bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity
Authors: Zhang Lu , Zhang Zhenmiao , Xiao Jin , Wang Hongbo , Yang Chao , Huang Yufen , Yue Zhen , Chen Yang , Han Lijuan , Yin Kejing , Lyu Aiping , Fang Xiaodong 
Published: September 2023

Abstract

Despite long-read sequencing enables to generate complete genomes of unculturable microbes, its high cost hinders its widespread application in large cohorts. An alternative method is to assemble short-reads with long-range connectivity, which can be a cost-effective way to generate high-quality microbial genomes. We developed Pangaea to improve metagenome assembly using short-reads with physical or virtual barcodes. It adopts a deep-learning-based binning algorithm to assemble the co-barcoded reads with similar sequence contexts and abundances to improve assemblies of high- and medium-abundance microbes. Pangaea also leverages a multi-thresholding reassembly strategy to refine assembly for low-abundance microbes. We benchmarked Pangaea with linked-reads and a combination of short- and long-reads from mock communities and human gut metagenomes. Pangaea achieved significantly higher contig continuity as well as more near-complete metagenome-assembled genomes (NCMAGs) than the existing assemblers. Pangaea was also observed to generate three complete and circular NCMAGs on the human gut microbiomes.
Large-scale green grabbing for wind and solar PV development in Brazil
Authors: Klingler Michael , Ameli Nadia , Rickman Jamie , Schmidt Johannes 
Published: September 2023

Abstract

Large-scale wind and solar photovoltaic (PV) infrastructures are expanding rapidly in Brazil. These projects can exacerbate struggles for land rooted in weak land governance, with negative impacts for traditional populations due to loss of access to common lands. Here, we trace how green grabbing, i.e. the large-scale appropriation and control of (undesignated) public lands, both formally legal and illicit, for low-carbon technologies, has developed in Brazil throughout 2000 to 2021. We find that global investors and owners, mainly from Europe, are involved in 78% of wind and 96% of solar PV parks, occupying 2,148 km2 and 102 km2 of land, respectively. We also show that land privatization is the prevalent land tenure regime for securing access to and control over land, indicating significant transformations of prior (undesignated) public land. We conclude that green grabbing is a persistent, critical phenomenon in Brazil, requiring transparency and close monitoring of land tenure modifications.
Residual networks without pooling layers improve the accuracy of genomic predictions
Authors: Xie Zhengchao , Xu Xiaogang , Li Ling , Wu Cuiling , Ma Yinxing , He Jingjing , Wei Sidi , Wang Jun , Feng Xianzhong 
Published: September 2023

Abstract

With the decrease in gene sequencing cost and the development of deep learning, phenotype prediction accuracy by genomic selection (GS) has been continuously improved. Residual networks, a widely validated deep learning technique, are introduced to deep learning for GS. Since each locus has a different weighted impact on the phenotype, strided convolutions are more suitable for GS problems than pooling layers. Through the above technological innovations, we propose a deep learning algorithm for GS, residual neural network genomic selection (ResGS). ResGS is the first neural network to reach 50 layers in GS. In 15 cases with four public data, the prediction accuracy of ResGS is higher than that of ridge-regression best linear unbiased prediction, support vector regression, random forest, gradient boosting regressor, and deep neural network genomic prediction in most cases. ResGS performs well in dealing with gene-environment interaction. Phenotypes from other environments are imported into ResGS along with genetic data. The prediction results are much better than just providing genetic data as input, which demonstrates the effectiveness of GS multi-modal learning. Standard deviation is recommended as an auxiliary GS evaluation metric, which could improve the distribution of predicted results. Deep learning for GS, such as ResGS, has increasingly apparent advantages compared with traditional GS algorithms.
Characterization of Xanthomonas isolates causal of citrus canker type A in Tucumán, Argentina, and biocontrol strategies using olive and wine-derived agro-industrial wastes.
Authors: Aguirre Constanza María , Viola Carolina , Salazar Sergio Miguel , Haelterman Raquel Mercedes , Arena Mario Eduardo 
Published: September 2023

