bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evolution of the genetic load during habitat loss and population fragmentation
Authors: Pinto Alessandro V. , Hansson Bengt , Patramanis Ioannis , Morales Hernán E. , Oosterhout Cock 
Published: October 2022

Abstract
Habitat loss and population fragmentation pose severe threats to the survival of many species. Population isolation and the decline in effective population size lead to increased genetic drift and inbreeding. In turn, this reduces neutral diversity, and it also affects the genetic load of deleterious mutations. Here, we analyse the effect of such genomic erosion by designing a spatially explicit model in SLiM to simulate the effects of the recorded habitat loss in Mauritius over the past ~ 250 years. We show that the loss of neutral nucleotide diversity was barely noticeable during the first 100 years of habitat loss, and that it only became apparent when the total amount of suitable habitat had been reduced to circa 25% of the native undisturbed forest. At that time, the census population size had dropped from circa 10,000 individuals to approximately N = 2000 (equivalent to Ne ~ 1000). The decline of neutral diversity continued after the metapopulation had stabilised at low numbers, consistent with the “drift debt” hypothesis. Although a considerable number of deleterious mutations were lost by drift, others increased in frequency. The masked load was thus converted into a realised load, which compromises individual fitness and population viability after much of the native habitat had been lost. Our study shows that historic habitat loss can pose a sustained threat to populations also in future generations, and that the resulting genetic erosion is likely to continue even without further habitat loss. The UN’s Decade on Ecosystem Restoration needs to lead to transformative change to save species from future extinction, and this requires the urgent restoration of natural habitats.
Nanoengineered Drug Delivery in Cancer Immunotherapy for Overcoming Immunosuppressive Tumor Microenvironment
Authors: Park Sei Hyun , Eun Ryounho , Heo Janghun , Lim Yong Taik 
Published: October 2022

Abstract
Almost like a living being in and of itself, tumors actively interact with and modify their environment to escape immune responses. Owing to the pre-formation of cancer favorable microenvironment prior to anti-cancer treatment, the numerous attempts that followed proposes limited efficacy in oncology. Immunogenicity by activation of immune cells within the tumor microenvironment or recruitment of immune cells from nearby lymph nodes is quickly offset as the immunosuppressive environment, rapidly converting immunogenic cells into immune suppressive cells, overriding the immune system. Tumor cells, as well as regulatory cells, namely M2 macrophages, Tregs, and MDSCs, derived by the immunosuppressive environment, also cloaks from potential anti-tumoral factors by directly or indirectly secreting cytokines, such as IL-10 and TGF-β, related to immune regulation. Enzymes and other metabolic or angiogenetic constituents – VEGF, IDO1, and iNOS - are also employed directed for anti-cancer immune cell malfunctioning. Therefore, the conversion of ‘cold’ immunosuppressive environment into ‘hot’ immune responsive environment is of paramount importance, bestowing the advances in the field of cancer immunotherapy the opportunity to wholly fulfill its intended purpose. This paper reviews the mechanisms by which tumors wield to exercise immune suppression and the nanoengineered delivery strategies being developed to overcome this suppression. Clinical advances based on transforming ‘cold’ into ‘hot’ tumors targeting various methods discussed in this paper will also be addressed for further understanding of the clinical applications of ongoing research in cancer immunotherapy.
Synthesis, Characterization, Analytical Application, and Theoretical Studies of a Schiff Base, (E)-2-(2-aminophenylthio)-N-(thiophen-2-yl-methylene) benzenamine
Authors: Berhanu Asnake Lealem , Mohiuddin Irshad , Malik Ashok Kumar , Aulakh Jatinder Singh 
Published: October 2022

Abstract
In this study, a new Schiff base, (E)-2-(2-aminophenylthio)-N-(thiophen-2-yl-methylene) benzenamine was synthesized for selective detection of Hg2+. This Schiff base was characterized by proton nuclear magnetic resonance (1HNMR) spectroscopy, carbon-13 nuclear magnetic resonance (13CNMR) spectroscopy, and Fourier-transform infrared (FTIR) spectroscopy. Binding interaction between (E)-2-(2-aminophenylthio)-N-(thiophen-2-yl-methylene)benzenamine and various metal ions has been studied by UV–Vis spectroscopic measurements and shows promising coordination towards Hg2+ and almost no interference from other metal ions ( Ag+, Mn2+, Fe3+, Al3+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Fe2+ and Cr3+).This Schiff base exhibiting detection limit of 3.8 × 10− 8 M. The Schiff base newly synthesized in this study was successfully applied to the determination of Hg2+ in water samples. In addition to the experimental study, a theoretical study was conducted using Gaussian 09 program to support the experimental findings. FTIR, NMR, bond angle, bond length, torsional angles and structural approximation were studied using theoretical consideration.
A simple soil mass correction factor for a more accurate determination of soil carbon stock changes
Authors: Fowler Ames , Basso Bruno , Millar Neville , Brinton William 
Published: October 2022

