bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opportunistic Muscle Evaluation During Chest CT Is Associated With Vertebral Compression Fractures in Old Adults: A Longitudinal Study
Authors: Wang Miaomiao , Tang Hongye , Chen Xin , Liu Jingjing , Hu Nandong , Cui Wenjing , Zhang Chao , Xie Chao , Chen Xiao 
Published: July 2023

Abstract

Background
Sarcopenia and bone loss are both common in older individuals. However, the association between sarcopenia and bone fractures has not been evaluated longitudinally. In this study, we evaluated the association between computed tomography (CT)-based erector spinae muscle area and attenuation and vertebral compression fracture (VCF) in elderly individuals in a longitudinal study.

Methods
This study recruited individuals 50 years of age and older, who did not have VCF and underwent CT imaging for lung cancer screening during January 2016 to December 2019. Participants were followed up annually until January 2021. Muscle CT value and muscle area of the erector spinae were determined for muscle assessment. Genant score was used to define new-onset VCF. Cox proportional hazards models were used to assess the association between muscle area/attenuation and VCF.

Results
Of the 7 906 included participants, 72 developed new VCF over a median follow-up of 2 years. Large area of the erector spinae (adjusted hazard ratio [HR] = 0.2, 95% confidence interval [CI]: 0.1–0.7) and high bone attenuation (adjusted HR = 0.2, 95% CI: 0.1–0.5) were independently associated with VCF. High muscle attenuation was associated with severe VCF (adjusted HR = 0.46, 95% CI: 0.24–0.86). The addition of muscle area improved the area under the curve of bone attenuation from 0.79 (95% CI: 0.74–0.86) to 0.86 (95% CI: 0.82–0.91; p = .001).

Conclusions
CT-based muscle area/attenuation of the erector spinae was associated with VCF in elderly individuals, independently of bone attenuation. The addition of muscle area improved the performance of bone attenuation in predicting VCF.
Seismic-phase detection using multiple deep learning models for global and local representations of waveforms
Authors: Tokuda Tomoki , Nagao Hiromichi 
Published: July 2023

SUMMARY
The detection of earthquakes is a fundamental prerequisite for seismology and contributes to various research areas, such as forecasting earthquakes and understanding the crust/mantle structure. Recent advances in machine learning technologies have enabled the automatic detection of earthquakes from waveform data. In particular, various state-of-the-art deep-learning methods have been applied to this endeavour. In this study, we proposed and tested a novel phase detection method using deep learning, which is based on a standard convolutional neural network in a new framework. The novelty of the proposed method is its separate explicit learning strategy for global and local representations of waveforms, which enhances its robustness and flexibility. Prior to modelling the proposed method, we identified local representations of the waveform by the multiple clustering of waveforms, in which the data points were optimally partitioned. Based on this result, we considered a global representation and two local representations of the waveform. Subsequently, different phase detection models were trained for each global and local representation. For a new waveform, the overall phase probability was evaluated as a product of the phase probabilities of each model. This additional information on local representations makes the proposed method robust to noise, which is demonstrated by its application to the test data. Furthermore, an application to seismic swarm data demonstrated the robust performance of the proposed method compared with those of other deep learning methods. Finally, in an application to low-frequency earthquakes, we demonstrated the flexibility of the proposed method, which is readily adaptable for the detection of low-frequency earthquakes by retraining only a local model.
3-D forward modelling of controlled-source frequency-domain electromagnetic data using the meshless generalized finite-difference method
Authors: Zhang Ming , Farquharson Colin G , Lin Tingting 
Published: July 2023

