bluuebunny/crossref_metadata_2025 huggingface dataset:
An improved passivity‐based control for suppressing the traction motor torque ripples due to traction network voltage fluctuation in high‐speed railways
Authors: Zhao Wenqing , Lu Bing , Liu Zhigang , Zhang Guinan
Published: July 2023

When the voltage fluctuation of the traction network occurs in high‐speed railways, the interharmonics in the grid‐side voltage will propagate to the traction motor, which results in the motor torque ripple of running trains. The ripple can cause abnormal vibrations of key train components and even influence train operation safety. However, the traditional proportional‐integral controller used in the inverter‐motor system has a weak anti‐interference capability when facing nonlinear disturbances. This paper proposes an improved passivity‐based control (IPBC) to suppress the impact of interharmonics on trains. First, the Euler‐Lagrange mathematical model of the traction inverter‐motor system is established. Then, the PBC for this system is designed by damping injection, ensuring the asymptotic stability of the system. Furthermore, to purposely suppress the impact of the periodic disturbance on the system, a repetitive controller is designed in parallel with the PBC to control the inverter‐motor system. Finally, through the offline simulation and HIL simulation, it has been verified that the proposed IPBC can effectively suppress the motor torque ripple and the vibrations of key train components. The control strategy proposed in this paper has a reference significance for improving the operational stability of high‐speed trains.
Additive manufacturing of polymer derived ceramics: Materials, methods, and applications
Authors: Lacelle Thomas , Sampson Kathleen L. , Yazdani Sarvestani Hamidreza , Rahimizadeh Amir , Barroeta Robles Julieta , Mirkhalaf Mohammad , Rafiee Mohammad , Jakubinek Michael B. , Paquet Chantal , Ashrafi Behnam
Published: July 2023

Owing to freedom of design, simplicity, and ability to handle complex structures, additive manufacturing (AM) or 3D printing of ceramics represents a promising enabling technology and has already been used to produce geometrically complex ceramic components and ceramic metamaterials. Consequently, novel applications for additively manufactured ceramics, which leverage their structural, high temperature, and chemical-resistant properties, have been proposed in areas ranging from electrical engineering and micro/nanoelectronics to chemical engineering to biology. Polymer derived ceramics (PDCs) represent a relatively new class of materials within additive manufacturing. PDCs enable the development of ceramic parts patterned via low-cost polymer 3D printing methods followed by pyrolysis in a high temperature process in which the polymer itself forms a ceramic often in the absence of any ceramic filler. PDCs have served as a feedstock for various 3D printing techniques for which a wide range of physiochemical factors can be tailored to optimize the ceramic manufacturing processes. In particular, the silicon and carbon-rich polymeric microstructure of PDCs offers a high degree of tunability and potential to achieve a closely defined combination of functional, thermomechanical, and chemical properties. In this review, we cover mechanisms underlying the design and manufacture of ceramics via 3D printing and pyrolysis of preceramic polymers, focusing on chemical formulations, printing technologies, and the mechanical performance of the ceramic network from microscale to scale. We also summarize experimental data from the literature and present qualitative and quantitative comparisons between different AM routes to provide a comprehensive review for 3D printing of PDCs and to highlight potential future research.
GsNAC2 gene enhances saline-alkali stress tolerance by promoting plant growth and regulating glutathione metabolism in Sorghum bicolor
Authors: Wu Rong , Kong Lingxin , Wu Xiao , Gao Jing , Niu Tingli , Li Jianying , Li Zhijiang , Dai Lingyan
Published: July 2023

