bluuebunny/crossref_metadata_2025_split huggingface dataset:
Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits
Authors: Zhao Pengju , Gu Lihong , Gao Yahui , Pan Zhangyuan , Liu Lei , Li Xingzheng , Zhou Huaijun , Yu Dongyou , Han Xinyan , Qian Lichun , Liu George E. , Fang Lingzhao , Wang Zhengguang 
Published: August 2023

AbstractTransposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.
Rapid and biased evolution of canalization during adaptive divergence revealed by dominance in gene expression variability during Arctic charr early development
Authors: Horta-Lacueva Quentin Jean-Baptiste , Jónsson Zophonías Oddur , Thorholludottir Dagny A. V. , Hallgrímsson Benedikt , Kapralova Kalina Hristova 
Published: August 2023

AbstractAdaptive evolution may be influenced by canalization, the buffering of developmental processes from environmental and genetic perturbations, but how this occurs is poorly understood. Here, we explore how gene expression variability evolves in diverging and hybridizing populations, by focusing on the Arctic charr (Salvelinus alpinus) of Thingvallavatn, a classic case of divergence between feeding habitats. We report distinct profiles of gene expression variance for both coding RNAs and microRNAs between the offspring of two contrasting morphs (benthic/limnetic) and their hybrids reared in common conditions and sampled at two key points of cranial development. Gene expression variance in the hybrids is substantially affected by maternal effects, and many genes show biased expression variance toward the limnetic morph. This suggests that canalization, as inferred by gene expression variance, can rapidly diverge in sympatry through multiple gene pathways, which are associated with dominance patterns possibly biasing evolutionary trajectories and mitigating the effects of hybridization on adaptive evolution.
Plasma metabolomic profiling in two rabbit lines divergently selected for intramuscular fat content
Authors: Zubiri-Gaitán Agostina , Blasco Agustín , Hernández Pilar 
Published: August 2023

AbstractThis study provides a thorough comparison of the plasma metabolome of two rabbit lines divergently selected for intramuscular fat content (IMF). The divergent selection led to a correlated response in the overall adiposity, turning these lines into a valuable animal material to study also the genetics of obesity. Over 900 metabolites were detected, and the adjustment of multivariate models, both discriminant and linear, allowed to identify 322 with differential abundances between lines, which also adjusted linearly to the IMF content. The most affected pathways were those of lipids and amino acids, with differences between lines ranging from 0.23 to 6.04 standard deviations, revealing a limited capacity of the low-IMF line to obtain energy from lipids, and a greater branched-chain amino acids catabolism in the high-IMF line related to its increased IMF content. Additionally, changes in metabolites derived from microbial activity supported its relevant role in the lipid deposition. Future research will focus on the analysis of the metabolomic profile of the cecum content, and on the integration of the several -omics datasets available for these lines, to help disentangle the host and microbiome biological mechanisms involved in the IMF deposition.
Using surface plasmon resonance, capillary electrophoresis and diffusion-ordered NMR spectroscopy to study drug release kinetics
Authors: Libánská Alena , Špringer Tomáš , Peštová Lucie , Kotalík Kevin , Konefał Rafał , Šimonová Alice , Křížek Tomáš , Homola Jiří , Randárová Eva , Etrych Tomáš 
Published: August 2023

AbstractNanomedicines, including polymer nanocarriers with controlled drug release, are considered next-generation therapeutics with advanced therapeutic properties and reduced side effects. To develop safe and efficient nanomedicines, it is crucial to precisely determine the drug release kinetics. Herein, we present application of analytical methods, i.e., surface plasmon resonance biosensor technology (SPR), capillary electrophoresis, and 1H diffusion-ordered nuclear magnetic resonance spectroscopy, which were innovatively applied for drug release determination. The methods were optimised to quantify the pH-triggered release of three structurally different drugs from a polymer carrier. The suitability of these methods for drug release characterisation was evaluated and compared using several parameters including applicability for diverse samples, the biological relevance of the experimental setup, method complexity, and the analysis outcome. The SPR method was the most universal method for the evaluation of diverse drug molecule release allowing continuous observation in the flow-through setting and requiring a small amount of sample.
The integrity of dopaminergic and noradrenergic brain regions is associated with different aspects of late-life memory performance
Authors: Dahl Martin J. , Bachman Shelby L. , Dutt Shubir , Düzel Sandra , Bodammer Nils C. , Lindenberger Ulman , Kühn Simone , Werkle-Bergner Markus , Mather Mara 
Published: August 2023

