bluuebunny/crossref_metadata_2025_split huggingface dataset:
Light Sketching for Ecology: A cooperative design tool for balancing human experience and ecological impact
Authors: Ross Philip R , Rutten Niek 
Published: November 2022

Abstract
The impact of artificial light at night on ecology is an urgent and continuous consideration in lighting design. People’s needs and wishes for light in urban areas often conflict with demands for minimising ecological impact. For example, in city parks people may desire light that offers a pleasant experience of nature and the feeling of safety, while the fauna may thrive best with no light at all. How to overcome this seemingly unresolvable conflict, especially in hybrid environments like city parks? This paper presents Light Sketching for Ecology, a cooperative lighting design tool to help balance lighting demands from the human experience side with demands for minimising ecological impact. Results from a pilot study show the potential of Light Sketching for Ecology to create a win-win situation in which park users are more positive about the park lighting while the lighting’s ecological impact is significantly lowered.
Microstructure, mechanical properties and tear toughness of laser-welded DP980 dual phase steel
Authors: Huang Jiajin , Li Shengci , Ren Yupeng , Zhang Zhiqian , Li Dehua 
Published: November 2022

Abstract
In this study, DP980 steel sheets were laser welded with a laser power of 4.5 kW and a welding speed of 4.5 m min−1. The microstructural evolution and mechanical properties of the welded joint and the effect of notch location on tear toughness were evaluated. Results show that the fusion zone (FZ) was composed of lath martensite, the hardness (276 HV) of the heat-affected zone (HAZ) was lower than that of the base metal (305 HV) resulting from martensite tempering. The welded specimens failed at the soft HAZ with a 98.4% joint efficiency during the tensile test, and the ultimate tensile strength of the as-recieved steel and welded joint was 1026 MPa and 1010 MPa, respectively. The tear energy of the FZ and HAZ was lower than DP980 base metal (BM). Thus, it is considered that the fracture toughness of the joint decreased after welding. The crack growth path of the FZ gradually deviated toward the HAZ during tearing due to the asymmetrical plastic zone at the crack tip. Compared with the ductile fracture of the base metal, the significant decrease in the fracture toughness of the welded joint is due to the weak deformation resistance of tempered martensite.
Quantum capsule networks
Authors: Liu Zidu , Shen Pei-Xin , Li Weikang , Duan L-M , Deng Dong-Ling 
Published: November 2022

Abstract
Capsule networks (CapsNets), which incorporate the paradigms of connectionism and symbolism, have brought fresh insights into artificial intelligence (AI). The capsule, as the building block of CapsNets, is a group of neurons represented by a vector to encode different features of an entity. The information is extracted hierarchically through capsule layers via routing algorithms. Here, we introduce a quantum capsule network (dubbed QCapsNet) together with an efficient quantum dynamic routing algorithm. To benchmark the performance of the QCapsNet, we carry out extensive numerical simulations on the classification of handwritten digits and symmetry-protected topological phases, and show that the QCapsNet can achieve an enhanced accuracy and outperform conventional quantum classifiers evidently. We further unpack the output capsule state and find that a particular subspace may correspond to a human-understandable feature of the input data, which indicates the potential explainability of such networks. Our work reveals an intriguing prospect of QCapsNets in quantum machine learning, which may provide a valuable guide towards explainable quantum AI.
HCDT: an integrated highly confident drug–target resource
Authors: Chen Jiaqi , Chen Zhengxin , Chen Rufei , Feng Dehua , Li Tianyi , Han Huirui , Bi Xiaoman , Wang Zhenzhen , Li Kongning , Li Yongsheng , Li Xia , Wang Limei , Li Jin 
Published: November 2022