The quality and yields of Sorghum bicolor plants are seriously affected by saline-alkali conditions. NAC (NAM, ATAF, and CUC) transcription factors are plant specific and have various functions in plant development and response to various stresses. To investigate how GsNAC2 functions in sorghum responses to saline-alkali treatment, the characteristics of GsNAC2 were analysed by bioinformatics methods, and NaHCO3:Na2CO3 (5:1, 75 mM, pH 9.63) saline-alkali stress solution was applied when sorghum plants were 2 weeks old. The research results show that GsNAC2 belongs to the NAC gene family. GsNAC2 was significantly induced by saline-alkali treatment and strongly expressed in sorghum leaves. GsNAC2-overexpressing sorghum plants had increased plant height, dry weight, moisture content, root activity, leaf length, chlorophyll content, stomatal conductance, relative root activity, relative chlorophyll content, relative stomatal conductance, and relative transpiration rate after saline-alkali treatment. Lower H2O2 and O2− levels, relative permeability of the plasma membrane, and malondialdehyde (MDA) content were found in GsNAC2-overexpressing sorghum. In transcriptome analysis, clusters of orthologous groups (COG) analysis showed that a high proportion of differentially-expressed genes (DEGs) participated in defence mechanisms at each processing time, and 18 DEGs related to synthetic glutathione were obtained. Gene expression analysis revealed that key genes in glutathione biosynthesis pathways were upregulated. GR and GSH-Px activities were increased, and GSH accumulated more with the overexpression of GsNAC2 after saline-alkali treatment. Furthermore, these results suggest that GsNAC2 acts as a potentially important regulator in response to saline-alkali stress and may be used in molecular breeding to improve crop yields under adverse environmental conditions.
Mpox knowledge, vaccination and intention to reduce sexual risk practices among men who have sex with men and transgender people in response to the 2022 mpox outbreak: a cross-sectional study in Victoria, Australia
Authors: Chow Eric P. F. , Samra Ranjit S. , Bradshaw Catriona S. , Chen Marcus Y. , Williamson Deborah A. , Towns Janet M. , Maddaford Kate , Mercury Finn , Fairley Christopher K.
Published: July 2023

Background The first mpox case was reported in May 2022 in Australia. Most cases have been diagnosed in men who have sex with men (MSM). This study aimed to examine community understanding of mpox, attitudes towards vaccination, and potential changes in sexual practices surrounding the mpox outbreak among MSM and transgender people in Victoria, Australia. Methods Participants were recruited from sexual health clinics and communities in Victoria, Australia, in August–October 2022. Participants were asked about their understanding and knowledge of mpox, vaccination uptake and intentions to change sexual practices. Univariable and multivariable logistic regression was performed to examine the factors associated with mpox vaccine uptake. Results Most participants (97.8%, 525/537) had heard about mpox and 10.5% (55/525) knew someone who had had mpox. Of the 12 mpox knowledge questions, the median score of correct answers was 10 (IQR = 8–11) out of a maximum of 12. More than a third (36.6%, 191/522) had been vaccinated against mpox. MSM who had a good knowledge of mpox had the highest odds of receiving mpox vaccine compared with those who had poor knowledge (aOR = 4.05; 95% CI: 1.54–10.61). To prevent mpox, half reported they would reduce having sex with casual partners, stop having chemsex (used drugs for the purpose of sex), stop attending sex-on-premises-venues, and stop having group sex. A quarter reported they would increase condom use for anal sex. Conclusions One-third of high-risk participants and a substantial proportion of participants intended to reduce or stop certain practices, which may explain the large reduction in mpox cases.
Supermassive Dark Star candidates seen by JWST
Authors: Ilie Cosmin , Paulin Jillian , Freese Katherine
Published: July 2023

The first generation of stars in the universe is yet to be observed. There are two leading theories for those objects that mark the beginning of the cosmic dawn: hydrogen burning Population III stars and Dark Stars, made of hydrogen and helium but powered by dark matter heating. The latter can grow to become supermassive (
M
⋆
∼ 10
6
M
⊙
) and extremely bright (
L
∼ 10
9
L
⊙
). We show that each of the following three objects—JADES-GS-z13-0, JADES-GS-z12-0, and JADES-GS-z11-0 (at redshifts
z
∈ [11, 14])—are consistent with a Supermassive Dark Star interpretation, thus identifying the first Dark Star candidates.
Helium bubble size effects on the surface morphological response of plasma-facing tungsten
Authors: Patel Omeet N , Dasgupta Dwaipayan , Wirth Brian D , Maroudas Dimitrios
Published: July 2023

