cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Three new flavonoid glycosides from the aerial parts of Allium sativum L. and their anti-platelet aggregation assessment
Creators: name: Hu, Bin
name: Hu, Haibo
name: Pu, Chuan
name: Wei, Zheng
name: Wang, Qiuhong
name: Kuang, Haixue
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
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

description: Three new flavonoid glycosides, Dasuanxinoside F–H (1–3), were isolated from the aerial parts of Allium sativum, together with eight known compounds which were firstly reported in this plant, including three flavonoid glycosides (4–6) and five phenylethanoid glycosides (7–11). Their structures were identified by UV-vis, IR, 1D and 2D NMR spectra, as well as HR-ESI-MS analyses. The inhibitory effect of the isolated compounds on platelet aggregation induced by adenosine diphosphate (ADP) was evaluated in vitro. The results showed that most compounds displayed different degrees of inhibition. Among them, 2, 5, 8 and 9 exhibited the strongest activity on platelet aggregation.
Additional file 1 of Association of H3K9me3 with breast cancer prognosis by estrogen receptor status
Creators: name: Zhou, Meng
name: Yan, Jin-qi
name: Chen, Qian-xin
name: Yang, Yuan-zhong
name: Li, Yue-lin
name: Ren, Yue-xiang
name: Weng, Zi-jin
name: Zhang, Xiao-fang
name: Guan, Jie-xia
name: Tang, Lu-ying
name: Ren, Ze-fang
Publisher: name: figshare
Year: 2022
Subjects: subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Plant Biology
subject: FOS: Biological sciences

description: Additional file 1. Figure S1. Flowchart of the study cohort. Figure S2. X-tile plot of the selected cut-off value for H3K9me3 in tumor tissues. Table S1. Univariate association between the demographic and clinicopathological characteristics and the outcomes.
MOESM1 of Establishment of an innovative and sustainable PCR technique for 1534 locus mutation of the knockdown resistance (kdr) gene in the dengue vector Aedes albopictus
Creators: name: Zhu, Cai-Ying
name: Zhao, Chun-Chun
name: Wang, Yi-Guan
name: Ma, De-Ling
name: Song, Xiu-Ping
name: Wang, Jun
name: Meng, Feng-Xia
Publisher: name: figshare
Year: 2019
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Virology

description: Additional file 1: Alignment S1. ClustalW alignment for eight genotypes in the 1534 locus of the kdr gene in Ae. albopictus. The underlined uppercase letters referring to the codons in the 1534 locus, and the letter highlighted in yellow corresponds to the insertion. All the alignments originate from the sequences sequenced in reverse direction by the primer aegSCR8.
Additional file 1: of The Mini-International Neuropsychiatric Interview is useful and well accepted as part of the clinical assessment for depression and anxiety in primary care: a mixed-methods study
Creators: name: Pettersson, Agneta
name: Modin, Sonja
name: WahlstrĂśm, Rolf
name: Hammarberg, Sandra Af Winklerfelt
name: Krakau, Ingvar
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology

description: Questionnaires and topic guides. (PDF 203Â kb)
The validity of situation awareness for performance: a meta-analysis
Creators: name: Bakdash, Jonathan Z.
name: Marusich, Laura R.
name: Cox, Katherine R.
name: Geuss, Michael N.
name: Zaroukian, Erin G.
name: Morris, Katelyn M.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Space Science
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: Situation awareness (SA) is a widely used cognitive construct in human factors, often theoretically posited to be a critical causal factor and/or construct for performance. However, there are concerns that SA may not sufficiently capture the psychological processes underlying performance. We address these conflicting perspectives using meta-analysis to evaluate the patterns of associations among SA-performance effect sizes. Specifically, we focus on the validity of SA for performance—how well SA captures the relevant psychological processes for task performance. In our systematic review of the empirical literature, we coded associations of ten unique measures of SA with performance: 678 effects from 77 papers. The meta-analytic means for SA measures were all of approximately medium or lower effect sizes. The overall mean effect, while significant, was also limited in magnitude (r = 0.26, p r = −0.15 to 0.60). The results indicate that SA’s validity for performance tends to be, on average, weak with large variations among effects. Interventions that improve SA may not correspond to meaningful improvements in task performance, and it may be appropriate to revise major theories of SA. Supplemental data for this article is available online at https://doi.org/10.1080/1463922X.2021.1921310.
title: ADCO, Sixième cartulaire de Saint-Étienne de Dijon (1662), Cart. 30 (G 133), 441 folios, f. 055
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2012
name: Petot, Frédéric
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: cartulaire
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge

description: Sixième cartulaire de Saint-Étienne de Dijon (1662), Archives départementales de la Côte-d'Or, Cart. 30 (G 133), 441 folios, f. 055, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Sixième cartulaire de Saint-Étienne de Dijon (1662), Archives départementales de la Côte-d'Or, Cart. 30 (G 133), 441 folios, f. 055, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https://manuscrits.cbma-project.eu/
description: Provenance: abbaye Saint-Étienne de Dijon
description: Provenance: http://www.wikidata.org/entity/Q15945019
Additional file 1: of Role of HIV in the desire of procreation and motherhood in women living with HIV in Spain: a qualitative approach
Creators: name: Arco, Debora Alvarez-Del
name: Sabela Rodríguez
name: Mª. Pérez-Elías
name: Blanco, Jose
name: Cuellar, Sandra
name: Romero, Jorge Del
name: Santos, Ignacio
name: Boix, Vicente
name: Masiá, Mar
name: Pascual, Lydia
name: Hernando, Victoria
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Computational Biology

description: “Interview script”. Interview script used to develop the interviews. In the Additional file 1 we included both, the original Spanish version and the English translation of the script. (DOCX 20 kb)
Effects of supplementing herb mixed drinking water on productive performance, carcass quality, and caecal microbial population
Creators: name: Paweenisaras Khenjan, Ananthaya Sansawat
Publisher: name: Faculty of Agriculture
Year: 2022
Subjects: herb
coriander seed
oregano extract
productive performance
caecal microbial

description: Khon Kaen Agriculture Journal, 50, 3, 625-635
Factors affecting the successful operation of the extension and development for standards production of Pradu Hang Dam Chiang Mai chicken of business project of farmers in upper Northern region, Thailand
Creators: name: Panuphan Prapatigul And Wuttichai Khamdee
Publisher: name: Faculty of Agriculture
Year: 2022
Subjects: successful
Pradu Hang Dam Chiang Mai chicken
upper Northern region

description: Khon Kaen Agriculture Journal, 50, 3, 657-667
Guidelines for developing beef cattle raising among farmers in Rattaphum district, Songkhla province
Creators: name: Seksan Duangsingtham, Apinya Ratanachai
Publisher: name: Faculty of Agriculture
Year: 2022
Subjects: beef cattle raising
guideline for developing
Rattaphum district
Songkhla province

description: Khon Kaen Agriculture Journal, 50, 3, 668-681
Cost and revenue analysis of soybean production in the dry season of famers in Khon Kaen province
Creators: name: Yuwarut Boonkasem And Parichard Sangkumchaliang
Publisher: name: Faculty of Agriculture
Year: 2022
Subjects: soybean in dry season
cost and revenue
soybean production

description: Khon Kaen Agriculture Journal, 50, 3, 682-689
Needs for extension on hand reeled thai silk yarn production with TAS 80002555 Agricultural Standard of farmers in Chaiyaphum province
Creators: name: Napas Heamatorn, Sukanlaya Choenkwan
Publisher: name: Faculty of Agriculture
Year: 2022
Subjects: needs for extension
hand reeled Thai silk yarn production with TAS 8000 - 2555 agricultural standard
hand reeled Thai silk yarn production
silk thread value addition

description: Khon Kaen Agriculture Journal, 50, 3, 690-702
MEТAФOPA B OБPAЗOBAНИИ ТEPMИНOB B OБЛAСТИ ЯДEPНOЙ ЭНEPГEТИКИ
Creators: name: Боқиева Муқаддас Обиджоновна
Publisher: name: Zenodo
Year: 2024

description: Aннoтaция. Дaннaя cтaтья пpедcтaвляет cобой aнaлиз теpминов, обpaзовaнных c помощью метaфоpичеcкого пеpеноca. Aктyaльноcть иccледовaния зaключaетcя в чacтом иcпользовaнии в cовpеменном языке нayки эмоционaльно- экcпpеccивных и изобpaзительных cpедcтв языкa, котоpые зaметно выделяютcя нa фоне чиcто нayчного изложения и пpидaют нayчной пpозе добaвочнyю yбедительноcть.

