bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using design of experiments to guide genetic optimization of engineered metabolic pathways
Authors: Moon Seonyun , Saboe Anna , Smanski Michael J 
Published: March 2024

Abstract

Design of experiments (DoE) is a term used to describe the application of statistical approaches to interrogate the impact of many variables on the performance of a multivariate system. It is commonly used for process optimization in fields such as chemical engineering and material science. Recent advances in the ability to quantitatively control the expression of genes in biological systems open up the possibility to apply DoE for genetic optimization. In this review targeted to genetic and metabolic engineers, we introduce several approaches in DoE at a high level and describe instances wherein these were applied to interrogate or optimize engineered genetic systems. We discuss the challenges of applying DoE and propose strategies to mitigate these challenges.

One-Sentence Summary
This is a review of literature related to applying Design of Experiments for genetic optimization.
Comparative transcriptomic and metabolomics analysis of modified atmosphere responses in Tribolium castaneum (Coleoptera: Tenebrionidae)
Authors: Zhou Min , Pan Biying , Guan Liwen , Wang Yuanyuan , Xu Kangkang , Wang Shigui , Tang Bin , Li Can 
Published: March 2024

Abstract
Modified atmosphere is effective in controlling Tribolium castaneum Herbst, but it has adaptations. Comprehending the potential mechanism of resistance to T. castaneum in a modified atmosphere will help advance related management methods. This study conducted a comparative transcriptomic and metabolomic analysis to understand the physiological mechanism of T. castaneum in adapting to CO2 stress. Results showed that there were a large number of differentially expressed genes (DEGs) in T. castaneum treated with different concentrations of CO2. Gene ontology (GO) analysis revealed significant enrichment of DEGs mainly in binding, catalytic activity, cell, membrane, membrane part, protein-containing complex, biological regulation, and cellular and metabolic process. Kyoto Encyclopedia of Genes and Genomes analysis showed that different treatments had different effects on the metabolic pathways of T. castaneum. DEGs induced by 25% CO2 were involved in arginine and proline metabolism, and 50% air + 50% CO2 treatment affected most kinds of metabolic pathways, mainly the signal transduction pathway, including PI3K-Akt signaling pathway, AMPK signaling pathway, neurotrophin signaling pathway, insulin signaling pathway, and thyroid hormone signaling. Ribosome and DNA replication were enriched under high CO2 stress (75% and 95%). The metabolomics revealed that different concentrations of CO2 treatments might inhibit the growth of T. castaneum through acidosis, or they may adapt to anoxic conditions through histamine and N-acetylhistamine. Multiple analyses have shown significant changes in histamine and N-acetylhistamine levels, as well as their associated genes, with increasing CO2 concentration. In conclusion, this study comprehensively revealed the molecular mechanism of T. castaneum responding to CO2 stress and provided the basis for an effectively modified atmosphere in the T. castaneum.
New records of three parasitoids, Pteroptrix chinensis, Aphytis hispanicus, and Marlattiella prima (Hymenoptera: Aphelinidae) associated with an exotic scale, Lopholeucaspis japonica (Hemiptera: Diaspididae) in Tennessee
Authors: Daniel Johnson Alfred , Woolley James B , Addesso Karla M 
Published: March 2024

Abstract
A survey for parasitoids of Lopholeucaspis japonica Cockerell (Hemiptera: Diaspididae), an exotic scale of woody ornamentals, resulted in the discovery of 3 species of aphelinid parasitoid wasps, Pteroptrix chinensis (Howard), Aphytis hispanicus (Mercet), and Marlattiella prima Howard. This serves as the first report of these parasitoids reared from a host in the state of Tennessee, USA. Despite routine pesticide applications in the surveyed nursery and directed treatments of the infested plants to control the scale outbreak, the percentage of parasitized scale in privet and euonymus shrubs averaged 7.0% and 7.9%, respectively. These parasitoids may be useful in the natural or managed control of this pest in the United States, but additional research is needed to understand how these parasitoids contribute to the control of L. japonica in the landscape and how nursery production practices can be modified to promote parasitoid populations.
Implementing the human right to science in the context of health-related data processing
Authors: Molnár-Gábor Fruzsina 
Published: March 2024