Abstract

Agricultural soils can act as a sink for large quantities of soil organic carbon (SOC), but can also be sources of carbon to the atmosphere. The international standard for SOC stock assessment relies on a 30cm fixed depth sample. The tendency of bulk density (BD) to decrease with decreasing disturbance and increasing SOC concentration and the assumption of constant SOC and BD within this depth profile introduces error into the estimates of SOC stock. A change in BD from 1.5 to 1.1 in the top 30cm underestimates SOC stocks by 17%. Significant effort has been made to evaluate and reduce this fixed depth error by using the equivalent soil mass (ESM) approach, but with limited adoption.
We evaluate the error in SOC stock assessment generated from fixed depth measurements relative to the ESM approach and propose correction factors that can be readily adopted under current sampling and analytical methods. Our approach provides a more accurate estimate of SOC stock accumulation or loss that will help incentivize management practice changes that reduce the environmental impacts of agriculture and further legitimize the accounting practices used by the emerging carbon market and organizations that have pledged to reduce their supply chain GHG footprints.
Improvement of face recognition performance using a new hybrid subspace classifier
Authors: Keser Serkan 
Published: October 2022

Abstract
Multiple Classification Systems (MCS) play an important role in increasing recognition performance, especially when using heterogeneous classifiers effectively improves performance. In this study, a new hybrid classifier was designed using heterogeneous Fisherface and Discriminative common vector approach (DCVA) subspace recognition methods, which gave successful results in face recognition. The main feature of the hybrid classifier is that it can assign the misclassified parts to the correct class. While DCVA is based on the common properties of the signals belonging to the classes for classification, Fisherface is based on the different properties of the signals. In order to create a hybrid classifier, called the Hybrid DCVA-Fisherface (HDF), the classifiers' decision rules were combined using the Minimum Proportional Score Algorithm (MPSA) and Recognition Update Algorithm (RUA). To better examine the efficiency of the algorithms, tests were also carried out by downsampling the images. When the experimental results were analyzed, the proposed hybrid classifier gave higher recognition rates than other classifiers.
Assessing the learning curve of robot-assisted total mesorectal excision. A multi-centre study considering procedural safety, pathological safety and efficiency
Authors: Burghgraef Thijs A. , Sikkenk D. J. , Crolla R. M.P.H. , Fahim M. , Melenhorst J. , Moumni M. El , Schelling G. , Smits A. B. , Stassen L. P.S. , Verheijen P. M. , Consten E. C.J. 
Published: October 2022

Abstract

Purpose
Evidence regarding the learning curve of robot-assisted total mesorectal excision is scarce and of low quality. Case-mix is mostly not taken into account, and learning curves are based on operative time, while preferably clinical outcomes and literature-based limits should be used. Therefore this study aims to assess the learning curve of robot-assisted total mesorectal excision.
Methods
A retrospective study was performed in four Dutch centres. The primary aim was to assess the safety of the individual and institutional learning curves using a RA-CUSUM analysis based on intraoperative complications, major postoperative complications and compound pathological outcome (positive circumferential margin or incomplete TME specimen). The learning curve for efficiency was assessed using a LC-CUSUM analysis for operative time. Outcomes of patients before and after the learning curve were compared.
Results
In this study, seven participating surgeons performed robot-assisted total mesorectal excisions in 531 patients. Learning curves for intraoperative complications, postoperative complications, and compound pathological outcome did not exceed predefined literature-based limits. The LC-CUSUM for operative time showed lengths of the learning curve ranging from 12–35 cases. Intraoperative, postoperative and pathological outcome did not differ between patients operated during and after the learning curve.
Conclusion
The learning curve of robot-assisted total mesorectal excision based on intraoperative complications, postoperative complications and compound pathological outcome did not exceed predefined limits, and is therefore suggested to be safe. Using operative time as a surrogate for efficiency, the learning curve is estimated to be between 12 and 35 procedures.
Application of laser desorption/ionization for investigation of phosphomolybdic acid
Authors: Minenkova Irina V. , Emel’yanov Anton M. , Tarkhanova Irina G. , Buryak Aleksey K. 
Published: October 2022