Abstract
Drug–target association plays an important role in drug discovery, drug repositioning, drug synergy prediction, etc. Currently, a lot of drug-related databases, such as DrugBank and BindingDB, have emerged. However, these databases are separate, incomplete and non-uniform with different criteria. Here, we integrated eight drug-related databases; collected, filtered and supplemented drugs, target genes and experimentally validated (highly confident) associations and built a highly confident drug–target (HCDT: http://hainmu-biobigdata.com/hcdt) database. HCDT database includes 500 681 HCDT associations between 299 458 drugs and 5618 target genes. Compared to individual databases, HCDT database contains 1.1 to 254.2 times drugs, 1.8–5.5 times target genes and 1.4–27.7 times drug–target associations. It is normative, publicly available and easy for searching, browsing and downloading. Together with multi-omics data, it will be a good resource in analyzing the drug functional mechanism, mining drug-related biological pathways, predicting drug synergy, etc.
Database URL: http://hainmu-biobigdata.com/hcdt
Genome assembly and transcriptomic analyses of the repeatedly rejuvenating jellyfish Turritopsis dohrnii
Authors: Hasegawa Yoshinori , Watanabe Takashi , Otsuka Reo , Toné Shigenobu , Kubota Shin , Hirakawa Hideki 
Published: November 2022

Abstract
Only two hydromedusan species, Turritopsis dohrnii and T. sp., have exhibited experimental multiple-repeat life cycle reversion in the laboratory, which can be artificially induced by various means such as incubation with CsCl, heat shock, and mechanical damage with needles. In the present study, we constructed a genome assembly of T. dohrnii using Pacific Biosciences long-reads and Illumina short-reads, for which the genome DNA was extracted from 1,500 young medusae originated from a single clone. The total length of the draft genome sequence of T. dohrnii was 435.9 Mb (N50 length 747.2 kb). We identified 23,314 high-confidence genes and found the characteristics of RNA expression amongst developmental stages. Our genome assembly and transcriptome data provide a key model system resource that will be useful for understanding cyclical rejuvenation.
The effect of a Prasugrel- vs. a Ticagrelor-based strategy on total ischaemic and bleeding events in patients with acute coronary syndromes
Authors: Aytekin Alp , Coughlan J J , Ndrepepa Gjin , Cassese Salvatore , Lahu Shqipdona , Kufner Sebastian , Mayer Katharina , Xhepa Erion , Gewalt Senta , Joner Michael , Hapfelmeier Alexander , Angiolillo Dominick J , Menichelli Maurizio , Richardt Gert , Neumann Franz J , Schunkert Heribert , Kastrati Adnan 
Published: November 2022

AbstractAimsThe effect of a prasugrel vs. a ticagrelor based strategy on total (including both first and recurrent) ischaemic and bleeding events in patients with acute coronary syndromes (ACS) has not been evaluated. The aim of this analysis was to investigate the treatment effect of a prasugrel vs. a ticagrelor based strategy in patients with ACS undergoing an invasive management strategy when both first and recurrent non-fatal ischaemic and bleeding events are taken into account.Methods and resultsThis is a post-hoc analysis of the ISAR-REACT 5 randomized control trial, including all 4018 patients in the trial. The main clinical endpoints of interest included ischaemic events [myocardial infarction (MI) and stroke] and bleeding events [Bleeding Academic Research Consortium (BARC) type 3 to 5 bleeding]. An additional endpoint of interest was definite/probable stent thrombosis. The effect of the prasugrel vs. ticagrelor based strategies on these endpoints was evaluated on both time-to-first event and total events analyses. Patients in the prasugrel group had a lower risk of MI in comparison to the ticagrelor group on both time-to-first event [hazard ratio (HR) = 0.61; 95% confidence interval 0.44–0.85] and total events [HR = 0.62 (0.45–0.86)] analysis. The risk of BARC type 3 to 5 bleeding was comparable between the prasugrel and ticagrelor groups on both time-to-first event [HR = 0.96 (0.75–1.25)] and total events [HR = 0.99 (0.76–1.31)] analysis.ConclusionA prasugrel based strategy was associated with a reduction in total MI events in comparison to a ticagrelor based strategy in patients with ACS undergoing invasive assessment. Total BARC type 3 to 5 bleeding events were comparable between the two groups. Given the importance of this topic, future studies to confirm these findings would be welcome.ClinicalTrials.gov identifier: NCT01944800
In Vitro Dissolution Profile of Antihypertensive Mixture: Comparison Between Multivariate Methods and Statistical and Graphical Representation of Different Univariate Spectrophotometric Data
Authors: Magdy Ragaa , Hemdan Ahmed , Farouk Maha , Fares Nermine V 
Published: November 2022

Abstract

Background
Triplixam® is a new antihypertensive drug combination consisting of perindopril, amlodipine, and indapamide, which have a synergistic mechanism of action in combination with each other.