Abstract
This paper contributes to the exploration of the potential application of duties related to the diligent anticipation of the (imminent) harms and (potential) benefits to humans that scientific innovation engenders to health-related contexts. In particular, it addresses the intersection between the human right to science and health-related data processing, which plays a key role in the production, translation and implementation of biomedical knowledge. The first part of the paper provides a brief recap of the interpretation of the right to science based on Art. 15 (1) (b) of the United Nations International Covenant on Economic, Social and Cultural Rights (hereafter ICESCR or Covenant) and the resulting obligations for States in the context of health and related data processing. The second part of the paper defines the relevance of the ICESCR for EU Member States and the European Union. In the third part, theses are put forward on how the human right to science and the obligations under Art. 15 (1) (b) ICESCR influence the interpretation and application of the General Data Protection Regulation as secondary EU law. By examining the justifications for using the right to science to interpret EU data protection law and by providing interpretation and application guidance on the main data protection principles in the area of health-related data processing, taking this right into account, the aim is to shape the EU data governance framework to meet the requirements of this human right. In doing so, the paper aims to close the gaps in the interpretation and application of the main rules of EU data protection law. Such standardization in the health-related context can contribute to a coherent interpretation and application of existing rules by referring to this emerging human right. Against this background, the paper identifies governance measures that the EU legislator could take to guide the processing of health-related data in line with the requirements of the right to science.
Randomized trial promoting cancer genetic risk assessment when genetic counseling cost removed: 1-year follow-up
Authors: An Jinghua , McDougall Jean , Lin Yong , Lu Shou-En , Walters Scott T , Heidt Emily , Stroup Antoinette , Paddock Lisa , Grumet Sherry , Toppmeyer Deborah , Kinney Anita Y 
Published: March 2024

Abstract

Purpose
Cancer genetic risk assessment (CGRA) is recommended for women with ovarian and high-risk breast cancer. However, the underutilization of CGRA has long been documented, and cost has been a major barrier. In this randomized controlled trial, a tailored counseling and navigation (TCN) intervention significantly improved CGRA uptake at 6-month follow-up, compared with targeted print (TP) and usual care (UC). We aimed to examine the effect of removing genetic counseling costs on CGRA uptake by 12 months.

Methods
We recruited racially and geographically diverse women with breast and ovarian cancer from cancer registries in Colorado, New Jersey, and New Mexico. Participants assigned to TCN received telephone-based psychoeducation and navigation. After 6 months, the trial provided free genetic counseling to participants in all arms.

Results
At 12 months, more women in TCN obtained CGRA (26.6%) than those in TP (11.0%; odds ratio [OR] = 2.77, 95% confidence interval [CI] = 1.56 to 4.89) and UC (12.2%; OR = 2.46, 95% CI = 1.41 to 4.29). There were no significant differences in CGRA uptake between TP and UC. The Kaplan-Meier curve shows that the divergence of cumulative incidence slopes (TCN vs UC, TCN vs TP) appears primarily within the initial 6 months.

Conclusion
TCN significantly increased CGRA uptake at the 12-month follow-up. Directly removing the costs of genetic counseling attenuated the effects of TCN, highlighting the critical enabling role played by cost coverage. Future policies and interventions should address multilevel cost-related barriers to expand patients’ access to CGRA.

Trial Registration
This trial was registered with the NIH clinical trial registry, clinicaltrials.gov, NCT03326713. https://clinicaltrials.gov/ct2/show/NCT03326713.
Biopsychosocial determinants of sexual health in older age: the role of health-related, relationship, and psychosexual factors
Authors: Vasconcelos Priscila A , Paúl Constança , Nobre Pedro J 
Published: March 2024

Abstract

Background
Given the unprecedented aging of the population and the increased focus on overall well-being in older age, investigating the determining factors of sexual well-being in older adults becomes essential as it offers insights into promoting healthy aging and overall quality of life.

Aim
By applying the biopsychosocial model of sexuality in older age, we aimed to identify the role of biomedical and psychosocial factors in predicting sexual well-being in partnered older adults (≥55 years old).

Methods
A total of 111 participants (mean [SD], 63.2 [5.96]) completed a self-report questionnaire assessing biopsychosocial dimensions. Bivariate correlational analyses and hierarchical multiple regression were conducted to investigate factors associated with sexual well-being. Health-related factors were entered into the first regression model. The second model included factors pertaining to relationship dimensions. Sexual beliefs were introduced in the third regression model.

