bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of nitrate and abscisic acid signaling in plants
Authors: Xu Yiran , Qi Shengdong , Wang Yong , Jia Jingbo 
Published: April 2024

Abstract
To meet the demands of the new Green Revolution and sustainable agriculture, it is important to develop crop varieties with improved yield, nitrogen use efficiency, and stress resistance. Nitrate is the major form of inorganic nitrogen available for plant growth in many well-aerated agricultural soils, and acts as a signaling molecule regulating plant development, growth, and stress responses. Abscisic acid (ABA), an important phytohormone, plays vital roles in integrating extrinsic and intrinsic responses and mediating plant growth and development in response to biotic and abiotic stresses. Therefore, elucidating the interplay between nitrate and ABA can contribute to crop breeding and sustainable agriculture. Here, we review studies that have investigated the interplay between nitrate and ABA in root growth modulation, nitrate and ABA transport processes, seed germination regulation, and drought responses. We also focus on nitrate and ABA interplay in several reported omics analyses with some important nodes in the crosstalk between nitrate and ABA. Through these insights, we proposed some research perspectives that could help to develop crop varieties adapted to a changing environment and to improve crop yield with high nitrogen use efficiency and strong stress resistance.
A probabilistic graphical model for assessing equivocal evidence
Authors: Taroni Franco , Garbolino Paolo , Bozza Silvia 
Published: April 2024

Abstract
The Bayes’ theorem can be generalized to account for uncertainty on reported evidence. This has an impact on the value of the evidence, making the computation of the Bayes factor more demanding, as discussed by Taroni, Garbolino, and Bozza (2020). Probabilistic graphical models can however represent a suitable tool to assist the scientist in their evaluative task. A Bayesian network is proposed to deal with equivocal evidence and its use is illustrated through examples.
Potential climates and habitability on Gl 514 b: a super-Earth exoplanet with high eccentricity
Authors: Biasiotti L , Simonetti P , Vladilo G , Ivanovski S , Damasso M , Sozzetti A , Monai S 
Published: April 2024

ABSTRACT
The recently discovered super-Earth Gl 514 b, orbiting a nearby M0.5-1.0 star at 7.6 pc, is one of the best benchmark exoplanets for understanding the potential climate states of eccentric planets. The elongated (e = 0.45$^{+0.15}_{-0.14}$) orbit of Gl 514 b, which only partially lies in the Conservative Habitable Zone, suggests a dynamically young system, where the spin-orbit tidal synchronization may not have yet occurred up to the present time. In the present work, we use a seasonal-latitudinal energy balance model, EOS-ESTM, to explore the potential impact of both constrained and unconstrained planetary, orbital, and atmospheric parameters on the Gl 514 b habitability, mapped in terms of surface temperature. We test three distinct CO2-dominated atmospheres by varying the CH4 concentration values (0 per cent, 0.1 per cent, and 1 per cent) and the total surface pressure. As a general trend, we find that habitable conditions are favoured by high-CH4 and high-pressure regimes. Habitability also increases for high-axis obliquities (at least until the appearance of an icebelt), long-rotation periods, and high-ocean fractional coverage. If the ocean fraction is low, then also the argument of periastron becomes relevant. Our results are robust against changes of the continental distribution. Thus, we conclude that Gl 514 b can potentially maintain temperate surface conditions with modest seasonal temperature variations under a wide variety of planetary, orbital, and atmospheric conditions. Despite no transit have been detected yet, the results found in this work should motivate the community to invest time in future observations.
Probing primordial black holes at high redshift with future gravitational wave detectors
Authors: Marcoccia Paolo , Nardini Germano , Pieroni Mauro 
Published: April 2024

ABSTRACT
We analyse the detection prospects for potential Primordial Black Hole Binary (PBHB) populations buried in the Stellar-Origin Black Hole Binary (SOBHB) population inferred by the LVK collaboration. We consider different PBHB population scenarios and several future Gravitational Wave (GW) detectors. To separate the PBHB component from the SOBHB one, we exploit the prediction that the PBHB merger rate does not decline as fast as the SOBHB one at high redshift. However, only a tiny fraction of PBHB events may be resolved individually, and the sub-threshold events may yield an undetectable Stochastic GW Background (SGWB). For this reason, we determine the statistical significance of the PBHB contributions in the number of resolvable events seen in future Earth-based detectors and the SGWB measured at LISA. We quantify them in the limit that SOBHB population uncertainties are small, as one may optimistically expect at the time that future detectors will operate. In general, we find the synergy between these probes will consistently help assess whether or not a sizeable PBHB population is present.
A High-Coverage Mesolithic Aurochs Genome and Effective Leveraging of Ancient Cattle Genomes Using Whole Genome Imputation
Authors: Erven Jolijn A M , Scheu Amelie , Verdugo Marta Pereira , Cassidy Lara , Chen Ningbo , Gehlen Birgit , Street Martin , Madsen Ole , Mullin Victoria E 
Published: April 2024