Abstract
Heteropoly compounds are of great practical importance as components of catalysts. In particular, phosphomolybdic acid H3PMo12O40 is widely used in catalytic oxidation processes. For heterogeneous catalysts, one of the effective methods for studying their structure is mass spectrometry. In this work, the main patterns of fragmentation of crystalline phosphomolybdic acid and its aqueous solutions are studied by laser desorption/ionization. It has been found that during laser desorption/ionization, acid crystals tend to form particles of the cluster type (MoO3)n and HPO3∙(MoO3)n. When registering positive ions, particles with a mixed oxidation state of Mo+ 5 and Mo+ 6 were detected. Clusters of molybdenum (VI) oxide were found in the study of aqueous solutions of acid. In the study of aqueous solutions together with a matrix of 2,5-dihydroxybenzoic acid, particles containing a hydrated molecular ion were found. Clusters with a molecular ion were identified: H3PMo12O40∙(MoO3)3, H3PMo12O40∙(MoO3)4, H3PMo12O40∙MoO3∙4H2O, H3PMo12O40∙(MoO3)2∙2H2O, H3PMo12O40∙(MoO3)2∙4H2O, and H3PMo12O40∙(MoO3)3∙2H2O. When studying the influence of the LDI parameters on the informativity of the mass spectrum, it was found that, in the general case, the values of the peak intensity and the laser power, as well as the number of shots, are in symbatic dependence. The intensity of the peak depends largely on the power of the laser than on the number of shots. Thus, it has been shown that, upon ionization, phosphomolybdic acid can generate both fragments and cluster ions containing mainly the adduct of the molecular ion with molybdenum oxide and water.
Plasma exosomal miR-199a-3p downregulates cell proliferation and migration in Hirschsprung’s disease by targeting mTOR
Authors: Yu Daiyue , Yang Yang , Huang Zhaorong , Lu Yi , Wang Chen , Luo Caiyun , Su Yuqian , Yang Liucheng , Wu Kai 
Published: October 2022

Abstract
Background
Plasma exosomal microRNAs have been suggested to be potential biomarkers of disease. However, the exosomal microRNAs in Hirschsprung’s disease (HSCR) are still unclear. In this study, we analyzed the miRNA profiles of HSCR and elucidated the mechanism of the selected miR-199a-3p in the development of HSCR.
Methods
Plasma exosomes were isolated, and exosomal miRNA high-throughput sequencing was performed to obtain differentially expressed miRNAs. CCK-8 and Transwell assay were used to determine the function of the most differentially expressed miRNA, which was confirmed in tissue specimen. Thereafter, target genes of the selected miRNAs were predicted by the databases. Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes Genomes (KEGG) analysis, and protein–protein interaction network (PPI) construction of possible target genes were used to perform enrichment analysis and interaction. Finally, the PCR, Western blot and recovery experiment were used to confirm the function of target gene, mammalian target of rapamycin (mTOR), in vitro.
Results
The expression of miR-199a-3p was upregulated in plasma exosomes and diseased colonic tissues of patients with HSCR. In vitro, miR-199a-3p can inhibit cell proliferation and migration. Bioinformatic analysis suggested that mTOR might be a potential target of miR-199a-3p in HSCR. mTOR was discovered to be downregulated by miR-199a-3p in vitro. The negative connection between mTOR and miR-199a-3p was confirmed in tissue samples. mTOR can partially reverse the effect of miR-199a-3p on cell proliferation and migration function in vitro.
Conclusions
miR-199a-3p suppresses cell growth and motility, partially by targeting mTOR. Plasma exosomal miR-199a-3p, a diagnostic marker, is crucial for the development of HSCR.
Using spatially variable nitrogen application and crop responses to evaluate crop nitrogen use efficiency
Authors: Hegedus Paul B. , Ewing Stephanie , Jones Clain , Maxwell Bruce D. 
Published: October 2022

