal-Domańska Beata 
Published: July 2021

AbstractThe presented article follows the research mainstream of econometric analyses focused on the assessment of correlations between youth unemployment rate and market and macroeconomic determinants, including economic growth and productivity of the economy, its structure in terms of NACE Rev.2 sections as well as the labor market tools. The research addresses 28 European Union (EU) countries. The analysis period covers the years 2008–2018. The econometric methods dedicated to panel data were used. The research results confirm the importance of the general economic condition as well as the development of knowledge-based economy for the improvement of the youth situation in the labor market. With regard to the economy structure, the development of manufacturing section importance turned out to be a major factor in female youth unemployment rate reduction. The growing importance of the construction sector translated into a decline in the unemployment rate among young men.
This time is different?—on the use of emergency measures during the corona pandemic
Authors: Bjørnskov Christian , Voigt Stefan 
Published: July 2021

AbstractThe COVID-19 pandemic has not only caused millions to die and even more to lose their jobs, it has also prompted more governments to simultaneously declare a state of emergency than ever before enabling us to compare their decisions more directly. States of emergency usually imply the extension of executive powers that diminishes the powers of other branches of government, as well as to the civil liberties of individuals. Here, we analyze the use of emergency provisions during the first wave of the COVID-19 pandemic and find that it can be largely explained by drawing on political economy. It does, hence, not constitute an exception. We show that many governments have (mis-)used the pandemic as a pretext to curtail media freedom. We further show that executive decrees are considered as a substitute for states of emergency by many governments.
On the Contingency of Universalism
Authors: Calosi Claudio 
Published: July 2021

AbstractThe paper presents different arguments against the necessity of mereological universalism. First, it argues that they are examples of a much more general argumentative structure. It then contends that some of these arguments cannot be resisted by distinguishing different variants of universalism that have been recently proposed in the literature—in contrast with recent suggestions to the contrary. Finally, it provides different ways to resist such contingentist arguments on behalf of universalists.
Preliminary hemocompatibility assessment of an innovative material for blood contacting surfaces
Authors: Todesco Martina , Pontara Elena , Cheng Chunyan , Gerosa Gino , Pengo Vittorio , Bagno Andrea 
Published: July 2021

AbstractOver the years, several devices have been created (and the development of many others is currently in progress) to be in permanent contact with blood: mechanical circulatory supports represent an example thereof. The hemocompatibility of these devices largely depends on the chemical composition of blood-contacting components. In the present work, an innovative material (hybrid membrane) is proposed to fabricate the inner surfaces of a pulsatile ventricular chamber: it has been obtained by coupling a synthetic polymer (e.g., commercial polycarbonate urethane) with decellularized porcine pericardium. The hemocompatibility of the innovative material has been preliminarily assessed by measuring its capacity to promote thrombin generation and induce platelet activation. Our results demonstrated the blood compatibility of the proposed hybrid membrane.
Computing directed Steiner path covers
Authors: Gurski Frank , Komander Dominique , Rehs Carolin , Rethmann Jochen , Wanke Egon 
Published: July 2021

AbstractIn this article we consider the Directed Steiner Path Cover problem on directed co-graphs. Given a directed graph $$G=(V,E)$$

G
=
(
V
,
E
)

and a set $$T \subseteq V$$

T
⊆
V

of so-called terminal vertices, the problem is to find a minimum number of vertex-disjoint simple directed paths, which contain all terminal vertices and a minimum number of non-terminal vertices (Steiner vertices). The primary minimization criteria is the number of paths. We show how to compute in linear time a minimum Steiner path cover for directed co-graphs. This leads to a linear time computation of an optimal directed Steiner path on directed co-graphs, if it exists. Since the Steiner path problem generalizes the Hamiltonian path problem, our results imply the first linear time algorithm for the directed Hamiltonian path problem on directed co-graphs. We also give binary integer programs for the (directed) Hamiltonian path problem, for the (directed) Steiner path problem, and for the (directed) Steiner path cover problem. These integer programs can be used to minimize change-over times in pick-and-place machines used by companies in electronic industry.
What is life?
Authors: Gómez-Márquez Jaime 
Published: July 2021

Abstract
Background
Many traditional biological concepts continue to be debated by biologists, scientists and philosophers of science. The specific objective of this brief reflection is to offer an alternative vision to the definition of life taking as a starting point the traits common to all living beings.

Results and Conclusions
Thus, I define life as a process that takes place in highly organized organic structures and is characterized by being preprogrammed, interactive, adaptative and evolutionary. If life is the process, living beings are the system in which this process takes place. I also wonder whether viruses can be considered living things or not. Taking as a starting point my definition of life and, of course, on what others have thought about it, I am in favor of considering viruses as living beings. I base this conclusion on the fact that viruses satisfy all the vital characteristics common to all living things and on the role they have played in the evolution of species. Finally, I argue that if there were life elsewhere in the universe, it would be very similar to what we know on this planet because the laws of physics and the composition of matter are universal and because of the principle of the inexorability of life.