Abstract
Ancient genomic analyses are often restricted to utilizing pseudohaploid data due to low genome coverage. Leveraging low-coverage data by imputation to calculate phased diploid genotypes that enables haplotype-based interrogation and single nucleotide polymorphism (SNP) calling at unsequenced positions is highly desirable. This has not been investigated for ancient cattle genomes despite these being compelling subjects for archeological, evolutionary, and economic reasons. Here, we test this approach by sequencing a Mesolithic European aurochs (18.49×; 9,852 to 9,376 calBCE) and an Early Medieval European cow (18.69×; 427 to 580 calCE) and combine these with published individuals: two ancient and three modern. We downsample these genomes (0.25×, 0.5×, 1.0×, and 2.0×) and impute diploid genotypes, utilizing a reference panel of 171 published modern cattle genomes that we curated for 21.7 million (Mn) phased SNPs. We recover high densities of correct calls with an accuracy of &gt;99.1% at variant sites for the lowest downsample depth of 0.25×, increasing to &gt;99.5% for 2.0× (transversions only, minor allele frequency [MAF] ≥ 2.5%). The recovery of SNPs correlates with coverage; on average, 58% of sites are recovered for 0.25× increasing to 87% for 2.0×, utilizing an average of 3.5 million (Mn) transversions (MAF ≥2.5%), even in the aurochs, despite the highest temporal distance from the modern reference panel. Our imputed genomes behave similarly to directly called data in allele frequency-based analyses, for example consistently identifying runs of homozygosity &gt;2 Mb, including a long homozygous region in the Mesolithic European aurochs.
Comparative Analysis of Maternal Gene Expression Patterns Unravels Evolutionary Signatures Across Reproductive Modes
Authors: Kagan Ferenc , Hejnol Andreas 
Published: April 2024

Abstract
Maternal genes have a pivotal role in regulating metazoan early development. As such their functions have been extensively studied since the dawn of developmental biology. The temporal and spatial dynamics of their transcripts have been thoroughly described in model organisms and their functions have been undergoing heavy investigations. Yet, less is known about the evolutionary changes shaping their presence within diverse oocytes. Due to their unique maternal inheritance pattern, a high degree is predicted to be present when it comes to their expression. Insofar only limited and conflicting results have emerged around it. Here, we set out to elucidate which evolutionary changes could be detected in the maternal gene expression patterns using phylogenetic comparative methods on RNAseq data from 43 species. Using normalized gene expression values and fold change information throughout early development we set out to find the best-fitting evolutionary model. Through modeling, we find evidence supporting both the high degree of divergence and constraint on gene expression values, together with their temporal dynamics. Furthermore, we find that maternal gene expression alone can be used to explain the reproductive modes of different species. Together, these results suggest a highly dynamic evolutionary landscape of maternal gene expression. We also propose a possible functional dichotomy of maternal genes which is influenced by the reproductive strategy undertaken by examined species.
Towards parsimonious generative modeling of RNA families
Authors: Calvanese Francesco , Lambert Camille N , Nghe Philippe , Zamponi Francesco , Weigt Martin 
Published: April 2024