Abstract
Low nitrogen use efficiency (NUE) is ubiquitous in agricultural systems, with mounting global scale consequences for both atmospheric aspects of climate and downstream ecosystems. Since NUE related soil characteristics such as water holding capacity and organic matter are likely to vary at small scales (<1 ha), understanding the influence of soil characteristics on NUE at the subfield scale (<32 ha) could increase fertilizer NUE. Here, we quantify NUE in four conventionally managed dryland winter-wheat fields in Montana following multiple years of sub-field scale variation in experimental N fertilizer applications. To inform farmer decisions that incorporates NUE, we developed a generalizable model to predict subfield scale NUE by comparing six candidate models, using ecological and biogeochemical data gathered from open-source data repositories and from normal farm operations, including yield and protein monitoring data. While NUE varied across fields and years, efficiency was highest in areas of fields with low N availability from both fertilizer and estimated mineralization of soil organic N (SON). At low levels of applied N, distinct responses among fields suggest distinct capacities to supply non-fertilizer plant-available N, suggesting that mineralization supplies more available N in locations with higher total N, reducing efficiency for any applied rate. Comparing modelling approaches, a random forest regression model of NUE provided predictions with the least error relative to observed NUE. Subfield scale predictive models of NUE can help to optimize efficiency in agronomic systems, maximizing both economic net return and NUE, which provides a valuable approach for optimization of nitrogen fertilizer use.
Hepatocellular carcinoma risk-stratification based on ASGR1 in circulating epithelial cells for cancer interception
Authors: Colomo Amparo Roa , Garrido María Ángeles López , Molina-Vallejo Pilar , Rojas Angela , Sanchez Mercedes González , Aranda-García Violeta , Salmeron Javier , Romero-Gomez Manuel , Muntane Jordi , Padillo Javier , Alamo Jose María , Lorente Jose A. , Serrano María José , Garrido-Navas M. Carmen 
Published: October 2022

Abstract
Purpose: Lack of diagnostic and prognostic biomarkers in hepatocellular carcinoma impedes stratifying patients based on their risk of developing cancer. The aim of this study was to evaluate phenotypic and genetic heterogeneity of circulating epithelial cells (CECs) based on asialoglycoprotein receptor 1 (ASGR1) and miR-122-5p expression as potential diagnostic and prognostic tools in patients with hepatocellular carcinoma (HCC) and liver cirrhosis (LC).
Methods: Peripheral blood samples were extracted from LC and HCC patients at different disease stages. CECs were isolated using positive immunomagnetic selection. Genetic and phenotypic characterization was validated by double immunocytochemistry for cytokeratin (CK) and ASGR1 or by in-situ hybridization with miR-122-5p and CECs were visualized by confocal microscopy.
Results: The presence of CECs increased HCC risk by 2.58-fold, however, this was only significant for patients with previous LC (p=0.028) and not for those without prior LC (p=0.23). Furthermore, the number of CECs lacking ASGR1 expression correlated significantly with HCC incidence and absence of miR-122-5p expression (p=0.014; r=0.23). Finally, overall survival was significantly greater for patients at earlier cancer stages (p=0.018), but this difference was only maintained in the group with the presence of CECs (p=0.021) whereas progression-free survival was influenced by the absence of ASGR1 expression.
Conclusion: Identification and characterization of CECs by ASGR1 and/or miR-122-5p expression may be used as a risk-stratification tool in LC patients, as it was shown to be an independent prognostic and risk-stratification marker in LC and early disease stage HCC patients.
Revealing the Crystalline Packing Structure of Y6 in the Active Layer of Organic Solar Cells: The Critical Role of Solvent Additives
Authors: Xia Xinxin , Mei Le , He Chengliang , Chen Zeng , Yao Nannan , Qin Minchao , Sun Rui , Pan Yuyu , Xiao Yiqun , Min Jie , Zhang Fengling , Zhu Haiming , Bredas Jean-Luc , Chen Hongzheng , Chen Xian-Kai , Lu Xinhui 
Published: October 2022

