bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental chemicals and endogenous metabolites in bile of USA and Norway patients with primary sclerosing cholangitis
Authors: Grant Caroline W , Juran Brian D , Ali Ahmad H , Schlicht Erik M , Bianchi Jackie K , Hu Xin , Liang Yongliang , Jarrell Zachery , Liu Ken H , Go Young-Mi , Jones Dean P , Walker Douglas I , Miller Gary W , Folseraas Trine , Karlsen Tom H , LaRusso Nicholas F , Gores Gregory J , Athreya Arjun P , Lazaridis Konstantinos N 
Published: January 2023

Abstract
Primary sclerosing cholangitis (PSC) is a complex bile duct disorder. Its etiology is incompletely understood, but environmental chemicals likely contribute to risk. Patients with PSC have an altered bile metabolome, which may be influenced by environmental chemicals. This novel study utilized state-of-the-art high-resolution mass spectrometry (HRMS) with bile samples to provide the first characterization of environmental chemicals and metabolomics (collectively, the exposome) in PSC patients located in the United States of America (USA) (n = 24) and Norway (n = 30). First, environmental chemical- and metabolome-wide association studies were conducted to assess geographic-based similarities and differences in the bile of PSC patients. Nine environmental chemicals (false discovery rate, FDR &lt; 0.20) and 3143 metabolic features (FDR &lt; 0.05) differed by site. Next, pathway analysis was performed to identify metabolomic pathways that were similarly and differentially enriched by the site. Fifteen pathways were differentially enriched (P &lt; .05) in the categories of amino acid, glycan, carbohydrate, energy, and vitamin/cofactor metabolism. Finally, chemicals and pathways were integrated to derive exposure–effect correlation networks by site. These networks demonstrate the shared and differential chemical–metabolome associations by site and highlight important pathways that are likely relevant to PSC. The USA patients demonstrated higher environmental chemical bile content and increased associations between chemicals and metabolic pathways than those in Norway. Polychlorinated biphenyl (PCB)-118 and PCB-101 were identified as chemicals of interest for additional investigation in PSC given broad associations with metabolomic pathways in both the USA and Norway patients. Associated pathways include glycan degradation pathways, which play a key role in microbiome regulation and thus may be implicated in PSC pathophysiology.
Maternal anaemia and birth weight: a cross-sectional study from Jiangxi Province, China
Authors: Xiong Jun , Zhou Wei , Huang Shaofang , Xu Kangxiang , Xu Yuqi , He Xiaoju 
Published: January 2023

Abstract

Background
Association between maternal haemoglobin (Hb) and low birth weight (LBW) remains a controversial topic, and data in China were sparse.

Aims
We aimed to investigate the association between maternal Hb and LBW among pregnant women in Jiangxi Province, China.

Methods
In this cross-sectional study, 1,029 participants were enrolled. Anaemia was classified according to World Health Organization’s definition of anaemia in pregnancy. Logistic regression analysis was performed to evaluate the association between maternal Hb and LBW. Generalized additive model and smooth curve fitting (penalized spline method) were conducted to explore the exact shape of curve between them.

Results
The overall prevalence of anaemia was 58.2% in our study. A significantly higher risk of LBW was found in moderate anaemia subjects (odds ratio [OR] = 2.93; 95% confidence interval [CI]: 1.16–5.31) and severe anaemia subjects (OR = 63.86; 95% CI: 25.66–158.90) compared with maternal Hb concentration &gt;100 g/L. The fully adjusted smooth curve fitting presented an L-shaped association between the maternal Hb and LBW, with a turning point at about 110 g/L. Subgroup analyses showed that stronger associations between maternal Hb and LBW were detected in pregnant women with high education, long duration of gestation and multiple antenatal visits (all P for interaction &lt;0.05).

