cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Molecular dynamic simulation and DFT study on the Drug-DNA interaction; Crocetin as an anti-cancer and DNA nanostructure model
Creators: name: Azarhazin, Ebrahim
name: Izadyar, Mohammad
name: Housaindokht, Mohammad Reza
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: Hematology

description: In this research, the interaction of Crocetin as an anti-cancer drug and a Dickerson DNA has been investigated. 25 ns molecular dynamic simulations of Crocetin and DNA composed of 12 base pairs and a sequence of d(CGCGAATTCGCG)2 were done in water. Three definite parts of the B-DNA were considered in analyzing the best interactive site from the thermodynamic point of view. Binding energy analysis showed that van der Waals interaction is the most important part related to the reciprocal O and H atoms of the Crocetin and DNA. Stabilizing interactions, obtained by ΔG calculations, showed that maximum and minimum interactions are related to the S1 and S3 regions, respectively. This means that the most probable van der Waals interaction site of the Dickerson B-DNA and Crocetin is located in the minor groove of DNA. Two sharp peaks at 2.55 and 1.75 Å in radial distribution functions of the PO⋯HO and NH⋯OC parts are related to new hydrogen bonds between the Crocetin and DNA in the complex which can be considered as the driving force of the anti-cancer mechanism of the Crocetin. Average values of 0.3 au and zero for the electron densities of the H⋯O bonds for DNA and complex, obtained by Quantum theory of atoms in molecules (QTAIM), means that the origin of DNA instability after complexation may be related to the H-bond denaturation by Crocetin. Finally, the evaluation of the dispersion interactions using the dispersion functional, -148.76 kcal.mol−1, confirmed the importance of the dispersion interaction in drug-DNA complex.
Laboratory and pilot-scale field experiments for application of iron oxide nanoparticle-loaded chitosan composites to phosphate removal from natural water
Creators: name: Kim, Jae-Hyun
name: Song-Bae Kim
name: Sang-Hyup Lee
name: Choi, Jae-Woo
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Plant Biology

description: The aim of this study was to apply iron oxide nanoparticle-chitosan (ION-chitosan) composites to phosphate removal from natural water collected from the Seoho Stream in Suwon, Republic of Korea. Laboratory batch experiments showed that phosphate removal by the ION-chitosan composites was not sensitive to pH changes between pH values of 5.0 and 9.0. During six cycles of adsorption–desorption, the composites could be successfully regenerated with 5 mM NaOH solution and reused for phosphate removal. Laboratory fixed-bed column experiments (column height = 10 and 20 cm, inner diameter = 2.5 cm, flow rate = 8.18 and 16.36 mL/min) demonstrated that the composites could be successfully applied for phosphate removal under dynamic flow conditions. A pilot-scale field experiment was performed in a pilot plant, which was mainly composed of chemical reactor/dissolved air flotation and an adsorption tower, built nearby the Seoho Stream. The natural water was pumped from the Seoho Stream into the pilot plant, passed through the chemical reactor/dissolved air flotation process, and then introduced into the adsorption tower (height = 100 cm, inner diameter = 45 cm, flow rate = 7.05 ± 0.18 L/min) for phosphate removal via the composites (composite volume = 80 L, composite weight = 85.74 kg). During monitoring of the adsorption tower (33 days), the influent total phosphorus (T-P) concentration was in the range of 0.020–0.046 mgP/L, whereas the effluent T-P concentration was in the range of 0.010–0.028 mgP/L. The percent removal of T-P in the adsorption tower was 52.3% with a phosphate removal capacity of 0.059 mgP/g.
Inhibitory potential of strepthonium A against Shiga toxin production in enterohemorrhagic Escherichia coli (EHEC) strain EDL933
Creators: name: Cheng, Cheng
name: Balasubramanian, Srikkanth
name: Fekete, Agnes
name: Krischke, Markus
name: J. Mueller, Martin
name: Hentschel, Ute
name: A. Oelschlaeger, Tobias
name: Ramadan Abdelmohsen, Usama
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: The production of shiga toxin (Stx) is a critical step in the establishment and progress of enterohemorrhagic Escherichia coli (EHEC) infections. The possible release of Stx from dead and dying bacteria, and the risk of resistance development have restricted the usage of antibiotics against EHEC. The chlorinated quaternary ammonium compound, strepthonium A, was isolated from the culture of Streptomyces sp. SBT345 that was cultivated from the Mediterranean sponge Agelas oroides. The structure was elucidated and confirmed by spectroscopic analyses including 1D and 2D NMR, ESI-HRMS, as well as ESI-HRMS2. Strepthonium A follows Lipinski’s rule of five with respect to its molecular weight, CLogP values and the number of hydrogen acceptors and donors. Verotoxin ELISA assay demonstrated that Strepthonium A reduced the Stx production in EHEC strain EDL933 at 80 μM concentration without growth inhibition. This study demonstrates the potential of strepthonium A in restraining the production of Stx in EHEC infections.
An efficient semi-synthesis of 1-hydroxyl oleanolic acid analogs
Creators: name: Zhang, Da-Hui
name: Wei-Shuo Fang
name: Wang, Shao-Rong
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: An efficient route for the semi-synthesis of either 1α- or 1β-OH epimers of 1-hydroxy-3-deoxyolean-12-en-28-oic acid (1), 6–8 steps from oleanolic acid is reported. The synthesis involves stereoselective formation of α,β-unsaturated epoxy ketone and subsequent Wharton reaction as key steps, offering a new access to the 1-O-substituted oleanolic acid-type pentacyclic triterpenoids.
Antioxidant and anti-osteoporotic effects of anthraquinones and related constituents from the aqueous dissolved Aloe exudates
Creators: name: Sun, Ya Nan
name: Li, Wei
name: Lee, Sang Hyun
name: Jang, Hae Dong
name: Yeul Ma, Jin
name: Kim, Young Ho
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified

description: In this study, 25 known anthraquinones and related compounds were isolated from aqueous dissolved Aloe exudates. The antioxidant and anti-osteoporotic activities of the isolated compounds were then investigated. Compounds 8, 11, 20, and 23 showed good antioxidant activity based on peroxyl radical-scavenging and reducing capacity assays at a concentration of 10.0 μM. Additionally, compounds 7, 9, 15–16, 18, 21–22 and 24–25 showed potent peroxyl radical-scavenging activities with values ranging from 5.28 to 14.60 at 10.0 μM. Moreover, compounds 8, 11, 15, 20 and 22 exhibited significantly suppressed tartrate-resistant acid phosphatase (TRAP) activity in nuclear factor-κB ligand-activated osteoclastic RAW 264.7 cells, with values of 125.67, 118.54, 127.64, 125.82 and 124.98%, respectively. These results indicate that Aloe is an excellent source of antioxidant and anti-osteoporotic phytochemicals.
Structure revision of aspergicin by the crystal structure of aspergicine, a co-occurring isomer produced by co-culture of two mangrove epiphytic fungi
Creators: name: Zhu, Feng
name: Li, Jie-sen
name: Xie, Wu-cheng
name: Shi, Jun-jun
name: Xu, Feng
name: Song, Zhao-feng
name: Liu, Yi-lu
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Hematology
subject: Plant Biology

description: The structure of aspergicin (1), an antibacterial alkaloid produced by co-culture of two marine-derived mangrove epiphytic fungi, were revised by the co-occurring isomer named as aspergicine (2), whose structure was determined on the basis of spectroscopic analysis and X-ray crystallography.
Evaluation of two promising genes from the target region of SSC13 with susceptibility towards the ETEC F4ac adhesion in pigs
Creators: name: Liu, Yang
name: Hu, Zhengzheng
name: Yang, Chen
name: Wang, Lina
name: Wang, Shiwei
name: Wang, Wenwen
name: Zhang, Qin
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Virology
subject: Computational Biology

description: Enterotoxigenic Escherichia coli (ETEC) expressing F4 fimbria is the major pathogenic bacteria causing diarrhoea in neonatal and post-weaned piglets. Based on our previous GWAS results from 301 pigs in a two generation family-based population, two promising candidate genes (HEG1 and ITGB5) from a 0.65 Mb region on pig chromosome 13 for susceptibility to ETEC F4ac infection were investigated for the presence of possible causative mutations. A total of 23 polymorphisms in their coding regions were identified, and two previous uppermost GWAS significant SNPs (ALGA0072075; GenBank NC_010455.4:g.145009857 A > G) were also chosen for genotyping in the three pig breeds. The genotyping data and association analysis results showed that a C to T polymorphism in exon7, and a G to T polymorphism in exon14 of the HEG1 gene significant increased the effects on the ETEC F4ac adhesion traits (p = 2.853E − 11; p = 1.410E − 09). Although the identified polymorphisms were not causal mutations, these results indicate that the HEG1 gene is an important adhesion molecule, and it could serve as a genetic marker for selecting ETEC F4ac-resistant pigs in breeding programmes.
Acetylation targets HSD17B4 for degradation via the CMA pathway in response to estrone
Creators: name: Zhang, Ye
name: Xu, Ying-Ying
name: Yao, Chuan-Bo
name: Li, Jin-Tao
name: Zhao, Xiang-Ning
name: Yang, Hong-Bin
name: Zhang, Min
name: Yin, Miao
name: Chen, Jing
name: Lei, Qun-Ying
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy
subject: Plant Biology

description: Dysregulation of hormone metabolism is implicated in human breast cancer. 17β-hydroxysteroid dehydrogenase type 4 (HSD17B4) catalyzes the conversion of estradiol (E2) to estrone (E1), and is associated with the pathogenesis and development of various cancers. Here we show that E1 upregulates HSD17B4 acetylation at lysine 669 (K669) and thereby promotes HSD17B4 degradation via chaperone-mediated autophagy (CMA), while a single mutation at K669 reverses the degradation and confers migratory and invasive properties to MCF7 cells upon E1 treatment. CREBBP and SIRT3 dynamically control K669 acetylation level of HSD17B4 in response to E1. More importantly, K669 acetylation is inversely correlated with HSD17B4 in human breast cancer tissues. Our study reveals a crosstalk between acetylation and CMA degradation in HSD17B4 regulation, and a critical role of the regulation in the malignant progression of breast cancer.
MOSES concept and innovations: Indicators of success and ambition
Creators: name: Prof. Nikolaos Ventikos
Publisher: name: Zenodo
Year: 2022

