bluuebunny/crossref_metadata_2025_split huggingface dataset:
KnotAli: Informed Energy Minimization Through the Use of Evolutionary Information
Authors: Gray Mateo , Chester Sean , Jabbari Hosna 
Published: September 2021

Abstract
BackgroundImproving the prediction of structures, especially those containing pseudoknots (structures with crossing base pairs) is an ongoing challenge. Homology-based methods utilize structural similarities within a family to predict the structure. However, their prediction is limited to the consensus structure, and the quality of the alignment. Minimum free energy (MFE) based methods, on the other hand, do not rely on familial information and can predict structures of novel RNA molecules. Their prediction normally suffers from inaccuracies due to their underlying energy parameters. ResultsWe present a new method for prediction of RNA pseudoknotted secondary structures that combines the strengths of MFE prediction and alignment-based methods. KnotAli takes a multiple RNA sequence alignment and uses covariation and thermodynamic energy minimization to predict secondary structures for each individual sequence in the alignment. We compared KnotAli’s performance to that of three other alignment-based programs, on a large data set of 10 families with pseudoknotted and pseudoknot-free reference structures. We produced sequence alignments for each family using two well-known sequence aligners (MUSCLE and MAFFT). We found KnotAli to be superior in 6 of the 10 families for MUSCLE and 7 of the 10 for MAFFT. ConclusionsWe find KnotAli’s predictions to be less dependent on alignment quality. In particular, KnotAli is shown to have more accurate predictions compared to other leading methods as alignment quality deteriorates. KnotAli can be found online on github at https://github.com/mateog4712/KnotAli
Enhanced Cellulase Production by Talaromyces Amestolkiae CMIAT055 using Banana Pseudostem
Authors: Faheina Genilton S , Sousa Kally A , Zilli Jerri E , Vergara Carlos , Pinto Gustavo A. Saavedra , de Santiago-Aguiar Rilvia Saraiva 
Published: September 2021

Abstract
Cellulases are a complex of enzymes necessary for the complete solubilization of cellulose in sugars, thus playing a key role in the natural carbon cycle through the hydrolysis of lignocellulosic structures. The aim of this study was to evaluate the increase in the capacity of Talaromyces amestolkiae CMIAT 055 to produce cellulases by optimizing the components of the culture medium containing banana pseudostem as an inducer, as well as in different agitation configurations in a bioreactor. Optimization was performed through statistical experimental design (Plackett-Burman and DCCR), a study of pH control in bioreactors, and a study of the agitation system by comparing impellers with different flow profiles in the liquid medium. For this purpose, a wild strain of Talaromyces amestolkiae CMIAT 055 was used. In the Plackett-Burman and DCCR statistical design, four components of the culture medium were significant and optimized for greater synthesis of FPase: banana pseudostem, CaCl2, KH2PO4, and urea. In bioreactors tests, these parameters were beneficial for greater enzyme activities: maintenance of pH at 5.0, use of Pitched blade impeller, and rotation speed at 300 rpm. Comparing the first test using banana pseudostem in an Erlenmeyer flask to the last fermentation process in bioreactors, it was observed that the total cellulase activity increased from 424.7 FPU/L to 2172.8 FPU/L. This fact showed that the strategies adopted in this study are a pertinent way to reduce the cost of enzyme production through the use of lignocellulosic materials.
Do the prices of a preventive animal health product affect dairy farmers’ willingness to pay and product use? Evidence from an experimental study
Authors: Cariappa A G , Chandel Balwant , Sendhil R , Dixit Anil , Sankhala Gopal , Mani Veena , Meena Brajendra 
Published: September 2021

Abstract

Should we distribute preventive animal health products for free or charge a positive price? The decision depends on the price sensitivity of the product and the effect prices have on product use. We explore this idea through a field experiment in which we randomize the price a farmer faces for an animal health product. We find that the demand for the product is highly sensitive to prices; willingness to pay (WTP) decreased from 44% at ₹ 100 to 18% at ₹ 500. Further, among farmers who were willing to pay, the product usage rate was 71% and usage did not increase in prices (lack of screening effect). Furthermore, we find that farmers whose animals were sick in the baseline had a higher WTP. These findings support the human capital model relating to demand for human health products. We argue that individuals behave in a similar way when the decisions concern their own health or the health of an animal they rear for commercial purposes. A highly subsidized distribution of the product is recommended due to high price sensitivity, lack of screening effect, equitable distribution among poor and lesser implementation costs found in this study.
Sustainability Analysis of Improvement of Contaminated Clayey Soil Using Lime Piles Technique
Authors: Karkush Mahdi O. , Kareem Mahmoud S. Abdul , Babu Sivakumar 
Published: September 2021