Abstract

Argentina ranks fourth as a lemon producer worldwide and first in lemon industrialization. At the same time, Tucumán (NW region of Argentina) is the leading national producer and exporter of lemons and the fourth largest exporter of fresh lemons worldwide. Citrus canker is one of the major diseases that threaten citrus production, and its causal agent, Xanthomonas citri subsp. citri is present in all citrus-growing areas worldwide, including Tucumán. Due to the current global awareness of environmental care and the demand for organic food, the present study aims to characterize Xanthomonas strains in Tucumán and further evaluate the potential of wine-derived agro-industrial wastes as a natural alternative to control citrus canker. In this vein, we focused on those by-products derived from the olive (‘Alperujo’) and wine (‘Orujo’) industries. The current study provides an updated characterization of the Xanthomonas species isolated in Tucumán and confirms that all the isolates pertained to citrus canker type A. Such strains were clustered into four groups according to their distinctive features: in vitro growth, biofilm formation, metabolic activity, exopolysaccharide content, swarming mobility, and pathogenicity. We further demonstrated that ‘Alperujo’ extracts mainly inhibited bacterial growth, while ‘Orujo’ extracts were most active against biofilm production and bacterial motility, with evident antibacterial activity. Overall, this study confirms the presence of pathotype A of X. citri subsp. citri strains in Tucumán, Argentina, and proposes to use olive and wine agro-industrial sub-products as an efficient bio-input to control the causal agent of citrus canker in lemons.
Ecological consequences of low ampicillin concentrations on an ex-vivo biofilm model of the human oral microbiome
Authors: Petersen Fernanda C. , Brar Navdeep Kaur , Dhariwal Achal , Aar Heidi , Junges Roger , Salvadori Gabriela , Baker Jonathon , Edlund Anna 
Published: September 2023

Abstract
Antibiotics at low concentration can promote processes such as biofilm formation, virulence and antibiotic resistance. This can be of high relevance in microbial communities like the oral microbiome, where commensals and pathogens share a common habitat and where the abundance of antibiotic resistance genes surpasses the abundance in the gut. Here, we used an ex vivo model of human oral biofilms to investigate the impact of ampicillin on biofilm viability. Further, the ecological impact on the microbiome and resistomes was investigated using shotgun metagenomics. The results showed that low concentrations promoted significant shifts in microbial taxonomic profile and could enhance biofilm viability by up to 1 to 2-log. For the resistome, low concentrations had no significant impact on antibiotic resistance gene (ARG) diversity, while ARG abundance decreased by up to 84%. A positive correlation was observed between reduced microbial diversity and reduced ARG abundance. The WHO priority pathogens Streptococcus pneumoniae and Staphylococcus aureus were identified in some of the samples, but their abundance was not significantly altered by ampicillin. Yet, most of the antibiotic resistance genes that increased in abundance in the ampicillin group were associated with streptococci, including Streptococcus mitis, a well-known potential donor of ARGs to S. pneumoniae. To our knowledge, this is the first report on antibiotic effects on oral microbial communities using an ex-vivo human microbiome model combining biofilms and shotgun metagenomics. Overall, the results highlight the potential of using the model to further our understanding of ecological and evolutionary forces driving antimicrobial resistance in oral microbiomes.
Leveraging sampling schemes on skewed class distribution to enhance male fertility detection with ensemble AI learners
Authors: GhoshRoy Debasmita , Alvi P. A. , Santosh KC 
Published: September 2023

Abstract
Designing effective AI models becomes a challenge when dealing with imbalanced/skewed class distributions in datasets. Addressing this, re-sampling techniques often come into play as potential solutions. In this investigation, we delve into the male fertility dataset, exploring fifteen re-sampling approaches to understand their impact on enhancing predictive model performance. The research employs conventional AI learners to gauge male fertility potential. Notably, five ensemble AI learners are studied, their performances compared, and their results are evaluated using four measurement indices. Through comprehensive comparative analysis, we identify substantial enhancement in model effectiveness. Our findings showcase that the LightGBM model with SMOTE-ENN re-sampling stands out, achieving an efficacy of 96.66% and an F1-score of 95.60% through 5-fold cross-validation. Interestingly, the CatBoost model, without re-sampling, exhibits strong performance, achieving an efficacy of 86.99% and an F1-score of 93.02%. Furthermore, we benchmark our approach against state-of-the-art methods in male fertility prediction, particularly highlighting the use of re-sampling techniques like SMOTE and ESLSMOTE. Consequently, our proposed model emerges as a robust and efficient computational framework, promising accurate male fertility prediction.
Efficient ring-opening polymerization of epsilon-caprolactone catalyzed by iron(III) chloride under mild reaction conditions
Authors: Wu Hai-Bo , Zhou Xiantai , Zhou Xiao-Wu , Fang Yan-Xiong 
Published: September 2023

