bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disentangling structural and functional responses of native versus alien communities by canonical ordination analyses and variation partitioning with multiple matrices
Authors: Sîrbu Ioan , Benedek Ana-Maria , Brown Bryan L. , Sîrbu Monica 
Published: July 2022

AbstractFreshwaters are under accelerated human pressure, and mollusk communities are among its most sensitive, threatened, and valuable components. To the best of our knowledge, the overall effects of damming, environment, space, time, and invasive alien mollusk species, on structural and functional responses of native mollusk communities were not yet compared. Using historical information and recent data from a river, we aimed to investigate and disentangle these effects and evaluate the differences in structural and functional responses of natives and alien invasives to the same predictors. Variation partitioning showed that alien species were as important predictors as were environmental factors and time in explaining species composition of native freshwater mollusk communities. Aliens were more independent of environmental conditions than natives and responded to different drivers, partially explaining their invasion success. The increased abundance of some alien gastropods was positively related to taxonomic diversity, while certain alien bivalves were negatively associated with the functional diversity of native communities. We introduce a cumulative variation partitioning with multiple response (native and alien) and predictor matrices, along with a diagram to show their relations, advocating for a conceptual shift in future community ecology, from “variables to matrices” and from “multivariate analyses to multi-matrix statistical modeling”.
The coupled photocycle of phenyl-p-benzoquinone and Light-Harvesting Complex II (LHCII) within the biohybrid system
Authors: Łazicka Magdalena , Palińska-Saadi Adriana , Piotrowska Paulina , Paterczyk Bohdan , Mazur Radosław , Maj-Żurawska Magdalena , Garstka Maciej 
Published: July 2022

AbstractThe combination of trimeric form of the light-harvesting complex II (LHCII3), a porous graphite electrode (GE), and the application of phenyl-p-benzoquinone (PPBQ), the quinone derivative, allow the construction of a new type of biohybrid photoactive system. The Chl fluorescence decay and voltammetric analyzes revealed that PPBQ impacts LHCII3 proportionally to accessible quenching sites and that PPBQ forms redox complexes with Chl in both ground and excited states. As a result, photocurrent generation is directly dependent on PPBQ-induced quenching of Chl fluorescence. Since PPBQ also undergoes photoactivation, the action of GE-LHCII3-PPBQ depends on the mutual coupling of LHCII3 and PPBQ photocycles. The GE-LHCII3-PPBQ generates a photocurrent of up to 4.5 µA and exhibits considerable stability during operation. The three-dimensional arrangement of graphite scraps in GE builds an active electrode surface and stabilizes LHCII3 in its native form in low-density multilayers. The results indicate the future usability of such designed photoactive device.
A two-layer mono-objective algorithm based on guided optimization to reduce the computational cost in virtual screening
Authors: Ferrández Miriam R. , Puertas-Martín Savíns , Redondo Juana L. , Pérez-Sánchez Horacio , Ortigosa Pilar M. 
Published: July 2022

AbstractVirtual screening methods focus on searching molecules with similar properties to a given compound. Molecule databases are made up of large numbers of compounds and are constantly increasing. Therefore, fast and efficient methodologies and tools have to be designed to explore them quickly. In this context, ligand-based virtual screening methods are a well-known and helpful tool. These methods focus on searching for the most similar molecules in a database to a reference one. In this work, we propose a new tool called 2L-GO-Pharm, which requires less computational effort than OptiPharm, an efficient and robust piece of software recently proposed in the literature. The new-implemented tool maintains or improves the quality of the solutions found by OptiPharm, and achieves it by considerably reducing the number of evaluations needed. Some of the strengths that help 2L-GO-Pharm enhance searchability are the reduction of the search space dimension and the introduction of some circular limits for the angular variables. Furthermore, to ensure a trade-off between exploration and exploitation of the search space, it implements a two-layer strategy and a guided search procedure combined with a convergence test on the rotation axis. The performance of 2L-GO-Pharm has been tested by considering two different descriptors, i.e. shape similarity and electrostatic potential. The results show that it saves up to 87.5 million evaluations per query molecule.
Isolation, characterization and complete genome analysis of a novel bacteriophage vB_EfaS-SRH2 against Enterococcus faecalis isolated from periodontitis patients
Authors: Pazhouhnia Setareh , Bouzari Majid , Arbabzadeh-Zavareh Farahnaz 
Published: August 2022