description: NOVIMOVE Joint EU Smart Shipping & Logistics Platform meeting took place on the 6th of April 2022, as an online meeting (MS Teams), between 13.00h – 15.00h. The meeting started with a Tour de Table per project (PLATINA3, ENTRANCE, BOOSTLOG, IW-NET, AUTOSHIP, AEGIS, Current Direct, ST4W, NOVIMOVE) and, then, it was followed by three presentations from MOSES, AUTOBarge, and LASTING project. Finally, the meeting concluded with discussions on the identification of relevant opportunities for joint activities between the participated projects. MOSES was represented by its coordinator Prof Nikolaos Ventikos, who made a presentation on ‘MOSES concept and innovations: Indicators of success and ambition‘.
Asymptotic distributions in affiliation networks with an increasing sequence
Creators: name: Luo, Jing
name: Qin, Hong
name: Hu, Jianwei
name: Zhang, Yong
Publisher: name: Taylor & Francis
Year: 2017
Subjects: Medicine
Cell Biology
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Mathematical Sciences not elsewhere classified
Science Policy

description: A central limit theorem for a linear combination of all the maximum likelihood estimators with an increasing dimension for affiliation networks has been established. Simulation studies are provided to illustrate the asymptotic results.
Diet-dependent immunohistochemical evaluation of connexin 43 in the sheep rumen
Creators: name: Ahmed, Rasha S.
name: Martens, Holger
name: Muelling, Christoph
Publisher: name: Freie Universität Berlin
Year: 2016
Subjects: subject: sheep
subject: rumen
subject: connexin 43
subject: feed
subject: immunohistochemistry
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::616 Krankheiten
subject: 500 Naturwissenschaften und Mathematik::590 Tiere (Zoologie)::590 Tiere (Zoologie)

description: The objective of this study was to characterize the immunohistochemical localization of plasma membrane connexin 43 in the rumen of sheep after changing the diet from hay (ad libitum) to a mixed hay/concentrate diet. A total of 24 sheep were fed mixed hay/concentrate for different periods ranging from 0 weeks (control; hay ad libitum) to 12 weeks (1-1.5 kg hay plus 780 g concentrate per day in two equal portions). Using immunohistochemical technique the present study confirmed the existence of plasma membrane connexin 43 in the sheep rumen epithelium. Plasma membrane connexin 43 immunostaining was most intense at the stratum basale and stratum spinosum (suprabasal layer) and decreased iron intensity through stratum spinosum (superficial layers) to stratum granulosum. Meanwhile, stratum corneum was negative. The reaction around the cells gave a syncitial appearance with more apical-immunostaining concentration. Moreover, the present study confirmed a significant effect of concentrate diet on the immunoreactivity of plasma membrane connexin 43 in the rumen of sheep. A very strong degree of antibody reaction was seen in 4 to 12 weeks concentrate-fed groups.
A new fluorescence chemosensor based on benzothiazole derivative for Zn2+ and its logic gate behavior
Creators: name: Hu, Jing-Han
name: Qi, Jing
name: Sun, You
name: Pei, Peng-Xiang
Publisher: name: Taylor & Francis
Year: 2017
Subjects: Biochemistry
Space Science
Neuroscience
Biotechnology
Chemical Sciences not elsewhere classified

description: A novel benzothiazole derivative J as a fluorescent chemosensor for Zn2+ has been designed and synthesized. The chemosensor J exhibits high selectivity and sensitivity to Zn2+ as fluorescence “turn-on” behavior, which the other cations do not make sense. The detection limit calculated by fluorescence titration method was 1.64 × 10−8 M. Furthermore, the generated J-Zn2+ ensemble could recover the enhanced fluorescence upon the addition of EDTA generating an “on-off-on” recycle. In addition, the test strip based on J was fabricated, which could act as a convenient and efficient Zn2+ test kit.
Artepillin C, is it a good marker for quality control of Brazilian green propolis?
Creators: name: Zhang, Cui-ping
name: Shen, Xiao-ge
name: Chen, Jia-wei
name: Jiang, Xia-sen
name: Wang, Kai
name: Hu, Fu-liang
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Medicine
subject: Cell Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy

description: As commercialisation of Brazilian green propolis is going on, quality evaluation and authenticity are important. The result demonstrated that artepillin C found by far in Brazilian green propolis by HPLC-ESI-MS/MS analysis, while a small interferent may be mistaken as artepillin C in some propolis from China. A new HPLC quality control method as artepillin C for marker was developed, which is the primary assessment criteria for quality control of Brazilian green propolis.
Removal of five fluoroquinolone antibiotics during broiler manure composting
Creators: name: Yang, Bing
name: Meng, Lei
name: Xue, Nandong
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Virology