AbstractChanges in dopaminergic neuromodulation play a key role in adult memory decline. Recent research has also implicated noradrenaline in shaping late-life memory. However, it is unclear whether these two neuromodulators have distinct roles in age-related cognitive changes. Here, combining longitudinal MRI of the dopaminergic substantia nigra–ventral tegmental area (SN-VTA) and noradrenergic locus coeruleus (LC) in younger (n = 69) and older (n = 251) adults, we found that dopaminergic and noradrenergic integrity are differentially associated with memory performance. While LC integrity was related to better episodic memory across several tasks, SN-VTA integrity was linked to working memory. Longitudinally, we found that older age was associated with more negative change in SN-VTA and LC integrity. Notably, changes in LC integrity reliably predicted future episodic memory. These differential associations of dopaminergic and noradrenergic nuclei with late-life cognitive decline have potential clinical utility, given their degeneration in several age-associated diseases.
Modulation of Small-Intestine Morphology in Mice by a Novel Supplement Containing Silybum marianum, Yeast β-Glucan, Prebiotics, and Minerals
Authors: Nucci Ricardo Aparecido Baptista , Nehmi-Filho Victor Abou , Bastos Marta Ferreira , de Freitas Jéssica Alves , Otoch José Pinhata , Pessoa Ana Flávia Marçal , Jacob-Filho Wilson 
Published: August 2023

AbstractSilymarin, derived from Silybum marianum, has recently demonstrated its potential to improve health in conditions such as obesity and metabolic disturbances. Understanding the impact of nutraceuticals on intestinal morphology is crucial for developing supplements that promote a higher quality of life. Therefore, this study aimed to investigate the effects of nutraceutical supplementation with silymarin on the morphology of the small intestine. Sixty-day-old adult male C57BL/6 mice were divided into two groups: one receiving a standard chow (control) and the other receiving a novel silymarin supplement (experimental). Following the experimental period, the animals were euthanized, and fragments of the small intestine were collected for histochemical analysis using Masson's trichrome and periodic acid-Schiff with Alcian blue staining techniques. Our results revealed an increase in the number of villi per analyzed field in the experimental group, accompanied by a decrease in basic mucin, crypt depth, mucosal thickness, and villus spacing. In conclusion, this novel nutraceutical supplementation may play a crucial role in modulating small intestine morphology and enhancing absorption capacity.
CT MRI LI-RADS in Routine Practice
Authors: Ganesan Karthik , Jalkote Shivsamb , Nellore Swarup 
Published: August 2023

AbstractPrimary liver cancer is the third most common cause of cancer-related deaths worldwide with hepatocellular carcinoma (HCC) comprising the vast majority of the cases. HCC unlike most solid cancers can be diagnosed based on imaging findings alone using multiphasic contrast-enhanced computed tomography (CT) or magnetic resonance imaging (MRI) without the need for histopathological confirmation in the majority of the cases. Liver Imaging Reporting and Data System (LI-RADS) was first introduced by the American College of Radiology in 2011 with the help of a multidisciplinary team of liver disease experts to improve the accuracy, consistency, and clarity of communication of imaging findings between radiologists and treating physicians. To date, LI-RADS has undergone four major updates in 2013, 2014, 2017, and 2018. This article reviews the technical aspects, categorization, and major and ancillary imaging features for the application of LI-RADS version 2018 using CT and MRI in routine clinical practice.
Lessons from Real Life Experience: Importance of In-House Sequencing and Smart Ratio-Based Real-Time PCR Outperform Multiplex Ligation-Dependent Probe Amplification in Prenatal Diagnosis for Spinal Muscular Atrophy: Bench to Bedside Diagnosis
Authors: Tuncel Gulten , Sanlıdag Burcin , Dirik Eray , Baris Tugba , Ergoren Mahmut Cerkez , Temel Sehime Gulsun 
Published: August 2023

AbstractSpinal muscular atrophy (SMA) is a rare, recessively inherited neurodegenerative disorder caused by the presence of pathogenic variants in the SMN gene. As it is the leading inherited cause of infant mortality, identification of SMN gene pathogenic variant carriers is important for diagnostic purposes with effective genetic counseling. Multiple ligation probe analysis (MLPA), a probe-based method, is considered as the gold standard for SMA carrier analysis. However, MLPA might give false-negative results in cases with variations in the probe-binding regions. Here, we present a case born to consanguineous SMA carrier parents. Prenatal diagnosis with MLPA failed to detect the compound heterozygous mutant state of the proband and she was born unfortunately with SMA phenotype. Further analysis with a real-time polymerase chain reaction kit was able to detect the compound heterozygous state of the patient and was confirmed with targeted next-generation sequencing technology.
MSSA-based adaptive low-frequency noise reduction using spectrum overlap measure
Authors: Kuang Weichao , Yang Ping , Miao Qing , Ling Wing-Kuen 
Published: August 2023