Objective
Comparative study of different spectrophotometric approaches used for the simultaneous determination of perindopril, indapamide, and amlodipine in bulk powder and in dosage form Triplixam.

Method
The methods include univariate and multivariate spectrophotometric methods depending on either mathematical calculation or graphical representation of data. For the univariate methods: perindopril was resolved from other components using constant multiplication followed by spectrum subtraction resolution technique, and then two base point, AUC, constant value, and concentration value (CNV) methods were applied. For both amlodipine and indapamide: constant multiplication resolution technique was used, and then constant value and CNV methods were applied. CNV depends on graphical representation of data rather than statistical data. PLS and PCR chemometric assisted spectrophotometric techniques were also applied. The proposed methods are considered a green alternative to the reported methods as the greenness of the proposed methods was evaluated qualitatively and quantitatively by four green analytical evaluation tools.

Results
The methods were applied for the analysis of the mixture in the pharmaceutical dosage form Triplixam and in vitro release at intestinal pH (7.4) using a USP dissolution tester.

Conclusions
The proposed green analytical methods are considered to be greener than the reported methods and simpler, so they could be used as an alternative for routine analysis of the mixture in quality control laboratories for the reason of their accurate results beside minimum manipulation steps that reduced the error and time required of the analysis with no harmful effect on analyst health as well as the environment.

Highlights
The study was the first in vitro dissolution profiling of perindopril, amlodipine, and indapamide. The developed methods were excellent green methods without compromising the analytical criteria.
Functional engineering strategies of 3D printed implants for hard tissue replacement
Authors: Chen Cen , Huang Bo , Liu Yi , Liu Fan , Lee In-Seop 
Published: November 2022

AbstractThree-dimensional printing technology with the rapid development of printing materials are widely recognized as a promising way to fabricate bioartificial bone tissues. In consideration of the disadvantages of bone substitutes, including poor mechanical properties, lack of vascularization and insufficient osteointegration, functional modification strategies can provide multiple functions and desired characteristics of printing materials, enhance their physicochemical and biological properties in bone tissue engineering. Thus, this review focuses on the advances of functional engineering strategies for 3D printed biomaterials in hard tissue replacement. It is structured as introducing 3D printing technologies, properties of printing materials (metals, ceramics and polymers) and typical functional engineering strategies utilized in the application of bone, cartilage and joint regeneration.
Fructobacillus apis sp. nov., isolated from the gut of honeybee (Apis mellifera)
Authors: Chen Yi-sheng , Wang Li-Ting , Lin Shih-Ting , Lee Yun-Shien , Chang Yu-Chung , Wu Hui-Chung , Liao Chia-Yu , Chen Wei-Hua , Deng Jin-Nan , Wang Yu-Hsuan 
Published: November 2022

A Gram-positive, facultatively anaerobic, catalase-negative, fructose-dependent strain (W13T) was isolated from the gut of honeybee (Apis mellifera). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain W13T represents a distinct line of descent within the genus

Fructobacillus

, with the closest neighbours being

Fructobacillus broussonetiae

BCRC 81240T (98.9 % sequence similarity) and

Fructobacillus durionis

DSM 19113T (96.8 % sequence similarity). Comparative sequencing of the additional phylogenetic markers rpoC and recA confirmed the 16S rRNA gene tree topology. The complete genome of strain W13T consisted of 1 292 712 bp with a G+C content of 48.3 mol%. Pairwise comparisons of the average nucleotide identity values and digital DNA–DNA hybridization values between the genomes of W13T and its close phylogenetic neighbours,

F. broussonetiae

BCRC 81240T and

F. durionis

DSM 19113T, resulted in 76.2–84.1 % and 20.2–27.6 %, respectively. The main cellular fatty acids of strain W13T were C16 : 0, C18 : 1
ω9c and C18 : 1
ω7c. Thus, we propose a novel species within the genus

Fructobacillus

, with the name Fructobacillus apis sp. nov. and the type strain is W13T (= NBRC 115637T=BCRC 81365T).
Amyloid Beta Peptides Inhibit Glucose Transport at the Blood-brain Barrier by Disrupting Insulin-Akt Pathway in Alzheimer’s Disease
Authors: Wang Lushan , Curran Geoffry L. , Min Paul H. , Li Ling , Lowe Val J. , Kandimalla Karunya K. 
Published: November 2022