description: Composting is a cost-effective approach for the removal of antibiotics from the environment; however, the consequence of this approach on fluoroquinolone antibiotics is limited. The fate of five representative fluoroquinolone antibiotics, namely ciprofloxacin, enrofloxacin, lomefloxacin, norfloxacin, and sarafloxacin, was investigated in a pilot-scale composting of broiler manure over 42 days. The effect of antibiotic concentrations (at a dose of 15, 30, or 60 mg/kg for each and a control without antibiotic addition) on the composting process was also assessed. The 42-day composting showed 45.3–75.4% of antibiotic removal with species-specific patterns. However, the observed variations in such removal among both antibiotics concentrations and composting times were not significant in most cases, possibly indicating a slight side-effect of the tested antibiotic concentrations on the composting process. To the best of our knowledge, this study is among few studies with a focus on the persistence of fluoroquinolone antibiotics during a pilot-scale composting, which warrants further study in regards to the mechanism underlying the removal of these compounds during composting.
Dethreading of a Photoactive Azobenzene-Containing Molecular Axle from a Crown Ether Ring
Creators: name: Tabacchi, Gloria
name: Silvi, Serena
name: Venturi, Margherita
name: Credi, Alberto
name: Fois, Ettore
Publisher: name: figshare
Year: 2017
Subjects: subject: Computational Chemistry
subject: 30302 Nanochemistry and Supramolecular Chemistry
subject: FOS: Chemical sciences
subject: 30304 Physical Chemistry of Materials
subject: 30699 Physical Chemistry not elsewhere classified
subject: 30701 Quantum Chemistry
subject: Supramolecular Chemistry
subject: 30799 Theoretical and Computational Chemistry not elsewhere classified
subject: 100704 Nanoelectromechanical Systems
subject: FOS: Nanotechnology
subject: 100706 Nanofabrication, Growth and Self Assembly
subject: 100708 Nanomaterials
subject: 100799 Nanotechnology not elsewhere classified
subject: 39999 Chemical Sciences not elsewhere classified
subject: Molecular Physics

description: Green open access version of the article:"Dethreading of a Photoactive Azobenzene-Containing Molecular Axle from a Crown Ether Ring: A Computational Investigation"
published in: ChemPhysChem 2016, 17, 1913-1919. DOI: 10.1002/cphc.201501160 which should be cited to refer to this work.
The links below refer to: the paper at publisher's site; supporting data; popular summaries of the research; two movies of the dethreading process of the two rotaxanes; high resolution figures
Isolation, physicochemical properties, and in vitro antioxidant activity of polysaccharides extracted from different parts of Pinus koraiensis
Creators: name: Zhang, Hua
name: Zhao, Haitian
name: Yao, Lei
name: Yang, Xin
name: Shen, Siyan
name: Wang, Jing
name: Wang, Zhenyu
name: Regenstein, Joe M.
name: Geng, Lin
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Physiology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Plant Biology

description: The isolation and purification of polysaccharides extracted from the cones, bark, and needles of Pinus koraiensis (Korean pine) were studied. The amounts of polysaccharides were 42.7%, 53.4%, and 48.4% for cones, bark, and needles, respectively. All these samples contained uronic acid. The total protein and polyphenols were <4.5% for all three samples. With acid hydrolysis, seven polysaccharides were found in different molar ratios in each sample: D-ribose, L-rhamnose, L-arabinose, D-xylose, D-mannose, D-glucose, and D-galactose. The relationships between in vitro antioxidant properties (AOP) of polysaccharides extracted from different parts of the P. koraiensis tree are correlated with physicochemical properties (the amount of neutral sugars, uronic acid, and proteins). Moreover, the pinecone polysaccharides (PKCP) confirmed previously observed beneficial antioxidant capacity with an EC50 of OH radical, ABTS radical scavenging, and reducing power of 6.54, 5.06, and 9.15 mg/mL, respectively. PKCP had the best antioxidant activity among the three samples.
title: 01_2612
Creators: name: Wesley Baldwin, John
name: Baldwin, John W.
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2018
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: L'ensemble de ces notes ont été crée par John Baldwin lors d'une de ses premières périodes de résidence à Paris. Ces documents comprennent tous les magistri qu’il avait pu rencontrer dans ses sources. Aux XIIème et XIIIème siècles, les universités n'existant pas encore, le titre de magister s'il évoque certainement une compétence n'est pas rattaché de façon systématique au passage par les écoles. De surcroît, les magistris sont le plus souvent désignés par leur seul prénom. La lecture de ces données est donc difficile et suppose un long travail pour tenter d'identifier un individu auquel on pourrait rattacher plusieurs mentions. John Baldwin avait donc renoncé à utiliser ces données pour donner un prolongement à sa magnifique étude sur les gradués d'université et leur emploi par les Capétiens et les Plantagenêts. Néanmoins, il a conservé ces données et elles sont potentiellement très utile dans le cadre de Studium, comme le sont toutes les mentions dans les volumes des Fasti Ecclesiae Gallicanae de chanoines portant ce titre de magister sans autres précisions. L'ampleur des dépouillements rend ces données très utiles et nous devons une grande reconnaissance à John Baldwin pour avoir pris la peine de faire photocopier ses fiches et de nous les avoir transmises amicalement.
Les données ainsi que les images des fiches sont accessibles sur le site Internet à l'adresse suivante : http://studium-baldwin.lamop.fr/.
Les transcriptions des fiches ont été effectuées par des étudiants de Paris 1 Panthéon - Sorbonne mais elles n'ont pas été corrigées par la suite.
description: Relation: https://lamop.hypotheses.org/
Anaerobic acidogenic fermentation of food waste for mixed-acid production
Creators: name: Li, Yeqing
name: Su, Dongfang
name: Feng, Hao
name: Yan, Fang
name: Liu, Hong
name: Feng, Lu
name: Liu, Guangqing
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified

description: In this study, three batch tests were conducted to investigate the effect of total solids loading, substrate to inoculum ratio, and fermentation temperatures on mixed-acids (total volatile fatty acids, TVFA) production from food waste (FW). Results showed that adding anaerobic inoculum could largely increase the extent of acidification of FW. Temperature could significantly influence the mixed-acids yield. Increasing S/I (substrate to inoculum ratio (on volatile solid basis)) ratio from 3 to 9 resulted in lower TVFA yields. The highest TVFA production with a concentration of 18.4 g/L (as acetic acid) was found at 6.0% TS (total solid) loading, 3 S/I ratio, and 37°C.
Phenolic constituents from Rheum nobile and their antioxidant activity
Creators: name: Fei, Ye
name: Wang, Juan
name: Peng, Bing
name: Peng, Jiangnan
name: Hu, Jing-Hong
name: Zeng, Zu-Ping
name: Chen, Jing
name: Li, Qi-En
name: Gao, Zeng-Ping
name: Yan, Xing-Li
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biochemistry
subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Plant Biology

description: Although the rhizomes of Rheum nobile Hook. f. et Thoms (Polygonaceae) are widely used in Tibetan medicine, no previous investigations regarding the biological activities and rarely chemical constituents of this plant have been reported. As part of an ongoing search for novel bioactive agents, a phytochemical investigation of R. nobile led to the isolation of two new compounds Rheumone B (1) and piceatannol-4′-O-β-D-(6″-O-acetyl)-glucoside (2), together with 15 known compounds by gel filtration over Sephadex LH-20 and preparative HPLC. Their structures were determined by combined spectroscopic methods. Compounds 1–10 were evaluated for their ability to scavenge 2,2-diphenyl-1-picrylhydzyl (DPPH) radical and compounds 7–10 showed relatively strong scavenging abilities with IC50 values from 2.76 μM to 11.80 μM. In conclusion, naphthalene glycosides, stilbene glycosides, flavanols, especially anthraquinones are main chemical constituents of this plant. The ability to scavenge DPPH radical of compound 8 was the highest among compounds 1–10.
Operational and biological analyses of branched water-adjustment and combined treatment of wastewater from a chemical industrial park
Creators: name: Xu, Ming
name: Cao, Jiashun
name: Li, Chao
name: Tu, Yong
name: Wu, Haisuo
name: Liu, Weijing
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: The combined biological processes of branched water-adjustment, chemical precipitation, hydrolysis acidification, secondary sedimentation, Anoxic/Oxic and activated carbon treatment were used for chemical industrial wastewater treatment in the Taihu Lake Basin. Full-scale treatment resulted in effluent chemical oxygen demand, total nitrogen, NH3–N and total phosphorus of 35.1, 5.20, 3.10 and 0.15 mg/L, respectively, with a total removal efficiency of 91.1%, 67.1%, 70.5% and 89.3%, respectively. In this process, short-circuited organic carbon from brewery wastewater was beneficial for denitrification and second-sulfate reduction. The concentration of effluent fluoride was 6.22 mg/L, which also met the primary standard. Gas Chromatography-Mass Spectrometry analysis revealed that many types of refractory compounds were present in the inflow. Microbial community analysis performed in the summer by PCR-denaturing gradient gel electrophoresis and MiSeq demonstrated that certain special functional bacteria, such as denitrificans, phosphorus-accumulating bacteria, sulfate- and perhafnate-reducing bacteria, aromatic compound-degrading bacteria and organic fluoride-degrading bacteria, present in the bio-tanks were responsible for the acceptable specific biological pollutant reduction achieved.
YWP 2017 Flash Abstract
Creators: name: O. Bailey
name: M. Carvalho
name: E. Castrignano
name: A. Cauchois
name: Y-H Cho
name: J Chouler
name: N. Deering
name: E. Gallagher
name: W-T. Huang
name: O.M. Imonikhe
name: A. Iqbal
name: L. Krieger
name: E. Losty
name: I. Markidis
name: H.S. Muhammad
name: M. Nguyen Quang
name: J. Rice
name: L. Richards
name: K.J. Russell
name: J. Webber
name: K. Zakaria
Publisher: name: figshare
Year: 2017
Subjects: subject: 60204 Freshwater Ecology
subject: FOS: Biological sciences
subject: 90508 Water Quality Engineering
subject: FOS: Civil engineering
subject: 90410 Water Treatment Processes
subject: FOS: Chemical engineering
subject: 90409 Wastewater Treatment Processes
subject: 90509 Water Resources Engineering
subject: 40608 Surfacewater Hydrology
subject: FOS: Earth and related environmental sciences