Abstract
This study aims to use the concept of sustainability and provide guidance to geotechnical engineers to contribute towards greater sustainability in geotechnical design and construction. The methodology of the sustainability framework aims to support indicators and tools used in the sustainability concept in geotechnical engineering. In addition, available indicators will be used to analyze the role of natural resources, social impacts, environmental and economic aspects. In order to demonstrate the sustainability assessment approach, a case study is evaluated using the methodology of sustainability framework by using Multi-Criteria Analysis (MCA). The assessment is studied for raft footing and deep foundations (driven and bored piles A foundation treatment of 15×15 m and 0.45 m thickness to carry a high static load or to carry cyclic loading is analyzed. The results indicate the calculations of sustainability indices from the multicriteria analysis show that the option of raft footing than deep foundation if raft provides adequate allowable load by improving the soil using lime piles technique is sustainable.
Do Adsorbent Pore Size and Specific Surface Area Affect The Kinetics of Methyl Orange Aqueous Phase Adsorption?
Authors: IWUOZOR KINGSLEY OGEMDI , Ighalo Joshua O. , Emenike Ebuka Chizitere , Igwegbe Chinenye Adaobi , Adeniyi Adewale George 
Published: September 2021

Abstract
The kinetics of any adsorption reaction gives more information on the rate at which the adsorbate is taken up by the adsorbent, which is responsible for the residence time of an adsorbate uptake at the adsorbent-aqueous phase interface. This study was aimed at determining the effect of pore size as well as specific surface area (SSA) on the kinetics of the uptake of methyl orange (MO). The basis of the analysis was from data on kinetic models sourced from recent literature. ANOVA of the data revealed that statistical significance was achieved for SSA but not for pore size (at a significance level of 0.05). This called for a more theoretical perspective on the research data. The kinetics constant for micropores is far higher than for the two selected regimes of the mesopore. For the SSA, 100–10 m2/g adsorbents had a higher mean k2 value. This suggested that adsorbents in the SSA range had pore sizes that favour rapid uptake. However, further studies will be needed to gain a better understanding of how SSA affects adsorption kinetics. The study also discussed the technical limitations that could arise due to the use of kinetic model linearisation.
Attitudes Toward End-Of-Life Decisions Other Than Assisted Death Amongst Doctors in Northern Portugal
Authors: Gonçalves José António Ferraz 
Published: September 2021

Abstract
Background

Doctors often deal with end-of-life issues other than assisted death, such as incompetent patients and treatment withdrawal, including food and fluids.
Methods

A link to a questionnaire was sent by email three times, at intervals of one week, to the doctors registered in the Northern Section of the Portuguese Medical Association.
Results

The questionnaire was returned by 1148 (9%) physicians. This study shows that only a minority of Portuguese doctors were willing to give one or more drugs in lethal doses to cognitively incompetent patients with an incurable, advanced, and progressive disease at the request of a family member or other close person, and even less would do it on their own initiative. Concerning the withdrawal of support of life measures in advanced and progressive diseases at the patient’s request, most doctors were in favor, but much fewer doctors agreed with the suspension of supportive life measures at the request of a family member, another close person, or by their own unilateral decision. However, concerning the suspension of food and fluids, fewer agreed with that action. Portuguese doctors favor the administration of drugs for suffering control, even foreseeing they could shorten life,
Conclusion

Most doctors in this study respect patients’ autonomy, but do not agree with measures decided by others that have an impact on patients’ survival. They also agree with the administration of drugs for suffering control, even considering the possibility of shortening life.
Obesity is Not Associated with Perioperative Adverse Events in Patients Undergoing Complex Revision Surgery for the Thoracolumbar Spine
Authors: Hirase Takashi , Ling Jeremiah F. , Haghshenas Varan ,   Richard Fuld 3rd, Dong David , Hanson Darrell S. , Meyer B. Christoph , Marco Rex A.W. 
Published: September 2021