AbstractDisruptions in glucose uptake and metabolism in the brain are implicated in metabolic disorders and Alzheimer’s disease (AD). Toxic soluble amyloid-beta (sAß) peptides accumulating in the brain and plasma of AD patients were suggested to promote blood-brain barrier (BBB) dysfunction, brain hypometabolism, and cognitive decline. Exposure to sAß peptides is reported to interfere with glucose metabolism in the brain parenchyma, although their effects on the BBB have not been fully characterized. Our data showed that the brain uptake of glucose surrogate, [18F]-fluorodeoxyglucose (18FDG), was reduced significantly in APP/PS1 transgenic mice (overproduce Aß) compared to wild-type (WT) mice. In addition, the influx rate of18FDG was also decreased in both Aß40 and Aß42 pre-infused mice compared to control mice. Glucose is primarily delivered from blood into the brain via glucose transporter 1 (GLUT1). The confocal microscopy experiment showed that Aß40 and Aß42 peptides significantly decreased GLUT1 expression in polarized human cerebral microvascular endothelial cell (hCMEC/D3) monolayers. Insulin-AKT pathway has been observed to induce glucose uptake via regulating the expression of TXNIP, the only α-arrestin protein known to bind to thioredoxin. We found that Aß40 and Aß42 peptides decreased p-AKT and increased TXNIP expression in the hCMEC/D3 cell monolayers. MK2206, a kinase inhibitor of AKT, was used to confirm that inhibition of insulin/AKT pathway reduced GLUT1 expression in an insulin-independent manner in the hCMEC/D3 cell monolayers. These results suggest that inhibitory effects of sAß on GLUT1 expression are mediated by inhibition of the insulin/AKT pathway. The role of TXNIP on endothelial GLUT1 expression was investigated using resveratrol, which has been reported to downregulate TXNIP overexpression. Consistently, resveratrol treatment led to a significant increase in GLUT1 expression in the hCMEC/D3 cell monolayers. Furthermore, by co-incubation of resveratrol and sAß peptides in hCMEC/D3 cell monolayers, we found that resveratrol rectified the aberrant TXNIP expression caused by sAß peptides. Together, these findings provide novel evidence that toxic sAß peptide exposure inhibits glucose transport at the BBB by decreasing GLUT1 expression via the insulin/Akt/TXNIP axis.
Smurfness-based two-phase model of ageing helps deconvolve the ageing transcriptional signature
Authors: Zane Flaminia , Bouzid Hayet , Marmol Sofia Sosa , Brazane Mira , Besse Savandara , Molina Julia Lisa , Cansell Céline , Aprahamian Fanny , Durand Sylvère , Ayache Jessica , Antoniewski Christophe , Todd Nicolas , Carré Clément , Rera Michael 
Published: November 2022

AbstractAgeing is characterised at the molecular level by six transcriptional ‘hallmarks of ageing’, that are commonly described as progressively affected as time passes. By contrast, the ‘Smurf’ assay separates high-and-constant-mortality risk individuals from healthy, zero-mortality risk individuals, based on increased intestinal permeability. Performing whole body total RNA sequencing, we found that Smurfness distinguishes transcriptional changes associated with chronological age from those associated with biological age. We show that transcriptional heterogeneity increases with chronological age in non-Smurf individuals preceding the other five hallmarks of ageing, that are specifically associated with the Smurf state. Using this approach, we also devise targeted pro-longevity genetic interventions delaying entry in the Smurf state. We anticipate that increased attention to the evolutionary conserved Smurf phenotype will bring about significant advances in our understanding of the mechanisms of ageing.Graphical abstractThe two-phase model of ageing allows to study separately the effect of chronological and physiological age.(A)Classic approaches for studying ageing tend to consider it as a black box affecting all individuals progressively from birth to death. Instead, the Smurf phenotype shows that life can be divided into two consecutive phases separated by an abrupt transition.(B)All individuals undergo this transition at a different moment in their life, prior to death. This allows us to switch from population based approaches, comparing bulks of age-matched individuals through time, to individuals-centred approaches relying on direct access to their transition status.(C)Such paradigm shift shows that hallmarks of ageing long thought to progressively change with age are actually mostly affected in a growing proportion of Smurfs, allowing for the identification of the chain of events accompanying ageing and death from natural causes.(D)By studying the behaviour of the ageing transcriptome as a function of chronological age and Smurfness separately, we demonstrate that the progressively changing transcriptional ageing signature, as described in Frenk & Houseley (2018), is in fact the convolution changes accompanying chronological age signature (increased transcriptional noise) and changes associated with Smurfness (or biological age) signature (increased stress response and inflammation, decreased expression of ribosomal and mitochondrial genes). We also identified a hallmark partially associated with only old Smurfs (ATH5), suggesting that chronological age can affect, late in life, the Smurf response.
Generating synthetic data with a mechanism-based Critical Illness Digital Twin: Demonstration for Post Traumatic Acute Respiratory Distress Syndrome
Authors: Cockrell Chase , Schobel-McHugh Seth , Lisboa Felipe , Vodovotz Yoram , An Gary 
Published: November 2022

