bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pleiotropic genetic architecture and novel loci for C-reactive protein levels
Authors: Koskeridis Fotios , Evangelou Evangelos , Said Saredo , Boyle Joseph J. , Elliott Paul , Dehghan Abbas , Tzoulaki Ioanna 
Published: November 2022

AbstractC-reactive protein is involved in a plethora of pathophysiological conditions. Many genetic loci associated with C-reactive protein are annotated to lipid and glucose metabolism genes supporting common biological pathways between inflammation and metabolic traits. To identify novel pleiotropic loci, we perform multi-trait analysis of genome-wide association studies on C-reactive protein levels along with cardiometabolic traits, followed by a series of in silico analyses including colocalization, phenome-wide association studies and Mendelian randomization. We find 41 novel loci and 19 gene sets associated with C-reactive protein with various pleiotropic effects. Additionally, 41 variants colocalize between C-reactive protein and cardiometabolic risk factors and 12 of them display unexpected discordant effects between the shared traits which are translated into discordant associations with clinical outcomes in subsequent phenome-wide association studies. Our findings provide insights into shared mechanisms underlying inflammation and lipid metabolism, representing potential preventive and therapeutic targets.
Social affective forecasting and social anhedonia in schizophrenia-spectrum disorders: a daily diary study
Authors: Shovestul Bridget , Saxena Abhishek , Reda Stephanie , Dudek Emily , Wu Chenwei , Lamberti J. Steven , Dodell-Feder David 
Published: November 2022

AbstractSocial anhedonia (SA) is a trait-like phenomenon observed across schizophrenia-spectrum disorders (SSDs). While in-the-moment social pleasure experiences are intact in SSDs, anticipatory pleasure experiences may be disrupted. Thus, the prediction of future emotions in social situations, or social affective forecasting (SAF), may play a role in SA. Therefore, we utilized daily diary methods to examine SAF in SSD and the association between SAF and SA in 34 SSD and 43 non-SSD individuals. SAF was calculated as the absolute difference between anticipatory and consummatory ratings of 13 positive and negative emotions for daily social interactions reported across eight days. Results suggest that individuals with SSDs are less accurate in forecasting negative, but not positive emotions, for future social interactions. Further, poorer forecasting accuracy of negative emotions were associated with elevated levels of SA and lower social pleasure. Together, these data suggest that inaccuracies in forecasting negative emotions may be a worthwhile intervention target for reducing SA in SSDs.
Ansatz-Independent Variational Quantum Classifiers and the Price of Ansatz
Authors: Miyahara Hideyuki , Roychowdhury Vwani 
Published: November 2022

AbstractThe paradigm of variational quantum classifiers (VQCs) encodes classical information as quantum states, followed by quantum processing and then measurements to generate classical predictions. VQCs are promising candidates for efficient utilizations of noisy intermediate scale quantum (NISQ) devices: classifiers involving M-dimensional datasets can be implemented with only $$\lceil \log _2 M \rceil $$

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log
2

M
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qubits by using an amplitude encoding. A general framework for designing and training VQCs, however, is lacking. An encouraging specific embodiment of VQCs, quantum circuit learning (QCL), utilizes an ansatz: a circuit with a predetermined circuit geometry and parametrized gates expressing a time-evolution unitary operator; training involves learning the gate parameters through a gradient-descent algorithm where the gradients themselves can be efficiently estimated by the quantum circuit. The representational power of QCL, however, depends strongly on the choice of the ansatz, as it limits the range of possible unitary operators that a VQC can search over. Equally importantly, the landscape of the optimization problem may have challenging properties such as barren plateaus and the associated gradient-descent algorithm may not find good local minima. Thus, it is critically important to estimate (i) the price of ansatz; that is, the gap between the performance of QCL and the performance of ansatz-independent VQCs, and (ii) the price of using quantum circuits as classical classifiers: that is, the performance gap between VQCs and equivalent classical classifiers. This paper develops a computational framework to address both these open problems. First, it shows that VQCs, including QCL, fit inside the well-known kernel method. Next it introduces a framework for efficiently designing ansatz-independent VQCs, which we call the unitary kernel method (UKM). The UKM framework enables one to estimate the first known computationally-determined bounds on both the price of ansatz and the price of any speedup advantages of VQCs: numerical results with datatsets of various dimensions, ranging from 4 to 256, show that the ansatz-induced gap can vary between 10 and 20$$\%$$
%
, while the VQC-induced gap (between VQC and kernel method) can vary between 10 and 16$$\%$$
%
. To further understand the role of ansatz in VQCs, we also propose a method of decomposing a given unitary operator into a quantum circuit, which we call the variational circuit realization (VCR): given any parameterized circuit block (as for example, used in QCL), it finds optimal parameters and the number of layers of the circuit block required to approximate any target unitary operator with a given precision.
Water provisioning increases caged worker bee lifespan and caged worker bees are living half as long as observed 50 years ago
Authors: Nearman Anthony , vanEngelsdorp Dennis 
Published: November 2022