Abstract
As a biodegradable polyester, the commercialized synthesis protocol of poly(ε-caprolactone) (PCL) under mild conditions is of great significance and attractive. Herein, the ring-opening polymerization (ROP) of ε-caprolactone (ε-CL) using FeCl3 catalyst and benzyl alcohol (BnOH) as the initiator was developed. FeCl3 has been proved to be an efficient catalyst for the ROP of ε-CL under mild conditions. The conversion of ε-CL to PCL was 98.8% at 60 oC within 4 h, with number-average molecular weight (Mn) and dispersity (PDI) of 16500 g/mol and 1.28, respectively. Moreover, a coordination-insertion ring-opening polymerization mechanism mediated by FeCl3 was proposed. Overall, this work is expected to provide a feasible industrial method for the preparation of PCL from the direct aerobic oxidation of cyclohexanone.
The Safety and Efficacy of Systemic Delivery of a New Liver-de-targeted TGFβ Signaling Inhibiting Adenovirus in an Immunocompetent Triple Negative Mouse Mammary Tumor Model
Authors: Xu Weidong , Shin Soon Cheon , Vickman Renee , Filimon Beniamin , Yang Yuefeng , Hu Zebin , Mangold Kathy , Prabhakar Bellur , Schreiber Hans 
Published: September 2023

Abstract
Aberrant TGFβ signaling is linked to metastasis and tumor immune escape of many cancers including metastatic triple negative breast cancer (mTNBC). Previously, we have found that oncolytic adenoviruses expressing a TGFβ signaling inhibitory protein (sTGFβRIIFc) induced immune activation in a mouse TNBC (4T1) immunocompetent subcutaneous model with intratumoral injection. Systemic administration of adenoviruses can be a superior route to treat mTNBC but faces the challenges of increased toxicity and viral clearance. Thus, we created a liver-de-targeted sTGFβRIIFc- and LyP-1 peptide-expressing adenovirus (mHAdLyp.sT) with enhanced breast cancer cell tropism. Its safety and immune response features were profiled in the 4T1 model. Our data showed that the systemic administration of mHAdLyp.sT resulted in reduced hepatic and systemic toxicity. mHAdLyp.sT was also effective in increasing Th1 cytokines and anti-tumor cell populations by cytokine analysis, spleen/tumor qRT-PCR, and flow cytometry. We further tested the therapeutic effects of mHAdLyp.sT alone and in combination with immune checkpoint inhibitors (ICIs). mHAdLyp.sT alone and with all ICI combinations elicited significant inhibition of lung metastasis by histological analysis. When mHAdLyp.sT was combined with both anti-PD-1 and anti-CTLA-4 antibodies, primary 4T1 tumor growth was also significantly inhibited. We are confident in advancing this new treatment option for mTNBC.
Proteinuria frequency and subsequent renal dysfunction in bevacizumab-treated patients: A single center, retrospective, observational study
Authors: Kataoka Shigeki , Nishikawa Yoshitaka , Funakoshi Taro , Horimatsu Takahiro , Sakuragi Minoru , Uchino Eiichiro , Hiragi Shusuke , Yamamoto Shinya , Sakai Kaoru , Matsubara Takeshi , Yanagita Motoko , Muto Manabu 
Published: September 2023

Abstract
Background
Proteinuria is a common adverse event observed during treatment with antivascular endothelial growth factor (VEGF) antibodies. Proteinuria is a risk factor for renal dysfunction and cardiovascular complications in patients with chronic kidney disease. However, the association between anti-VEGF antibody-induced proteinuria and renal dysfunction or cardiovascular complications remains unclear.
Methods
The medical records of patients treated with bevacizumab (BV) at Kyoto University Hospital (Kyoto, Japan) between January 2006 and March 2018 were retrospectively reviewed. Adverse event rates were compared between patients who developed qualitative ≥ 2 + proteinuria and those who developed < 1 + proteinuria. Adverse events were defined as renal dysfunction (i.e., ≥ 57% decrease in the eGFR, compared to the rate at the initial treatment) and hospitalization due to BV-associated cardiovascular complications and other adverse events.
Results
In total, 734 patients were included in this analysis. Renal dysfunction was more common in patients with ≥ 2 + proteinuria than in those with < 1 + proteinuria (13/199, 6.5% vs. 13/535, 2.4%). Seven of these 13 patients with ≥ 2 + proteinuria had transient reversible renal dysfunction. Only four (2.0%) patients had BV-associated renal dysfunction. Of the 734 patients, 6 patients, 16 patients, and 13 patients were hospitalized because of the adverse events of cardiovascular complications, thromboembolisms, and cerebrovascular complications, respectively. No relationship was observed between these adverse events and proteinuria.
Conclusion
BV treatment-induced proteinuria was not associated with renal dysfunction or other adverse events. Continuing BV with caution is a possible treatment option, even after proteinuria develops, in patients with cancer and a limited prognosis.
Structural basis for the dynamic chaperoning of disordered clients by Hsp90
Authors: Huang Chengdong , Qu Xiaozhan , Zhao Shuo , Wan Chanjuan , Zhu Lei , Rossi Paolo , Wang Junfeng , Kalodimos Charalampos , Wang Chao , Xu Weiya 
Published: September 2023