Ключeвыe cлoвa: теpмин, метафopа, ядеpная энеpгетика, кoнцепт, слoвooбpазoвание.

Abstract. This article is an analysis of terms formed with the help of metaphorical transfer. The relevance of the study lies in the frequent use of emotional-expressive and figurative means of language in the modern language of science, which noticeably stand out against the background of purely scientific presentation and give scientific prose added persuasiveness.

Keywords: term, metaphor, nuclear energy, concept, word formation.
The deleterious variants of N-acetylgalactosamine-6-sulfatase (GalN6S) enzyme trigger Morquio a syndrome by disrupting protein foldings
Creators: name: Li, Jiuyi
name: Khalid, Waqas Ahmad
name: Imtiaz, Hina
name: Huang, Lingkun
name: Ali, Yasir
name: Yousaf, Rimsha
name: Gul, Fouzia
name: Mahmood, Arif
name: Shah, Abid Ali
name: Deng, Huiyin
name: Khattak, Saadullah
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Genetics
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Virology
subject: Computational Biology

description: Lysosomal enzymes degrade cellular macromolecules, while their inactivation causes human hereditary metabolic disorders. Mucopolysaccharidosis IVA (MPS IVA; Moquio A syndrome) is one of the lysosomal storage disorders caused by a defective Galactosamine-6-sulfatase (GalN6S) enzyme. In several populations, disease incidence is elevated due to missense mutations brought on by non-synonymous allelic variation in the GalN6S enzyme. Here, we studied the effect of non-synonymous single nucleotide polymorphism (nsSNPs) on the structural dynamics of the GalN6S enzyme and its binding with N-acetylgalactosamine (GalNAc) using all-atom molecular dynamics simulation and an essential dynamics approach. Consequently, in this study, we have identified three functionally disruptive mutations in domain-I and domain-II, that is, S80L, R90W, and S162F, which presumably contribute to post-translational modifications. The study delineated that both domains work cooperatively, and alteration in domain II (S80L, R90W) leads to conformational changes in the catalytic site in domain-I, while mutation S162F mainly provokes higher residual flexibility of domain II. These results show that these mutations impair the hydrophobic core, implying that Morquio A syndrome is caused by misfolding of the GalN6S enzyme. The results also show the instability of the GalN6S-GalNAc complex upon substitution. Overall, the structural dynamics resulting from point mutations give the molecular rationale for Moquio A syndrome and, more importantly, the Mucopolysaccharidoses (MPS) family of diseases, re-establishing MPS IVA as a protein-folding disease. Communicated by Ramaswamy H. Sarma
‘Computational studies on coumestrol-ArlR interaction to target ArlRS signaling cascade involved in MRSA virulence’
Creators: name: Verma, Abhishek Kumar
name: Jaiswal, Grijesh
name: Sultana, Kazi Nasrin
name: Srivastava, Sandeep Kumar
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Two component signaling system ArlRS (Autolysis-related locus) regulates adhesion, biofilm formation and virulence in methicillin resistant Staphylococcus aureus. It consists of a histidine kinase ArlS and response regulator ArlR. ArlR is composed of a N-terminal receiver domain and DNA-binding effector domain at C-terminal. ArlR receiver domain dimerizes upon signal recognition and activates DNA binding by effector domain and subsequent virulence expression. In silico simulation and structural data suggest that coumestrol, a phytochemical found in Pueraria montana, forges a strong intermolecular interaction with residues involved in dimer formation and destabilizes ArlR dimerization, an essential conformational switch required for downstream effector domain to bind to virulent loci. Structural and energy profiles of simulated ArlR-coumestrol complexes suggest lower affinity between ArlR monomers due to structural rigidity at the dimer interface hindering the conformational rearrangements relevant for dimer formation. These analyses could be an attractive strategy to develop therapeutics and potent leads molecules response regulators of two component systems in which are involved in MRSA virulence as well as other drug-resistant pathogens. Communicated by Ramaswamy H. Sarma
Additional file 1 of Network meta-analysis on the efficacy and safety of finerenone versus SGLT2 inhibitors on reducing new-onset of atrial fibrillation in patients with type 2 diabetes mellitus and chronic kidney disease
Creators: name: Zhang, Yaofu
name: Wang, Junheng
name: Jiang, Li
name: Wang, Tongxin
name: Li, Zhuang
name: Fu, Xiaozhe
name: Huang, Weijun
name: Xiao, Yonghua
name: Wang, Shidong
name: Zhao, Jinxi
Publisher: name: figshare
Year: 2022
Subjects: Space Science
Medicine
Biological Sciences not elsewhere classified
Marine Biology
Cancer
Science Policy

