bluuebunny/crossref_metadata_2025_split huggingface dataset:
An efficient algorithm for gravity forward modelling (GFM) with masses of arbitrary shapes and density distributions
Authors: Chen Wenjin , Tan Xiaolong 
Published: September 2024

SUMMARY
Currently, gravimetric forward modelling of mass density structures with arbitrary geometries and density distributions typically involves subdividing the mass body into individual geometric elements (such as rectangular prisms), calculating their gravitational contributions that are then summed up to obtain the gravitational attraction of the whole body. To achieve a more accurate approximation of the true geometric shape and density distribution, this rectangular prism model requires fine dividing, which significantly increases computational load and reduces numerical efficiency. To address this issue, we propose the algorithm for gravimetric forward modelling of arbitrary geometric shapes and density distributions in spectral domain that significantly improves numerical efficiency while preserves computational accuracy. The novelty of our proposed algorithm lies in dividing the masses into multiple layers of equal thickness in the vertical direction, providing constant upper and lower bounds. This allows to extended Parker's formulas and apply the Fast Fourier Transform to increase numerical efficiency. The algorithm is tested using synthetic models and then used to compute gravitational effects of topography and sediments using real data from Tibet. Results show high accuracy and numerical efficiency than rectangular prism approach.
Chromatin accessibility profile and the role of PeAtf1 transcription factor in the postharvest pathogen Penicillium expansum
Authors: Wang Yiran , Wang Kaili , Yang Qiya , Wang Zhaoting , Su Yingying , Chen Xifei , Zhang Hongyin 
Published: September 2024

Abstract
Gene transcription is governed by a complex regulatory system involving changes in chromatin structure, the action of transcription factors, and the activation of cis-regulatory elements. Postharvest fruits are threatened by Penicillium expansum, a leading causal agent of blue mold disease and one of the most economically significant postharvest pathogens worldwide. However, information on its transcription regulatory mechanism is lagging. Here, we conducted an assay for transposase accessible chromatin sequencing (ATAC-seq) for P. expansum during vegetative growth and infection phase and then studied the function of a basic leucine zipper (bZIP) transcription factor PeAtf1. Results highlighted the role of promoter regions in gene transcription and the significant difference in P. expansum between these two phases. Six footprint-supported cis-regulatory elements of active transcription factors were obtained and analyzed. We then identified a homolog of the bZIP regulator Atf1, PeAtf1, and found it positively regulated vegetative growth, reproduction, and osmotic stress response in P. expansum. Furthermore, PeAtf1 deletion enhanced the fungus's tolerance to oxidative, cell wall, and membrane stresses, which might contribute to the virulence of deletion mutants in apple fruits, leading to similar pathogenicity between mutants and the wild type. Overall, this study provides new insights into the transcription regulatory profile of P. expansum, aiding in the future development of strategies to control P. expansum.
Oligo-FISH barcode chromosome identification system provides novel insights into the natural chromosome aberrations propensity in the autotetraploid cultivated alfalfa
Authors: Meng Zhuang , Zheng Qian , Wang Wei , Zhu Yuanbin , Li Yuanhao , Dong Fulin , Luo Wenjun , Zhang Zhiliang , Wang Fei , Shen Haitao , Xie Quanliang , Li Hongbin 
Published: September 2024

Abstract
Alfalfa is one of the most economically valuable forage crops in the world. However, molecular cytogenetic studies in alfalfa lag far behind other cash crops and have reached a bottleneck. Here, we developed a novel chromosome identification system by designing 21 oligo probes in specific regions of each chromosome, which can be used as a barcode to simultaneously distinguish all chromosomes in a cell. Using this system, we revealed the chromosome karyotype features and evolutionary differences among 10 cultivated alfalfa varieties. Interestingly, we also found two chromosomal variation types, i.e. aneuploidy and large chromosomal segment deletions in the seeds of three alfalfa varieties. Variation frequency analysis showed that only 7/173 seeds in those three alfalfa varieties had chromosome aberrations, which indicated that the inheritance and meiosis of alfalfa had evolved to a relatively stable state. Remarkably, 4/7 variation seeds were chromosome 2 aberrations, suggesting that chromosome 2 appears to be more susceptible to natural chromosomal aberrations than other chromosomes during inheritance. DNA sequence variation analysis showed that the difference of presence and absence variations (PAVs) among homologous copies of chromosome 2 was larger than that of the other seven chromosomes. We suggest that such large PAV divergence among homologous copies may provide the physical basis for natural chromosome 2 aberrations propensity. Our study provides a valuable and efficient tool for alfalfa’s molecular cytogenetics and sheds new insights into the propensity for natural chromosome aberrations during autopolyploid inheritance.
Care as a constitutional value
Authors: Fredman Sandra 
Published: September 2024