Outcomes
Self-rated health, psychological distress, subjective cognitive decline, sexual beliefs, duration of the relationship, relationship satisfaction, and sexual well-being were assessed.

Results
Findings from the hierarchical regression revealed that duration of relationship [t(104) = −3.07, P &lt; .01], relationship satisfaction [t(104) = 8.49, P &lt; .001], and age-related sexual beliefs [t(104) = −2.75, P &lt; .01] were significant predictors of sexual well-being of partnered older adults [F(6, 104) = 22.77, P &lt; .001, R2 = .57], after controlling for health-related factors. These findings suggest that relationship factors and sexual beliefs play a significant role in predicting sexual well-being of older adults, above and beyond health-related dimensions.

Clinical implications
Interventional approaches aimed at promoting sexual well-being in older age might benefit from incorporating exercises that demystify age-related sexual beliefs, by normalizing changes that occur with aging and fostering positive attitudes toward sexual expression in older age; particularly for older adults in long-term relationships, relationship satisfaction must also be considered as an important intervention target.

Strengths and limitations
Further investigation using longitudinal designs is required to examine the causal links between these factors and sexual well-being in older age.

Conclusion
Findings from this study underscore the role of relationship dimensions and age-related sexual beliefs for the sexual well-being of partnered older adults.
Dorsoventrally asymmetric expression of miR319/TCP generates dorsal-specific venation patterning in petunia corolla tube
Authors: Zhang Bin , Qin Xiaoting , Han Yao , Li Mingyang , Guo Yulong 
Published: March 2024

Abstract
Vein-associated pigmentation (venation) is a type of floral coloration adopted by plants to attract pollinators. Several petunia (Petunia hybrida) lines generate dorsoventrally asymmetric venation patterning of the corolla tube, in which venation is only present in the dorsal tube. The molecular mechanism underlying this trait is unknown. Here, we demonstrate that miR319 is preferentially expressed in the dorsal corolla tube, leading to dorsoventrally asymmetric expression of its target genes. Transgenic lines overexpressing phy-miR319a generated uniform venation patterning of the corolla tube. Knockout of TCP genes targeted by miR319 promoted venation patterning in the ventral and dorsal tube, while overexpression of the miR319 target gene, PhTCP6, completely inhibited corolla tube venation patterning. In addition, miR319-targeted TCPs negatively regulated venation patterning, probably by repressing the regulator of venation patterning, AN4. Together, our data demonstrate that asymmetric expression of miR319 promotes venation patterning in the petunia dorsal tube alone by repressing the expression of its target TCP genes, which negatively regulate corolla tube venation patterning. These findings provide novel insights into how the dorsoventrally asymmetric distribution of venation patterning is established in zygomorphic flowers.
Microbes as a tool for the bioremediation of fish waste from the environment and the production of value-added compounds: a review
Authors: Kumari Neha , Hussain Ahmed , Ghosh Sachan Shashwati 
Published: March 2024

Abstract
Fish are the most edible protein source worldwide and generate several remnants such as scales, viscera, head, bone, and skin. Fish wastes are not disposed of properly, which adversely affects the environment, especially the water bodies where fish processing industries dispose of their waste. Fish waste mainly contains nitrogen, oil, fat, salts, heavy metals, and organic compounds, which increase the biological oxygen demand and chemical oxygen demand. Fish waste can degrade in various ways, such as physicochemical or by enzymatic action, but using microbes is an environmentally friendly approach that can provide valuable compounds such as products such as collagen, chitin, minerals, and fish protein concentrates. This review is designed to focus on the suitability of microbes as tools for fish waste degradation and the production of certain associated. This study also provides insight into the production of other compounds such as protease, chitinase, and chitin applicability of these products. After processing, fish waste as a microbial growth media for enzyme production since microorganisms synthesize enzymes such as proteases, protein hydrolysates, lipids, and chitinase, which have broader applications in the pharmaceutical, cosmetic, biomedical material, and food processing industries.
Completeness of tableau calculi for two-dimensional hybrid logics
Authors: Nishimura Yuki 
Published: March 2024