AbstractMachine learning (ML) and Artificial Intelligence (AI) approaches are increasingly applied to predicting the development of sepsis and multiple organ failure. While there has been success in demonstrating the clinical utility of such systems in terms of affecting various outcomes, there are fundamental challenges to the ML/AI approach in terms of improving the actual predictive performance and future robustness of such systems. Given that one of the primary proposed avenues for improving algorithmic performance is the addition of molecular/biomarker/genetic features to the data used to train these systems, the overall sparsity of such available data suggests the need to generate synthetic data to aid in training, as has been the case in numerous other ML/AI tasks, such as image recognition/generation and text analysis/generation. We propose the need to generate synthetic molecular/mediator time series data coincides with the advent of the concept of medical digital twins, specifically related to interpretations of medical digital twins that hew closely to the original description and use of industrial digital twins, which involve simulating multiple individual twins from a common computational model specification. Herein we present an example of generating synthetic time series data of a panel of pro- and anti-inflammatory cytokines using the Critical Illness Digital Twin (CIDT) regarding the development of post-traumatic acute respiratory distress syndrome.
Rasputin/G3BP mediates o’nyong-nyong virus subversion of antiviral immunity in Anopheles coluzzii
Authors: Cottis Solène , Blisnick Adrien , Mitri Christian , Brito-Fravallo Emma , Matondo Mariette , Failloux Anna-Bella , Vernick Kenneth D. 
Published: November 2022

ABSTRACTThe G3BP proteins in vertebrates and Aedes mosquito ortholog, Rasputin, are essential for alphavirus infection, but the underlying mechanism of Rasputin/G3BP proviral activity is poorly understood. It has been suggested that G3BP could influence host immune signaling, but this has not been functionally demonstrated. Here, we find that depletion of Rasputin activity in Anopheles mosquitoes, the primary vectors of the alphavirus o’nyong-nyong (ONNV), provokes dysregulation of the antiviral Imd, JAK/STAT and RNAi pathways, indicating that Rasputin is required for expression of normal basal immunity in uninfected mosquitoes. Depletion of Rasputin during ONNV bloodmeal infection causes increased transcript abundance of genes in the Imd pathway including positive regulator Rel2, and decreases ONNV infection in mosquitoes. Loss of Rasputin is complemented by co-depletion of Imd pathway positive regulator, Rel2, which restores normal ONNV infection levels. Thus, the presence of Rasputin is required for ONNV inhibition of Imd activity, and viral inhibition of Imd explains much of the Rasputin proviral activity. The viral non-structural protein 3 (nsP3) binds to Rasputin and alters the profile of cellular proteins binding to Rasputin. In the presence of nsP3, 48 Rasputin-binding proteins are unchanged but seven binding proteins are excluded and eight new proteins bind Rasputin. The Rasputin binding partners altered by nsP3 are candidate factors for ONNV immune manipulation and subversion through Rasputin. Overall, these results are consistent with and strongly suggest a mechanism in which ONNV, probably nsP3, co-opts the normal Rasputin function assuring basal cellular immune activity in order to inhibit antiviral immunity and promote infection. These observations may be generalizable for Rasputin function during alphavirus infection of other mosquitoes, as well as for G3BP function in the mammalian host, and could offer a target for vector-based control of arbovirus transmission.