Conclusions
Anaemia in delivering women was associated with an elevated risk of LBW and the risk increased with the severity of anaemia, especially among pregnant women with high education, long duration of gestation and multiple antenatal visits from Jiangxi Province, China.
Above- and below-ground microbiome in the annual developmental cycle of two olive tree varieties
Authors: Kakagianni Myrsini , Tsiknia Myrto , Feka Maria , Vasileiadis Sotirios , Leontidou Kleopatra , Kavroulakis Nektarios , Karamanoli Katerina , Karpouzas Dimitrios G , Ehaliotis Constantinos , Papadopoulou Kalliope K 
Published: January 2023

Abstract
The olive tree is a hallmark crop in the Mediterranean region. Its cultivation is characterized by an enormous variability in existing genotypes and geographical areas. As regards the associated microbial communities of the olive tree, despite progress, we still lack comprehensive knowledge in the description of these key determinants of plant health and productivity. Here, we determined the prokaryotic, fungal and arbuscular mycorrhizal fungal (AMF) microbiome in below- (rhizospheric soil, roots) and above-ground (phyllosphere and carposphere) plant compartments of two olive varieties ‘Koroneiki’ and ‘Chondrolia Chalkidikis’ grown in Southern and Northern Greece respectively, in five developmental stages along a full fruit-bearing season. Distinct microbial communities were supported in above- and below-ground plant parts; while the former tended to be similar between the two varieties/locations, the latter were location specific. In both varieties/locations, a seasonally stable root microbiome was observed over time; in contrast the plant microbiome in the other compartments were prone to changes over time, which may be related to seasonal environmental change and/or to plant developmental stage. We noted that olive roots exhibited an AMF-specific filtering effect (not observed for bacteria and general fungi) onto the rhizosphere AMF communities of the two olive varieties/locations/, leading to the assemblage of homogenous intraradical AMF communities. Finally, shared microbiome members between the two olive varieties/locations include bacterial and fungal taxa with putative functional attributes that may contribute to olive tree tolerance to abiotic and biotic stress.
Spatial Spillover Effects of Pine Sawtimber Stumpage Prices in the US South
Authors: Lamichhane Sabhyata , Mei Bin , Siry Jacek 
Published: January 2023

AbstractTimberland returns have three main drivers: biological growth, timber price, and land value. Among three of these drivers, timber price is the most volatile. Therefore, modeling and predicting timber prices has been of great concern for timberland investors and other stakeholders. In this study, the spatial dependency and spillover effect of sawtimber prices were investigated across 11 southern states with three different spatial panel models. The findings revealed a strong positive spatial dependency in sawtimber prices across these states, and the observed spillover effect for significant independent variables was over 35% of the total effect. Similarly, pulpwood prices not only have positive impact on the sawtimber prices of a given state but also on its contiguous states. In addition, the impact of COVID-19 pandemic on sawtimber prices was positive and significant. These results would facilitate the valuation of timberland investments as well as predict future timber prices.Study Implications: The sawtimber prices of one state positively affect the future sawtimber prices of neighboring states in addition to its own. Similarly, a shock in a given state also affects the sawtimber prices of its neighbors. Given the volatile nature of timber prices, gaining a better understanding of spatial integration of timber markets improves prediction of sawtimber price fluctuations and trends that ultimately help timberland investors to make effective decisions.
Some Assembly Required: Explaining Variations in Legislative Oversight over the Armed Forces
Authors: Auerswald David , Lagassé Philippe , Saideman Stephen M 
Published: January 2023

AbstractLegislatures vary widely in how they affect democratic civil–military relations. In some countries, legislative oversight plays a critical role in guiding their defense establishment. In others, legislators are largely ignorant and happily so. In this article, we explain the sources of these variations in fifteen democratic states. After discussing the importance of the legislature's role in democratic civil–military relations, we clarify what we mean by oversight. We argue that variations in oversight are explained by the number and scope of legislative committees charged with military oversight and party politics within those committees. After reviewing alternative explanations, we present oversight patterns in fifteen democratic countries across the world. We then briefly examine Germany's Bundestag and Japan's Diet, as the comparison of these cases challenges most existing explanations of legislative oversight and serve as hard cases for our argument. We conclude with implications of legislative oversight for broader debates about civilian control of the military.
Integrative cytology and proteome alterations unravel the multitarget effect of a novel alkaloid antofine againstPenicillium italicum
Authors: Peng Xuan , Wan Chunpeng , Zhang Yajie , Chen Jinyin , Yang Zhicheng , Zhang Xinyu , Chen Chuying 
Published: January 2023