SUMMARY
This paper proposes a procedure of forward modelling 3-D frequency-domain wire-source electromagnetic data using the meshless generalized finite-difference (MGFD) method. This method is based on Taylor series expansions and the weighted least-squares method, and its basic principle is to express the partial derivatives of the unknown function on a particular central point by a linear combination of function values on the adjacent points. The advantages of the method over mainstream forward-modelling methods, for example, the regular finite-difference (FD) method, or the finite-element (FE) method, is that mesh generation is not needed: a discretization in the form of just points is applied instead. This allows the points to be distributed freely to fit the arbitrary shape of the structures in the model, which is helpful in the modelling of complex earth structures. It makes the MGFD method more suitable to deal with complex model than FD method. Also, unlike that in the FE method, interpolation functions are not required and no integral needs to be calculated in MGFD method. This results in high computational efficiency and a concise forward-modelling process. In this paper, the particulars of the MGFD method are introduced, the discretized MGFD system of equations (for an ${\boldsymbol{A}} - {\rm{\ }}\varphi $ potential decomposition of the fields, with the Coulomb gauge condition enforced and a primary–secondary separation approach to deal with the singularity of the source) are solved using a direct solver, and the forward-modelling code are programmed. To test the method and code, we compare the MGFD solutions for three 3-D earth models with the equivalent solutions calculated by other methods, and verify the correctness of the MGFD solution by the good agreement between the corresponding results (with relative error of the electric field ${{\boldsymbol{E}}}_{\boldsymbol{x}}$ smaller than 4.89 per cent). We also investigate the performance of this method when applying different discretizations of points, and when using different weighting functions, to assess the influence of these two factors on the forward-modelling accuracy and efficiency. Results indicate that denser point distributions and straightforward weighting functions result in better accuracy and efficiency.
Rigid widths of active block boundary faults and crustal layered anisotropy in the intersection of faults Honghe and Xiaojiang in the SE margin of the Tibetan Plateau
Authors: Li Ying , Gao Yuan 
Published: July 2023

SUMMARYThe distribution of block boundary faults, both horizontally and vertically, has significant implications for crustal movements and structural variations. In the SE margin of the Tibetan Plateau, the south part of the Sichuan–Yunnan block is surrounded by the first-order block boundaries of the Honghe faults (HHF) trending NW–SE and the Xiaojiang faults (XJF) trending N–S. Crustal anisotropy provides valuable insights into the ongoing deformation and evolution. This study investigates the upper-crustal anisotropy at 26 stations, using local seismic waveforms from the temporary linear Honghe–Xiaojiang seismic broad-band Array (i.e. the HX Array) in 2017–2019 and regional permanent stations in 2012–2019. The PFS (i.e. polarization of fast S wave) shows an abrupt change in the Yimen region, which is the middle of the HX Array survey line between two large faults. The NW–SE dominant PFS orientations across the HHF agree well with the strike of faults and the direction of regional principal compressive stress, illustrating cracks or minerals aligned with the HHF, influenced by regional stress. The NE–SW dominant PFS orientations crossing the XJF differ from the faults strike or regional stress orientation, suggesting alignment with microcracks caused by the in situ principal compressive stress. The comparison between the upper-crustal and whole-crustal anisotropy demonstrates a noticeable PFS consistency across the two large faults, the HHF and the XJF. This observation implies that these two large faults may tectonically control a wide zone, with wide rigid widths of approximately 150 and 200 km, respectively. This study presents a new pattern indicating the control of deep physical properties on the boundary faults and uncovering the layered deformation in the upper and lower crust.
Genetic diversity, population structure, and genome-wide association analysis of ginkgo cultivars
Authors: Hu Yaping , Yu Zhaoyan , Gao Xiaoge , Liu Ganping , Zhang Yun , Šmarda Petr , Guo Qirong 
Published: July 2023

Abstract
Ginkgo biloba is an economically valuable tree worldwide. The species has nearly become extinct during the Quaternary, which has likely resulted in reduction of its genetic variability. The genetic variability is now conserved in few natural populations in China and a number of cultivars that are, however, derived from a few ancient trees, helping the species survive in China through medieval times. Despite the recent interest in ginkgo, however, detailed knowledge of its genetic diversity, conserved in cultivated trees and cultivars, has remained poor. This limits efficient conservation of its diversity as well as efficient use of the existing germplasm resources. Here we performed genotyping-by-sequencing (GBS) on 102 cultivated germplasms of ginkgo collected to explore their genetic structure, kinship, and inbreeding prediction. For the first time in ginkgo, a genome-wide association analysis study (GWAS) was used to attempt gene mapping of seed traits. The results showed that most of the germplasms did not show any obvious genetic relationship. The size of the ginkgo germplasm population expanded significantly around 1500 years ago during the Sui and Tang dynasties. Classification of seed cultivars based on a phylogenetic perspective does not support the current classification criteria based on phenotype. Twenty-four candidate genes were localized after performing GWAS on the seed traits. Overall, this study reveals the genetic basis of ginkgo seed traits and provides insights into its cultivation history. These findings will facilitate the conservation and utilization of the domesticated germplasms of this living fossil plant.
Genome assembly of Polygala tenuifolia provides insights into its karyotype evolution and triterpenoid saponin biosynthesis
Authors: Meng Fanbo , Chu Tianzhe , Feng Pengmian , Li Nan , Song Chi , Li Chunjin , Leng Liang , Song Xiaoming , Chen Wei 
Published: July 2023