AbstractThe high loss rates of honey bee colonies drive research for solutions aimed to mitigate these losses. While honey bee colonies are superorganisms, experiments that measure the response to stressors often use caged individuals to allow for inference in a controlled setting. In an initial experiment, we showed that caged honey bees provisioned with various types of water (deionized, 1%NaCl in deionized, or tap) have greater median lifespans than those that did not. While researching the history of water provisioning in cage studies, we observed that the median lifespan of caged honey bees has been declining in the US since the 1970’s, from an average of 34.3 days to 17.7 days. In response to this, we again turned to historical record and found a relationship between this trend and a decline in the average amount of honey produced per colony per year in the US over the last 5 decades. To understand the relationship between individual bee lifespan and colony success we used an established honey bee population model (BEEHAVE) to simulate the predicted effects of decreased worker lifespans. Declines in downstream measures of colony population, overall honey production, and colony lifespan resulted from reduced worker bee lifespans. Modeled colony lifespans allowed us to estimate colony loss rates in a beekeeping operation where lost colonies are replaced annually. Resulting loss rates were reflective of what beekeepers’ experience today, which suggests the average lifespan of individual bees plays an important role in colony success.
Curvature and van der Waals interface effects on thermal transport in carbon nanotube bundles
Authors: Valadkhani Mostafa , Chen Shunda , Kowsary Farshad , Benenti Giuliano , Casati Giulio , Allaei S. Mehdi Vaez 
Published: November 2022

AbstractA van der Waals (vdW) heterostructure, can be used in efficient heat management, due to its promising anisotropic thermal transport feature, with high heat conductance in one direction and low conductance in the rest. A carbon nanotube (CNT) bundle, can be used as one of the most feasible vdW heterostructures in a wide range of nanoscale devices. However, detailed investigations of heat transport in CNT bundles are still lacking. In this paper, we study heat transport in different CNT bundles—homogeneous bundles consisting of the one CNT radius (curvature) and inhomogeneous bundles constructed from different CNTs with different curvatures. We also investigate the comparison between two possible thermostatting configurations: the two ends connected (TEC) case in which there is at least a direct covalently connected path between the hot and cold heat baths, and the one end connected (OEC) case in which the system can be divided at least into two parts, by a vdW interacting interface. Nonequilibrium molecular dynamics simulations have been carried out for a wide range of configurations and curvature differences. We find that, in homogeneous bundles, by increasing the number of outer CNTs, the heat conductance increases. In inhomogeneous bundles, the total heat flux shows dependence on the difference between the curvature of the core and outer CNTs. The less the difference between the curvature of the core and the outer CNTs, the more the thermal conductance in the system. By investigating the spectral heat conductance (SHC) in the system, we found that a larger curvature difference between the core and outer CNTs leads to a considerable decrease in the contribution of 0–10 THz phonons in the bundled zone. These results provide an insightful understanding of the heat transport mechanism in vdW nano-heterostructures, more important for designing nanoelectronic devices as well as systems in which asymmetry plays a significant role.
Mathematical analysis of phototransduction reaction parameters in rods and cones
Authors: Takeda Yukari , Sato Kazuma , Hosoki Yukari , Tachibanaki Shuji , Koike Chieko , Amano Akira 
Published: November 2022