Abstract
Generative probabilistic models emerge as a new paradigm in data-driven, evolution-informed design of biomolecular sequences. This paper introduces a novel approach, called Edge Activation Direct Coupling Analysis (eaDCA), tailored to the characteristics of RNA sequences, with a strong emphasis on simplicity, efficiency, and interpretability. eaDCA explicitly constructs sparse coevolutionary models for RNA families, achieving performance levels comparable to more complex methods while utilizing a significantly lower number of parameters. Our approach demonstrates efficiency in generating artificial RNA sequences that closely resemble their natural counterparts in both statistical analyses and SHAPE-MaP experiments, and in predicting the effect of mutations. Notably, eaDCA provides a unique feature: estimating the number of potential functional sequences within a given RNA family. For example, in the case of cyclic di-AMP riboswitches (RF00379), our analysis suggests the existence of approximately 1039 functional nucleotide sequences. While huge compared to the known &lt;4000 natural sequences, this number represents only a tiny fraction of the vast pool of nearly 1082 possible nucleotide sequences of the same length (136 nucleotides). These results underscore the promise of sparse and interpretable generative models, such as eaDCA, in enhancing our understanding of the expansive RNA sequence space.
Multivalent DNAzyme agents for cleaving folded RNA
Authors: Dubovichenko Mikhail V , Batsa Michael , Bobkov Gleb A , Vlasov Gleb S , El-Deeb Ahmed A , Kolpashchikov Dmitry M 
Published: April 2024

Abstract
Multivalent recognition and binding of biological molecules is a natural phenomenon that increases the binding stability (avidity) without decreasing the recognition specificity. In this study, we took advantage of this phenomenon to increase the efficiency and maintain high specificity of RNA cleavage by DNAzymes (Dz). We designed a series of DNA constructs containing two Dz agents, named here bivalent Dz devices (BDD). One BDD increased the cleavage efficiency of a folded RNA fragment up to 17-fold in comparison with the Dz of a conventional design. Such an increase was achieved due to both the improved RNA binding and the increased probability of RNA cleavage by the two catalytic cores. By moderating the degree of Dz agent association in BDD, we achieved excellent selectivity in differentiating single-base mismatched RNA, while maintaining relatively high cleavage rates. Furthermore, a trivalent Dz demonstrated an even greater efficiency than the BDD in cleaving folded RNA. The data suggests that the cooperative action of several RNA-cleaving units can significantly improve the efficiency and maintain high specificity of RNA cleavage, which is important for the development of Dz-based gene knockdown agents.
TTSBBC: triplex target site biomarkers and barcodes in cancer
Authors: Ylagan Maya , Xu Qi , Kowalski Jeanne 
Published: April 2024

Abstract
The technology of triplex-forming oligonucleotides (TFOs) provides an approach to manipulate genes at the DNA level. TFOs bind to specific sites on genomic DNA, creating a unique intermolecular triple-helix DNA structure through Hoogsteen hydrogen bonding. This targeting by TFOs is site-specific and the locations TFOs bind are referred to as TFO target sites (TTS). Triplexes have been observed to selectively influence gene expression, homologous recombination, mutations, protein binding, and DNA damage. These sites typically feature a poly-purine sequence in duplex DNA, and the characteristics of these TTS sequences greatly influence the formation of the triplex. We introduce TTSBBC, a novel analysis and visualization platform designed to explore features of TTS sequences to enable users to design and validate TTSs. The web server can be freely accessed at https://kowalski-labapps.dellmed.utexas.edu/TTSBBC/.
Perceptions of Heated Tobacco Products (HTPs) Versus Cigarettes and e-Cigarettes in Relation to Likelihood of Trying HTPs or Suggesting HTPs to Those who Smoke Cigarettes
Authors: Duan Zongshuan , Berg Carla J , Bar-Zeev Yael , Abroms Lorien C , Wang Yan , Khayat Amal , Cui Yuxian , LoParco Cassidy R , Levine Hagai 
Published: April 2024

Abstract

Introduction
Heated tobacco products (HTPs), like IQOS, are marketed as innovative, stylish, harm-reduction products distinct from cigarettes and e-cigarettes. Research is needed to better understand how adults who are newly introduced to HTPs perceive them relative to cigarettes and e-cigarettes, and the impact of these perceptions on use outcomes.

Aims and Methods
We analyzed 2021 cross-sectional survey data from 1914 adults who never used HTPs from the United States and Israel, two countries where IQOS has unique histories and markets. Exploratory factor analysis examined perceptions of HTPs (vs. cigarettes and e-cigarettes) across 12 perception measures (eg, innovative, trendy, harmful, addictive). Multivariable linear regression examined these factors in relation to self-reported likelihood to: (1) “try HTPs in the next year” (1 = not–7 = extremely) and (2) “suggest IQOS to a friend who smokes cigarettes” (1 = not–5 = very), controlling for demographics and past-month cigarette and e-cigarette use (10.1% dual use, 15.4% cigarette-only, 5.7% e-cigarette-only, 68.8% neither).