AbstractPeriodontitis is a chronic inflammatory condition that can damage soft tissues and supporting teeth.Enterococcus faecalisis an opportunistic pathogen usually living in the oral cavity and plays a critical role in apical periodontitis that significantly threatens human health. The use of bacteriophages as an alternative way to eliminate bacterial infections is a promising approach.E. faecaliswas isolated from the depth of dental packets of patients with periodontitis. Antimicrobial susceptibility was tested using 16 antimicrobial agents. Also, a specific virulent bacteriophage (vB_EfaS-SRH2) with an irregular pentagonal morphology of the head and a non-contractile tail belonging to theSiphoviridae,was isolated from wastewater in East of Isfahan, Iran, and its physiological and genomic specifications were investigated. The genome was double-strand DNA with 38,746 bp length and encoded 62 putative ORFs. In addition, eight Anti-CRISPERs and 30 Rho-dependent terminators were found. No tRNA was found. It had a short latent period of 15 min and a large burst size of~125. No undesirable genes (antibiotic resistance, lysogenic dependence, and virulence factors) were identified in the genome. Based on physiological properties and genomic characteristics, this phage can be used as a suitable choice in phage therapy for periodontitis and root canal infection.
An ANN-based advancing double-front method for automatic isotropic triangle generation
Authors: Lu Peng , Wang Nianhua , Chang Xinghua , Zhang Laiping , Wu Yadong , Zhang Hongying 
Published: July 2022

AbstractThe advancing front method (AFM) is one of the widely used unstructured grid generation techniques. However, the efficiency is relatively low because only one cell is generated in the advancing procedure. In this work, a novel automatic isotropic triangle generation technique is developed by introducing an artificial neural network (ANN) based advancing double-front method (ADFM) to improve the mesh generation efficiency. First, a variety of different patterns are extracted from the AFM mesh generation method and extended to the ADFM method. The mesh generation process in each pattern is discussed in detail. Second, an initial isotropic triangular mesh is generated by the traditional mesh generation method, and then an approach for automatic extraction of the training dataset is proposed. The preprocessed dataset is input into the ANN to train the network, then some typical patterns are obtained through learning. Third, after inputting the initial discrete boundary as initial fronts, the grid is generated from the shortest front and adjacent front. The coordinates of the points contained in the dual fronts and the adjacent points are sent into the neural network as the grid generation environment to obtain the most possible mesh generation pattern, the corresponding methods are used to update the advancing front until the whole computational domain is covered by initial grids, and finally, some smoothing techniques are carried out to improve the quality initial grids. Several typical cases are tested to validate the effectiveness. The experimental results show that the ANN can accurately identify mesh generation patterns, and the mesh generation efficiency is 50% higher than that of the traditional single-front AFM.
Modulation of dielectric properties in low-loss polypropylene-based composites at GHz frequencies: theory and experiment
Authors: Wilczyński Konrad , Wróblewska Anna , Daniszewska Agata , Krupka Jerzy , Mrozowski Michał , Zdrojek Mariusz 
Published: July 2022

AbstractPolymer composites with high dielectric constant and low loss tangent are highly regarded as substrates for modern high-speed electronics. In this work, we analyze the high-frequency dielectric properties of two types of composites based on polypropylene infused with high-dielectric-constant microparticles. Two types of fillers are used: commercial ceramics or titanium oxide (TiO2) with different concentrations. The key observation is that adding the fillers causes an increase of dielectric constants by around 100% (for highest loading) up to 4.2 and 3.4, for micro-ceramics and TiO2 based composites, respectively. Interestingly, for the TiO2 composite, the loss tangent depends on the filler loading volume, whereas the other composite has a slightly increasing tendency, however, being at the level ~ 10–3. To explain the experimental results, a theoretical model determined by microwave reflection and transmission through a representative volume element is proposed, which allows the investigation of the impact of volume ratio, grain shape, aggregation, and size on the loss tangent and permittivity evolution. This approach could be used for modeling other low dielectric loss materials with inclusions.
Risk assessment for the native anurans from an alien invasive species, American bullfrogs (Lithobates catesbeianus), in South Korea
Authors: Park Hye-Rin , Rahman Md Mizanur , Park Seung-Min , Choi Jae-Hyeok , Kang Hee-Jin , Sung Ha-Cheol 
Published: July 2022