AbstractRetinal photoreceptor cells, rods and cones, convert photons of light into chemical and electrical signals as the first step of the visual transduction cascade. Although the chemical processes in the phototransduction system are very similar to each other in these photoreceptors, the light sensitivity and time resolution of the photoresponse in rods are functionally different than those in the photoresponses of cones. To systematically investigate how photoresponses are divergently regulated in rods and cones, we have developed a detailed mathematical model on the basis of the Hamer model. The current model successfully reconstructed light intensity-, ATP- and GTP-dependent changes in concentrations of phosphorylated visual pigments (VPs), activated transducins (Tr*s) and phosphodiesterases (PDEs) in rods and cones. In comparison to rods, the lower light sensitivity of cones was attributed not only to the lower affinity of activated VPs for Trs but also to the faster desensitization of the VPs. The assumption of an intermediate inactive state, MIIi, in the thermal decay of activated VPs was essential for inducing faster inactivation of VPs in rods, and possibly also in cones.
Vasculature–function relationship in open-angle glaucomatous eyes with a choroidal microvasculature dropout
Authors: Lee Anna , Shin Joong Won , Lee Jin Yeong , Baek Min Su , Kook Michael S. 
Published: November 2022

AbstractIdentifying biomarkers associated with functional impairment is important in monitoring glaucoma patients. This retrospective cross-sectional study investigated the vasculature–function relationship in open-angle glaucoma (OAG) eyes with choroidal microvasculature dropout (CMvD) versus in OAG eyes without. Optical coherence tomography (OCT) angiography-derived circumpapillary (cpVD) and macular vessel densities (mVD) were measured in 159 early-stage OAG eyes (mean deviation >  −6 dB) in accordance with the presence or not of a CMvD. OCT-derived circumpapillary retinal nerve fibre layer thickness (cpRNFLT) and macular ganglion cell-inner plexiform layer thicknesses (mGCIPLT) were also measured as reference standards. The vasculature (cpVD and mVD)–function [24-2 visual field mean sensitivity (VFMS) and central 10° VFMS (cVFMS)] and structure (cpRNFLT and mGCIPLT)–function (24-2 VFMS and cVFMS) relationships were compared using global and sectoral maps between OAG eyes with (CMvD+) and without CMvD (CMvD−). The CMvD+ eyes showed significantly steeper cpVD-24-2 VFMS and mVD-cVFMS correlations (P < 0.05). In contrast, there were no significant differences in the cpRNFLT-24-2 VFMS and mGCIPLT-cVFMS relationships between the two groups (P > 0.05). In conclusion, OAG eyes with a CMvD have significantly stronger vasculature–function relationships than eyes without. Vessel density parameters may be useful biomarkers of disease progression in early-stage OAG patients with a CMvD.
Spectrally selective antireflection of nanoimprint lithography-formed 3D spherical structures on film coated with a silver layer
Authors: Chiou A. H. , Chang C. W. , Ting C. J. 
Published: November 2022

AbstractWe fabricate moth-eye antireflection (AR) coatings using high-resolution and low-cost UV nanoimprint lithography with polyethylene terphthalate (PET) molds. Several various thicknesses of silver films placed on the moth-eye structure were analyzed for reflectance and transmission. On PET, the conical nanostructured surface arrays had a spatial period length of approximately 250 nm, a diameter of approximately 200 nm, and a height of approximately 160 nm. After them, a silver (Ag) layer of 18 nm is deposited satisfactorily on the PET substrate surface. The never-ending moth-eye formations of the imprinted mold were fabricated by Ni mold electroplating, interference lithography, and replication. We found that an Ag layer of suitable thickness on AR film in the spectrum range that can be seen has high transmittance (Highest value is 72%) while in the infrared spectrum it has high reflectance (At least 60%). For an optical film with a silver coating has been placed on an anti-reflection subwavelength-structured (ASS) surface, such properties, including heat insulation, have obvious applications in windows for homes and vehicles.
Single-cell transcriptomics defines an improved, validated monoculture protocol for differentiation of human iPSC to microglia
Authors: Washer Sam J. , Perez-Alcantara Marta , Chen Yixi , Steer Juliette , James William S. , Trynka Gosia , Bassett Andrew R. , Cowley Sally A. 
Published: November 2022