Abstract
This article explores the potential of regarding care as a constitutional issue, rather than addressing it solely through legislation, the family, or the market. It is argued that care is best regarded as a constitutional value, reflecting the reality of our interdependence, and functioning as a crucial counterweight to the fiction that individual freedom can be constituted independently of our social relations. Care as a constitutional value should be regarded as complementing express constitutional commitments to freedom, dignity, and equality, recognizing that relationships are constitutive of the self, and that individuals are partly constituted by society. Just as freedom, dignity, and equality perform important expressive functions in a constitution, so the recognition of care, implicit or explicit, signals the foundational importance of care to everyone throughout our lives and to society’s ability to reproduce itself. Care as a constitutional value should permeate the interpretation of constitutional and other provisions, and enhance accountability for care-related decisions, encouraging decision-makers to pay attention to care, and prompting courts to interpret constitutional and legislative measures with the value of care in mind. In this way, the gaps in welfare law, labor law, and free market regulation can be addressed to face the challenges of care. Equally importantly, care as a constitutional value can act as a catalyst for political activism, legitimizing grassroots campaigns for better recognition of care. This article is normative and exploratory. At the same time, its propositions are tested against constitutional jurisprudence in India, South Africa, Canada, and the United Kingdom.
Bi-stochastically normalized graph Laplacian: convergence to manifold Laplacian and robustness to outlier noise
Authors: Cheng Xiuyuan , Landa Boris 
Published: September 2024

Abstract
Bi-stochastic normalization provides an alternative normalization of graph Laplacians in graph-based data analysis and can be computed efficiently by Sinkhorn–Knopp (SK) iterations. This paper proves the convergence of bi-stochastically normalized graph Laplacian to manifold (weighted-)Laplacian with rates, when $n$ data points are i.i.d. sampled from a general $d$-dimensional manifold embedded in a possibly high-dimensional space. Under certain joint limit of $n \to \infty $ and kernel bandwidth $\epsilon \to 0$, the point-wise convergence rate of the graph Laplacian operator (under 2-norm) is proved to be $ O( n^{-1/(d/2+3)})$ at finite large $n$ up to log factors, achieved at the scaling of $\epsilon \sim n^{-1/(d/2+3)} $. When the manifold data are corrupted by outlier noise, we theoretically prove the graph Laplacian point-wise consistency which matches the rate for clean manifold data plus an additional term proportional to the boundedness of the inner-products of the noise vectors among themselves and with data vectors. Motivated by our analysis, which suggests that not exact bi-stochastic normalization but an approximate one will achieve the same consistency rate, we propose an approximate and constrained matrix scaling problem that can be solved by SK iterations with early termination. Numerical experiments support our theoretical results and show the robustness of bi-stochastically normalized graph Laplacian to high-dimensional outlier noise.
Sustainability performance of food supply chains with internal and external evaluation perspectives
Authors: Gürül Binnur , Yilmaz Dilek , Kiriş Sinem Büyüksaatçı 
Published: September 2024