AbstractThe invasive species are of global concern, and the Invasive American Bullfrog (IAB;Lithobates catesbeianus) is one of the worst invasive amphibian species worldwide. Like other countries, South Korea is also facing challenges from IAB. Although many studies indicated impacts of IAB on native anurans in Korea, the actual risk at the specific level is yet to evaluate. Considering the putative invasiveness of IAB, it is hypothesized that any species with the possibility of physical contact or habitat sharing with them, will have a potential risk. Thus, we estimated and observed their home range, preferred habitats, morphology, behavior, and ecology. Then, comparing with existing knowledge, we assessed risks to the native anurans. We found a home range of 3474.2 ± 5872.5 m2and identified three types of habitats for IAB. The analyses showed at least 84% of native anurans (frogs and toads) were at moderate to extreme risks, which included all frogs but only 33% of toads. Finally, we recommended immediate actions to conserve the native anurans based on our results. As this study is the first initiative to assess the specific risk level from the invasiveness ofL. catesbeianus, it will help the managers to set conservation priorities and strategies.
Integrated genomic sequencing in myeloid blast crisis chronic myeloid leukemia (MBC-CML), identified potentially important findings in the context of leukemogenesis model
Authors: Kazemi-Sefat Golnaz Ensieh , Keramatipour Mohammad , Vaezi Mohammad , Razavi Seyed Mohsen , Kavousi Kaveh , Talebi Amin , Rostami Shahrbano , Yaghmaie Marjan , Chahardouli Bahram , Talebi Saeed , Mousavizadeh‬ Kazem 
Published: July 2022

AbstractChronic myeloid leukemia (CML) is a model of leukemogenesis in which the exact molecular mechanisms underlying blast crisis still remained unexplored. The current study identified multiple common and rare important findings in myeloid blast crisis CML (MBC-CML) using integrated genomic sequencing, covering all classes of genes implicated in the leukemogenesis model. Integrated genomic sequencing via Whole Exome Sequencing (WES), Chromosome-seq and RNA-sequencing were conducted on the peripheral blood samples of three CML patients in the myeloid blast crisis. An in-house filtering pipeline was applied to assess important variants in cancer-related genes. Standard variant interpretation guidelines were used for the interpretation of potentially important findings (PIFs) and potentially actionable findings (PAFs). Single nucleotide variation (SNV) and small InDel analysis by WES detected sixteen PIFs affecting all five known classes of leukemogenic genes in myeloid malignancies including signaling pathway components (ABL1, PIK3CB, PTPN11), transcription factors (GATA2, PHF6, IKZF1, WT1), epigenetic regulators (ASXL1), tumor suppressor and DNA repair genes (BRCA2, ATM, CHEK2) and components of spliceosome (PRPF8). These variants affect genes involved in leukemia stem cell proliferation, self-renewal, and differentiation. Both patients No.1 and No.2 had actionable known missense variants on ABL1 (p.Y272H, p.F359V) and frameshift variants on ASXL1 (p.A627Gfs*8, p.G646Wfs*12). The GATA2-L359S in patient No.1, PTPN11-G503V and IKZF1-R208Q variants in the patient No.3 were also PAFs. RNA-sequencing was used to confirm all of the identified variants. In the patient No. 3, chromosome sequencing revealed multiple pathogenic deletions in the short and long arms of chromosome 7, affecting at least three critical leukemogenic genes (IKZF1, EZH2, and CUX1). The large deletion discovered on the short arm of chromosome 17 in patient No. 2 resulted in the deletion of TP53 gene as well. Integrated genomic sequencing combined with RNA-sequencing can successfully discover and confirm a wide range of variants, from SNVs to CNVs. This strategy may be an effective method for identifying actionable findings and understanding the pathophysiological mechanisms underlying MBC-CML, as well as providing further insights into the genetic basis of MBC-CML and its management in the future.
Identification of Daboia siamensis venome using integrated multi-omics data
Authors: Saethang Thammakorn , Somparn Poorichaya , Payungporn Sunchai , Sriswasdi Sira , Yee Khin Than , Hodge Kenneth , Knepper Mark A. , Chanhome Lawan , Khow Orawan , Chaiyabutr Narongsak , Sitprija Visith , Pisitkun Trairak 
Published: July 2022

AbstractSnakebite, classified by World Health Organization as a neglected tropical disease, causes more than 100,000 deaths and 2 million injuries per year. Currently, available antivenoms do not bind with strong specificity to target toxins, which means that severe complications can still occur despite treatment. Moreover, the cost of antivenom is expensive. Knowledge of venom compositions is fundamental for producing a specific antivenom that has high effectiveness, low side effects, and ease of manufacture. With advances in mass spectrometry techniques, venom proteomes can now be analyzed in great depth at high efficiency. However, these techniques require genomic and transcriptomic data for interpreting mass spectrometry data. This study aims to establish and incorporate genomics, transcriptomics, and proteomics data to study venomics of a venomous snake, Daboia siamensis. Multiple proteins that have not been reported as venom components of this snake such as hyaluronidase-1, phospholipase B, and waprin were discovered. Thus, multi-omics data are advantageous for venomics studies. These findings will be valuable not only for antivenom production but also for the development of novel therapeutics.
Mechanical strength and shape accuracy optimization of polyamide FFF parts using grey relational analysis
Authors: Shakeri Zohreh , Benfriha Khaled , Zirak Nader , Shirinbayan Mohammadali 
Published: July 2022

AbstractThis paper investigates the effect of different additive manufacturing process parameters such as chamber temperature, Printing temperature, layer thickness, and print speed on five essential parameters that characterize the manufactured components: cylindricity, circularity, strength, and Young’s modulus, and deformation by Gray Relational Analysis method simultaneously. Taguchi method was used to design the experiments, and the PA6 cylindrical parts were fabricated using a German RepRap X500® 3D printer. Then the Gray Relational Grade (GRG) values were calculated for all experiments. In the 8th trial, the highest value of GRG was observed. Then, to discover the optimal parameters, the GRG data were analyzed using ANOVA and S/N analysis, and it was determined that the best conditions for enhancing GRG are 60 °C in the chamber temperature, 270 °C in the printing temperature, 0.1 mm layer thickness, and 600 mm/min print speed. Finally, by using optimal parameters, a verification test was performed, and new components were investigated. Finally, comparing the initial GRG with the GRG of the experiments showed an improvement in the gray relational grade (14%) which is accompanying with improving of GRG value.
Managed pollination is a much better way of increasing productivity and essential oil content of dill seeds crop
Authors: Meena Narottam Kumar , Meena Ram Swaroop , Singh Ravindra , Verma Arvind Kumar , Choudhary Sharda , Singh Balraj , Meena Ram Dayal , Y Ravi , Meena Murlidhar 
Published: July 2022

AbstractDill seeds (Anethumgraveolens L.) is the most valuable medicinal seed spice crop of Apiaceae. It bears small yellow flowers in the form of umbels. Being a cross-pollinated crop, floral visitors play vital role in pollination and seed sets. Hence, the present study was conducted at the ICAR-National Research Centre on Seed Spices, Ajmer (Rajasthan), India to discover the pollinator’s community, foraging behaviour and abundance of most frequent pollinators and different modes of pollination on seed yield and quality of this seed spice crop. The insect visitors community of dill seeds was composed of 28 insect species belonging to 14 families of 6 orders. Most of floral visitors started their foraging activity at 8.00 h, reached peak activity between 12.00 and 14.00 h and their activity ceased at 18.00 h. Apisflorea,A.dorsata,A.mellifera, solitary bee, Halictus sp. and two unidentified species of Hymenoptera; Episyrphusbalteatus (DeGeer), Episyrphus sp., Eristalis sp and two other Musca species of Diptera were identified as potential and regular floral visitors of dill seeds. The highest seed yield of 1505.63 kg/ha was recorded in the treated plots provided with only 10% jaggery solution and was at par with the open pollination. A lower seed yield of 1432.5 kg/ha was recorded in plots pollinated only with A.mellifera inside insect cages. Open pollination with 10% jaggery solution spray increased the seed yield of dill seed crop by 57%, one-thousand seed test weight by 96% and the essential oil content by 27% over control plots. These results show that managed pollination is a much better way to enhance yields and quality of dill seed crop than other treatments including only honeybee-based pollination.
Calorie restriction has no effect on bone marrow tumour burden in a Vk*MYC transplant model of multiple myeloma
Authors: Bradey Alanah L. , Fitter Stephen , Duggan Jvaughn , Wilczek Vicki , Williams Connor M. D. , Cheney Emma AJ. , Noll Jacqueline E. , Tangseefa Pawanrat , Panagopoulos Vasilios , Zannettino Andrew C. W. 
Published: July 2022

AbstractMultiple myeloma (MM) is an incurable haematological malignancy, caused by the uncontrolled proliferation of plasma cells within the bone marrow (BM). Obesity is a known risk factor for MM, however, few studies have investigated the potential of dietary intervention to prevent MM progression. Calorie restriction (CR) is associated with many health benefits including reduced cancer incidence and progression. To investigate if CR could reduce MM progression, dietary regimes [30% CR, normal chow diet (NCD), or high fat diet (HFD)] were initiated in C57BL/6J mice. Diet-induced changes were assessed, followed by inoculation of mice with Vk*MYC MM cells (Vk14451-GFP) at 16 weeks of age. Tumour progression was monitored by serum paraprotein, and at endpoint, BM and splenic tumour burden was analysed by flow cytometry. 30% CR promoted weight loss, improved glucose tolerance, increased BM adiposity and elevated serum adiponectin compared to NCD-fed mice. Despite these metabolic changes, CR had no significant effect on serum paraprotein levels. Furthermore, endpoint analysis found that dietary changes were insufficient to affect BM tumour burden, however, HFD resulted in an average two-fold increase in splenic tumour burden. Overall, these findings suggest diet-induced BM changes may not be key drivers of MM progression in the Vk14451-GFP transplant model of myeloma.
Ym155 localizes to the mitochondria leading to mitochondria dysfunction and activation of AMPK that inhibits BMP signaling in lung cancer cells
Authors: Mondal Arindam , Jia Dongxuan , Bhatt Vrushank , Akel Moumen , Roberge Jacques , Guo Jessie Yanxiang , Langenfeld John 
Published: July 2022

AbstractThe imidazolium compound Ym155 was first reported to be a survivin inhibitor. Ym155 potently induces cell death of many types of cancer cells in preclinical studies. However, in phase II clinical trials Ym155 failed to demonstrate a significant benefit. Studies have suggested that the cytotoxic effects of Ym155 in cancer cells are not mediated by the inhibition of survivin. Understanding the mechanism by which Ym155 induces cell death would provide important insight how to improve its efficacy as a cancer therapeutic. We demonstrate a novel mechanism by which Ym155 induces cell death by localizing to the mitochondria causing mitochondrial dysfunction. Our studies suggest that Ym155 binds mitochondrial DNA leading to a decrease in oxidative phosphorylation, decrease in TCA cycle intermediates, and an increase in mitochondrial permeability. Furthermore, we show that mitochondrial stress induced by Ym155 and other mitochondrial inhibitors activates AMP-activated kinase leading to the downregulation to bone morphogenetic protein (BMP) signaling. We provide first evidence that Ym155 initiates cell death by disrupting mitochondrial function.
Exome sequencing revealed comparable frequencies of RNF43 and BRAF mutations in Middle Eastern colorectal cancer
Authors: Siraj Abdul Khalid , Bu Rong , Masoodi Tariq , Parvathareddy Sandeep Kumar , Iqbal Kaleem , Al-Haqawi Wael , Al-Dossari Hassan , Azam Saud , Qadri Zeeshan , Annaiyappanaidu Padmanaban , Al-Dayel Fouad , Al-Kuraya Khawla Sami 
Published: July 2022

AbstractMutation-induced activation of Wnt-β Catenin signaling pathway is frequent in CRC. The E3 ubiquitin ligase, RNF43, has been reported to negatively regulate the Wnt signaling pathway and RNF43 mutations are frequently seen in CRC. However, its role in Middle Eastern CRC remains unclear. Therefore, we employed Exome and Sanger sequencing technology to assess the frequency of RNF43 mutations and its association with other clinico-pathological features in Middle Eastern CRC. RNF43 mutations were found in 5.9% (13/220) of CRC cases and was inversely correlated to APC and TP53 mutations. A strong association of RNF43 mutations with right sided and sporadic microsatellite instable (MSI) CRC was observed. No association was identified between RNF43 mutation and other clinico-pathological features including BRAF mutation, age, tumor histological subtype, tumor grade or patients’ prognosis. Multivariate logistic regression analysis revealed that MSI status and wild type APC were independent predictor of RNF43 mutation. We conclude that RNF43 mutations occur in Middle Eastern CRC at comparable frequencies with BRAF mutations and represent a distinct molecular subtype which further enhances our understanding of how different mutational subsets of Wnt tumor suppressor genes link to distinct tumor characteristics, which might be considered for treatment strategies for CRC patients.