AbstractThere is increasing genetic evidence for the role of microglia in neurodegenerative diseases, including Alzheimer’s, Parkinson’s, and motor neuron disease. Therefore, there is a need to generate authentic in vitro models to study human microglial physiology. Various methods have been developed using human induced Pluripotent Stem Cells (iPSC) to generate microglia, however, systematic approaches to identify which media components are actually essential for functional microglia are mostly lacking. Here, we systematically assess medium components, coatings, and growth factors required for iPSC differentiation to microglia. Using single-cell RNA sequencing, qPCR, and functional assays, with validation across two labs, we have identified several medium components from previous protocols that are redundant and do not contribute to microglial identity. We provide an optimised, defined medium which produces both transcriptionally and functionally relevant microglia for modelling microglial physiology in neuroinflammation and for drug discovery.
A general framework for optimising cost-effectiveness of pandemic response under partial intervention measures
Authors: Nguyen Quang Dang , Prokopenko Mikhail 
Published: November 2022

AbstractThe COVID-19 pandemic created enormous public health and socioeconomic challenges. The health effects of vaccination and non-pharmaceutical interventions (NPIs) were often contrasted with significant social and economic costs. We describe a general framework aimed to derive adaptive cost-effective interventions, adequate for both recent and emerging pandemic threats. We also quantify the net health benefits and propose a reinforcement learning approach to optimise adaptive NPIs. The approach utilises an agent-based model simulating pandemic responses in Australia, and accounts for a heterogeneous population with variable levels of compliance fluctuating over time and across individuals. Our analysis shows that a significant net health benefit may be attained by adaptive NPIs formed by partial social distancing measures, coupled with moderate levels of the society’s willingness to pay for health gains (health losses averted). We demonstrate that a socially acceptable balance between health effects and incurred economic costs is achievable over a long term, despite possible early setbacks.
Spatial–temporal contrast sensitivity of the eye alignment reflex
Authors: Dhungel Deepa , Stevenson Scott B. 
Published: November 2022

AbstractThe binocular alignment of the eyes involves both voluntary and reflexive mechanisms, but little is known about the visual input and neurological pathway of the reflex component. Our studies examined the role of spatiotemporal frequency and contrast in the control of reflex eye alignment, and compared the contrast sensitivity of the alignment reflex with psychophysical contrast sensitivity. We measured the contrast sensitivity of vertical disparity-driven vergence eye movements in response to bandwidth filtered static or 6 Hz counterphase flickering noise and measured psychophysical detection sensitivity for the same stimuli. Contrast thresholds for producing a detectable vertical alignment change (measured with nonius lines) were determined using a staircase method for 7 spatial frequencies [0.25–16 cycles per degree] and 3 vertical disparities [5, 10, and 30 arcmin] in 7 adults with normal or corrected to normal vision. The main findings of this study are, (1) the vertical alignment reflex had overall relatively high contrast sensitivity, comparable to but somewhat less than visual detection thresholds, (2) the most effective stimulus spatial frequency scaled in inverse proportion to the disparity being stimulated, and (3) unlike psychophysical contrast sensitivity, the eye alignment reflex contrast sensitivity was not improved by flickering low spatial frequencies.
Failure energy evolution of coal–rock combination with different inclinations
Authors: Yu Yongjiang , Liu Jingjing , Yang Yuntao , Wang Pengbo , Wang Zhenmeng , Song Zhiyuan , Liu Jiaming , Zhao Shangqing 
Published: November 2022

AbstractIn this paper, in the deformation and damage process under different confining pressures, the energy evolution characteristics and damage mechanism of coal–rock combinations with different inclination angles are studied. Based on the brittleness indexes of coal rock combinations, the evolution rules between brittleness indexes and the inclination are explored, as well as the confining pressure of coal rock combinations; then, the influence mechanism of the inclination angle of coal rock combinations on the plastic yielding degree, energy dissipation level, crack extension and fracture speed in the pre-peak stage is revealed. The composite specimens are mainly damaged due to oblique shear and accompanied by tensile damage; In the deformation and damage, various energies of coal rock composites are distributed as a negative exponential function of the inclination angle, which is significantly affected by the change of the confining pressure.
Inducer-free cellulase production system based on the constitutive expression of mutated XYR1 and ACE3 in the industrial fungus Trichoderma reesei
Authors: Arai Toshiharu , Ichinose Sakurako , Shibata Nozomu , Kakeshita Hiroshi , Kodama Hiroshi , Igarashi Kazuaki , Takimura Yasushi 
Published: November 2022