Abstract
Polygala tenuifolia is a perennial medicinal plant that has been widely used in traditional Chinese medicine for treating mental diseases. However, the lack of genomic resources limits the insight into its evolutionary and biological characterization. In the present work, we reported the P. tenuifolia genome, the first genome assembly of the Polygalaceae family. We sequenced and assembled this genome by a combination of Illumnina, PacBio HiFi, and Hi-C mapping. The assembly includes 19 pseudochromosomes covering ~92.68% of the assembled genome (~769.62 Mb). There are 36 463 protein-coding genes annotated in this genome. Detailed comparative genome analysis revealed that P. tenuifolia experienced two rounds of whole genome duplication that occurred ~39–44 and ~18–20 million years ago, respectively. Accordingly, we systematically reconstructed ancestral chromosomes of P. tenuifolia and inferred its chromosome evolution trajectories from the common ancestor of core eudicots to the present species. Based on the transcriptomics data, enzyme genes and transcription factors involved in the synthesis of triterpenoid saponin in P. tenuifolia were identified. Further analysis demonstrated that whole-genome duplications and tandem duplications play critical roles in the expansion of P450 and UGT gene families, which contributed to the synthesis of triterpenoid saponins. The genome and transcriptome data will not only provide valuable resources for comparative and functional genomic researches on Polygalaceae, but also shed light on the synthesis of triterpenoid saponin.
Genes, Morphology, Performance, and Fitness: Quantifying Organismal Performance to Understand Adaptive Evolution
Authors: Matthews David G , Dial Terry R , Lauder George V 
Published: July 2023

Synopsis
To understand the complexities of morphological evolution, we must understand the relationships between genes, morphology, performance, and fitness in complex traits. Genomicists have made tremendous progress in finding the genetic basis of many phenotypes, including a myriad of morphological characters. Similarly, field biologists have greatly advanced our understanding of the relationship between performance and fitness in natural populations. However, the connection from morphology to performance has primarily been studied at the interspecific level, meaning that in most cases we lack a mechanistic understanding of how evolutionarily relevant variation among individuals affects organismal performance. Therefore, functional morphologists need methods that will allow for the analysis of fine-grained intraspecific variation in order to close the path from genes to fitness. We suggest three methodological areas that we believe are well suited for this research program and provide examples of how each can be applied within fish model systems to build our understanding of microevolutionary processes. Specifically, we believe that structural equation modeling, biological robotics, and simultaneous multi-modal functional data acquisition will open up fruitful collaborations among biomechanists, evolutionary biologists, and field biologists. It is only through the combined efforts of all three fields that we will understand the connection between evolution (acting at the level of genes) and natural selection (acting on fitness).
Event-Related Potential Markers of Suicidality in Adolescents
Authors: Doruk Camsari Deniz , Lewis Charles P , Sonmez Ayse Irem , Ozger Can , Fatih Parmis , Yuruk Deniz , Shekunov Julia , Vande Voort Jennifer L , Croarkin Paul E 
Published: July 2023

Abstract

Background
Implicit cognitive markers may assist with the prediction of suicidality beyond clinical risk factors. The aim of this study was to investigate neural correlates associated with the Death/Suicide Implicit Association Test (DS-IAT) via event-related potentials (ERP) in suicidal adolescents.

Methods
Thirty inpatient adolescents with suicidal ideations and behaviors (SIBS) and 30 healthy controls from the community were recruited. All participants underwent 64-channel electroencephalography, DS-IAT, and clinical assessments. Hierarchical generalized linear models with spatiotemporal clustering were used to identify significant ERPs associated with the behavioral outcome of DS-IAT (D scores) and group differences.