Abstract
Accepted by: M. Zied Babai
The challenges of food security, water use, energy consumption and the growing global demand for food raise the importance of ensuring sustainability of the food supply chains (FSCs). Studies in relevant literature discuss the sustainability performances of FSCs generally without distinguishing between the internal and external stakeholders’ concerns or clarifying the existence of greenwashing or bluewashing attempts, jeopardizing true sustainability. This is why modelling towards some holistic treatment of the problem that satisfies those concerns is required. This paper proposes a framework to evaluate the true sustainability performance of FSCs by considering triple bottom line indicators, i.e. economic, environmental and social. In light of the proposed framework, two models have been developed, one calculating the internal and the other an external sustainability score. The presented models can handle interval or ordinal qualitative and quantitative indicators concurrently while considering desirable and undesirable factors. These novel models have been implemented on data from 50 FSCs in Istanbul, using a two-stage imprecise data envelopment analysis with a special multiplier. To facilitate visualization of true sustainability assessment, an internal–external sustainability performance matrix is proposed. Results reveal that the internal sustainability performance of the focal FSCs is better than the external one. The economic dimension predominates in Turkish FSCs’ internal sustainability performance, while the environmental and social dimensions predominate in the external sustainability performance of the FSCs.
Comparative Emergence of Maribavir and Ganciclovir Resistance in a Randomized Phase 3 Clinical Trial for Treatment of Cytomegalovirus Infection
Authors: Chou Sunwen , Winston Drew J , Avery Robin K , Cordonnier Catherine , Duarte Rafael F , Haider Shariq , Maertens Johan , Peggs Karl S , Solano Carlos , Young Jo-Anne H , Gu Joan , Pocock Ginger , Papanicolaou Genovefa A 
Published: September 2024

Abstract

Background
Among 547 patients receiving maribavir or valganciclovir for first-episode cytomegalovirus infection after hematopoietic cell transplant, the treatment response rate was 69.6% and 77.4% respectively. Development of maribavir and ganciclovir resistance was compared after receiving either drug.

Methods
Viral mutations conferring drug resistance were analyzed in plasma DNA extracts at baseline and posttreatment.

Results
Prior antiviral drug exposure was limited, with only 2 instances of baseline drug resistance detected. An equal number (n = 241) received valganciclovir or maribavir for at least 21 days (median, 55–56 days). Among them, drug resistance mutations were detected in 24 (10%) maribavir recipients at 35–125 days (median, 56 days) after starting therapy, including in 12 of 14 who experienced a viral load rebound while on therapy. Ganciclovir resistance mutations developed in 6 (2.5%) valganciclovir recipients at 66–110 days (median, 90 days). One maribavir recipient developed a novel UL97 gene mutation (P-loop substitution G343A) that conferred strong maribavir and ganciclovir resistance in vitro. Viral clearance was confirmed in 17 (74%) of 23 patients with emergent maribavir resistance after retreatment with an alternative CMV antiviral drug.

Conclusions
After 3–8 weeks of therapy, maribavir resistance emerged earlier and more frequently than ganciclovir resistance but was usually treatable using alternative therapy.
Clinical Trials Registration. NCT02927067 (AURORA).
Bacillus subtilis B55 degraded the ferulic acid and p-coumaric acid and changed the soil bacterial community in soils
Authors: Liu Dongli , Ge Xin , Pan Dandan , Zheng Xianqing , Zhou Xingang 
Published: September 2024

Abstract

Aims
This study aimed to assess the effects of phenolic acid-degrading bacteria strains on phenolic acid content, plant growth, and soil bacterial community in phenolic acid-treated soils.

Methods and results
The strain of interest coded as B55 was isolated from cucumber root litter, and its degradation rates of ferulic acid and p-coumaric acid were 81.92% and 72.41% in Luria-Bertani solution, respectively, and B55 was identified as Bacillus subtilis. B55 had plant growth-promoting attributes, including solubilization of inorganic phosphate and production of siderophore and indole acetic acid. Both ferulic acid and p-coumaric acid significantly restrained an increase in cucumber seedling dry biomass, while the B55 inoculation not only completely counteracted the damage of phenolic acids to cucumber seedlings and decreased the content of ferulic acid and p-coumaric acid in soil, but also promoted cucumber seedlings growth. Amplicon sequencing found that B55 inoculation changed the cucumber rhizosphere bacterial community structure and promoted the enrichment of certain bacteria, such as Pseudomonas, Arthrobacter, Bacillus, Flavobacterium, Streptomyces, and Comamonas.