description: Abstracts submitted to the 18th IWA-UK Young Water Professionals Conference and awarded for Flash presentation
Machine Learning of Three-Dimensional Protein Structures to Predict the Functional Impacts of Genome Variation
Creators: name: Schoenberger, Stephen P.
name: Brunk, Elizabeth
name: Naradikian, Martin
name: Ting, Stephanie
name: Shukla, Kriti
name: Idanwekhai, Kelvin
Publisher: name: American Chemical Society (ACS)
Year: 2024

description: Research in the human genome sciences generates a substantial amount of genetic data for hundreds of thousands of individuals, which concomitantly increases the number of variants of unknown significance (VUS). Bioinformatic analyses can successfully reveal rare variants and variants with clear associations with disease-related phenotypes. These studies have had a significant impact on how clinical genetic screens are interpreted and how patients are stratified for treatment. There are few, if any, computational methods for variants comparable to biological activity predictions. To address this gap, we developed a machine learning method that uses protein three-dimensional structures from AlphaFold to predict how a variant will influence changes to a gene's downstream biological pathways. We trained state-of-the-art machine learning classifiers to predict which protein regions will most likely impact transcriptional activities of two proto-oncogenes, nuclear factor erythroid 2 (NFE2L2)-related factor 2 (NRF2) and c-Myc. We have identified classifiers that attain accuracies higher than 80%, which have allowed us to identify a set of key protein regions that lead to significant perturbations in c-Myc or NRF2 transcriptional pathway activities.
Association of fractures with the incidence of amyotrophic lateral sclerosis
Creators: name: L. Peters, Tracy
name: E. Weibull, Caroline
name: Fang, Fang
name: P. Sandler, Dale
name: C. Lambert, Paul
name: Ye, Weimin
name: Kamel, Freya
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Mathematical Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Objective: Elevated bone turnover observed in ALS patients suggests poor bone health and increased fracture risk. We therefore evaluated the relationship of fracture to subsequent ALS risk. Methods: We followed 4,529,460 Swedes from 1987 to 2010 and identified ALS and fractures from the Swedish National Patient Register. We examined associations of ALS risk with all fractures, osteoporotic and non-osteoporotic fractures, and traumatic and non-traumatic fractures among individuals aged 30–80 years. We used Cox proportional hazards models to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). We analysed the association of ALS with time since fracture using a Poisson regression model. Results: All fractures (HR: 1.51, 95% CI 1.39–1.65) as well as osteoporotic (HR: 1.59, 95% CI 1.41–1.79), non-osteoporotic (HR: 1.46, 95% CI 1.31–1.63), traumatic (HR: 1.50, 95% CI 1.37–1.63), and non-traumatic (HR: 1.80, 95% CI 1.35–2.40) fractures were associated with a higher incidence of ALS. Increased ALS incidence was associated with fractures occurring from one (HR: 2.33, 95% CI 2.04–2.66) to 18 (HR: 1.19, 95% CI 1.01–1.43) years before ALS diagnosis. Conclusions: Poor bone health may be related to ALS. These findings may offer insight into ALS pathophysiology.
YWP 2017 Flash presentations
Creators: name: O. Bailey
name: M. Carvalho
name: E. Castrignano
name: A. Cauchois
name: Y-H Cho
name: J Chouler
name: N. Deering
name: E. Gallagher
name: W-T. Huang
name: O.M. Imonikhe
name: A. Iqbal
name: L. Krieger
name: E. Losty
name: I. Markidis
name: H.S. Muhammad
name: M. Nguyen Quang
name: J. Rice
name: L. Richards
name: K.J. Russell
name: J. Webber
name: K. Zakaria
Publisher: name: figshare
Year: 2017
Subjects: subject: 60204 Freshwater Ecology
subject: FOS: Biological sciences
subject: 90508 Water Quality Engineering
subject: FOS: Civil engineering
subject: 90410 Water Treatment Processes
subject: FOS: Chemical engineering
subject: 90409 Wastewater Treatment Processes
subject: 90509 Water Resources Engineering
subject: 40608 Surfacewater Hydrology
subject: FOS: Earth and related environmental sciences

description: Abstracts submitted to the 18th IWA-UK Young Water Professionals Conference and awarded for Flash presentation
In vitro inhibitory effects of farnesol and interactions between farnesol and antifungals against biofilms of Candida albicans resistant strains
Creators: name: Xia, Jinping
name: Qian, Fang
name: Xu, Wenqian
name: Zhang, Zhenzhen
name: Wei, Xin
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Virology