We report a simulation study on the effects of helium (He) bubble size on the morphological evolution and pattern formation on the surface of tungsten used as a plasma-facing component (PFC) in nuclear fusion devices. We have carried out a systematic investigation based on self-consistent dynamical simulations of surface morphological evolution according to an atomistically-informed, 3D continuum-scale model that captures well the relevant length and time scales of surface nanostructure formation in PFC tungsten. The model accounts for PFC surface diffusion, driven by the biaxial compressive stress originating from the over-pressurized He bubbles in the near-surface region of PFC tungsten as a result of He plasma exposure, combined with the formation of self-interstitial atoms in tungsten that diffuse toward the PFC surface and the flux of surface adatoms generated as a result of surface vacancy-adatom pair formation upon He implantation; this transport of surface adatoms contributes to the anisotropic growth of surface nanostructural features due to the different rates of adatom diffusion along and across step edges of islands on the tungsten surface. Our detailed analysis reveals that varying the average He bubble size plays an important role in the PFC surface growth kinetics as well as the resulting surface topography. Specifically, we find that an increase in the He bubble size leads to a deceleration in the growth rate of the tungsten nanotendrils that emanate from the PFC surface. We also find that the separation distance between the resulting surface features increases with increasing He bubble size, as well as over time. This coarsening effect is a thermally activated process resulting in an accurate description of the temperature dependence of the average surface feature separation by an Arrhenius relation.
Dissecting T-cell heterogeneity in esophageal squamous cell carcinoma reveals the potential role of LAIR2 in antitumor immunity
Authors: Wang Ping , Zhuang Weitao , Zheng Zhuojun , Zhang Liyun , Zhang Xu , Chen Qingyun
Published: July 2023

Esophageal squamous cell carcinoma (ESCC), one of the most commonly diagnosed and lethal malignant diseases, has a complex tumor ecosystem. An obvious requirement for T-cell-mediated tumor control is the infiltration of tumor-reactive T cells into the tumor. Here, we obtained detailed T-cell compositions in both ESCC tumors and matched peripheral blood mononuclear cells (PBMCs) at single-cell resolution. We demonstrated that T cells in tumors and PBMCs had different compositions and functional states. ESCC tumors were rich in Treg and exhausted T cells but poor in cytotoxic and naïve T cells compared with PBMCs. The exhausted T cells showed higher exhausted signature in tumors than in PBMCs, while the cytotoxic T cells exhibited higher cytotoxic signature in PBMCs than in tumors. Our data indicated an immunosuppressive status and a defect at the level of T-cell priming in the tumor microenvironment. Leukocyte-associated Ig-like receptor-2 (LAIR2), a soluble collagen receptor that prevents the binding of human leukocyte-associated Ig-like receptor-1 (LAIR1) to collagens, was predominantly expressed in proliferating CD8+ T and Treg cells in tumors but in cytotoxic cells in PBMCs. LAIR2 could inhibit tumor metastasis, invasion, and collagen deposition via suppressing transforming growth factor-β signaling. These findings revealed differential T-cell populations in tumors and PBMCs and provided convincing evidence that LAIR2 acted as a tumor suppressor.
Upadacitinib Salvage Therapy for Infliximab-Experienced Patients with Acute Severe Ulcerative Colitis
Authors: Gilmore Robert , Tan Wei Lian , Fernandes Richard , An Yoon-Kyo , Begun Jakob
Published: July 2023

Background and Aims

Acute severe ulcerative colitis [ASUC] is a medical emergency treated with intravenous steroids followed by infliximab or cyclosporin in the case of steroid failure with emergent colectomy required in refractory or severe cases. Case series have reported on the effectiveness of tofacitinib for refractory disease, but data regarding the effectiveness of upadacitinib in this setting have not been previously reported. We describe the use of upadacitinib therapy for steroid-refractory ASUC in patients with prior loss of response to infliximab.

Methods

Six patients who received upadacitinib for steroid-refractory ASUC were identified at two Australian tertiary inflammatory bowel disease centres. Patients were followed for up to 16 weeks after discharge with clinical, biochemical and intestinal ultrasound [IUS] outcomes.

Results

All six patients demonstrated clinical response to upadacitinib induction during their inpatient admission. Four patients achieved corticosteroid-free clinical remission by week 8, including complete resolution of rectal bleeding and transmural healing assessed by IUS, and sustained clinical remission at week 16. One patient proceeded to colectomy at week 15 due to refractory disease. No adverse events directly attributable to upadacitinib were identified.