Conclusions
B55 not only promoted cucumber seedling growth, and decreased the content of ferulic acid and p-coumaric acid in soil, but it also increased the relative abundance of beneficial microorganisms in the cucumber rhizosphere.
Enhancing skeletal muscle fiber characteristics, intramuscular fat deposition, and fatty acid composition in broilers under heat stress through combined selenomethionine and Bacillus subtilis supplementation in the diet
Authors: Yang Weiguang , Xue Junjing , Zhang Sha , Yao Chenge , Zhang Na , Fang Rejun 
Published: September 2024

Abstract
Heat stress is the most common environmental stressor in poultry production, negatively affecting growth performance, meat quality, and welfare. Therefore, the aim of this study was to compare the nutritional effects of dietary supplementation with selenomethionine, Bacillus subtilis (BS), and a combination of selenomethionine and BS on broilers challenged with heat stress. A total of 300 21-day-old male broilers (Ross 308) were randomly assigned to 5 groups with 6 replicates of 10 broilers per each: control group (CON, broilers raised at 22 ± 2 °C), heat stress exposure group (HS, broilers raised at 32 ± 2 °C for 8 h/d), HSS group (HS group supplemented with 0.3 mg/kg selenomethionine), HSB group (HS group supplemented with 1 × 109 cfu/kg BS), and HSBS group (HS group supplemented with 0.3 mg/kg selenomethionine and × 109 cfu/kg BS). The experiment lasted for 21 d. The results indicated that, compared to the CON group, heat stress reduces (P &lt; 0.05) broiler growth performance and damages the meat quality in breast and thigh muscles. Dietary supplementation with selenomethionine and BS did not improve the growth performance of broilers under heat stress. However, compared to the HS group, the HSS, HSB, and HSBS groups showed significantly increased (P &lt; 0.05) pH45 min, redness (a*) and yellowness (b*), muscle fiber density, intramuscular fat, triglyceride content, and expression levels of Myf5, CAPN 2, FM, SLC27A1, A-FABP, H-FABP, APOB-100, and ACC in breast and thigh muscles. Meanwhile, these groups showed reduced (P &lt; 0.05) lightness (L*), drip loss, shear force, muscle fiber cross-sectional area, and FM gene expression level. The HSBS group showed greater improvement in the physicochemical quality of muscle and volatile substances compared to the HSS and HSB groups. In conclusion, selenomethionine and BS improved meat quality and flavor in broilers under heat stress by modulating muscle fiber composition and characteristics, as well as increasing intramuscular fat deposition.
Safety of Silver Dressings in Infants; a Systematic Scoping Review
Authors: O’Donohoe Patrick K , Leon Ryan , Orr David J A , de Blacam Catherine 
Published: September 2024

Abstract
Silver-based dressings are used to reduce infection risk and optimize conditions for wound healing. They are widely used in the management of burns and other complex wounds. However, reports of elevated serum silver and concern over systemic toxicity have meant that their use in young children has been questioned. The aim of the current study was to map the literature relating to the use of silver-based dressings in children under 1 year of age. A systematic scoping review was conducted according to the methodology described by the Joanna Briggs Institute. Sources were identified from major medical databases as well as the gray literature. Inclusion criteria were the use of silver-based dressing in children under 1 year of age. Outcomes of interest were complications or adverse events attributed to silver-based dressings and elevated serum silver levels. A total of 599 sources were identified through the search strategy, with 110 included for review. Complications were described in 31 sources, with the most frequent being wound infection. No cases of argyria, kernicterus, or methemoglobinemia were reported. Six sources documented elevated serum silver levels in infants but none reported adverse events related to this. On the basis of current evidence, we suggest reserving silver dressings in infants under 1 for wounds that are at high risk of infection. Wound area and duration of treatment should be considered when assessing the risk of systemic absorption of silver. Standardized data collection and recording of complications and adverse events is recommended to better inform future clinical decision-making.
Linking transcriptome and morphology in bone cells at cellular resolution with generative AI
Authors: Lu Lu , Ono Noriaki , Welch Joshua D 
Published: September 2024