AbstractPenicillium italicum is the causal agent of citrus blue mold, which is a major threat to the global citrus fruit industry. Antofine, a natural phenanthroindolizidine alkaloid, is water-soluble and exhibits a broad range of biological activities. However, whether it can inhibit P. italicum growth and the potential inhibitory mechanism remains to be elucidated. This study aimed to investigate the antifungal mechanism of antofine against P. italicum using scanning electron microscopy, transmission electron microscopy (TEM), propidium iodide staining, and tandem mass tag-labeled quantitative proteomic analysis. Antofine was found to exhibit its preeminent antifungal activity against P. italicum with a minimum inhibitory concentration of 1.56 mg/L and a minimum fungicidal concentration of 6.25 mg/L. The challenge test revealed that antofine inhibited the development of citrus blue mold during a 6-d P. italicum-infected period. Antofine acted on its potential multitargets to inhibit P. italicum growth by synergistically activating oxidative stress through accumulating excess reactive oxygen species, impairing membrane integrity, inducing membrane lipid peroxidation, and disrupting mitochondrial function, thereby disrupting the membrane system and reducing cell viability. Moreover, antofine treatment downregulated most differentially expressed proteins involved in carbon metabolism, pyruvate metabolism, and the tricarboxylic acid cycle (TCA) in P. italicum mycelia, which may explain the mitochondrial decomposition observed by TEM and the declines in ATP levels as well as the activities of TCA-related enzymes. These results indicate that antofine treatment inhibited P. italicum growth by targeting the cell membrane and mitochondria.
Achieving robustness to temperature change of a NIR model for apple soluble solids content
Authors: Jiang Xiaogang , Yao Jinliang , Zhu Mingwang , Li Bin , Liu Yande , Ou Yang Aiguo 
Published: January 2023

AbstractThe temperature difference of fruit itself will affect its near infrared spectrum and the accuracy of its soluble solids content (SSC) prediction model. To eliminate the influence of apple temperature difference on the SSC model, a diffuse transmission dynamic online detection device was used to collect the spectral data of apples at different temperatures, and four methods were used to establish partial least squares correction models: global correction, orthogonal signal processing, generalized least squares weighting and external parameter orthogonal (EPO). The results show that the temperature has a strong influence on the diffuse transmission spectrum of apples. The 20 ºC model can get a satisfactory prediction result when the temperature is constant, and there will be great errors when detecting samples at other temperatures. The effect of temperature must be corrected to establish a more general model. These methods all improve the accuracy of the model, with the EPO method giving the best results; the prediction set correlation coefficient is 0.947, the root mean square error of prediction is 0.489%, and the prediction bias is 0.009%. The research results are of great significance to the practical application of SSC prediction of fruits in sorting workshops or orchards.
Non-destructive detection of tea stalk and insect foreign bodies based on THz-TDS combination of electromagnetic vibration feeder
Authors: Sun Xudong , Xu Chao , Luo Chagen , Xie Dongfu , Fu Wei , Gong Zhiyuan , Wang Xinpeng 
Published: January 2023

AbstractBackground and objectivesCurrent technology of X-ray imaging can recognize hard foreign materials (FMs) such as metal and high-density plastic. However, low-density foreign bodies are still a challenge for food quality and safety assessment.Materials and methodsAn electromagnetic vibration feeder aided by terahertz time-domain spectroscopy (THz-TDS) and imaging was investigated for non-destructively detecting tea stalk and insect FMs mixed with tea leaves.ResultsTHz time-domain signals were employed directly to develop the K-nearest neighbor model with a precision of 100%, accuracy of 95.6% and recall of 98.7% in predicting the unknown samples. High contrast THz-TDS images were obtained by the separation method for the samples using electromagnetic vibration feeder. The characteristic parameters of the ratio of maximum length (L) to maximum width (W) and hue extracted from THz-TDS images indicated significant difference between tea leaves and FMs.ConclusionsThe results suggested that electromagnetic vibration feeder combination with THz-TDS was feasible for detecting FMs in finishing tea products.
The gyrfalcon (Falco rusticolus) genome
Authors: Zuccolo Andrea , Mfarrej Sara , Celii Mirko , Mussurova Saule , Rivera Luis F , Llaca Victor , Mohammed Nahed , Pain Arnab , Alrefaei Abdulmajeed Fahad , Alrefaei Abdulwahed Fahad , Wing Rod A 
Published: January 2023

