bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-based analysis of biosynthetic potential from antimycotic Streptomyces rochei strain A144
Authors: Zhang Li-juan , Wang Ning , Huang Wei , Wu Long-yuan , Song Bo , Wang Su-ling , Sheng Jian-dong , Wang Wei 
Published: November 2024

Abstract
Streptomyces rochei is a species of Streptomyces with a diverse range of biological activities. Streptomyces rochei strain A144 was isolated from desert soils and exhibits antagonistic activity against several plant pathogenic fungi. The genome of S. rochei A144 was sequenced and revealed the presence of one linear chromosome and one plasmid. The chromosome length was found to be 8 085 429 bp, with a GC content of 72.62%, while the Plas1 length was 177 399 bp, with a GC content (proportion of guanine and cytosine in DNA sequences) of 69.08%. Comparative genomics was employed to analyse the S. rochei group. There is a high degree of collinearity between the genomes of S. rochei strains. Based on pan-genome analysis, S. rochei has 10 315 gene families, including 4051 core and 2322 unique genes. AntiSMASH was used to identify the gene clusters for secondary metabolites, identifying 33 secondary metabolite genes on the A144 genome. Among them, 18 clusters were found to be &gt;70% identical to known biosynthetic gene clusters (BGCs), indicating that A144 has the potential to synthesize secondary metabolites. The majority of the BGCs were found to be conserved within the S. rochei group, including those encoding polyketide synthases, terpenes, non-ribosomal peptide synthetases, other ribosomally synthesized and post-translationally modified peptides, nicotianamine-iron transporters, lanthipeptides, and a few other types. The S. rochei group can be a potential genetic source of useful secondary metabolites with applications in medicine and biotechnology.
Chromosome-Scale Genomes of the Flightless Caterpillar Hunter Beetles Calosoma tepidum and Calosoma wilkesii From British Columbia (Coleoptera: Carabidae)
Authors: Gauthier Jérémy , Blanc Mickael , Toussaint Emmanuel F A 
Published: November 2024

Abstract
The giant ground beetle genus Calosoma (Coleoptera, Carabidae) comprises ca. 120 species distributed worldwide. About half of the species in this genus are flightless due to a process of wing reduction likely resulting from the colonization of remote habitats such as oceanic islands, highlands, and deserts. This clade is emerging as a new model to study the genomic basis of wing evolution in insects. In this framework, we present the de novo assemblies and annotations of two Calosoma species genomes from British Columbia, Calosoma tepidum and Calosoma wilkesii. Combining PacBio HiFi and Hi-C sequencing, we produce high-quality reference genomes for these two species. Our annotation using long-read RNAseq and existing Coleoptera protein evidence identified a total of 21,976 genes for C. tepidum and 26,814 genes for C. wilkesii. Using synteny analyses, we provide an in-depth comparison of genomic architectures in these two species. We infer an overall pattern of chromosome-scale conservation between the two species, with only minor rearrangements within chromosomes. These new reference genomes represent a major step forward in the study of this group, providing high-quality references that open the door to different approaches such as comparative genomics or population scale resequencing to study the implications of flight evolution.
Associations Between Deficit Accumulation Frailty and Baseline Markers of Lifestyle in the U.S. POINTER Trial
Authors: Espeland Mark A , Demesie Yitbarek N , Olson KayLoni , Lockhart Samuel N , Farias Sarah E Tomaszewski , Cleveland Maryjo L , Tangney Christy C , Crivelli Lucia , Snyder Heather M , York Michele K , Baker Laura D , Whitmer Rachel A , Wing Rena R , Garcia Katelyn R , Callahan Kathryn E 
Published: November 2024

Abstract

Background
Multidomain lifestyle interventions may have the potential to slow biological aging as captured by deficit accumulation frailty indices. We describe the distribution and composition of the 49-component frailty index developed by the U.S. POINTER clinical trial team of investigators and assess its cross-sectional associations with sociodemographic factors and markers chosen to be representative of behaviors targeted by the trial’s multidomain interventions.

Methods
We draw baseline data from the 2 111 volunteers enrolled in U.S. POINTER who were ages 60–79 years and at increased risk for cognitive decline. Frailty components were grouped into 9 domains. Associations that frailty index scores and their domains had with behavioral markers were described with correlations and canonical correlation.