Conclusions

Upadacitinib may have a role as a safe and effective salvage therapy for steroid-refractory ASUC in patients who have previously failed to respond to infliximab therapy. Prospective studies are required to determine the safety and efficacy of upadacitinib use in this setting before routine use can be recommended.
Declining Trends of Reoperations and Disease Behaviour Progression in Crohn’s Disease over Different Therapeutic Eras—A Prospective, Population-Based Study from Western Hungary between 1977–2020, Data from the Veszprem Cohort
Authors: Gonczi Lorant , Lakatos Laszlo , Golovics Petra A , Ilias Akos , Pandur Tunde , David Gyula , Erdelyi Zsuzsanna , Szita Istvan , Al Khoury Alex , Lakatos Peter L
Published: July 2023

Background and Aims

Few population-based studies have investigated long-term surgery rates for Crohn’s disease [CD]. Our aim was to analyse disease progression and surgery rates in a population-based cohort over different therapeutic eras, based on the time of diagnosis: cohort-A [1977–1995], cohort-B [1996–2008], and cohort-C [2009–2018].

Methods

A total of 946 incident CD patients were analysed (male/female: 496/450; median age at diagnosis: 28 years [y]; interquartile range [IQR]: 22–40]). Patient inclusion lasted between 1977 and 2018. Immunomodulators have become widespread in Hungary since the mid-1990s and biologic therapies since 2008. Patients were followed prospectively, with both in-hospital and outpatient records reviewed regularly.

Results

The probability of disease behaviour progression from inflammatory [B1] to stenosing or penetrating phenotype [B2/B3] significantly decreased (27.1 ± 5.3%/21.5 ± 2.5%/11.3 ± 2.2% in cohorts A/B/C, respectively, after 5 years; 44.3 ± 5.9%/30.6 ± 2.8%/16.1 ± 2.9% after 10 years, respectively; [pLogRank <0.001]). The probability of first resective surgery between cohorts A/B/C were 33.3 ± 3.8%/26.5 ± 2.1%/28.1 ± 2.4%, respectively, after 5 years; 46.1 ± 4.1%/32.6 ± 2.2%/33.0 ± 2.7% after 10 years, respectively; and 59.1 ± 4.0%/41.4 ± 2.6% [cohorts A/B] after 20 years. There was a significant decrease in first resective surgery risk between cohorts A and B [plog rank = 0.002]; however, no further decrease between cohorts B and C [plog rank = 0.665]. The cumulative probability of re-resection in cohorts A/B/C was decreasing over time (17.3 ± 4.1%/12.6 ± 2.6%/4.7 ± 2.0%, respectively, after 5 years [plog rank = 0.001]).

Conclusion

We report a continuous decline in reoperation rates and disease behaviour progression in CD over time, with the lowest values in the biologic era. In contrast, there was no further decrease in the probability of first major resective surgery after the immunosuppressive era.
Using evolutionary principles to make clinical decisions: a case series of urinary tract infections
Authors: Blyth Michelle
Published: July 2023

The principles of evolutionary medicine have significant potential to be useful in a wide variety of clinical situations. Despite this, few demonstrations of clinical applications exist. To address this paucity, a case series applying evolutionary medicine principles to urinary tract infections, a common medical condition is presented. This series demonstrates how applying evolutionary medicine principles can be used to augment clinical decision-making.
Denitrification in hypersaline and coastal environments
Authors: Torregrosa-Crespo Javier , Miralles-Robledillo Jose María , Bernabeu Eric , Pire Carmen , Martínez-Espinosa Rosa María
Published: July 2023

As the association of denitrification with global warming and nitrogen removal from ecosystems has gained attention in recent decades, numerous studies have examined denitrification rates and the distribution of denitrifiers across different environments. In this minireview, reported studies focused on coastal saline environments, including estuaries, mangroves, and hypersaline ecosystems, have been analysed to identify the relationship between denitrification and saline gradients. The analyses of the literature and databases stated the direct effect of salinity on the distribution patterns of denitrifiers. However, few works do not support this hypothesis thus making this topic controversial. The specific mechanisms by which salinity influences denitrifier distribution are not fully understood. Nevertheless, several physical and chemical environmental parameters, in addition to salinity, have been shown to play a role in structuring the denitrifying microbial communities. The prevalence of nirS or nirK denitrifiers in ecosystems is a subject of debate in this work. In general terms, in mesohaline environments, the predominant nitrite reductase is NirS type and, NirK is found predominantly in hypersaline environments. Moreover, the approaches used by different researchers are quite different, resulting in a huge amount of unrelated information, making it difficult to establish comparative analysis. The main techniques used to analyse the distribution of denitrifying populations along salt gradients have been also discussed.
Phenotypic Frailty Assessment in SAMP8 Mice: Sex Differences and Potential Role of miRNAs as Peripheral Biomarkers
Authors: Musazzi Laura , Carini Giulia , Barbieri Silvia S , Maggi Stefania , Veronese Nicola , Popoli Maurizio , Barbon Alessandro , Ieraci Alessandro
Published: July 2023