Abstract
A multistage singular spectrum analysis based method is presented to extract the useful component from the residue stage by stage. In every stage of the decomposition, the sum of the signal-dominated SSA components is treated as the denoised signal. The signal-to-noise ratios of the denoised signals first increase and then decrease. A measurement called spectrum overlap factor (SOF) is proposed to estimate the optimal stage which achieves the highest SNR. First, the factor is calculated to measure the spectrum overlap degree between the residue and the denoised signal in every stage. Then, the curve of the SOF with respect to the number of stages is analyzed. Further, the minimum of the SOFs, which indicates the less spectrum overlap, allows for the estimation of the optimal stage. The proposed strategy avoids inappropriate parameter selection effectively since the estimation of the optimal stage is automatic. Besides, simulation results show that the proposed method has satisfactory denoising performance in different test scenarios.
A refractive three-dimensional reconstruction method for fringe projection with a planar medium
Authors: Chen Chao , Li Zhaonan , Lu Wenzhen , Wang Yuzhu , Wang Huaiwen 
Published: August 2023

Abstract
In special measurement situations, a vision measurement system needs to measure objects through a viewing observation window made of a planar transparent medium. The refraction at the interface between a medium and air leads to large measurement errors in the pin-hole imaging model. Most existing solutions require complex processes of calculating refracted light equations and/or matching stereo images. Here, we propose a refractive three-dimensional (3D) reconstruction method for fringe projection with a planar medium. We derive a coordinate conversion relationship from a pseudo-object point caused by light refraction to a real-object point based on flat refractive geometry. Then, we integrate the relationship into regular fringe projection framework for unbiased 3D reconstruction. Two experiments, including 3D shape measurements of a step and a regular sphere are performed. The results verify the effectiveness and accuracy of the proposed refractive 3D reconstruction method.
Absolute continuity of non-homogeneous Gibbs measures of the Ising model on the Cayley tree
Authors: Mukhamedov Farrukh , Khakimov Otabek 
Published: August 2023

Abstract
In this paper, for the Ising model on the Cayley tree of order

k
⩾
2

, a sequence

{

h
n

}

of boundary conditions is constructed depending on an initial value h which defines a Gibbs measure µ

h
. By investigating the dynamical behaviour of the renormalisation group map associated with the model, we prove that each measure µ

h
is equivalent to the disordered phase

μ
∗

. This result shines a new light to the question closely related to the classical result by Kakutani which asserts that any two locally-equivalent probability product measures are either equivalent or mutually-singular.
Towards simulation-free MR-linac treatment: utilizing male pelvis PSMA-PET/CT and population-based electron density assignments
Authors: Carr Madeline E , Jelen Urszula , Picton Maddison , Batumalai Vikneswary , Crawford David , Peng Valery , Twentyman Tania , de Leon Jeremy , Jameson Michael G 
Published: August 2023

Abstract

Objective. This study aimed to investigate the dosimetric impact of using population-based relative electron density (RED) overrides in lieu of simulation computerized tomography (CT) in a magnetic resonance linear accelerator (MRL) workflow for male pelvis patients. Additionally, the feasibility of using prostate specific membrane antigen positron emission tomography/CT (PSMA-PET/CT) scans to assess patients’ eligibility for this proposed workflow was examined. Approach. In this study, 74 male pelvis patients treated on an Elekta Unity 1.5 T MRL were retrospectively selected. The patients’ individual RED values for 8 organs of interest were extracted from their simulation-CT images to establish population-based RED values. These values were used to generate individual (IndD) and population-based (PopD) RED dose plans, representing current and proposed MRL workflows, respectively. Lastly, this study compared RED values obtained from CT and PET-CT scanners in a phantom and a subset of patients. Results. Population-based RED values were mostly within two standard deviations of ICRU Report 46 values. PopD plans were comparable to IndD plans, with the average %difference magnitudes of 0.5%, 0.6%, and 0.6% for mean dose (all organs), D0.1cm
3 (non-target organs) and D95%/D98% (target organs), respectively. Both phantom and patient PET-CT derived RED values had high agreement with corresponding CT-derived values, with correlation coefficients ≥ 0.9. Significance. Population-based RED values were considered suitable in a simulation-free MRL treatment workflow. Utilizing these RED values resulted in similar dosimetric uncertainties as per the current workflow. Initial findings also suggested that PET-CT scans may be used to assess prospective patients’ eligibility for the proposed workflow. Future investigations will evaluate the clinical feasibility of implementing this workflow for prospective patients in the clinical setting. This is aimed to reduce patient burden during radiotherapy and increase department efficiencies.
HIRA: Heart Rate Interval based Rapid Alert score to characterize autonomic dysfunction among patients with sepsis-related acute respiratory failure (ARF)
Authors: Krishnan Preethi , Rad Milad G , Agarwal Palak , Marshall Curtis , Yang Philip , Bhavani Sivasubramanium V , Holder Andre L , Esper Annette , Kamaleswaran Rishikesan 
Published: August 2023