Results
The 25th, 50th, and 75th percentiles of the frailty index score distribution were 0.153, 0.189, and 0.235. Higher frailty scores tended to occur among individuals who were older, male, and living in areas of greater deprivation (all p &lt; .001). They were also associated with poorer self-reported diet, less physical activity, and higher Framingham risk scores (all p &lt; .001). Associations were diffusely distributed among the frailty component domains, indicating that no individual domain was dominating associations.

Conclusions
The U.S. POINTER deficit accumulation frailty index had expected relationships with sociodemographic factors and sensitivity to the behaviors targeted by the trial’s interventions. Our analysis supports its use as a secondary outcome to assess whether the multidomain interventions differentially impact an established marker of biological aging. ClinicalTrials.gov Identifier: NCT03688126.
Integrating deep learning and discrete cosine transform for surface waves full-waveform inversion
Authors: Rincón Felipe , Berti Sean , Aleardi Mattia , Tognarelli Andrea , Stucchi Eusebio 
Published: November 2024

SUMMARY
Accurate estimations of near-surface S-wave velocity (Vs) models hold particular significance in geological and engineering investigations. On the one hand, the popular multichannel analysis of surface waves (MASWs) is limited to the 1-D and the plane wave assumptions. On the other hand, the more advanced and computationally expensive full-waveform inversion (FWI) approach is often solved within a deterministic framework that hampers an accurate uncertainty assessment and makes the final predictions heavily reliant on the starting model. Here we combine deep learning with discrete cosine transform (DCT) to solve the FWI of surface waves and to efficiently estimate the inversion uncertainties. Our neural network approach effectively learns the inverse non-linear mapping between DCT-compressed seismograms and DCT-compressed S-velocity models. The incorporation of DCT into the deep learning framework provides several advantages: it notably reduces parameter space dimensionality and alleviates the ill-conditioning of the problem. Additionally, it decreases the complexity of the network architecture and the computational cost for the training phase compared to training in the full domain. A Monte Carlo simulation is also used to propagate the uncertainties from the data to the model space. We first test the implemented inversion method on synthetic data to showcase the generalization capabilities of the trained network and to explore the implications of incorrect noise assumptions in the recorded seismograms and inaccurate wavelet estimations. Further, we demonstrate the applicability of the implemented method to field data. In this case, available borehole information is used to validate our predictions. In both the synthetic and field applications, the predictions provided by the proposed method are compared with those of a deterministic FWI and the outcomes of a network trained in the full data and model spaces. Our experiments confirm that the implemented deep-learning inversion efficiently and successfully solves the FWI problem and yields more accurate and stable results than a network trained without the DCT compression. This opens the possibility to efficiently train a neural network that provides accurate instantaneous predictions of Vs near-surface models and related uncertainties.
High-precision identification and prediction of low-voltage load characteristics in smart grids based on hybrid deep learning framework
Authors: Cui Ziti , Wang Wei , Jiang Wei , Guo Jun , Liu Yang 
Published: November 2024

Abstract
This paper proposes a hybrid deep learning framework (HDLF) that combines improved convolutional neural networks (CNNs), long short-term memory (LSTM) networks, and transformer models. First, feature selection and dimensionality reduction are performed using XGBoost and principal component analysis, respectively. Secondly, CNN is enhanced by multiscale convolution, residual connection, and attention mechanism. Then, the bidirectional LSTM is combined with temporal convolutional network to improve the LSTM. Then, an improved dynamic focusing mechanism of transformer is introduced. The experimental results show that the HDLF has an accuracy of 0.945 in identifying low-pressure load characteristics.
Beyond Seeing and Listening: Children Born from Conflict-Related Sexual Violence
Authors: Távara Gabriela 
Published: November 2024