AbstractTrichodermareesei is a widely used host for producing cellulase and hemicellulase cocktails for lignocellulosic biomass degradation. Here, we report a genetic modification strategy for industrial T.reesei that enables enzyme production using simple glucose without inducers, such as cellulose, lactose and sophorose. Previously, the mutated XYR1V821F or XYR1A824V was known to induce xylanase and cellulase using only glucose as a carbon source, but its enzyme composition was biased toward xylanases, and its performance was insufficient to degrade lignocellulose efficiently. Therefore, we examined combinations of mutated XYR1V821F and constitutively expressed CRT1, BGLR, VIB1, ACE2, or ACE3, known as cellulase regulators and essential factors for cellulase expression to the T.reesei E1AB1 strain that has been highly mutagenized for improving enzyme productivity and expressing a ß-glucosidase for high enzyme performance. The results showed that expression of ACE3 to the mutated XYR1V821F expressing strain promoted cellulase expression. Furthermore, co-expression of these two transcription factors also resulted in increased productivity, with enzyme productivity 1.5-fold higher than with the conventional single expression of mutated XYR1V821F. Additionally, that productivity was 5.5-fold higher compared to productivity with an enhanced single expression of ACE3. Moreover, although the DNA-binding domain of ACE3 had been considered essential for inducer-free cellulase production, we found that ACE3 with a partially truncated DNA-binding domain was more effective in cellulase production when co-expressed with a mutated XYR1V821F. This study demonstrates that co-expression of the two transcription factors, the mutated XYR1V821F or XYR1A824V and ACE3, resulted in optimized enzyme composition and increased productivity.
Factors associated with meeting the WHO physical activity recommendations in pregnant Colombian women
Authors: López-Gil José Francisco , Izquierdo Mikel , García-Hermoso Antonio , Alonso-Martínez Alicia M. , Rincón-Pabón David , Morales-Osorio Marco Antonio , Ramírez-Vélez Robinson 
Published: November 2022

AbstractIn the absence of medical contraindications, physical activity (PA) can offer health maternal and fetal health outcomes during pregnancy. However, most pregnant women may not consider PA to be feasible, suitable and safe. Hence, it is essential to determine the prevalence of pregnant women who meet the PA recommendations and the possible factors associated with that meeting, since it might be important from the perspective of pregnant women's health. The aim of the present study was to establish the prevalence of meeting the World Health Organization PA recommendations for Colombian pregnant women, as well as possible factors that may be associated with meeting that recommendations. A cross-sectional study including representative data from the National Nutritional Situation Survey (2015) in Colombia was performed. Data were collected in 2015–2016. From an initial sample of 1140 Colombian pregnant women, 702 participants with complete data were included in the final analysis. PA was assessed by self-reported information through the long version of the International Physical Activity Questionnaire. Several potential factors were analysed according to four levels of the socioecological model: the individual, interpersonal, organizational and community levels. The prevalence of Colombian pregnant women who met with the PA recommendations was 7.5%. Indigenous and Mestizo pregnant women showed lower probabilities of meeting the PA recommendations [Indigenous: OR 0.05, 95% CI (0.01–0.18); Mestizo: OR 0.12, 95% CI (0.06–0.22)] than Afro-Colombian participants. Additionally, participants who lived near green and safe spaces for PA were more likely to meet the PA recommendations [OR 2.30, 95% CI (1.06–4.79)] than those who did not live near green areas. In conclusion, a low percentage of Colombian pregnant women met the new PA recommendations. The associations found according to race/ethnicity and living near green and safe areas underline the presence of fundamental disparities associated with meeting PA recommendations.