Abstract

Molecular chaperone Hsp90 is a ubiquitous regulator that fine-tunes and remodels diverse client proteins, exerting profound effects on normal biology and diseases. However, the atomic-level chaperoning mechanism of Hsp90 remains elusive. Here, using NMR spectroscopy in combination with other techniques, we determined the solution structure of the initial encounter complex in the chaperone cycle, wherein Hsp90 adopts an open conformation while engaging with a disordered client. Our structure reveals a dual-binding mechanism, as Hsp90 utilizes two distinct sites that synergistically capture hydrophobic segments within client proteins, forming a bipartite complex that enables rapid conformational samplings. Furthermore, we demonstrate that the chaperone cycle triggers significant conformational and dynamic transformations. Distant client binding effectively primes Hsp90's global dynamics and conformational equilibrium, ultimately unleashing its ATPase potential for efficient client remodeling. These findings offer fundamental insights into the dynamic machinery of Hsp90, contributing to a unified conceptual and mechanistic understanding of Hsp90-client interactions.
A large-scale, multi-centre, prospective observational study to treat hepatitis C in Pakistan and assess resistance to antiviral drugs (HepFREEPak): study protocol
Authors: Arif Ambreen , Hasnain Aliya , Chaudhry Auj , Asim Muhammad , Shafqat Muhammad Nabeel , Altaf Abeer , Saba Noor , Kemos Polychronis , Ansari M. Azim , Barnes Eleanor , Metcalfe Chris , Vickerman Peter , Qureshi Huma , Hamid Saeed , Choudhry Asad Ali , Niaz Saad Khalid , Foster Graham R , Choudhry Naheed 
Published: September 2023

Abstract
Background: Pakistan has one of the highest burdens of Hepatitis C virus (HCV) infection globally. To achieve the World Health Organization’s goals for HCV elimination, there is a need for substantial scale-up in testing, treatment, and a reduction in new infections. Data on the population impact of scaling up treatment is not available in Pakistan, nor is there reliable data on the incidence of infection/reinfection. This project will fill this gap by providing important empirical data on the incidence of infection (primary and reinfection) in Pakistan. Then, by using this data in epidemic models, the study will determine whether response rates achieved with affordable therapies (sofosbuvir plus daclatasvir) will be sufficient to eliminate HCV in Pakistan.Methods: This prospective multi-centre cohort study will screen 25,000 individuals for HCV antibody (Ab) and RNA (if Ab-positive) at various centers in Pakistan - Karachi (Sindh) and Punjab, providing estimates of the disease prevalence. HCV positive patients will be treated with sofosbuvir and daclatasvir for 12-weeks, (extended to 24-weeks in those with cirrhosis) and the proportion responding to this first-line treatment estimated. Patients who test HCV Ab negative will be recalled 12 months later to test for new HCV infections, providing estimates of the incidence rate. Patients diagnosed with HCV (~ 4,000) will be treated and tested for Sustained Virological Response (SVR). Questionnaires to assess risk factors, productivity, health care usage and quality of life will be completed at both the initial screening and at 12-month follow-up, allowing mathematical modelling and economic analysis to assess the current treatment strategies. Viral resistance will be analysed and patients who have successfully completed treatment will be retested 12 months later to estimate the rate of re-infection.Conclusion The HepFREEPak study will provide evidence on the efficacy of available and widely used treatment options in Pakistan. It will also provide data on the incidence rate of primary infections and re-infections. Data on incidence risk factors will allow us to model and incorporate heterogeneity of risk and how that affects screening and treatment strategies. These data will identify any gaps in current test-and-treat programs to achieve HCV elimination in Pakistan.Study registration This study was registered on clinicaltrials.gov (NCT04943588) on June 29, 2021.
Seed hydropriming to alleviate drought stress in germination of two cotton (Gossypium hirsutum L.) varieties
Authors: BOKOBANA Atalaèsso , GNOFAM Nambou , KOFFI Zovodu Kokou , ASSIH Alèdi , AKANTETOU Komlan Pikassalé , BASSAROU Ayeva , TOZO Koffi 
Published: September 2023