ABSTRACT
This essay discusses some points made by the three books under review regarding how children born of conflict-related sexual violence have not been seen and listened to by those working in the field of transitional justice. To this end, it explores some of the reasons behind this oversight, including generalized assumptions about their relationships with their mothers, families and communities. It also discusses some of the limitations of the current transitional justice framework to address the plight of these children. Finally, the essay emphasizes the importance of analyzing more deeply the particular context in which these children are embedded. To this end it draws from some of the frameworks presented in the three books under review, which allow for a more capacious comprehension of the situation of children born of conflict-related sexual violence.
Inoculation with PGPR co-fermented broths promotes growth, yields, and quality of pepper by increasing soil nutrients and changing soil bacterial community
Authors: Han Yujie , Tian Lei , Luo Yu , Han Lizhen 
Published: November 2024

Abstract

Aims
The purpose of this study was to explore impacts of different combinations of co-fermentation plant growth-promoting rhizobacteria (PGPR) broth on the growth and yield of pepper.

Methods and results
The effects of co-fermentation broth containing a random combination of two PGPR strains on the growth of pepper were analyzed. All inoculation treatments promoted growth, yield, and quality of peppers. The relative abundance of the dominant Proteobacteria and Sphingomonas was significantly higher in the planted soil at the seedling and fruiting stages, and the soil available nitrogen, phosphorus, and potassium contents were correspondingly higher. In addition, the co-fermented broth of Bacillus velezensis HP9 and Burkholderia pyrrocinia P10 treatment had the most pronounced effect on plant growth, while the combination of Bacillus flexus HGD12 and P10 had the greatest impact on fruit nutritional indices. This is consistent with the highest enrichment of beneficial bacterial genera at the seedling stage in the HP9 and P10 treatment and at the fruiting stage in the P10 and HGD12 treatment groups, respectively.

Conclusions
Different combinations of co-fermented bacterial broths increased soil nutrient contents and changed the bacterial community, which in turn promoted the growth, yield, and quality of pepper.
An efficient deep learning method for amino acid substitution model selection
Authors: Tinh Nguyen Huy , Vinh Le Sy 
Published: November 2024

Abstract
Amino acid substitution models play an important role in studying the evolutionary relationships among species from protein sequences. The amino acid substitution model consists of a large number of parameters; therefore, it is estimated from hundreds or thousands of alignments. Both general models and clade-specific models have been estimated and widely used in phylogenetic analyses. The maximum likelihood method is normally used to select the best-fit model for a specific protein alignment under the study. A number of studies have discussed theoretical concerns as well as the computational burden of the maximum likelihood methods in model selection. Recently, machine learning methods have been proposed for selecting nucleotide models. In this article, we propose a method to measure substitution rates among amino acids (called summary statistics) from protein alignments to efficiently train a deep learning network of so-called ModelDetector for detecting amino acid substitution models. The ModelDetector network was trained from 2,246,400 alignments on a computer with eight cores (without GPU) in about 3.3 hr. Experiments on simulation data showed that the accuracy of the ModelDetector was comparable with that of the maximum likelihood method ModelFinder. It was orders of magnitude faster than the maximum likelihood method in inferring amino acid substitution models and able to analyze genome alignments with millions of sites in minutes. The results indicate that the deep learning network can play as a promising tool for amino acid substitution model selection.
Pancreaticoduodenectomy after Roux-en-Y gastric bypass and novel endoscopic ultrasound-directed transgastric ERCP procedure
Authors: Orsi Carolina , Davis Tyler , Moudy Paige , Ismael Hishaam 
Published: November 2024

Abstract
Performing a pancreaticoduodenectomy (PD) in patients having undergone a Roux-en-Y gastric bypass (RNYGB) poses a significant surgical challenge. We present a patient with a history of RNYGB and endoscopic ultrasound-directed transgastric ERCP (EDGE) procedure who underwent a successful PD. This 77-year-old female with history of open RNYBG presented with resectable pancreatic adenocarcinoma. A preoperative EDGE procedure was required for biliary decompression. A PD was performed by removing the entire biliopancreatic limb for oncologic resection. The reconstructive technique here involved utilizing the old common channel for the hepaticojejunostomy, pancreaticojejunostomy, and remnant gastrojejunostomy. The case also included Axios stent placement during a preoperative EDGE procedure. This case describes the first reported successful PD in a patient with prior RNYGB and EDGE procedure. Although the optimal technique for this clinical scenario remains unestablished, this unique case contributes to the literature by demonstrating an effective approach for practicing surgeons.
Preliminary Description of the Jewish Arabic Dialect of Ghardaïa (Central Algeria) with Elements of Phonology, Socio-Phonetics, and Morphology
Authors: Gębski Wiktor 
Published: November 2024