Abstract
Recent advancements in deep learning (DL) have revolutionized the capability of artificial intelligence (AI) by enabling the analysis of large-scale, complex datasets that are difficult for humans to interpret. However, large amounts of high-quality data are required to train such generative AI models successfully. With the rapid commercialization of single-cell sequencing and spatial transcriptomics platforms, the field is increasingly producing large-scale datasets such as histological images, single-cell molecular data, and spatial transcriptomic data. These molecular and morphological datasets parallel the multimodal text and image data used to train highly successful generative AI models for natural language processing and computer vision. Thus, these emerging data types offer great potential to train generative AI models that uncover intricate biological processes of bone cells at a cellular level. In this Perspective, we summarize the progress and prospects of generative AI applied to these datasets and their potential applications to bone research. In particular, we highlight three AI applications: predicting cell differentiation dynamics, linking molecular and morphological features, and predicting cellular responses to perturbations. To make generative AI models beneficial for bone research, important issues, such as technical biases in bone single-cell datasets, lack of profiling of important bone cell types, and lack of spatial information, needs to be addressed. Realizing the potential of generative AI for bone biology will also likely require generating large-scale, high-quality cellular-resolution spatial transcriptomics datasets, improving the sensitivity of current spatial transcriptomics datasets, and thorough experimental validation of model predictions.
Testing for heterogeneous rates of discrete character evolution on phylogenies
Authors: Revell Liam J , Schliep Klaus P , Mahler D Luke , Ingram Travis 
Published: September 2024

Abstract
Many hypotheses in the field of phylogenetic comparative biology involve specific changes in the rate or process of trait evolution. This is particularly true of approaches designed to connect macroevolutionary pattern to microevolutionary process. We present a method to test whether the rate of evolution of a discrete character has changed in one or more clades, lineages, or time periods. This method differs from other related approaches (such as the “covarion” model) in that the “regimes” in which the rate or process is postulated to have changed are specified a priori by the user, rather than inferred from the data. Similarly, it differs from methods designed to model a correlation between two binary traits in that the regimes mapped onto the tree are fixed. We apply our method to investigate the rate of dewlap colour and/or caudal vertebra number evolution in Caribbean and mainland clades of the diverse lizard genus Anolis. We find little evidence to support any difference in the evolutionary process between mainland and island evolution for either character. We also examine the statistical properties of the method more generally and show that it has acceptable type I error, parameter estimation, and power. Finally, we discuss some general issues of frequentist hypothesis testing and model adequacy, as well as the relationship of our method to existing models of heterogeneity in the rate of discrete character evolution on phylogenies.
Interferon lambda signaling in neutrophils enhances the pathogenesis of Bordetella pertussis infection
Authors: Kumar Amit , Johnson Da’Kuawn , Bukowski Alicia , Noto Michael J , Carbonetti Nicholas H 
Published: September 2024

Abstract
Interferon lambda plays diverse roles in bacterial infections. Previously, we showed that interferon lambda is induced in the lungs of Bordetella pertussis-infected adult mice and exacerbates inflammation. Here, we report that mice lacking the interferon lambda receptor 1 specifically on neutrophils (MRP8creIFNLR1fl/fl mice) exhibit reduced lung bacterial load and inflammation compared to wild-type mice during B. pertussis infection. In B. pertussis-infected wild-type mice, lung type I and III IFN responses were higher than in MRP8creIFNLR1fl/fl mice, correlating with increased lung inflammatory pathology. There was an increased proportion of interferon gamma-producing neutrophils in the lungs of MRP8creIFNLR1fl/fl mice compared to wild-type mice. IFNLR1−/− neutrophils incubated with B. pertussis exhibited higher killing compared to wild-type neutrophils. Treatment of wild-type neutrophils with interferon lambda further decreased their bacterial killing capacity and treatment of wild-type mice with interferon lambda increased lung bacterial loads. Contributing to the differential killing, we found that IFNLR1−/− neutrophils exhibit higher levels of reactive oxygen species, myeloperoxidase, matrix metalloproteinase-9 activity, neutrophil extracellular traps, and interferon gamma secretion than wild-type neutrophils, and inhibiting NADPH oxidase inhibited bacterial killing in IFNLR1−/− neutrophils. B. pertussis-induced interferon lambda secretion and IFNLR1 gene expression in mouse and human neutrophils and this was dependent on the bacterial virulence protein pertussis toxin. Pertussis toxin enhanced bacterial loads in wild type but not in MRP8creIFNLR1fl/fl or IFNLR1−/− mice. Thus, pertussis toxin disrupts neutrophil function by enhancing type III IFN signaling, which prevents neutrophils from effectively clearing B. pertussis during infection, leading to higher bacterial loads and exacerbation of lung inflammation.