Abstract
Hybrid logic is one of the extensions of modal logic. The many-dimensional product of hybrid logic is called hybrid product logic (HPL). We construct a sound and complete tableau calculus for two-dimensional HPL. Also, we made a tableau calculus for hybrid dependent product logic (HdPL), where one dimension depends on the other. In addition, we add a special rule to the tableau calculus for HdPL and show that it is still sound and complete. All of them lack termination, however.
Asymetrical shape of C–He lines in the ultraviolet
Authors: Allard Nicole F , Spiegelman Fernand 
Published: March 2024

ABSTRACT
We present the first theoretical line profile calculations of the ultraviolet spectral lines of carbon perturbed by helium using a semiclassical collision approach and high-quality ab initio potentials and electronic transition dipole moments. The temperature range is from 5000 to 8000 K. These results are important for astrophysical modelling of spectra in atmospheres of white dwarf stars showing atomic carbon in an helium atmosphere. Beyond the conventional symmetrical Lorentzian core at low He density, these lines exhibit a blue asymmetric behaviour. This blue asymmetry is a consequence of low maxima in the corresponding C–He potential energy difference curves at short internuclear distances. The collisional profiles are carefully examined and their perturber density dependence allow to understand the various line shapes of the observed carbon spectral lines in helium-rich white dwarf photosphere where the He perturber densities reach several 1021 cm−3.
The escape of fast radio burst emission from magnetars
Authors: Lyutikov Maxim 
Published: March 2024

ABSTRACT
We reconsider the escape of high-brightness coherent emission of fast radio bursts (FRBs) from magnetars’ magnetospheres, and conclude that there are numerous ways for the powerful FRB pulse to avoid non-linear absorption. Sufficiently strong surface magnetic fields, $\ge 10{{\ \rm per\ cent}}$ of the quantum field, limit the waves’ non-linearity to moderate values. For weaker fields, the electric field experienced by a particle is limited by a combined ponderomotive and parallel-adiabatic forward acceleration of charges by the incoming FRB pulse along the magnetic field lines newly opened during FRB/coronal mass ejection. As a result, particles surf the weaker front part of the pulse, experiencing low radiative losses, and are cleared from the magnetosphere for the bulk of the pulse to propagate. We also find that initial mildly relativistic radial plasma flow further reduces losses.
Angular correlations of cosmic microwave background spectrum distortions from photon diffusion
Authors: Starkman Nathaniel , Starkman Glenn , Kosowsky Arthur 
Published: March 2024

ABSTRACT
During cosmic recombination, charged particles bind into neutral atoms and the mean free path of photons rapidly increases, resulting in the familiar diffusion damping of primordial radiation temperature variations. An additional effect is a small photon spectrum distortion, because photons arriving from a particular sky direction were originally in thermal equilibrium at various spatial locations with different temperatures; the combination of these different blackbody temperature distributions results in a spectrum with a Compton y-distortion. Using the approximation that photons had zero mean free path prior to their second-to-last scattering, we derive an expression for the resulting y-distortion, and compute the angular correlation function of the diffusion y-distortion and its cross-correlation with the square of the photon temperature fluctuation. Detection of the cross-correlation is within reach of existing arcminute-resolution microwave background experiments such as the Atacama Cosmology Telescope and the South Pole Telescope.
Searching for NLTE effects in the high-resolution transmission spectrum of WASP-121 b with cloudy for exoplanets
Authors: Young M E , Spring E F , Birkby J L 
Published: March 2024

ABSTRACT
Ultrahot Jupiters (UHJs) undergo intense irradiation by their host stars and are expected to experience non-local thermodynamic equilibrium (NLTE) effects in their atmospheres. Such effects are computationally intensive to model but, at the low pressures probed by high-resolution cross-correlation spectroscopy (HRCCS), can significantly impact the formation of spectral lines. The UHJ WASP-121 b exhibits a highly inflated atmosphere, making it ideal for investigating the impact of NLTE effects on its transmission spectrum. Here, we formally introduce cloudy for exoplanets, a cloudy-based modelling code, and use it to generate 1D LTE and NLTE atmospheric models and spectra to analyse archival HARPS WASP-121 b transmission spectra. We assessed the models using two HRCCS methods: (i) Pearson cross-correlation, and (ii) a method that aims to match the average observed line depth for given atmospheric species. All models result in strong detections of Fe i (7.5 &lt; S/N &lt; 10.5). However, the highest S/N model (LTE) does not agree with the best-matching model of the average line depth (NLTE). We also find degeneracy, such that increasing the isothermal temperature and metallicity of the LTE models can produce average line depths similar to cooler, less metal rich NLTE models. Thus, we are unable to conclusively remark on the presence of NLTE effects in the atmosphere of WASP-121 b. We instead highlight the need for standardized metrics in HRCCS that enable robust statistical assessment of complex physical models, e.g. NLTE or 3D effects, that are currently too computationally intensive to include in HRCCS atmospheric retrievals.
Unveiling two expanding stellar groups formed through violent relaxation in the lagoon nebula cluster
Authors: Bonilla-Barroso Andrea , Ballesteros-Paredes Javier , Hernández Jesús , Aguilar Luis , Zamora-Avilés Manuel 
Published: March 2024