description: Antifungal resistance is a serious problem in clinical infections. Farnesol, which is a potential antifungal agent against biofilms formed by Candida albicans resistant strains (a fluconazole-resistant isolate derived from SC5314 and two clinical Candida resistant isolates), was investigated in this study. The inhibitory effects of farnesol on biofilms were examined by XTT assay. The morphological changes and biofilm thicknesses were analyzed by scanning electron microscopy and confocal laser scanning microscopy, respectively. Additionally, the checkerboard microdilution method was used to investigate the interactions between farnesol and antifungals (fluconazole, amphotericin B, caspofungin, itraconazole, terbinafine and 5-flurocytosine) against biofilms. The results showed decreased SMICs of farnesol and thinner biofilms in the farnesol-treated groups, indicating that farnesol inhibited the development of biofilms formed by the resistant strain. Furthermore, there were synergistic effects between farnesol and fluconazole/5-flurocytosine, while there were antagonistic effects between farnesol and terbinafine/itraconazole, respectively, on the biofilms formed by the resistant strains.
Identification and characterization of the BmCyclin L1-BmCDK11A/B complex in relation to cell cycle regulation
Creators: name: Liu, Tai-hang
name: Wu, Yun-fei
name: Dong, Xiao-long
name: Pan, Cai-xia
name: Du, Guo-yu
name: Yang, Ji-gui
name: Wang, Wei
name: Bao, Xi-yan
name: Chen, Peng
name: Pan, Min-hui
name: Lu, Cheng
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Developmental Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Cyclin proteins are the key regulatory and activity partner of cyclin-dependent kinases (CDKs), which play pivotal regulatory roles in cell cycle progression. In the present study, we identified a Cyclin L1 and 2 CDK11 2 CDK11 splice variants, CDK11A and CDK11B, from silkworm, Bombyx mori. We determined that both Cyclin L1 and CDK11A/B are nuclear proteins, and further investigations were conducted to elucidate their spatiofunctional features. Cyclin L1 forms a complex with CDK11A/B and were co-localized to the nucleus. Moreover, the dimerization of CDK11A and CDK11B and the effects of Cyclin L1 and CDK11A/B on cell cycle regulation were also investigated. Using overexpression or RNA interference experiments, we demonstrated that the abnormal expression of Cyclin L1 and CDK11A/B leads to cell cycle arrest and cell proliferation suppression. Together, these findings indicate that CDK11A/B interacts with Cyclin L1 to regulate the cell cycle.
Comparison of Regression Methods with Non-Convex Penalties
Creators: name: Pipher, Brandon P.
Publisher: name: Zenodo
Year: 2019

description: We examine a solution to the problem of sparse selection in linear models. The method used is a mixed norm ℓp-ℓq algorithm with a focus on non-convex, q < 1, penalty parameters. Classical regression, Ordinary Least Squares, has low bias but high variance and prediction accuracy can sometimes be improved by increasing bias to decrease variance. By inducing sparsity we can improve model interpretability, especially in the setting of high-dimensional data. These methods of penalized regression also provide solutions when the Ordinary Least Squares solution is ill-posed under a high-dimensional setting, and have a history of producing accurate and parsimonious models. A simulation study is conducted utilizing another method of penalized regression using non-convex penalties, the SparseNet algorithm, which had previously been compared independently against several other proposed sparsity inducing non-convex solutions. We also include a comparison with other more common penalties such as LASSO, Ridge/Tikhonov, and Elastic Net.
Identification and Characterization of the BmCyclin L1-BmCDK11A/B complex in relation to cell cycle regulation
Creators: name: Liu, Tai-hang
name: Wu, Yun-fei
name: Dong, Xiao-long
name: Pan, Cai-xia
name: Du, Guo-yu
name: Yang, Ji-gui
name: Wang, Wei
name: Bao, Xi-yan
name: Chen, Peng
name: Pan, Min-hui
name: Lu, Cheng
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Developmental Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Cyclin proteins are the key regulatory and activity partner of cyclin-dependent kinases (CDKs), which play pivotal regulatory roles in cell cycle progression. In the present study, we identified a Cyclin L1 and two CDK11 two CDK11 splice variants, CDK11A and CDK11B, from silkworm, Bombyx mori. We determined that both Cyclin L1 and CDK11A/B are nuclear proteins, and further investigations were conducted to elucidate their spatiofunctional features. Cyclin L1 forms a complex with CDK11A/B and were co-localized to the nucleus. Moreover, the dimerization of CDK11A and CDK11B and the effects of Cyclin L1 and CDK11A/B on cell cycle regulation were also investigated. Using overexpression or RNA interference experiments, we demonstrated that the abnormal expression of Cyclin L1 and CDK11A/B leads to cell cycle arrest and cell proliferation suppression. Together, these findings indicate that CDK11A/B interacts with Cyclin L1 to regulate the cell cycle.
The age of the Takatika Grit, Chatham Islands, New Zealand
Creators: name: Hollis, Christopher J.
name: Stickley, Catherine E.
name: K. Bijl, Peter
name: Schiøler, Poul
name: Clowes, Christopher D.
name: Li, Xun
name: Campbell, Hamish
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: Hollis, C.J, Stickley, C.E., Bijl, P.K., Schiøler, P., Clowes, C.D., Li, X, Campbell, H. March 2017. The age of the Takatika Grit, Chatham Islands, New Zealand. Alcheringa 41, xxx–xxx. ISSN 0311-5518. The oldest Paleogene strata on Chatham Islands, east of New Zealand, are the phosphatized conglomerates and sandstones of the Takatika Grit that crops out on the northeastern coast at Tioriori and unconformably overlies the Chatham Schist. An intact Cretaceous–Paleogene boundary transition is not preserved at this locality. New biostratigraphic analysis of dinoflagellate, diatom and radiolarian microfossil assemblages confirms that the Takatika Grit is of late early–middle Paleocene (New Zealand Teurian stage) age but contains reworked microfossils of early Campanian (Early Haumurian) age. Vertebrate fossils found in this unit are inferred to be a mixture of reworked Cretaceous and in situ Paleocene bones and teeth. The overlying Tutuiri Greensand is of middle–late Paleocene age in its lower part and also contains reworked Cretaceous microfossils. Christopher J. Hollis [c.hollis@gns.cri.nz], Chris Clowes [c.clowes@gns.cri.nz], Xun Li [x.li@gns.cri.nz], Hamish Campbell [h.campbell@gns.cri.nz], GNS Science, PO Box 30-368, Lower Hutt 5040, New Zealand; Catherine Stickley, Evolution Applied Limited, 50 Mitchell Way, Upper Rissington, Cheltenham GL54 2PL, UK [catherine.stickley@gmail.com]; Peter Bijl [p.k.bijl@uu.nl], Marine Palynology and Paleoceanography, Department of Earth Sciences, Utrecht University, 3584 CS Utrecht, the Netherlands; Poul Schiøler [poul.schioler@mgpalaeo.com.au], Morgan Goodall Palaeo, Unit 1/5 Arvida St, Malaga, WA 6090, Australia.
IYPT 2024 Problem No. 7 : Giant Sounding Plate ISL TEAM A
Creators: name: Ali, Murtaza
name: Ahmad, Muhammad
name: Tariq, Muhammad Yusuf
name: Ijaz, Hania
name: Faisal, Muhammad Ibraheem
Publisher: name: Zenodo
Year: 2024