Abstract

Background Drought is a serious threat to the farming community, biasing the crop productivity in arid and semi-arid regions of the world. This study aims to evaluate effect of hydropriming on seed germination of two varieties of cotton, STAM 129A and STAM 190, under drought stress. The seed imbibition kinetics allowed to fix various hydropriming delays (3, 6, 9, 12, 15 and 18 hours). The germination test was conducted in four completely randomized repetitions of 25 seeds for each of the four induced osmotic water stress modalities (0 bar, -3bar, -6 bar, -9 bar), which required the use of PEG-6000 for adjustment. Calculus of germination percentage (GP), mean germination time (MGT), germination index (GI) and the relative PEG injury rate (RPIR) made it possible to evaluate the germinative behavior of the seeds following the different treatments. Results Drought stress-induced damage to seed germination was significantly reduced by priming seeds for 12 hours for both cotton varieties. Under drought stress (average of values measured at -3 bar, -6 bar and − 9 bar), 12H-hydropriming increased the GP by 206.25% for STAM 190 and 179.26% for STAM 190. Germination, previously nil at -6 bar and − 9 bar for unprimed seeds, becomes possible with priming and better with 12H-hydropriming. Increases of 250.76% and 289.55% of GI for respectively STAM 129A and STAM 190 are noted under drought stress. In general, primed seeds germinated one day earlier than unprimed seeds under normal hydrous conditions. Under drought conditions, however, MGT did not vary significantly from the control, approximately 4.56–4.77 days. Longer priming (18H-hydropriming) had a repressive effect on seed germination with total PEG damage, the few seeds that germinated doing so earlier than all the other treatments, at around 3.83–4.02 days under normal hydrous conditions, and 4.33–4.46 days under drought conditions. RPIR was reduced 35.89% (for STAM 129A) and 27.10% (for STAM 190) with 12H-hydropriming. Conclusions Thus, for growing cotton varieties STAM 129A and STAM 190, hydropriming seeds for 12 hours can be recommended to maintain germinative vigor whatever rainfall conditions may arise.
Transfer of heavy metals in topsoils, based on sequential extraction and statistical tools in Northeast Brazil
Authors: Fernández Zahily Herrero , Júnior José Araújo dos Santos , Amaral Romilton dos Santos , Coutinho Artur Paiva , Bezerra Mariana Brayner Cavalcanti Freire , Santos Josineide Marques do Nascimento , Milan Marvic Ortueta , Rojas Lino Angel Valcarcel , Yinusa Taiwo Saheed , Melo Robert Fernandes , de Oliveira Marcela Ferreira Marques , Santos Yasmin Marques dos 
Published: September 2023

Abstract

Trace metals are associated with various organic and inorganic components, appearing in different chemical forms, which regulate their solubility, mobility, and availability to biological systems. Given this, it is necessary to know the chemical form in which these elements are found since this defines their potential for remobilization. Thus, this work aimed to evaluate the distribution and mobility of Pb, Cu, Cd, Cr, Ni, and Zn in eight types of soils from Northeast Brazil. The concentration in the fractions was determined through sequential extraction using the procedure outlined by the Community Bureau of Reference (BCR). Cu was extracted using oxidizing conditions and in the residual fraction. The Principal Component Analysis (PCA) and Pearson correlation matrix were used in fifty topsoil samples to investigate the relationship between metals and physical-chemical parameters. The results revealed that metals were prevalent in the residual fraction. Cd, Ni, and Zn were primarily detected in the mobile fraction. Cd and Pb were associated with Fe and Mn oxides, suggesting the mobility of these metals within the environment. The organic matter and texture influenced the mobility of metals in the soil. The PCA analysis shows that the pH correlates positively with Ni, Cu, and Cr and negatively with Zn, Cd, and Pb. The parameters analyzed showed significant variations across different soil classes, highlighting their diverse nature. The findings highlighted the significance of sequential metal extraction in soil and the utilization of PCA to predict changes in solubility and determine its availability to plants.