ABSTRACT
The current kinematic state of young stellar clusters can give clues on their actual dynamical state and origin. In this contribution, we use Gaia DR3 data of the Lagoon Nebula Cluster (LNC) to show that the cluster is composed of two expanding groups, likely formed from different molecular cloud clumps. We find no evidence of massive stars having larger velocity dispersion than low-mass stars or being spatially segregated across the LNC, as a whole, or within the Primary group. However, the Secondary group, with 1/5th of the stars, exhibits intriguing features. On the one hand, it shows a bipolar nature, with an aspect ratio of ∼3:1. In addition, the massive stars in this group exhibit larger velocity dispersion than the low-mass stars, although they are not concentrated towards the centre of the group. This suggests that this group may have undergone dynamical relaxation, first, and some explosive event afterward. However, further observations and numerical work have to be performed to confirm this hypothesis. The results of this work suggest that, although stellar clusters may form by the global and hierarchical collapse of their parent clump, still some dynamical relaxation may take place.
Concerning SH0ES data: discrepant W0, VI absolute magnitudes for Cepheids in the keystone galaxy NGC4258
Authors: Majaess Daniel 
Published: March 2024

ABSTRACT
SH0ES VI-band photometry for classical Cepheids in the keystone galaxy NGC4258 yield discrepant absolute magnitudes. Specifically, the 2016 and 2022 published SH0ES Cepheid data for NGC4258 exhibit a substantial offset of ΔW0, VI ≃ 0m.3. That adds to a suite of existing concerns associated with the SH0ES analysis, which in sum imply that their relatively non-changing Hubble constant for nearly 20 years warrants scrutiny.
Mutual occurrence ratio of planets – I. New clues to reveal origins of hot and warm Jupiter from the RV sample
Authors: Su Xiang-Ning , Zhang Hui , Zhou Ji-Lin 
Published: March 2024

ABSTRACT
Many studies have analysed planetary occurrence rates and their dependence on the host’s properties to provide clues to planet formation, but few have focused on the mutual occurrence ratio of different kinds of planets. Such relations reveal whether and how one type of planet evolves into another, e.g. from a cold Jupiter (CJ) to a warm Jupiter (WJ) or even hot Jupiter (HJ), and demonstrate how stellar properties impact the evolution history of planetary systems. We propose a new classification of giant planets, i.e. CJ, WJ, and HJ, according to their position relative to the snow line in the system. Then, we derive their occurrence rates (ηHJ, ηWJ, ηCJ) with the detection completeness of radial velocity (RV) surveys (HARPS and CORALIE) considered. Finally, we analyse the correlation between the mutual occurrence ratios, i.e. ηCJ/ηWJ, ηCJ/ηHJ, or ηWJ/ηHJ, and various stellar properties, e.g. effective temperature Teff. Our results show that the ηHJ, ηWJ, and ηCJ are increasing with the increasing Teff when Teff ∈ (4600, 6600] K. Furthermore, the mutual occurrence ratio between CJ and WJ, i.e. ηCJ/ηWJ, shows a decreasing trend with the increasing Teff. But, both ηCJ/ηHJ and ηWJ/ηHJ are increasing when the Teff increases. Further consistency tests reveal that the formation processes of WJ and HJ may be dominated by orbital change mechanisms rather than the in situ model. However, unlike WJ, which favours gentle disc migration, HJ favours a more violent mechanism that requires further investigation.