description: This study investigates the phenomenon of "howling" sounds emitted by large, flexible plates, such as metal or plastic, when bent. We aimed to understand the underlying mechanics and acoustic properties that generate this distinct sound by experimenting with various materials, plate shapes, and bending techniques. Using sound meters and waveform analysis, we measured the amplitude and frequency of sounds produced under controlled bending. Our findings suggest that the sound’s amplitude and tonal characteristics are influenced by factors such as material composition, plate thickness, and the type of bending (e.g., half vs. full bend). We observed that resonance, displacement of air, and wave diffraction play central roles in sound generation, with different plate materials demonstrating unique damping qualities that affect sound decay. The project’s mathematical modeling component provides a framework for quantifying these effects, offering new insights into sound production in bent plates and broader applications in acoustics and materials science.
Fetal growth pathology score: a novel ultrasound parameter for individualized assessment of third trimester growth abnormalities
Creators: name: L. Deter, Russell
name: Lee, Wesley
name: C. P. Kingdom, John
name: Romero, Roberto
Publisher: name: Taylor & Francis
Year: 2017
Subjects: Space Science
Physical Sciences not elsewhere classified
Medicine
Cell Biology
Biotechnology
Chemical Sciences not elsewhere classified
Mathematical Sciences not elsewhere classified
Developmental Biology
Hematology

description: Objectives: To study fetal growth in pregnancies at risk for growth restriction (GR) using, for the first time, the fetal growth pathology score (FGPS1). Methods: A retrospective cohort study of GR was carried out in 184 selected SGA singletons using a novel, composite measure of growth abnormalities termed the FGPS1. Serial fetal biometry was used to establish second trimester Rossavik size models and determine FGPS1 values prior to delivery. FGPS1 data were compared to neonatal growth outcomes assessed using growth potential realization index (GPRI) values (average negative pathological GPRI (av − pGPRI)). Growth at the end of pregnancy was evaluated from differences in negative, individual composite prenatal growth assessment scores (-icPGAS) measured at the last two ultrasound scans. The FGPS1 and av − pGPRI values were used to classify fetal growth and neonatal growth outcomes, respectively, as Normal (N) or Abnormal (A). Results: The risk of neonatal GR (based on birth weight (BW)) was moderate (MR: between 5th and10th percentiles (n = 113)) or significant (SR:<5th percentile) (n = 71)). Individual pregnancies were grouped into four categories, two representing agreement (N–N (29%), A–A (40%)) and two representing discordance (N–A (11%), A–N (20%)). In the largest and most variable subgroup (A–A,<5%tile, n = 49), there was a statistically significant correlation (0.63, p < .0001) between the FGPS1 and av − pGPRI. In N–A, all 20 cases (100%) had long last-scan-to-delivery intervals (1.9 weeks or greater), suggesting late development of the growth abnormality. For A–N, in approximately equal proportions, GR was improving, progressing or unclassifiable at the end of pregnancy. Conclusions: Significant agreement between prenatal and postnatal growth assessments was found using a novel approach for quantifying fetal growth pathology (FGPS1). Discordances appear to be due to lack of appropriate prenatal scans or an inadequate set of neonatal measurements. Evidence for a quantitative relationship between assessment methods was seen in the largest and most variable subgroup. The FGPS1 has the potential for characterizing GR in the third trimester and may provide a means for predicting the severity of corresponding abnormal neonatal growth outcomes.