Abstract
The bulk heterojunction morphology of photovoltaic materials for organic solar cells (OSCs) is crucial to the fundamental optoelectronic properties. However, in the photoactive layer, the intrinsic crystalline packing structure of Y6, currently the hallmark molecule among the Y-series non-fullerene acceptors (NFAs), is still unclear. Here, employing grazing-incidence wide-angle x-ray scattering (GIWAXS), we resolved the crystalline packing structure of Y6 in the active layer thin film obtained under actual device fabrication conditions. It is found that the film with solvent additive 1-chloronaphthalene (CN) presents a more ordered crystalline packing of Y6. Atomistic molecular dynamics simulations indicate that there exist additional π-π interactions between CN molecules and Y6 end groups, which provide more space for Y6 molecules to relax and form more ordered structures. Our work reveals the critical role of CN in the crystalline packing of Y6 in the device active layer and provides direct correlations between this crystalline packing and the device characteristics and photophysical properties.
EA-GAN: Ancient books text restoration model based on example attention
Authors: Zheng Wenjun , Su Benpeng , Feng Ruiqi , Peng Xihua , Chen Shanxiong 
Published: October 2022

Abstract
Ancient books are of great significance to historical research and cultural inheritance. Unfortunately, these books have been damaged and corroded in the process of long-term transmission. The restoration and digital preservation of ancient books is a new protection method. Traditional character restoration methods ensure the visual consistency of character images through the character features and the pixels around the damaged hole. However, character structure often causes errors, especially when there is a big hole in critical locations. Inspired by human copywriting behavior, a two-branch structure character restoration network EA-GAN is proposed, which is based on generative adversarial network and fuses reference examples. By referring to the feature of the example character, the damaged character can be repaired accurately even when the damaged area is large. EA-GAN first uses two branches to extract the features of the damaged character and example character respectively. Then, the damaged character is repaired according to their neighborhood information and example character features of different scales in the upsampling stage. To solve the problems that the example features and the fixed character features are not aligned and the convolution receptive field is too small, an Example Attention structure block is proposed to assin ist repair. Qualitative and quantitative analysis experiments are carried out on the self-built dataset MSACCSD and real scene pictures. Compared with the latest repair networks, EA-GAN can get the correct text structure through the guidance of the additional example in the Example Attention block. The peak signal-to-noise ratio (PSNR) and the structural similarity (SSIM) value were improved by 9.82% and 1.82%, and the learned perceptual image patch similarity (LPIPS) value calculated by VGG and AlexNet decreased by 35.04% and 16.36% respectively, which obtained better results than the current repair methods. It also has a good repair effect in the face of untrained characters ,which is helpful to the digital preservation of ancient books.
VdERG2 was involved in ergosterol biosynthesis, nutritional differentiation and virulence of Verticillium dahliae
Authors: Lv Junyuan , Liu Shichao , Zhang Xiaojian , Zhao Lihong , Zhang Tao , Zhang Zhigang , Feng Zili , Wei Feng , Zhou Jinglong , Zhao Ruiyuan , Feng Hongjie , Zhu Heqin , Li Caihong , Zhang Yalin 
Published: October 2022

Abstract
The ergosterol biosynthesis pathway plays an important role in model pathogenic bacteria Saccharomyces cerevisiae, but little is known about the biosynthesis of ergosterol in pathogenic fungus Verticillium dahliae. In this study, we identified the VdERG2 gene encoding sterol C-8 isomerase from V. dahliae and investigated its function in virulence by generating gene deletion mutants (ΔVdEGR2) and complemented mutants (C-ΔVdEGR2). Deletion of VdERG2 reduced ergosterol content. The conidial germination rate and conidial yield of ΔVdERG2 decreased significantly, and abnormal conidia were produced. In spite of VdERG2 did not affect the utilization of carbon sources by V. dahliae, but ΔVdERG2 observed a decrease in melanin production when cellulose and pectin were used as sole carbon sources, respectively. The ability of mutants ΔVdERG2 to produce microsclerotia and melanin decreased and the knockout of VdERG2 led to a significant decrease in the expression of microsclerotia and melanin-related genes VaflM, Vayg1, VDH1, VdLAC, VdSCD and VT4HR. In addition, mutants ΔVdEGR2-1 and ΔVdEGR2-2 were very sensitive to congo red (CR), sodium dodecyl sulfate (SDS) and hydrogen peroxide (H2O2) stresses, indicating that VdEGR2 was involved in cell wall and oxidative stress response. The absence of VdERG2 weakened the penetration ability of mycelium on cellophane and affected the growth of mycelium on cellophane. Although ΔVdERG2 could infect cotton, its pathogenicity was significantly impaired. These phenotypic defects in ΔVdERG2 could be complemented by reintroduction of a full-length VdERG2 gene. In summary, as a single conservative secretory protein, VdERG2 played a crucial role in ergosterol biosynthesis, nutritional differentiation and virulence in V. dahliae.