Results
Four factors were identified: HTPs’ health and utility (“health-utility”) and design and appeal (“design-appeal”) versus cigarettes and versus e-cigarettes, separately. More favorable perceptions of HTP versus e-cigarette design-appeal (B = 0.30, 95% CI = 0.18, 0.41) were associated with greater likelihood to try HTPs. More favorable perceptions of HTP versus cigarette design-appeal (B = 0.38, 95% CI = 0.26, 0.51) and health-utility (B = 0.25, 95% CI = 0.13, 0.36), and HTP versus e-cigarette design-appeal (B = 0.32, 95% CI = 0.20, 0.45) were associated with greater likelihood to suggest HTPs to smokers.

Conclusions
Monitoring perceptions of HTPs versus cigarettes and e-cigarettes is critical given the role of such perceptions in HTP use and their population-level impact.

Implications
This study examined the relationship of perceptions of HTPs relative to cigarettes and e-cigarettes, with regard to adults’ self-reported likelihood to use HTP or to suggest HTPs to those who smoke cigarettes. Favorable perceptions of HTPs’ design and appeal versus e-cigarettes correlated with greater likelihood to try HTPs. Favorable perceptions of HTPs’ design and appeal, as well as health and utility, versus cigarettes and e-cigarettes correlated with greater likelihood to suggest HTPs to those who smoke. Findings underscore the need for ongoing surveillance of HTP marketing and consumer perceptions to inform regulatory efforts and estimate the population-level impact of HTPs and other tobacco products.
Mapping the evidence of novel plant-based foods: a systematic review of nutritional, health, and environmental impacts in high-income countries
Authors: Nájera Espinosa Sarah , Hadida Genevieve , Jelmar Sietsma Anne , Alae-Carew Carmelia , Turner Grace , Green Rosemary , Pastorino Silvia , Picetti Roberto , Scheelbeek Pauline 
Published: April 2024

Abstract

Context
Shifting from current dietary patterns to diets rich in plant-based (PB) foods and lower in animal-based foods (ABFs) is generally regarded as a suitable strategy to improve nutritional health and reduce environmental impacts. Despite the recent growth in supply of and demand for novel plant-based foods (NPBFs), a comprehensive overview is lacking.

Objectives
This review provides a synthesis of available evidence, highlights challenges, and informs public health and environmental strategies for purposeful political decision-making by systematically searching, analyzing, and summarizing the available literature.

Data Sources
Five peer-reviewed databases and grey literature sources were rigorously searched for publications.

Data Extraction
Study characteristics meeting the inclusion criteria regarding NPBF nutrient composition and health and environmental outcomes in high-income countries were extracted.

Data analysis
Fifty-seven peer-reviewed and 36 grey literature sources were identified; these were published in 2016–2022. NPBFs typically have substantially lower environmental impacts than ABFs, but the nutritional contents are complex and vary considerably across brands, product type, and main primary ingredient. In the limited evidence on the health impacts, shifts from ABFs to PB meats were associated with positive health outcomes. However, results were mixed for PB drinks, with links to micronutrient deficiencies.

Conclusion
If carefully selected, certain NPBFs have the potential to be healthier and nutrient-rich alternatives to ABFs and typically have smaller environmental footprints. More disaggregated categorization of various types of NPBFs would be a helpful step in guiding consumers and key stakeholders to make informed decisions. To enable informed policymaking on the inclusion of NPBFs in dietary transitions as part of a wider net-zero and health strategy, future priorities should include nutritional food standards, labelling, and subdivisions or categorizations of NPBFs, as well as short- and long-term health studies evaluating dietary shifts from ABFs to NPBFs and standardized environmental impact assessments, ideally from independent funders.
Combination of Antistaphylococcal β-Lactam With Standard Therapy Compared to Standard Therapy Alone for the Treatment of Methicillin-Resistant Staphylococcus aureus Bacteremia: A Post Hoc Analysis of the CAMERA2 Trial Using a Desirability of Outcome Ranking Approach
Authors: Petersiel Neta , Davis Joshua S , Meagher Niamh , Price David J , Tong Steven Y C ,   Combination Antibiotics for MEthicillin Resistant Staphylococcus aureus (CAMERA2) Study Group, Lye David C , Yahav Dafna , Sud Archana , Robinson J Owen , Nelson Jane , Archuleta Sophia , Roberts Matthew A , Cass Alan , Paterson David L , Foo Hong , Paul Mical , Guy Stephen D , Tramontana Adrian R , Walls Genevieve B , McBride Stephen , Bak Narin , Ghosh Niladri , Rogers Benjamin A , Ralph Anna P , Davies Jane , Ferguson Patricia E , Dotel Ravindra , McKew Genevieve L , Gray Timothy J , Holmes Natasha E , Smith Simon , Warner Morgyn S , Kalimuddin Shirin , Young Barnaby E , Runnegar Naomi , Andresen David N , Anagnostou Nicholas A , Johnson Sandra A , Chatfield Mark D , Cheng Allen C , Fowler Vance G , Howden Benjamin P , Meagher Niamh , Price David J , van Hal Sebastiaan J , Sullivan Matthew V N O 
Published: April 2024