description: Additional file 1. Search strategies.
Discovery of novel PARP-1 inhibitors using tandem in silico studies: integrated docking, e-pharmacophore, deep learning based de novo and molecular dynamics simulation approach
Creators: name: Bhatnagar, Aayushi
name: Nath, Virendra
name: Kumar, Neeraj
name: Kumar, Vipin
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Cancer accounts for the majority of deaths worldwide, and the increasing incidence of breast cancer is a matter of grave concern. Poly (ADP-ribose) polymerase-1 (PARP-1) has emerged as an attractive target for the treatment of breast cancer as it has an important role in DNA repair. The focus of the study was to identify novel PARP-1 inhibitors using a blend of tandem structure-based screening (Docking and e-pharmacophore-based screening) and artificial intelligence (deep learning)-based de novo approaches. The scrutiny of compounds having good binding characteristics for PARP-1 was carried out using a tandem mode of screening along with parameters such as binding energy and ADME analysis. The efforts afforded compound Vab1 (PubChem ID 129142036), which was chosen as a seed for obtaining novel compounds through a trained artificial intelligence (AI)-based model. Resultant compounds were assessed for PARP-1 inhibition; binding affinity prediction and interaction pattern analysis were carried out using the extra precision (XP) mode of docking. Two best hits, Vab1-b and Vab1-g, exhibiting good dock scores and suitable interactions, were subjected to 100 nanoseconds (ns) of molecular dynamics simulation in the active site of PARP-1 and compared with the reference Protein-Ligand Complex. The stable nature of PARP-1 upon binding to these compounds was revealed through MD simulation. Communicated by Ramaswamy H. Sarma
Success factors of indigo fabric farmers in Phanna Nikhom district, Sakon Nakhon province
Creators: name: Wanattaya Ngoiphala, Chalathon Choocharoen
Publisher: name: Faculty of Agriculture
Year: 2022
Subjects: success
indigo fabric
Phanna Nikhom district

description: Khon Kaen Agriculture Journal, 50, 3, 703-709
Decision factors to participate the large-scale farming of farmer's cocoa (Theobroma cacao), Wang Nuea district, Lampang province
Creators: name: Chaweewan Jaroenpong, Chalathon Choocharoen
Publisher: name: Faculty of Agriculture
Year: 2022
Subjects: decision to participate
large-scale farming
cocoa
wang nuea

description: Khon Kaen Agriculture Journal, 50, 3, 710-718
Additional file 1 of Circular RNAs to predict clinical outcome after cardiac arrest
Creators: name: Stefanizzi, Francesca M.
name: Zhang, Lu
name: Salgado-Somoza, Antonio
name: Dankiewicz, Josef
name: Stammet, Pascal
name: Hassager, Christian
name: Wise, Matthew P.
name: Friberg, Hans
name: Cronberg, Tobias
name: Hundt, Alexander
name: Kjaergaard, Jesper
name: Nielsen, Niklas
name: Devaux, