bluuebunny/crossref_metadata_2025 huggingface dataset:
Importation of a novel Indian Ocean lineage carrying E1-K211E and E2-V264A of Chikungunya Virus in Zhejiang Province, China, in 2019
Authors: Su Lingxuan , Lou Xiuyu , Yan Hao , Yang Zhangnv , Mao Haiyan , Yao Wenwu , Sun Yi , Pan Junhang , Zhang Yanjun
Published: July 2023

The chikungunya virus (CHIKV) is widespread. In Zhejiang province, China, CHIKV infection is often associated with travelers from tropical and subtropical countries. In the present study, three CHIKV isolates from serum samples of travelers in Zhejiang province in 2019 were sequenced, and phylogenetically analyzed to study their molecular characteristics. Sequence analysis showed that the non-structural protein and the structural protein had 37 and 28 amino acid mutations, respectively; no mutation site was found at the E1-A226 residue, which could increase the adaptability of CHIKV to Aedes albopictus. All three samples carried two mutations, namely, E1-K211E and E2-V264A, which were introduced to Bangladesh around late 2015 and Thailand in early 2017. Phylogenetic analysis revealed that these three CHIKVs were Indian Ocean lineage of the East Africa/Central/South Africa genotype (ECSA) and that the MF773566 strain from Bangladesh (Australia/Bangladesh 2017) had the closest evolutionary relationship. The three CHICKs imported into Zhejiang province in 2019 belonged to the ECSA genotype and had multiple amino acid variation sites. The variation in the three samples provides a certain reference for the subsequent research on CHIKV evolution.
Short Communication — Stability of “Free” Norovirus RNA on Fresh Produce
Authors: D’Agostino Martin
Published: July 2023

The accuracy and dependability of results generated through molecular detection of specific target sequences of RNA, commonly used for detecting viruses in food, have been extensively debated within the scientific community. Such concerns have been raised by researchers, clients, and regulators alike, highlighting the need for further investigation and clarification. In particular, there has been debate about the possibility of molecular methods to detect enteric viruses, such as norovirus, in foods, producing false positive RT-PCR results due to the presence of “free” target RNA sequences in the food supply chain environment. This study aimed to investigate this issue by evaluating the recovery of “free” norovirus RNA from lettuce leaves. The “free” RNA was produced using heat treatment and chemical extraction methods. The study findings indicate that recovery of heat-extracted RNA from the lettuce leaves decreased markedly within 24 h, while recovery of chemically extracted RNA remained stable and even increased over time. The results of this study suggest that positive molecular detection of viruses in food is more likely to be associated with intact and potentially infectious virus particles, rather than “free” unprotected RNA. These findings have significant implications for the food industry and regulatory bodies in terms of the interpretation, accuracy and reliability of molecular detection methods for virus detection in food.
Participation in Online Mindfulness was Associated with Improved Self-Compassion and Prosocial Attitudes
Authors: Bailey Neil W. , Comte Whitney , Chambers Richard , Bartlett Larissa , Connaughton Sherelle , Hassed Craig
Published: July 2023

Objectives

Online mindfulness programs have become popular due to their increased accessibility compared to face-to-face programs. Although research has demonstrated that face-to-face mindfulness programs can increase trait mindfulness, self-compassion, and prosocial attitudes, fewer studies have explored these outcomes in online programs. This study aimed to test whether an online mindfulness program improved trait mindfulness, self-compassion, and prosocial attitudes, and whether improvements related to self-reported quality and quantity of mindfulness practice.

Method

Repeated-measures ANOVAs compared measures of trait mindfulness, self-compassion, and prosocial attitudes between 209 pre- and post-program survey responses from participants who completed a 4-week online mindfulness program. Regressions were used to test whether the quantity or quality of mindfulness practice predicted changes in these measures, and mediation analyses tested whether associations between mindfulness practice and outcomes were mediated by changes in trait mindfulness.

Results

The study found that participation in the mindfulness program was associated with improved trait mindfulness, self-compassion, and prosocial attitudes (all p < 0.01) and that males showed larger increases in prosocial attitudes (p < 0.05). The study also showed an association between the quality of formal mindfulness practice and improvements in both self-compassion and trait mindfulness (p < 0.01). Lastly, the mediation analysis suggested the association between the quality of formal practice and self-compassion was mediated by changes in trait mindfulness (p < 0.05).

Conclusion

These results suggest online mindfulness programs can lead to improved trait mindfulness, self-compassion, and prosocial attitudes. Our results also indicate that higher self-reported practice quality is related to improved trait mindfulness, and that changes in trait mindfulness mediated improved self-compassion.

Pre-registration

This study was not pre-registered.
Irony with a Point: Alan Turing and His Intelligent Machine Utopia
Authors: Gonçalves Bernardo
Published: July 2023

Turing made strong statements about the future of machines in society. This article asks how they can be interpreted to advance our understanding of Turing’s philosophy. His irony has been largely caricatured or minimized by historians, philosophers, scientists, and others. Turing is often portrayed as an irresponsible scientist, or associated with childlike manners and polite humor. While these representations of Turing have been widely disseminated, another image suggested by one of his contemporaries, that of a nonconformist, utopian, and radically progressive thinker reminiscent of the English Romantic poet Percy B. Shelley, has remained largely underexplored. Following this image, I will reconstruct the argument underlying what Turing called (but denied being guilty of) his “Promethean irreverence” (1947–1951) as a utopian satire directed against chauvinists of all kinds, especially intellectuals who might sacrifice independent thought to maintain their power. These, Turing hoped, would eventually be rivaled and surpassed by intelligent machines and transformed into ordinary people, as work once considered “intellectual” would be transformed into non-intellectual, “mechanical” work. I study Turing’s irony in its historical context and follow the internal logic of his arguments to their limit. I suggest that Turing genuinely believed that the possibilities of the machines he envisioned were not utopian dreams, and yet he conceived them from a utopian frame of mind, aspiring to a different society. His ever-learning child machines, whose intelligence would grow out of their own individual experiences, would help distribute power.
Beyond Anatomy: The Role of Molecular Imaging in the Evaluation of Low Back Pain
Authors: Sweetwood Kevin , Junn Jacqueline C. , Qiao Yujie , Berven Sigurd , Shah Vinil , Pampaloni Miguel Hernandez , Flavell Robert R. , Dillon William , Talbott Jason , Lawhn-Heath Courtney
Published: July 2023

Purpose of Review

To review the role of molecular imaging modalities in the evaluation of low back pain and identification of active pain generators.

Recent Findings

Low back pain is a common condition associated with high utilization of imaging. Identification of a pain source in patients with nonspecific low back pain is an important clinical challenge. However, there is inadequate correlation between anatomic findings on CT and MRI with symptoms of back pain, or clinical response to therapeutic procedures including injection or surgery. In contrast, molecular imaging modalities including single-photon emission-computed tomography (SPECT) or positron emission tomography (PET) with bone-targeting radiotracers like Tc-99m methylene diphosphonate (MDP) and18F-NaF paired with CT or MRI demonstrate promise to improve test specificity in identification of pain generators in the spine. An accurate identification of pain source in patients with back pain is important in guiding therapeutic interventions including injection and surgery.

Molecular imaging modalities have demonstrated improved diagnostic accuracy in identifying active pain generators and predicting response to therapeutic intervention compared to anatomic imaging alone.
A scalable physically consistent particle method for high-viscous incompressible flows
Authors: Kondo Masahiro , Matsumoto Junichi , Sawada Tomohiro
Published: July 2023

A scalable matrix solver was developed for the moving particle hydrodynamics for incompressible flows (MPH-I) method. Since the MPH-I method can calculate both incompressible and highly viscous flows while ensuring stability through physical consistency, a wide range of industrial applications is expected. However, in its implicit calculation, both the pressure and velocity must be solved simultaneously via a linear equation with a nondefinite symmetric coefficient matrix. In this study, this nondefinite linear system was converted into a symmetric positive definite (SPD) system where only the velocity is unknown. This conversion enabled us to solve the system with well-known solvers such as the conjugated gradient (CG) and conjugated residual (CR) methods. For scalability, bucket-based multigrid preconditioned CG and CR solvers were developed for the SPD system. To handle multidimensionality during preconditioning, an extended Jacobi smoother that is even applicable in a nondiagonally dominant matrix system was proposed. The numerical efficiency was confirmed via a simple high-viscosity incompressible dam break calculation, and the scalability within the presented case was confirmed. In addition, the performance under shared memory parallel computations was studied.
Distribution and Disputation: Net Benefits, Equity, and Public Decision-Making
Authors: Banzhaf H. Spencer
Published: July 2023

As its practitioners know well, benefit-cost analysis (BCA) walks a fine line between the positive and normative, between the science of economics and the art of political economy. Missteps threaten to undermine its credibility as a value-free science, while overcaution risks irrelevance to the pressing questions of the day. As BCA adapts to give more weight to distributional concerns, while operating in a more highly charged political environment than ever before, these tensions will only grow. For perspective, I reexamine three prominent episodes in the history of economics where these issues were vigorously debated: (i) The founding of the NBER by Wesley Clair Mitchell, who insisted that the organization eschew all policy recommendations; (ii) the introduction of the modern definition of economics as the study of tradeoffs by Lionel Robbins, who insisted welfare effects could never be aggregated; and (iii) the origins of BCA as a measure of income, which to first-generation practitioners seemed to foreclose the possibility of measuring “intangible” benefits like recreation opportunities, mortality risks, and equity. These episodes, together with critiques of economics from philosophers of science, suggest we are best served by being as transparent as possible about the ways values influence BCA reasoning, without arrogating political decisions into it.
Multiomics characterisation of the zoo-housed gorilla gut microbiome reveals bacterial community compositions shifts, fungal cellulose-degrading, and archaeal methanogenic activity
Authors: Houtkamp Isabel M. , van Zijll Langhout Martine , Bessem Mark , Pirovano Walter , Kort Remco
Published: July 2023

We carried out a comparative analysis between the bacterial microbiota composition of zoo-housed western lowland gorillas and their wild counterparts through 16S rRNA gene amplicon sequencing. In addition, we characterised the carbohydrate-active and methanogenic potential of the zoo-housed gorilla (ZHG) microbiome through shotgun metagenomics and RNA sequencing. The ZHG microbiota showed increased alpha diversity in terms of bacterial species richness and a distinct composition from that of the wild gorilla microbiota, including a loss of abundant fibre-degrading and hydrogenic Chloroflexi. Metagenomic analysis of the CAZyome indicated predominant oligosaccharide-degrading activity, while RNA sequencing revealed diverse cellulase and hemi-cellulase activities in the ZHG gut, contributing to a total of 268 identified carbohydrate-active enzymes. Metatranscriptome analysis revealed a substantial contribution of 38% of the transcripts from anaerobic fungi and archaea to the gorilla microbiome. This activity originates from cellulose-degrading and hydrogenic fungal species belonging to the class Neocallimastigomycetes, as well as from methylotrophic and hydrogenotrophic methanogenic archaea belonging to the classes Thermoplasmata and Methanobacteria, respectively. Our study shows the added value of RNA sequencing in a multiomics approach and highlights the contribution of eukaryotic and archaeal activities to the gut microbiome of gorillas.
Limited knowledge of national plastics policy effectiveness may hinder global progress
Authors: March Antaya , Karasik Rachel , Roberts Keiron , Evans Tegan
Published: July 2023

Policy effectiveness is a critical measure for assessing whether policies are working and determining necessary adjustments. However, understanding the effectiveness of plastic policies is a significant gap in the toolkit driving solutions to the plastics crisis. This review examines effectiveness evaluations and existing tools for assessing policy effectiveness. The review further identifies the barriers to understanding effectiveness before proposing ways forward. Most studies focus on plastic bag bans or taxes, neglecting other policy instruments. Additionally, these studies often employ simple attribution approaches, rather than causal inference methods, limiting our ability to determine the true impact of policies on desired outcomes. The lack of monitoring and evaluation of plastic policies further hampers knowledge acquisition. The global understanding of the plastics economy and measurable success metrics is insufficient, hindering the design of systemic interventions. These findings highlight the development and evaluation of plastic policies with limited information. A more nuanced understanding of effective plastic policies is necessary, including a harmonised approach to evaluations, a shared definition of effectiveness, the use of rapid assessment tools and the integration of monitoring and evaluation into policy instruments.
Atrial septal defect-associated pulmonary hypertension with decompensated heart failure: outcomes after fenestrated device closure
Authors: Deniwar Ahmed , Hernandez Jason , Aregullin Enrique O. , Khan Sana K. , Huang Sihong , Finn Michael T. , Vettukattil Joseph J.
Published: July 2023

Background:

Up to 90% of adults with untreated atrial septal defect will be symptomatic by 4th decade, and 30-49% will develop heart failure. 8–10% of these patients have pulmonary arterial hypertension with a female predominance regardless of age. We aimed to demonstrate that fenestrated closure can be safely performed in patients with decompensated heart failure and atrial septal defect-associated pulmonary arterial hypertension with improved outcome.

Methods:

Transcatheter fenestrated atrial septal defect closures (Occlutech GmbH, Jena, Germany) were performed on a compassionate-use basis in 5 consecutive adult patients with atrial septal defect-associated pulmonary arterial hypertension and severe heart failure with prohibitive surgical mortality risks. Change in systemic oxygen saturation, 6-minute walk test, NYHA class, echocardiographic and haemodynamic parameters were used as parameters of outcome.

Results:

All patients were female, mean age 48.8 ± 13.5 years, followed up for a median of 29 months (max 64 months). Significant improvements observed in the 6-minute walk test, and oxygen saturation comparing day 0 time point to all other follow-up time points data (B = 1.32, SE = 0.28, t (22.7) = -4.77, p = 0.0001); and in the haemodynamic data (including pulmonary vascular resistance and pulmonary pressure) (B = –0.60, SE = 0.22, t (40.2) = 2.74, p = .009). All patients showed improved right ventricular size and function along with NYHA class. There were no procedure-related complications.

Conclusion:

Fenestrated atrial septal defect closure is feasible in adults with decompensated heart failure and atrial septal defect-associated pulmonary arterial hypertension. It results in sustained haemodynamic and functional improvement
A Comparison of Plasticity Regularization Approaches for Geodynamic Modeling
Authors: Duretz Thibault , Räss Ludovic , de Borst René , Hageman Tim
Published: July 2023

The emergence, geometry and activation of faults are intrinsically linked to frictional rheology. The latter is thus a central element in geodynamic simulations which aim at modeling the generation and evolution of fault zones and plate boundaries. However, resolving frictional strain localization in geodynamic models is problematic. In simulations, equilibrium cannot always be attained and results can depend on mesh resolution. Spatial and temporal regularization techniques have been developed to alleviate these issues. Herein, we investigate three popular regularization techniques, namely viscoplasticity, gradient plasticity and the use of a Cosserat continuum. These techniques have been implemented in a single framework based on an accelerated pseudo‐transient solution strategy. The latter allows to explore the effects of regularization on shear banding using the same code and model configuration. We have used model configurations that involve three levels of complexity: from the emergence of a single isolated shear band to the visco‐elasto‐plastic stress buildup of a crust. All considered approaches allow to resolve shear banding, provide convergence upon mesh refinement and satisfaction of equilibrium. Viscoplastic regularization is straightforward to implement in geodynamic codes. Nevertheless, more stable shear banding patterns and strength estimates are achieved with computationally more expensive gradient and Cosserat‐type regularizations. We discuss the relative benefits of these techniques and their combinations for geodynamic modeling. Emphasis is put on the potential of Cosserat‐type media for geodynamic applications.
Characterising the RNA-binding protein atlas of the mammalian brain uncovers RBM5 misregulation in mouse models of Huntington’s disease
Authors: Mullari Meeli , Fossat Nicolas , Skotte Niels H. , Asenjo-Martinez Andrea , Humphreys David T. , Bukh Jens , Kirkeby Agnete , Scheel Troels K. H. , Nielsen Michael L.
Published: July 2023

RNA-binding proteins (RBPs) are key players regulating RNA processing and are associated with disorders ranging from cancer to neurodegeneration. Here, we present a proteomics workflow for large-scale identification of RBPs and their RNA-binding regions in the mammalian brain identifying 526 RBPs. Analysing brain tissue from males of the Huntington’s disease (HD) R6/2 mouse model uncovered differential RNA-binding of the alternative splicing regulator RBM5. Combining several omics workflows, we show that RBM5 binds differentially to transcripts enriched in pathways of neurodegeneration in R6/2 brain tissue. We further find these transcripts to undergo changes in splicing and demonstrate that RBM5 directly regulates these changes in human neurons derived from embryonic stem cells. Finally, we reveal that RBM5 interacts differently with several known huntingtin interactors and components of huntingtin aggregates. Collectively, we demonstrate the applicability of our method for capturing RNA interactor dynamics in the contexts of tissue and disease.
An unconventional proanthocyanidin pathway in maize
Authors: Lu Nan , Jun Ji Hyung , Li Ying , Dixon Richard A.
Published: July 2023

Proanthocyanidins (PAs), flavonoid polymers involved in plant defense, are also beneficial to human health and ruminant nutrition. To date, there is little evidence for accumulation of PAs in maize (Zea mays), although maize makes anthocyanins and possesses the key enzyme of the PA pathway, anthocyanidin reductase (ANR). Here, we explore whether there is a functional PA biosynthesis pathway in maize using a combination of analytical chemistry and genetic approaches. The endogenous PA biosynthetic machinery in maize preferentially produces the unusual PA precursor (+)-epicatechin, as well as 4β-(S-cysteinyl)-catechin, as potential PA starter and extension units. Uncommon procyanidin dimers with (+)-epicatechin as starter unit are also found. Expression of soybean (Glycine max) anthocyanidin reductase 1 (ANR1) in maize seeds increases the levels of 4β-(S-cysteinyl)-epicatechin and procyanidin dimers mainly using (-)-epicatechin as starter units. Introducing a Sorghum bicolor transcription factor (SbTT2) specifically regulating PA biosynthesis into a maize inbred deficient in anthocyanin biosynthesis activates both anthocyanin and PA biosynthesis pathways, suggesting conservation of the PA regulatory machinery across species. Our data support the divergence of PA biosynthesis across plant species and offer perspectives for future agricultrural applications in maize.
Tuning electronic and phononic states with hidden order in disordered crystals
Authors: Roth Nikolaj , Goodwin Andrew L.
Published: July 2023

Disorder in crystals is rarely random, and instead involves local correlations whose presence and nature are hidden from conventional crystallographic probes. This hidden order can sometimes be controlled, but its importance for physical properties of materials is not well understood. Using simple models for electronic and interatomic interactions, we show how crystals with identical average structures but different types of hidden order can have very different electronic and phononic band structures. Increasing the strength of local correlations within hidden-order states can open band gaps and tune mode (de)localisation—both mechanisms allowing for fundamental changes in physical properties without long-range symmetry breaking. Taken together, our results demonstrate how control over hidden order offers a new mechanism for tuning material properties, orthogonal to the conventional principles of (ordered) structure/property relationships.
Organization of the human intestine at single-cell resolution
Authors: Hickey John W. , Becker Winston R. , Nevins Stephanie A. , Horning Aaron , Perez Almudena Espin , Zhu Chenchen , Zhu Bokai , Wei Bei , Chiu Roxanne , Chen Derek C. , Cotter Daniel L. , Esplin Edward D. , Weimer Annika K. , Caraccio Chiara , Venkataraaman Vishal , Schürch Christian M. , Black Sarah , Brbić Maria , Cao Kaidi , Chen Shuxiao , Zhang Weiruo , Monte Emma , Zhang Nancy R. , Ma Zongming , Leskovec Jure , Zhang Zhengyan , Lin Shin , Longacre Teri , Plevritis Sylvia K. , Lin Yiing , Nolan Garry P. , Greenleaf William J. , Snyder Michael
Published: July 2023

The intestine is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota and affects overall health1. The intesting has a length of over nine metres, along which there are differences in structure and function2. The localization of individual cell types, cell type development trajectories and detailed cell transcriptional programs probably drive these differences in function. Here, to better understand these differences, we evaluated the organization of single cells using multiplexed imaging and single-nucleus RNA and open chromatin assays across eight different intestinal sites from nine donors. Through systematic analyses, we find cell compositions that differ substantially across regions of the intestine and demonstrate the complexity of epithelial subtypes, and find that the same cell types are organized into distinct neighbourhoods and communities, highlighting distinct immunological niches that are present in the intestine. We also map gene regulatory differences in these cells that are suggestive of a regulatory differentiation cascade, and associate intestinal disease heritability with specific cell types. These results describe the complexity of the cell composition, regulation and organization for this organ, and serve as an important reference map for understanding human biology and disease.
Chromosome-level genome assembly of watershield (Brasenia schreberi)
Authors: Lu Bei , Shi Tao , Chen Jinming
Published: July 2023

Watershield (Brasenia schreberi) is an aquatic plant that belongs to the basal angiosperm family Cabombaceae. This species has been cultivated as an aquatic vegetable for more than 3000 years in East Asia, but the natural populations have greatly declined in recent decades and have become endangered in several countries of East Asia. In this study, by using PacBio long reads, Illumina short reads, and Hi-C sequencing data, we assembled the genome of B. schreberi, which was approximately 1170.4 Mb in size with a contig N50 of 7.1 Mb. Of the total assembled sequences, 93.6% were anchored to 36 pseudochromosomes with a scaffold N50 of 28.9 Mb. A total of 74,699 protein-coding genes were predicted in the B. schreberi genome, and 558 Mb of repetitive elements occupying 47.69% of the genome were identified. BUSCO analysis yielded a completeness score of 95.8%. The assembled high-quality genome of B. schreberi will be a valuable reference for the study of conservation, evolution and molecular breeding in this species.
Biobank-scale methods and projections for sparse polygenic prediction from machine learning
Authors: Raben Timothy G. , Lello Louis , Widen Erik , Hsu Stephen D. H.
Published: July 2023

In this paper we characterize the performance of linear models trained via widely-used sparse machine learning algorithms. We build polygenic scores and examine performance as a function of training set size, genetic ancestral background, and training method. We show that predictor performance is most strongly dependent on size of training data, with smaller gains from algorithmic improvements. We find that LASSO generally performs as well as the best methods, judged by a variety of metrics. We also investigate performance characteristics of predictors trained on one genetic ancestry group when applied to another. Using LASSO, we develop a novel method for projecting AUC and correlation as a function of data size (i.e., for new biobanks) and characterize the asymptotic limit of performance. Additionally, for LASSO (compressed sensing) we show that performance metrics and predictor sparsity are in agreement with theoretical predictions from the Donoho-Tanner phase transition. Specifically, a future predictor trained in the Taiwan Precision Medicine Initiative for asthma can achieve an AUC of $$0.63_{(0.02)}$$

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, respectively, for UK Biobank trained predictors applied to a European population.
Occipital and parietal cortex participate in a cortical network for transsaccadic discrimination of object shape and orientation
Authors: Baltaretu B. R. , Stevens W. Dale , Freud E. , Crawford J. D.
Published: July 2023

Saccades change eye position and interrupt vision several times per second, necessitating neural mechanisms for continuous perception of object identity, orientation, and location. Neuroimaging studies suggest that occipital and parietal cortex play complementary roles for transsaccadic perception of intrinsic versus extrinsic spatial properties, e.g., dorsomedial occipital cortex (cuneus) is sensitive to changes in spatial frequency, whereas the supramarginal gyrus (SMG) is modulated by changes in object orientation. Based on this, we hypothesized that both structures would be recruited to simultaneously monitor object identity and orientation across saccades. To test this, we merged two previous neuroimaging protocols: 21 participants viewed a 2D object and then, after sustained fixation or a saccade, judged whether the shape or orientation of the re-presented object changed. We, then, performed a bilateral region-of-interest analysis on identified cuneus and SMG sites. As hypothesized, cuneus showed both saccade and feature (i.e., object orientation vs. shape change) modulations, and right SMG showed saccade-feature interactions. Further, the cuneus activity time course correlated with several other cortical saccade/visual areas, suggesting a ‘functional network’ for feature discrimination. These results confirm the involvement of occipital/parietal cortex in transsaccadic vision and support complementary roles in spatial versus identity updating.
Evolvable design of network-oriented services based on a core/periphery structure
Authors: Takagi Shiori , Arakawa Shin’ichi , Murata Masayuki
Published: July 2023

In recent years, many new network-oriented services have emerged, and such services will need to be virtualized in the multi-access edge computing environment, which is currently being standardized along with fifth-generation network technology. The environment surrounding the service functions network changes over time, such as breaking changes of APIs, and these changes impact the services. The service design should be adaptable to user requirements and environmental changes for accommodating a large number of services at low cost. In addition, it is required not only to assume environmental changes when initially designing the service functions network, but also to enable the network to continue to change its structure to adapt to new environmental changes in the future. In this paper, we propose a method to evolve the entire network of service functions based on a core/periphery structure. The advantage of the core/periphery structure is that it helps reduce the costs for maintaining or changing services by dividing the service functions into core and periphery functions. We propose a method to evolve a service functions network based on this core/periphery structure. Our method evolves the structure of the service functions network at low cost by keeping the core and peripheral functions at the appropriate scale. In addition, our proposed method accommodates almost 100% of randomly generated service chains, and holds their length to less than twice the minimum chain length. Our simulation results reveal that the structure of the service functions networks can continue to evolve at a low cost and maintain a high service accommodation ratio.
Influences of chemotype and parental genotype on metabolic fingerprints of tansy plants uncovered by predictive metabolomics
Authors: Dussarrat Thomas , Schweiger Rabea , Ziaja Dominik , Nguyen Thuan T. N. , Krause Liv , Jakobs Ruth , Eilers Elisabeth J. , Müller Caroline
Published: July 2023

Intraspecific plant chemodiversity shapes plant-environment interactions. Within species, chemotypes can be defined according to variation in dominant specialised metabolites belonging to certain classes. Different ecological functions could be assigned to these distinct chemotypes. However, the roles of other metabolic variation and the parental origin (or genotype) of the chemotypes remain poorly explored. Here, we first compared the capacity of terpenoid profiles and metabolic fingerprints to distinguish five chemotypes of common tansy (Tanacetum vulgare) and depict metabolic differences. Metabolic fingerprints captured higher variation in metabolites while preserving the ability to define chemotypes. These differences might influence plant performance and interactions with the environment. Next, to characterise the influence of the maternal origin on chemodiversity, we performed variation partitioning and generalised linear modelling. Our findings revealed that maternal origin was a higher source of chemical variation than chemotype. Predictive metabolomics unveiled 184 markers predicting maternal origin with 89% accuracy. These markers included, among others, phenolics, whose functions in plant-environment interactions are well established. Hence, these findings place parental genotype at the forefront of intraspecific chemodiversity. We recommend considering this factor when comparing the ecology of various chemotypes. Additionally, the combined inclusion of inherited variation in main terpenoids and other metabolites in computational models may help connect chemodiversity and evolutionary principles.
Segmentation of human functional tissue units in support of a Human Reference Atlas
Authors: Jain Yashvardhan , Godwin Leah L. , Ju Yingnan , Sood Naveksha , Quardokus Ellen M. , Bueckle Andreas , Longacre Teri , Horning Aaron , Lin Yiing , Esplin Edward D. , Hickey John W. , Snyder Michael P. , Patterson Nathan Heath , Spraggins Jeffrey M. , Börner Katy
Published: July 2023

The Human BioMolecular Atlas Program (HuBMAP) aims to compile a Human Reference Atlas (HRA) for the healthy adult body at the cellular level. Functional tissue units (FTUs), relevant for HRA construction, are of pathobiological significance. Manual segmentation of FTUs does not scale; highly accurate and performant, open-source machine-learning algorithms are needed. We designed and hosted a Kaggle competition that focused on development of such algorithms and 1200 teams from 60 countries participated. We present the competition outcomes and an expanded analysis of the winning algorithms on additional kidney and colon tissue data, and conduct a pilot study to understand spatial location and density of FTUs across the kidney. The top algorithm from the competition, Tom, outperforms other algorithms in the expanded study, while using fewer computational resources. Tom was added to the HuBMAP infrastructure to run kidney FTU segmentation at scale—showcasing the value of Kaggle competitions for advancing research.
Estimating an Enclosure Temperature During Solid Propellant Fires
Authors: Paquet A. F. , Paquet B. M.
Published: July 2023

In any industrial energetic facility, it is useful to predict the effect of an accidental fire. Solid propellants are designed to quickly transform into high temperature gases. It is therefore necessary to predict the pressure evolution during a confined fire. Some methods are semi-empirical and thus do not depend on many thermodynamic variables. Other methods are numerical and require that many variables be defined. In any safety application, choosing the right method will depend on the risks involved, possible consequences and means available. Lack of precise knowledge of these variables is often what discourages facilities and equipment designers from modelling the behaviour of their systems. One such variable is the temperature in an enclosure during a fire for which the pressure generation is the main concern. For events involving low charge densities, using the flame temperature is an over-approximation. Assuming instantaneous perfect mixing of the enclosure air and combustion gases results in an under-approximation. In this paper, these approximations will first be considered compared to an event sequence. Three temperature models will be reviewed. Firstly, a simple model will consider the geometric mean of the previously described extreme values. Secondly, the radiative heating of the enclosure air due to a localized fire source will be studied. Finally, a finite volume multidimensional numerical model which includes turbulence effects will be presented. These three methods are seen to be of increasing complexity and will be compared to the event timescale. This timescale will help indicate if the level of complexity is warranted.
Intraoperative assessment of resection margins by Raman spectroscopy to guide oral cancer surgery
Authors: Aaboubout Yassine , Nunes Soares Maria R. , Bakker Schut Tom C. , Barroso Elisa M. , van der Wolf Martin , Sokolova Elena , Artyushenko Viacheslav , Bocharnikov Alexey , Usenov Iskander , van Lanschot Cornelia G. F. , Ottevanger Lars , Mast Hetty , ten Hove Ivo , Jonker Brend P. , Keereweer Stijn , Monserez Dominiek A. , Sewnaik Aniel , Hardillo Jose A. , Baatenburg de Jong Rob J. , Koljenović Senada , Puppels Gerwin J.
Published: July 2023

Raman spectroscopic technology for quick and accurate assessment of tumor resection margins.
Advancements and future directions in cardiac biomarker detection using lateral flow assays
Authors: Schuster da Silva Stella , Cunha Mylena Lemes , Ayres Lucas B. , Garcia Carlos D. , Blanes Lucas
Published: July 2023

Lateral flow assays (LFAs) have emerged as one of the most prominent paper-based biosensor platforms for rapidly detecting and quantifying analytes linked to cardiovascular health.
Engineering hetero-structural iron nanozyme decorated liposome with a self-cascade catalysis performance
Authors: Wang Teng , Wu Qing , Wang Zhenyu , Hu Xi , Mao Xiang
Published: July 2023

Metal-based enzyme mimics are considered as acceptable agents in fabricating heterogeneous biocomposites through valency integrations because of their biomedical or biological properties.
Simultaneous adsorption of ciprofloxacin drug and methyl violet dye on boron nitride nanosheets: experimental and theoretical insights
Authors: Javanmard Keivan , Farhadi Saeed , Zabardasti Abedin
Published: July 2023

In this work, the adsorption of MV and CIP onto microwave-assisted synthesized BN nanosheets has been investigated experimentally and theoretically.
Prediction of a reservoir of N-rich high-energy density material at the Earth's mantle
Authors: Yang Kang , Shi Jingming , Cui Wenwen , Hao Jian , Li Yinwei
Published: July 2023

Superionic H2ON6 and H2ON10 compounds might be potential constitutes of the Earth's mantle. Additionally, H2ON6 shows a high energy density (6.53 kJ g−1), which shoud be a potentialhigh-energy density material.
A roadmap for achieving scalable, safe, and low-cost direct air carbon capture and storage
Authors: Küng Lukas , Aeschlimann Silvan , Charalambous Charithea , McIlwaine Fergus , Young John , Shannon Noah , Strassel Karen , Maesano Cara Nichole , Kahsar Rudy , Pike Daniel , van der Spek Mijndert , Garcia Susana
Published: July 2023

A roadmap that delineates the major hurdles and essential RD&D actions to enable large-scale DACCS deployment.
Operando deconvolution of the degradation mechanisms of iron–nitrogen–carbon catalysts in proton exchange membrane fuel cells
Authors: Liu Shiyang , Meyer Quentin , Jia Chen , Wang Shuhao , Rong Chengli , Nie Yan , Zhao Chuan
Published: July 2023

The degradation mechanisms of Fe–N–C catalysts in hydrogen fuel cells are deconvoluted using operando electrochemical methods.
A community-led calibration of the Zr isotope reference materials: NIST candidate RM 8299 and SRM 3169
Authors: Tissot François L. H. , Ibañez-Mejia Mauricio , Rabb Savelas A. , Kraft Rebecca A. , Vocke Robert D. , Fehr Manuela A. , Schönbächler Maria , Tang Haolan , Young Edward D.
Published: July 2023

We introduce a zirconium stable isotope reference material (RM) adhering to community-defined best practices: NIST RM 8299. Its calibration provides insights into mass-fractionation laws and accurate determination of absolute ratios using MC-ICP-MS.
Europium(ii) bis[tetrafluoro-2-(pentafluoroethoxy)ethanesulfonate] – structure and spectroscopic properties of a new near-UV emitter
Authors: Starynowicz Przemysław
Published: July 2023

A new complex of divalent europium with tetrafluoro-2-(pentafluoroethoxy)ethanesulfonic acid is an efficient UV (377.8 nm) emitter. In the excitation spectrum, marked Fano resonances, indicating positions of 4f7 → 4f7 transitions, may be observed.
Adsorption of Rhodamine B from aqueous solutions using polarity-tunable hyper-cross-linked resins
Authors: You Xiaofeng , Han Lin , Liu Qing
Published: July 2023

The use of a polarity tunable hyper-cross-linked resin modified with the 3-AC monomer as an adsorbent to remove RhB from wastewater.
Novel covalent adaptable networks (CANs) of ethylene/1-octene copolymers (EOCs) made by free-radical processing: comparison of structure–property relationships of EOC CANs with EOC thermosets
Authors: Chen Boran , Fenimore Logan M. , Chen Yixuan , Barbon Stephanie M. , Brown Hayley A. , Auyeung Evelyn , Shan Colin Li Pi , Torkelson John M.
Published: July 2023

Various ethylene/1-octene copolymers were upcycled into reprocessable covalent adaptable networks to study structure–property relationships relative to their thermoset counterparts.
Ladder-type boron-containing π-systems with enhanced open-shell characteristics and photothermal conversion properties
Authors: Li Zeyi , Sun Tingting , Guo Jiaxiang , Tian Xinyu , Liu Yujia , Sheng Shihou , Ye Kaiqi , Xie Zhigang , Dou Chuandong
Published: July 2023

We disclose two ladder-type boron-containing π-conjugated molecules with two embedded s-indacene cores and their enhanced open-shell characteristics and attractive photothermal conversion properties.
The link between relative stability constant of DNA- and BSA-chromenopyrimidine complexes and cytotoxicity towards human breast cancer cells (MCF-7)
Authors: Zamisa Sizwe J. , Adeleke Adesola A. , Devnarain Nikita , Rhman Mahasin Abdel , Owira Peter M. O. , Omondi Bernard
Published: July 2023

In this study, we synthesized and characterized ten chromenopyrimidine derivatives using analytical and spectroscopic methods.
Chemical sensors for imaging total cellular aliphatic aldehydes in live cells
Authors: Wills Rachel , Farhi Jonathan , Czabala Patrick , Shahin Sophia , M. Spangle Jennifer , Raj Monika
Published: July 2023