Abstract
High-quality genome assemblies are characterized by high-sequence contiguity, completeness, and a low error rate, thus providing the basis for a wide array of studies focusing on natural species ecology, conservation, evolution, and population genomics. To provide this valuable resource for conservation projects and comparative genomics studies on gyrfalcon (Falco rusticolus), we sequenced and assembled the genome of this species using third-generation sequencing strategies and optical maps. Here, we describe a highly contiguous and complete genome assembly comprising 20 scaffolds and 13 contigs with a total size of 1.193 Gbp, including 8,064 complete Benchmarking Universal Single-Copy Orthologs (BUSCOs) of the total 8,338 BUSCO groups present in the library aves_odb10. Of these BUSCO genes, 96.7% were complete, 96.1% were present as a single copy, and 0.6% were duplicated. Furthermore, 0.8% of BUSCO genes were fragmented and 2.5% (210) were missing. A de novo search for transposable elements (TEs) identified 5,716 TEs that masked 7.61% of the F. rusticolus genome assembly when combined with publicly available TE collections. Long interspersed nuclear elements, in particular, the element Chicken-repeat 1 (CR1), were the most abundant TEs in the F. rusticolus genome. A de novo first-pass gene annotation was performed using 293,349 PacBio Iso-Seq transcripts and 496,195 transcripts derived from the assembly of 42,429,525 Illumina PE RNA-seq reads. In all, 19,602 putative genes, of which 59.31% were functionally characterized and associated with Gene Ontology terms, were annotated. A comparison of the gyrfalcon genome assembly with the publicly available assemblies of the domestic chicken (Gallus gallus), zebra finch (Taeniopygia guttata), and hummingbird (Calypte anna) revealed several genome rearrangements. In particular, nine putative chromosome fusions were identified in the gyrfalcon genome assembly compared with those in the G. gallus genome assembly. This genome assembly, its annotation for TEs and genes, and the comparative analyses presented, complement and strength the base of high-quality genome assemblies and associated resources available for comparative studies focusing on the evolution, ecology, and conservation of Aves.
A toolkit for converting Gal4 into LexA and Flippase transgenes in Drosophila
Authors: Karuparti Sasidhar , Yeung Ann T , Wang Bei , Guicardi Pedro F , Han Chun 
Published: January 2023

Abstract
Drosophila has been a powerful model system for biological studies due to the wide range of genetic tools established for it. Among these tools, Gal4 is the most abundant, offering unparalleled tissue and developmental stage specificity for gene manipulation. In comparison, other genetic reagents are far fewer in choices. Here we present a genetic toolkit for converting Gal4 strains into LexA and Flippase transgenes through simple genetic crosses and fluorescence screening. We demonstrate the proof-of-principle by converting ten Gal4 lines that exhibit diverse tissue specificities and examined the activity patterns of the converted LexA and Flippase lines. Gal4-to-LexA and Flp conversion is fast and convenient and should greatly expand the choices of LexA and Flp for binary expression and FRT-based mosaic analysis, respectively, in Drosophila.
TargetingKRAS G12Cmutations in colorectal cancer
Authors: Zhao Ming-He , Wu Ai-Wen 
Published: January 2023

AbstractWith the advent of Kirsten rat sarcoma viral oncogene homologue G12C (KRAS G12C) inhibitors, RAS is no longer considered undruggable. For the suppression of RAS, new therapeutic approaches have been suggested. However, current clinical studies have indicated therapeutic resistance after short-lived tumour suppression. According to preclinical studies, this might be associated with acquired genetic alterations, reactivation of downstream pathways, and stimulation for upstream signalling. In this review, we aimed to summarize current approaches for combination therapy to alleviate resistance to KRAS G12C inhibitors in colorectal cancer with a focus on the mechanisms of therapeutic resistance. We also analysed the relationship between various mechanisms and therapeutic resistance.
Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi
Authors: Reynolds Nicole K , Stajich Jason E , Benny Gerald L , Barry Kerrie , Mondo Stephen , LaButti Kurt , Lipzen Anna , Daum Chris , Grigoriev Igor V , Ho Hsiao-Man , Crous Pedro W , Spatafora Joseph W , Smith Matthew E 
Published: January 2023