Abstract

Objective. To examine whether heart rate interval based rapid alert (HIRA) score derived from a combination model of heart rate variability (HRV) and modified early warning score (MEWS) is a surrogate for the detection of acute respiratory failure (ARF) in critically ill sepsis patients. Approach. Retrospective HRV analysis of sepsis patients admitted to Emory healthcare intensive care unit (ICU) was performed between sepsis-related ARF and sepsis controls without ARF. HRV measures such as time domain, frequency domain, and nonlinear measures were analyzed up to 24 h after patient admission, 1 h before the onset of ARF, and a random event time in the sepsis controls. Statistical significance was computed by the Wilcoxon Rank Sum test. Machine learning algorithms such as eXtreme Gradient Boosting and logistic regression were developed to validate the HIRA score model. The performance of HIRA and early warning score models were evaluated using the area under the receiver operating characteristic (AUROC). Main Results. A total of 89 (ICU) patients with sepsis were included in this retrospective cohort study, of whom 31 (34%) developed sepsis-related ARF and 58 (65%) were sepsis controls without ARF. Time-domain HRV for Electrocardiogram (ECG) Beat-to-Beat RR intervals strongly distinguished ARF patients from controls. HRV measures for nonlinear and frequency domains were significantly altered (p < 0.05) among ARF compared to controls. The HIRA score AUC: 0.93; 95% confidence interval (CI): 0.88–0.98) showed a higher predictive ability to detect ARF when compared to MEWS (AUC: 0.71; 95% CI: 0.50–0.90). Significance. HRV was significantly impaired across patients who developed ARF when compared to controls. The HIRA score uses non-invasively derived HRV and may be used to inform diagnostic and therapeutic decisions regarding the severity of sepsis and earlier identification of the need for mechanical ventilation.
Aligning incentives for carbon dioxide removal
Authors: Reinhard Christopher T , Planavsky Noah J , Khan Anu 
Published: August 2023

Abstract
Carbon dioxide removal (CDR) at the scale needed to meet key climate goals will require the development of a massive industry. The development of regulatory architecture and effective incentive structures must proceed in parallel if this industry is to function in a way that is technically rigorous, environmentally conscious, and socially responsible. Most of the current capital flow, overall technological development in CDR, and third-party monitoring and verification are occurring in the private sector. We argue here that this will need to change in order for robust, responsible carbon removal to be brought to scale. In the short term, a focus on removing flawed incentive structures will be a critical ingredient in the transition to a stable, large-scale marketplace for durable carbon removal.
Tracking and curating putative SARS-CoV-2 recombinants with RIVET
Authors: Smith Kyle , Ye Cheng , Turakhia Yatish 
Published: August 2023

Abstract

Motivation
Identifying and tracking recombinant strains of SARS-CoV-2 is critical to understanding the evolution of the virus and controlling its spread. But confidently identifying SARS-CoV-2 recombinants from thousands of new genome sequences that are being shared online every day is quite challenging, causing many recombinants to be missed or suffer from weeks of delay in being formally identified while undergoing expert curation.

Results
We present RIVET—a software pipeline and visual platform that takes advantage of recent algorithmic advances in recombination inference to comprehensively and sensitively search for potential SARS-CoV-2 recombinants and organize the relevant information in a web interface that would help greatly accelerate the process of identifying and tracking recombinants.

Availability and implementation
RIVET-based web interface displaying the most updated analysis of potential SARS-CoV-2 recombinants is available at https://rivet.ucsd.edu/. RIVET’s frontend and backend code is freely available under the MIT license at https://github.com/TurakhiaLab/rivet and the documentation for RIVET is available at https://turakhialab.github.io/rivet/. The inputs necessary for running RIVET’s backend workflow for SARS-CoV-2 are available through a public database maintained and updated daily by UCSC (https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/).
Anuran swingers: misdirected mating attempts occurred early during anuran diversification
Authors: Brischoux François , Lorrain-Soligon Léa 
Published: August 2023

Abstract
Promiscuity, explosive breeding and male-biased operational sex-ratios can affect the strength of male selectivity and may play major roles in the expression of misdirected matings (with conspecific males, other species, corpses or objects) in anuran amphibians. Yet, misdirected amplexus occur in multiple species diverging from these reproductive traits, suggesting that the expression of such behaviour is widespread, and may have occurred early during anuran diversification. Using two methods of ancestral-trait reconstruction which predict unknown states, we found a very high probability that most anuran genera express misdirected amplexus, suggesting that this by-product of anuran reproductive strategies is likely to have occurred early during anuran diversification. The persistence of misdirected amplexus suggests that its infrequent occurrence may outweigh individual costs of breeding attempts with unfit mates. We found a recent exponential increase in reported observations of misdirected amplexus, which, along with increased research effort and publication rate, may reveal an effect of environmental perturbations known to promote the occurrence of these behaviours.