Abstract

Study Design: Retrospective cohort studyObjective: This study sought to determine the relationship between obesity and perioperative adverse events (AEs) with patients undergoing complex revision thoracolumbar spine surgery while controlling for psoas muscle index (PMI) as a confounding variable.Methods: Between May 2016 and February 2020, a retrospective analysis of individuals undergoing complex revision surgery of the thoracolumbar spine was performed at a single institution. Obesity was defined as BMI ≥ 30.0 kg/m2. PMI < 500 mm2/m2 for males and < 412 mm2/m2 for females were used to define sarcopenia. A Spine Surgical Invasiveness Index (SSII) > 10 was used to define complex revision surgery. A multivariable logistic regression model was used to ascertain the effects of sarcopenia, obesity, age, and gender on the likelihood of the occurrence of any AE.Results: The study included 114 patients. 54 patients were in the obese cohort and 60 patients in the non-obese cohort. There was not a significant difference in perioperative outcomes of both the obese and non-obese patients. Multivariable analysis demonstrated that sarcopenic individuals had a significantly higher likelihood for an AE than non-sarcopenic individuals (OR: 7.53, 95% CI: 3.05-18.60). Obesity did not have a significant effect in predicting AEs.Conclusions: Obesity is not associated with perioperative AEs, 30-day readmission rates, 30-day re-operation rates, rate of discharge to a facility, or post-operative length of stay (LOS) among patients undergoing complex revision thoracolumbar spine surgery.Level of Evidence: III
Current Tobacco Use and Susceptibility To Using Tobacco Among Non-Users of Tobacco: A Cross-Sectional Study Among School-Going Adolescents in Sierra Leone
Authors: James Peter Bai , Kabba John Alimamy , Bah Abdulai Jawo , Idriss Ayesha , Kitchen Chenai , Conteh Eugene B , Lahai Michael , Dalinjong Philip Ayizem 
Published: September 2021

Abstract
Background
Tobacco use is a global health threat associated with a high disease burden and deaths. Studies concerning current tobacco use and susceptibility to using tobacco products among adolescents who are potential adult tobacco users in Sierra Leone have not been explored. We aimed to estimate the prevalence and correlates of current tobacco use and tobacco non-users susceptibility to using tobacco amongst Sierra Leonean high-school students.
Method
We used data obtained from the 2017 Sierra Leone Global Youth Tobacco Survey (GYTS), which presented information collected from 6680 students aged 11-17years nationwide. Gender-based correlates of current use and susceptibility to using tobacco among non-tobacco users were determined by complex sample logistic regression analyses. Adjusted odds ratios (AOR) and respective 95% confidence intervals (CIs) were reported. p-values less than 0.005 were considered significant.
Results
The prevalence of current tobacco use among high school adolescents in Sierra Leone was 10.7% and was higher in males (12.2%) than in females (7.4%). Male [AOR = 1.32 (95%CI:1.01–1.72)], exposure to household secondhand smoke [AOR = 2.68(95%CI:1.71–4.20)], having peers who smoke [AOR = 3.07(1.53–6.16)] were more likely to be currently using tobacco. On the other hand, adolescents exposed to antismoking media messages were less likely to be current tobacco users [AOR = 0.45(95%CI: 0.24–0.83)]. The overall tobacco non-users susceptibility to using tobacco among adolescents in Sierra Leone was 18.2% [male (18.0%), female (18.5%)]. Exposure to tobacco promotion [AOR = 1.50(95%CI:1.07–2.11)] and non-exposure to antismoking education [AOR = 1.39(95%CI:1.04–1.85)] were significantly associated with tobacco non-users’ susceptibility to using tobacco.
Conclusion
Our study suggests that one-in-ten school-going adolescents currently use tobacco, with nearly one in five non-users susceptible to using tobacco. Given the high prevalence of tobacco product use among Sierra Leonean adults, our findings highlight the need for policies and interventions to prevent tobacco use behaviour among adolescents aimed at averting tobacco use in adulthood.
Valorization of Fig (Ficus carica Linn.) Waste Leaves: HPLC-QTOF-MS/MS-DPPH System For Online Screening And Identification of Antioxidant Compounds
Authors: Li Chunying , Yu Meiting , Li Shen , Yang Xue , Qiao Bin , Shi Sen , Zhao Chunjian , Fu Yujie 
Published: September 2021

Abstract
Fig (Ficus carica Linn.) leaves are produced each year and often thrown away as wastes, resulting in a waste of resources. Fig waste leaves are rich in flavonoids, which have strong antioxidant activity, however, the antioxidant components are not clear. So as to take full advantage of fig waste leaves, antioxidant capacity of different extracts (petroleum ether, ethyl acetate and water) was evaluated by 1, 1-diphenyl-2-picrylhydrazyl (DPPH), 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic) acid (ABTS) and ferric-ion reducing antioxidant power (FRAP) methods. The results showed that flavonoids in ethyl acetate extraction had the highest content, 83.92 ± 0.01 mg/g, and maximum DPPH scavenging activity (IC50 0.54 mg/mL), highest ABTS scavenging rate (80.28%), FRAP (3.46 mmol/g). Furthermore, HPLC-QTOF-MS/MS-DPPH method was developed for the first time to identify 11 flavonoids in fig waste leaves. This rapid and efficient method can not only be used for screening the antioxidant components in fig waste leaves, but also can be combined with mass spectrometry to identify the compounds with antioxidant capacity. There are three flavonoids with significant antioxidant capacity, which are 3-O-(rhamnopyranosyl-glucopyranosyl)-7-O-(glucopyranosyl)-quercetin, isoschaftoside and rutin. The results confirmed that fig waste leaves contain a variety of antioxidant components, which contributed to increase the value of fig waste leaves as antioxidants.
Study on the Mechanism of Lactobacillus Rhamnosus Probio-M9 Combined With Antibiotics on Staphylococcus Aureus Mastitis in Rat
Authors: Bo Xu Rui , Zhang Heping 
Published: September 2021

Abstract
This study aims to investigate the potential anti-inflammatory mechanism of Lactobacillus rhamnosus Probio-M9 (Probio-M9) combined with antibiotics. Probio-M9, a probiotic strain previously isolated from the milk of healthy women. The Illumina Hiseq platform performs metagenomic sequencing on faeces samples at various time points; UPLC-Q-TOF/MS is used to detect a large number of endogenous metabolites in the serum of rats with mastitis induced by Staphylococcus aureus. The results show that the Probio-M9 combined with antibiotics increases beneficial intestinal bacteria (Lactobacillus murinus, Lactobacillus reuteri) and positively regulates metabolites (linoleic acid, glycerophospholipids, arachidonic acid, Sphingolipids. etc.), reduce inflammation in the body to play a protective role against mastitis. This research provides a new research method to relieve mastitis, and also provides a theoretical basis for the development and utilization of Probio-M9.
Screening and Purification of NanB Sialidase from Pasteurella Multocida with Activity in Hydrolyzing Sialic Acid Neu5Acα(2-6)Gal
Authors: Nugroho Christian Marco Hadi , Kurnia Ryan Septa , Tarigan Simson , Silaen Otto Sahat Martua , Widyaningtyas Silvia Tri , Wibawan I Wayan Teguh , Natalia Lily , Soebandrio Amin 
Published: September 2021

Abstract
Study on sialidases as antiviral agents has been widely performed, but many types of sialidase had not been tested for their antiviral activity. One of such sialidase is the NanB sialidase of Pasteurella multocida, which has never been isolated for further study. In this study, the activity of NanB sialidase was investigated in silico by docking the NanB sialidase of Pasteurella multocida to the Neu5Acα(2-6)Gal ligand. Additionally, some local isolates of Pasteurella multocida, which had the NanB gene were screened, and the proteins were isolated for further testing regarding their activity in hydrolyzing Neu5Acα(2-6)Gal. In silico studies showed that the NanB sialidase possesses an exceptional affinity towards forming a protein-ligand complex with Neu5Acα(2-6)Gal. This was further confirmed by showing that a dose of 0.258 U/ml (100%) NanB sialidase of Pasteurella multocida B018 can hydrolyze up to 44.28% of Neu5Acα(2-6)Gal in chicken red blood cells and 81.95% in rabbit red blood cells. This study suggested that the NanB sialidase of Pasteurella multocida B018 has a potent antiviral activity that can inhibit avian influenza virus infection.
Estimating the Two Graph Dextran-Stearic Acid-Spermine Polymers Based on Iron Oxide Nanoparticles as Carrier for Gene Delivery
Authors: Ashtiyani Mehrnoosh Kazemi , Hajipour-Verdom Behnam , Satari Mohammad , Abdolmaleki Parviz , Hosseinkhani Saman , Shaki Hossein 
Published: September 2021

Abstract
BackgroundNon-viral gene carriers because of their limited side effects, biocompatibility, simplicity and taking the advantages of electrostatic interactions have shown noticeable potential in gene delivery. The low transfection rate of non-viral vectors under physiological conditions is a significant issue. MethodsWe investigated the efficacy of hydrophilic and hydrophobic groups on gene carriers such as two synthesized amphiphilic polymer of dextran-stearic acid-spermine (DSASP) with verified lipid and amine conjugations that associated with Fe3O4 superparamagnetic nanoparticles to promote the target delivery and decrease the transfection time using static magnetic field.ResultsOur findings illustrate that magnetic nanoparticles are spherical with positive surface charges and superparamagnetic behaviors. The DSASP–pDNA/MNPs offered a strong pDNA condensation, protection against DNase degradation, significant cell viability in HEK 293T cells. Although conjugations of spermine play a critical role in transfection efficiency, amphiphilic polymer with more derivatives of stearic acid showed better transfection yields. ConclusionDSASP amphiphilic magnetic carriers offer new insights for gene delivery due to the amine contents and ameliorate the uptake of complexes via cell membrane based on its hydrophilic surface.
hsa-miR-124-3p: A New Potential Prognostic Target For Multiple Myeloma
Authors: Gong Hui , Kang Chunxiang , Du Fang , Zhou Shengtang 
Published: September 2021

Abstract
The relationship of Exosomal RNAs released within the bone marrow microenvironment and Prognosis of patients with multiple myeloma has not been thoroughly studied. This study aims to evaluate which exosomal RNAs can prompt the prognosis of patients with multiple myeloma. Exosomes were isolated from the bone marrow fluid of patients with good treatment effect or not. Then they were characterized by dynamic light scattering, transmission electron microscopy, and Western blot analysis. The isolated exosomes stimulate PRMI8226 cells, observe the migration ability and proliferation ability of PRMI8226 cells. Then we performed exosome miRNA sequencing, performed bioinformatics analysis of differential miRNAs, and evaluated several miRNAs that may affect the treatment effect. To determine the actual value of these miRNAs in clinical applications, we collected a collection of clinical samples for verification. We found that bone marrow-derived exosomes from patients with different therapeutic effects have different effects on PRMI8226 cells. Exosomes with a poor prognosis can promote the proliferation and migration of PRMI8226 cells, while exosomes with a good prognosis have no impact on PRMI8226 cells. The miRNA sequencing results showed differentially expressed miRNAs in exosomes from different sources. These differential miRNAs can be enriched in pathways related to cancer development. Validation in clinical specimens found that exosomal mir-124-3p are highly expressed in patients with poor therapeutic effects. This study suggested exosomal miRNA plays a vital role in the development and treatment of multiple myeloma. Some miRNAs that can promote tumor progression are highly expressed in bone marrow exosomes of patients with poor therapeutic effects, such as hsa-miR-124-3p, hsa-miR-451b, hsa-miR-509-3p. Among them, hsa-miR-124-3 is promising as a predictor of therapeutic effect.
Immunogenomic Analyses of the Prognostic Predictive Model for Patients with Renal Cancer
Authors: Feng Tao , Zhao Jiahui , Wei Dechao , Guo Pengju , Yang Xiaobing , Li Qiankun , Fang Zhou , Wei Ziheng , Li Mingchuan , Jiang Yongguang , Luo Yong 
Published: September 2021

Abstract
Background: Renal cell carcinoma (RCC) is associated with poor prognostic outcomes. The current stratifying system does not predict prognostic outcomes and therapeutic benefits precisely for RCC patients.Methods: Herein, an immune prognostic signature was developed, and its predictive ability was confirmed in the cohorts based on TCGA-KIRC dataset. Several immunogenomic analyses were conducted to investigate the correlations between immune risk scores and immune cell infiltrations, immune checkpoints, cancer genotypes, tumor mutational burden, and responses to chemotherapy and immunotherapy.Results: The immune prognostic signature contained 14 immune-associated genes and was found to be an independent prognostic factor for KIRC. Furthermore, the immune risk score was established as a novel marker for predicting the overall survival outcomes for RCC. The risk score was correlated with some significant immunophenotypic factors, including T cell infiltration, antitumor immunity, antitumor response, oncogenic pathways, and immunotherapeutic and chemotherapeutic response.Conclusions: The immune prognostic, predictive model can be effectively and efficiently used in the prediction of survival outcomes and immunotherapeutic responses of RCC patients.