Results
Behavioral results (D scores) showed that the adolescents with SIBS had stronger implicit associations between “death” and “self” than the healthy group (P = .02). Within adolescents with SIBS, participants with stronger implicit associations between “death” and “self” reported more difficulty in controllability of suicidal ideation in the past 2 weeks based on the Columbia-Suicide Severity Rating Scale (P = .03). For the ERP data, the D scores and N100 component over the left parieto-occipital cortex had significant correlations. Significant group differences without behavioral correlation were observed for a second N100 cluster (P = .01), P200 (P = .02), and late positive potential (5 clusters, all P ≤ .02). Exploratory predictive models combining both neurophysiological and clinical measures distinguished adolescents with SIBS from healthy adolescents.

Conclusions
Our results suggest that N100 may be a marker of attentional resources involved in the distinction of stimuli that are congruent or incongruent to associations between death and self. Combined clinical and ERP measures may have utility in future refinements of assessment and treatment approaches for adolescents with suicidality.
Differential Impacts of Endogenous Antioxidants on Clinical Symptoms and Cognitive Function in Acute and Chronic Schizophrenia Patients
Authors: Lin Chieh-Hsin , Li Tin-May , Huang Yu-Jhen , Chen Shaw-Ji , Lane Hsien-Yuan 
Published: July 2023

Abstract

Background
Impaired antioxidant defense is implicated in the pathophysiology of schizophrenia, and superoxide dismutase (SOD), catalase (CAT), and glutathione (GSH) are 3 first-line endogenous antioxidants. Various cognitive functions decline differently during the schizophrenia course. The characteristic roles of the 3 antioxidants in clinical and cognitive profiles in acute and chronic phases of schizophrenia require study.

Methods
We recruited 311 patients with schizophrenia, including 92 acutely exacerbated patients who had been off antipsychotics for at least 2 weeks and 219 chronic patients who had been stable on medication for at least 2 months. Blood SOD, CAT, and GSH levels; clinical symptoms; and 9 cognitive test scores were measured.

Results
Blood CAT levels were higher in the acute patients than in the chronic patients, whereas SOD and GSH levels were similar to one another. Higher CAT levels were correlated with less positive symptoms, better working memory and problem solving in the acute phase, and less negative symptoms, less general psychopathology, better global assessment of function, and better cognitive function (in speed of processing, attention, problem solving) in the chronic period. Higher SOD levels were correlated with better global assessment of function in the acute phase and better speed of processing, working memory, and verbal learning and memory in the chronic period. GSH influenced neither clinical nor cognitive manifestations.

Conclusions
This study showed that blood CAT affected different clinical and cognitive domains between acute and chronic stages of schizophrenia, SOD influenced cognitive functions in chronic state, but GSH affected none. Further studies are needed to explore the underlying mechanisms.
Production improvement of FK506 in Streptomyces tsukubaensis by metabolic engineering strategy
Authors: Chen Hai-Tao , Zhang Xiao-Ying , Wu Qing-Bin , Zhao Qing-Wei , Chen Xin-Ai , Li Yong-Quan 
Published: July 2023

Abstract

Aims
Study of the effect of isoleucine on the biosynthesis of FK506 and modification of its producing strain to improve the production of FK506.

Methods and Results
Metabolomics analysis was conducted to explore key changes in the metabolic processes of Streptomyces tsukubaensis Δ68 in medium with and without isoleucine. In-depth analysis revealed that the shikimate pathway, methylmalonyl-CoA, and pyruvate might be the rate-limiting factors in FK506 biosynthesis. Overexpression of involved gene PCCB1 in S. tsukubaensis Δ68, a high-yielding strain Δ68-PCCB1 was generated. Additionally, the amino acids supplement was further optimized to improve FK506 biosynthesis. Finally, FK506 production was increased to 929.6 mg L−1, which was 56.6% higher than that in the starter strain, when supplemented isoleucine and valine at 9 and 4 g L−1, respectively.