Abstract
Ghardaïa, situated in the centre of Saharan Algeria, is renowned for its well-preserved medieval architecture tracing back to its establishment by the puritanical Ibāḍiyyah sect in the 11th century CE. The city has been home to a Jewish community for centuries, although its exact origins remain debated. Evidence suggests migrations from Djerba, Marrakesh, and Tafilalt shaping a unique Jewish dialect that reflects ties to both Tunisia and Morocco. This paper presents a preliminary linguistic analysis of the Jewish dialect of Ghardaïa, shedding light on its historical layers and socio-linguistic dynamics. Through comparative analysis with neighbouring Muslim dialects, Jewish Djerba, and Jewish Marrakesh, it unravels the complexities of this distinct linguistic heritage, providing insights into its origins and evolution. Additionally, it delves into the nuanced variations between male and female lects within the Jewish community of Ghardaïa, elucidating socio-phonetic features that contribute to the rich diversity of the dialect.
Phytochrome-interacting factors PIF4 and PIF5 directly regulate autophagy during leaf senescence in Arabidopsis
Authors: Lee Juhyeon , Kang Myeong Hoon , Choi Da-Min , Marmagne Anne , Park Jeehye , Lee Heeho , Gwak Eunha , Lee Jong-Chan , Kim Jeong-Il , Masclaux-Daubresse Céline , Lim Pyung Ok 
Published: November 2024

Abstract
During leaf senescence, autophagy plays a critical role by removing damaged cellular components and participating in nutrient remobilization to sink organs. However, how AUTOPHAGY (ATG) genes are regulated during natural leaf senescence remains largely unknown. In this study, we attempted to identify upstream transcriptional regulator(s) of ATG genes and their molecular basis during leaf senescence in Arabidopsis through the combined analyses of promoter binding, autophagy flux, and genetic interactions. We found that PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and PIF5 directly bind to the promoters of ATG5, ATG12a, ATG12b, ATG8a, ATG8e, ATG8f, and ATG8g, inducing their transcription. These target ATG genes are down-regulated in pif4, pif5, and pif4pif5 mutants, resulting in decreased autophagic activity and slower degradation of chloroplast proteins and chlorophyll. Conversely, overexpression of ATG8 genes accelerated protein degradation with early leaf senescence. Moreover, our data suggested partial suppression of the pif4pif5 phenotype by ATG8a overexpression. PIF4/PIF5 also influence senescence induced by nutrient starvation, another hallmark of the autophagy pathway. Furthermore, we observed that the PIF4/PIF5–ATG regulatory module may contribute to seed maturation. Our study not only unveils transcriptional regulators of autophagy in natural leaf senescence but also underscores the potential role of PIF4/PIF5 as functional regulators in leaf senescence and nutrient remobilization.
A search for H i absorption in distant star-forming galaxies with ASKAP-FLASH – I. Selection and analysis of the radio sample
Authors: Eden Sophie L , Sadler Elaine M , Pimbblet Kevin A , Mahony Elizabeth K , Yoon Hyein 
Published: November 2024