Frailty is a geriatric syndrome characterized by age-related decline in physiological reserves and functions in multiple organ systems, including the musculoskeletal, neuroendocrine/metabolic, and immune systems. Animal models are essential to study the biological basis of aging and potential ways to delay the onset of age-related phenotypes. Unfortunately, validated animal models of frailty are still lacking in preclinical research. The senescence-accelerated prone-8 (SAMP8) mouse strain exhibits early cognitive loss that mimics the deterioration of learning and memory in the elderly and is widely used as a model of aging and neurodegenerative diseases. Here, we examined the frailty phenotype, which includes body weight, strength, endurance, activity, and slow walking speed, in male and female SAMP8 and senescence-accelerated mouse resistant (SAMR1) mice at 6- and 9-months of age. We found that the prevalence of frailty was higher in SAMP8 mice compared with SAMR1 mice, regardless of sex. The overall percentage of prefrail and frail mice was similar in male and female SAMP8 mice, although the percentage of frail mice was slightly higher in males than in females. In addition, we found sex- and frailty-specific changes in selected miRNAs blood levels. In particular, the levels of miR-34a-5p and miR-331-3p were higher in both prefrail and frail mice, whereas miR-26b-5p was increased only in frail mice compared with robust mice. Finally, levels of miR-331-3p were also increased in whole blood from a small group of frail patients. Overall, these results suggest that SAMP8 mice may be a useful mouse model for identifying potential biomarkers and studying biological mechanisms of frailty.
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

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

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

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

The 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

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

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

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

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

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

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

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 < 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.
Comparing the standardized amino acid digestibility of an alternative protein source with commercially available protein-based ingredients using the precision-fed cecectomized rooster assay
Authors: Oba Patrícia M , Utterback Pamela L , Longshaw Matt , Parsons Carl M , Swanson Kelly S
Published: July 2023

Using single-cell-based proteins in pet foods is of interest, but little testing has been done. Therefore, our objective was to determine the amino acid (AA) digestibilities, assess protein quality of a novel microbial protein (MP) (FeedKind), and compare it with other protein-based ingredients using the precision-fed cecectomized rooster assay. Test ingredients included: MP, chicken meal (CM), corn gluten meal (CGM), pea protein (PP), and black soldier fly larvae. Thirty cecectomized roosters (n = 6/ingredient) were randomly assigned to test ingredients. After 24 h of feed withdrawal, roosters were tube-fed 15 g test ingredient and 15 g corn, and then excreta were collected for 48 h. Endogenous AA corrections were made using additional roosters. Digestible indispensable AA score (DIAAS)-like values were calculated to determine protein quality according to Association of American Feed Control Officials (AAFCO), The European Pet Food Industry Federation, and National Research Council reference values for growing and adult dogs and cats. Data were analyzed using the Mixed Models procedure of SAS 9.4, with P ≤ 0.05 being significant. All reactive lysine:total lysine ratios, an indicator of heat damage, were higher than 0.9, except for CM (0.86). Digestibility of indispensable and dispensable AA were >85% and >80% for MP, respectively, with indispensable AA digestibilities being >80% for all other ingredients. In general, CGM had the highest, while CM had the lowest AA digestibilities. Two exceptions were lysine and tryptophan. Lysine digestibility for MP was higher than that of all other ingredients, while tryptophan digestibility for MP was higher than that of CM, CGM, and PP. Threonine digestibility was highest for CGM and MP. Valine digestibility was highest for CGM, PP, and MP. DIAAS-like calculations identified limiting AA of each ingredient and depended on the reference used and life stage and species of animal. Using AAFCO guidelines, all DIAAS-like values for MP were >100 suggesting that it could be used as the sole source of protein in adult dog and cat diets; only methionine had DIAAS-like values <100 for growing kittens. For dogs, limiting AA was most commonly methionine, threonine, and tryptophan in the other protein sources. For cats, limiting AA was most commonly lysine and methionine. Lysine was severely limited in CGM across all life stages considered. Further research in dogs and cats is necessary, but our data suggest that the MP tested has high AA digestibilities and is a high-quality protein source that may be useful in pet foods.