Conclusions
Methylmalonyl-CoA might be the key rate-limiting factors in FK506 biosynthesis and overexpression of the gene PCCB1 and further addition of isoleucine and valine could increase the yield of FK506 by 56.6%.
Antibacterial activity of 2-hydroxy-4-methoxybenzaldehyde and its possible mechanism against Staphylococcus aureus
Authors: Arunachalam Kannappan , Ravi Jothi , Tian Xiaorong , Shunmugiah Karutha Pandian , Shanmugaraj Gowrishankar , Shi Chunlei 
Published: July 2023

Abstract

Aim
Staphylococcus aureus causes several complicated infections. Despite decades of research on developing new antimicrobials, methicillin-resistant S. aureus (MRSA) remains a global health problem. Hence, there is a dire need to identify potent natural antibacterial compounds as an alternative to antimicrobials. In this light, the present work divulges the antibacterial efficacy and the action mechanism of 2-hydroxy-4-methoxybenzaldehyde (HMB) isolated from Hemidesmus indicus against S. aureus.

Methods and Results
Antimicrobial activity of HMB was assessed. HMB exhibited 1024 µg ml−1 as the minimum inhibitory concentration (MIC) and 2 × MIC as the minimum bactericidal concentration against S. aureus. The results were validated by spot assay, time kill, and growth curve analysis. In addition, HMB treatment increased the release of intracellular proteins and nucleic acid contents from MRSA. Additional experiments assessing the structural morphology of bacterial cells using SEM analysis, β-galactosidase enzyme activity, and the fluorescence intensities of propidium iodide and rhodamine123 dye divulged that the cell membrane as one of the targets of HMB to hinder S. aureus growth. Moreover, the mature biofilm eradication assay revealed that HMB dislodged nearly 80% of the preformed biofilms of MRSA at the tested concentrations. Further, HMB treatment was found to sensitize MRSA cells upon combining tetracycline treatment.

Conclusions
The present study suggests that HMB is a promising compound with antibacterial and antibiofilm activities and could act as a lead structure for developing new antibacterial drugs against MRSA.
Evaluating differences between formulated dietary net energy values and net energy values determined from growth performance in finishing beef steers
Authors: Galyean Michael L , Hales Kristin E , Smith Zachary K 
Published: July 2023

Abstract
Based on principles of the California Net Energy System, the dry matter intake (DMI) by feedlot cattle can be subdivided into DMI required for maintenance and DMI required for gain. Thus, if DMI along with body weight at a compositional endpoint and shrunk weight gain are known, dietary concentrations of net energy for maintenance and gain (NEm and NEg, respectively) can be calculated from growth performance data. Close agreement between growth performance-predicted and tabular NEm and NEg values implies the system can be used to accurately predict growth performance and be used to evaluate marketing and management decisions. We used 747 pen means from 21 research studies conducted at Texas Tech University and South Dakota State University to assess the agreement between growth performance-predicted NEm and NEg values and those calculated from tabular energy values for feeds reported by the 2016 National Academies of Science, Engineering, and Medicine publication on beef cattle nutrient requirements. Regression of growth performance-predicted values on tabular values with adjustment for random effects of study indicated that the intercepts of the two regressions did not differ from zero, and the slopes did not differ from one. Residuals (tabular minus growth performance-predicted values) for NEm and NEg averaged −0.003 and −0.005, respectively. Nonetheless, the precision of growth performance-predicted values was low, with approximately 40.3% of performance-predicted NEm values and 30.9% of NEg values falling within 2.5% of the corresponding tabular value. Residuals for NEm were divided into quintiles to evaluate dietary, growth performance, carcass, and energetics variables that might help explain lack of precision in growth performance-predicted values. Among the variables considered, gain:feed ratio was the most discriminating, with differences (P &lt; 0.05) among each of the quintiles. Despite these differences, however, gain:feed ratio did not explain important percentages of variation in components of growth performance-predicted NEm values like maintenance energy requirements (r2 = 0.112) and retained energy (r2 = 0.003). Further research with large datasets that include dietary composition, growth performance and carcass data, and environmental variables, along with fundamental research on maintenance requirements and energy retention, will be required to identify ways to improve the precision of growth performance-predicted NE values.