Abstract

Background
Desirability of outcome ranking (DOOR) is an emerging approach to clinical trial outcome measurement using an ordinal scale to incorporate efficacy and safety endpoints.

Methods
We applied a previously validated DOOR endpoint to a cohort of CAMERA2 trial participants with methicillin-resistant Staphylococcus aureus bacteremia (MRSAB). Participants were randomly assigned to standard therapy, or to standard therapy plus an antistaphylococcal β-lactam (combination therapy). Each participant was assigned a DOOR category, within which they were further ranked according to their hospital length of stay (LOS) and duration of intravenous antibiotic treatment. We calculated the probability and the generalized odds ratio of participants receiving combination therapy having worse outcomes than those receiving standard therapy.

Results
Participants assigned combination therapy had a 54.5% (95% confidence interval [CI], 48.9%–60.1%; P = .11) probability and a 1.2-fold odds (95% CI, .95–1.50; P = .12) of having a worse outcome than participants on standard therapy. When further ranked according to LOS and duration of antibiotic treatment, participants in the combination group had a 55.6% (95% CI, 49.5%–61.7%) and 55.3% (95% CI, 49.2%–61.4%) probability of having a worse outcome than participants in the standard treatment group, respectively.

Conclusions
When considering both efficacy and safety, treatment of MRSAB with a combination of standard therapy and a β-lactam likely results in a worse clinical outcome than standard therapy. However, a small benefit of combination therapy cannot be excluded. Most likely the toxicity of combination therapy outweighed any benefit from faster clearance of bacteremia.
Masqueraders Around Disaster: Clinical Features of Scrub Typhus in Fukushima, Japan
Authors: Narita Masashi , Monma Naota , Chiba Kazuki , Suzuki Rie , Fujita Shohei , Hoshino Chisho , Nakamura Kiwamu , Sekikawa Yoshiyuki , Ikeda Hiroshi , Inoue Minoru , Shimbo Takuro , Yamamoto Seigo , Ando Shuji , Takada Nobuhiro , Fujita Hiromi 
Published: April 2024

Abstract

Background
Scrub typhus (ST) is endemic in Fukushima, with the largest number of cases reported in Japan from 2009 to 2010. Although ST is highly treatable, its atypical clinical presentation impedes diagnosis, causing delays in treatment.

Methods
We review the clinical features of ST in adults from 2008 to 2017 at Ohta Nishinouchi General Hospital in Fukushima, Japan.

Results
Fifty-five cases (serotype Karp 24, Irie/Kawasaki 21, Hirano/Kuroki 10) of ST were confirmed via serology based on elevated immunoglobulin (Ig)M and IgG and polymerase chain reaction positivity of eschar samples. The mean age was 69 years, and 64% were female. The case fatality rate was 1.8% (1/55). Approximately 70% of cases (38/55) were not diagnosed as ST upon the initial clinic visit. Inappropriate use of antibiotics was identified in 22% of cases (12/55). In terms of atypical clinical features, 1 or more of the manifestations, fever, rash, and eschar, was absent in 31% of cases (17/55). Approximately 11% of cases presented without eschar (6/55; Karp 1, Irie/Kawasaki 1, Hirano/Kuroki 4). Moreover, severe complications were observed with shock and disseminated intravascular coagulation in 7% of cases (4/55), Thus, while 53% of cases presented with the typical triad (29/55), unusual complications and atypical features occurred in 40% (22/55).

Conclusions
Diagnosis of ST becomes clinically challenging in the absence of typical features. In Fukushima, an endemic area of ST, an atypical presentation involving multisystem disease is common.