We introduce “turn-on” non-toxic fluorescent sensors as a diagnostic tool to rapidly detect and quantify total aliphatic aldehyde levels in live cells.
A π-conjugated covalent organic framework enables interlocked nickel/photoredox catalysis for light-harvesting cross-coupling reactions
Authors: Jati Ayan , Dam Suranjana , Kumar Shekhar , Kumar Kundan , Maji Biplab
Published: July 2023

A mono-metal decorated covalent organic framework interlocked the catalysis mediated by light and the transition metal for light-fueled C–X cross-coupling reactions in excellent efficiency.
Probing fluorescence resonance energy transfer and hole transfer in organic solar cells using a tandem structure
Authors: Zhao Zhenmin , Chu Shenglong , Lv Jie , Chen Qianqian , Xiao Zhengguo , Lu Shirong , Kan Zhipeng
Published: July 2023

The energy transfer and hole transfer processes in thin films and devices were probed using a tandem structure composed of donors/hole materials/acceptors.
Efficacy of low-intensity pulsed ultrasound in the treatment of COVID-19 pneumonia
Authors: Li Wen , Li Xiao , Kong Zhibin , Chen Bin , Zhou Hongsheng , Jiang Yimin , Li Weimei , Zhong Lichang , Zhang Xinyu , Zhang Kaihua , Zhang Lili , Zong Xiangyun , Bai Wenkun , Zheng Yuanyi
Published: July 2023

Purpose As a public health emergency of international concern, coronavirus disease 2019 (COVID-19) still lacks specific antiviral drugs, and symptomatic treatment is currently the mainstay. The overactivated inflammatory response in COVID-19 patients is associated with a high risk of critical illness or even death. Low-intensity pulsed ultrasound (LIPUS) can mitigate inflammation and inhibit edema formation. We aimed to investigate the efficacy of LIPUS therapy for COVID-19 pneumonia.

Materials and Methods 62 patients were randomly assigned to a treatment group (LIPUS treatment area – Group 1; self-control area – Group 2) and an external control group (Group 3). The primary outcomes were the volume absorption rate (VAR) and the area absorption rate (AAR) of lung inflammation in CT images.

Results After an average duration of treatment 7.2 days, there were significant differences in AAR and VAR between Group 1 and Group 2 (AAR 0.25 vs 0.12, p=0.013; VAR 0.35 vs 0.11, p=0.005), and between Group 1 and Group 3 (AAR 0.25 vs 0.11, p=0.047; VAR 0.35 vs 0.19, p=0.042). Neither AAR nor VAR was statistically different between Group 2 and Group 3. After treatment, C-reactive protein, interleukin-6, leukocyte, and fingertip arterial oxygen saturation (SaO2) improved in Group 1, while in Group 3 only fingertip SaO2 increased.

Conclusion LIPUS therapy reduced lung inflammation and serum inflammatory factor levels in hospitalized COVID-19 patients, which might be a major advancement in COVID-19 pneumonia therapy.
Assessment and Techniques for Endoscopic Closure
Authors: Siddharthan Ragavan , Marcello Peter
Published: July 2023

Endoscopic closure is an essential technique to perform safe advanced endoscopy. Without appropriate closure of a defect, patients can experience spillage of fecal contents into the peritoneal cavity resulting in abdominal sepsis. The essential components to performing endoscopic closure are assessing the defect appropriately and choosing the correct closure technique. Assessing the defect involves five separate elements: timing, size, depth, shape, blood flow, and location in the colon or rectum. Understanding how each of these elements contributes toward a successful closure allows an endoscopist to choose the proper technique for closure. There have been many types of closure techniques described in the literature but the most common are through the scope clips, over the scope clips, and endoscopic suturing. There are advantages and disadvantages of each of these closure techniques. In this manuscript, we will discuss these common techniques as well as some additional techniques and the situations where they can be employed.
Full counting statistics of ultrafast quantum transport
Authors: Hübler M. , Belzig W.
Published: July 2023

Quantum transport in the presence of time-dependent drives is dominated by quantum interference and many-body effects at low temperatures. For a periodic driving, the analysis of the full counting statistics revealed the elementary events that determine the statistical properties of the charge transport. As a result, the noise correlations display quantum oscillation as functions of the ratio of the voltage amplitude and the drive frequency, reflecting the detailed shape of the drive. However, so far only continuous wave excitations were considered, but, recently, transport by few-cycle light pulses were investigated, and the need for a statistical interpretation became eminent. We address the charge transfer generated by single- or few-cycle light pulses. The fingerprints of these time-dependent voltage pulses are imprinted in the full counting statistics of a coherent mesoscopic conductor at zero temperature. In addition, we identify the elementary processes that occur in the form of electron–hole pair creations, which can be investigated by the excess noise. We study the quantum oscillations in the differential noise induced by a wave packet consisting of an oscillating carrier modulated by a Gaussian- or a box-shaped envelope. As expected, the differential noise exhibits an oscillatory behavior with increasing amplitude. In particular, we find clear signature of the so-called carrier-envelope phase in the peak heights and positions of these quantum oscillations. More carrier cycles under the Gaussian envelope diminish the influence of the carrier-envelope phase, while this is not true for the box pulses, probably related to the abrupt onset.