Abstract
Improved sequencing technologies have profoundly altered global views of fungal diversity and evolution. High-throughput sequencing methods are critical for studying fungi due to the cryptic, symbiotic nature of many species, particularly those that are difficult to culture. However, the low coverage genome sequencing (LCGS) approach to phylogenomic inference has not been widely applied to fungi. Here we analyzed 171 Kickxellomycotina fungi using LCGS methods to obtain hundreds of marker genes for robust phylogenomic reconstruction. Additionally, we mined our LCGS data for a set of nine rDNA and protein coding genes to enable analyses across species for which no LCGS data were obtained. The main goals of this study were to: 1) evaluate the quality and utility of LCGS data for both phylogenetic reconstruction and functional annotation, 2) test relationships among clades of Kickxellomycotina, and 3) perform comparative functional analyses between clades to gain insight into putative trophic modes. In opposition to previous studies, our nine-gene analyses support two clades of arthropod gut dwelling species and suggest a possible single evolutionary event leading to this symbiotic lifestyle. Furthermore, we resolve the mycoparasitic Dimargaritales as the earliest diverging clade in the subphylum and find four major clades of Coemansia species. Finally, functional analyses illustrate clear variation in predicted carbohydrate active enzymes and secondary metabolites (SM) based on ecology, that is biotroph versus saprotroph. Saprotrophic Kickxellales broadly lack many known pectinase families compared with saprotrophic Mucoromycota and are depauperate for SM but have similar numbers of predicted chitinases as mycoparasitic.
Estimating linkage disequilibrium and selection from allele frequency trajectories
Authors: Li Yunxiao , Barton John P 
Published: January 2023

Abstract
Genetic sequences collected over time provide an exciting opportunity to study natural selection. In such studies, it is important to account for linkage disequilibrium to accurately measure selection and to distinguish between selection and other effects that can cause changes in allele frequencies, such as genetic hitchhiking or clonal interference. However, most high-throughput sequencing methods cannot directly measure linkage due to short-read lengths. Here we develop a simple method to estimate linkage disequilibrium from time-series allele frequencies. This reconstructed linkage information can then be combined with other inference methods to infer the fitness effects of individual mutations. Simulations show that our approach reliably outperforms inference that ignores linkage disequilibrium and, with sufficient sampling, performs similarly to inference using the true linkage information. We also introduce two regularization methods derived from random matrix theory that help to preserve its performance under limited sampling effects. Overall, our method enables the use of linkage-aware inference methods even for data sets where only allele frequency time series are available.
Association Between Pain and Sarcopenia Among Adults Aged ≥65 Years from Low- and Middle-Income Countries
Authors: Smith Lee , López Sánchez Guillermo F , Veronese Nicola , Soysal Pinar , Kostev Karel , Jacob Louis , Rahmati Masoud , Kujawska Agnieszka , Tully Mark A , Butler Laurie , Il Shin Jae , Koyanagi Ai 
Published: January 2023

Abstract

Background
Pain may increase the risk for sarcopenia, but existing literature is only from high-income countries, while the mediators of this association are largely unknown. Thus, we aimed to investigate the association between pain and sarcopenia using nationally representative samples of older adults from 6 low- and middle-income countries (LMICs), and to identify potential mediators.

Methods
Cross-sectional data from the WHO Study on global AGEing and adult health (SAGE) were analyzed. Sarcopenia was defined as having low skeletal muscle mass and weak handgrip strength, while the presence and severity of pain in the last 30 days were self-reported. Multivariable logistic regression and mediation analyses were performed. The control variables included age, sex, education, wealth, and chronic conditions, while affect, sleep/energy, disability, social participation, sedentary behavior, and mobility were considered potential mediators.

Results
Data on 14,585 adults aged ≥65 years were analyzed (mean [SD] age 72.6 [11.5] years; 55.0% females). Compared to no pain, mild, moderate, severe, and extreme pain were associated with 1.42 (95% confidence interval [CI] = 1.05–1.94), 1.43 (95%CI = 1.02–2.00), 1.92 (95%CI = 1.09–3.37), and 2.88 (95%CI = 1.10–7.54) times higher odds for sarcopenia, respectively. Disability (mediated percentage 18.0%), sedentary behavior (12.9%), and low mobility (56.1%) were significant mediators in the association between increasing levels of pain and sarcopenia.

Conclusions
Higher levels of pain were associated with higher odds for sarcopenia among adults aged ≥65 years in 6 LMICs. Disability, sedentary behavior, and mobility problems were identified as potential mediators. Targeting these factors in people with pain may decrease the future risk of sarcopenia onset, pending future longitudinal research.