ABSTRACT
We present and discuss two catalogues of ultraviolet (UV)-selected (near-UV (NUV)$\lt 22.8$ mag) galaxies that lie within a 200 deg$^2$ area of sky covered by the ASKAP First Large Absorption Survey in H i (FLASH) and have an impact parameter of less than 20 arcsec to a FLASH radio continuum source. These catalogues are designed to enable a future search for 21 cm H i absorption in and around star-forming galaxies at redshift $0.4\lt z\lt 1$. We outline the production of this UV-bright data set, which has optical spectroscopy from the WiggleZ and Sloan Digital Sky Survey (SDSS) surveys and a median redshift of ${\sim} 0.6$. Analysis of the optical spectra, using multiple diagnostic diagrams, shows that galaxies with an impact parameter of less than 5 arcsec are likely to be physically associated with the radio source and are five times more likely to be an active galactic nucleus than objects without a radio match. Conversely, objects with impact factors between 5 and 20 arcsec are largely (&gt;80 per cent) star-forming and resemble the overall WiggleZ population. The ($g - i$) colour evolution with redshift is consistent with a history of active star formation, but the radio-associated objects are typically redder and have colours similar to high-excitation radio galaxies. The redshift distribution of the two catalogues matches the overall distribution for WiggleZ galaxies, despite their otherwise rare radio properties. These catalogues can be expanded in future as new radio data become available, and a forthcoming paper will present the H i absorption results.
Characterizing long-term astroclimate parameters at the Muztagh-Ata site in the Pamir plateau with ERA5 and MERRA-2 data
Authors: Zhang Jicheng , Zhao Yong , Gao Jian , Esamdin Ali , Zhang Wenzhao , Yuan Haibo , Feng Guojie , Niu Hubiao , Gu Wenbo , Zhang Xuan , Bai Chunhai 
Published: November 2024

ABSTRACT
The Muztagh-Ata site, an excellent high-altitude ground-based astronomical observing site was discovered and monitored in the eastern part of the Pamir Plateau in the southwestern Xinjiang Uygur Autonomous Region of China. This site has been systematically monitored using various observational parameters since the spring of 2017. Yet, the site lacks long-term monitoring and statistical characterization of key variables such as: precipitable water vapour (PWV) and air temperature. These factors directly influence whether a site is suitable for hosting large ground-based telescopes across optical, infrared, submillimeter, and millimeter wavelengths in later stages. In this study, we utilized atmospheric reanalysis data sets from the Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2) and ERA5, the fifth edition of the European Centre for Medium-Range Weather Forecasts (ECMWF). These data sets were combined with local observations from the weather station at the Muztagh-Ata site. Following the validation of ground-based and satellite data, we conducted a comparative analysis of PWV and temperature trends at the Muztagh-Ata site over a period of 24 yr. The weighted annual mean nighttime temperature and PWV increase at rates of 0.18 $\sim$ 0.38$^{\circ }$C decade$^{-1}$ and 0.02 $\sim$ 0.15 mm decade$^{-1}$, respectively. The nighttime PWV slightly decrease during the winter with rates of $-$0.01 $\sim \, -$0.03 mm decade$^{-1}$. This findings reveal that the PWV and temperature variation patterns at the Muztagh-Ata site are consistently stable, particularly in the results derived from the ERA5 data set. The comprehensive conditions at this site are highly suitable and advantageous for hosting large optical, infrared, submillimeter, and millimeter wavelengths telescope installations.
Battle of the CH motions: aliphatic versus aromatic contributions to astronomical PAH emission and exploration of the aliphatic, aromatic, and ethynyl CH stretches
Authors: Esposito Vincent J , Bejaoui Salma , Billinghurst Brant E , Boersma Christiaan , Fortenberry Ryan C , Salama Farid 
Published: November 2024

ABSTRACT
Strong anharmonic coupling between vibrational states in polycyclic aromatic hydrocarbons (PAH) produces highly mixed vibrational transitions that challenge the current understanding of the nature of the astronomical mid-infrared PAH emission bands. Traditionally, PAH emission bands have been characterized as either aromatic or aliphatic, and this assignment is used to determine the fraction of aliphatic carbon in astronomical sources. In reality, each of the transitions previously utilized for such an attribution is highly mixed with contributions from both aliphatic and aromatic CH motions as well as non-CH motions such as CC stretches. High-resolution gas-phase IR absorption measurements of the spectra of the aromatic molecules indene and 2-ethynyltoluene at the Canadian Light Source combined with high-level anharmonic quantum chemical computations reveal the complex nature of these transitions, implying that the use of these features as a marker for the aliphatic fraction in astronomical sources is not uniquely true or actually predictive. Further, the presence of aliphatic, aromatic, and ethynyl CH groups in 2-ethynyltoluene provides an internally consistent opportunity to simultaneously study the spectroscopy of all three astronomically important groups. Finally, this study makes an explicit connection between fundamental quantum mechanical principles and macroscopic astronomical chemical physics, an important link necessary to untangle the lifecycle of stellar and planetary systems.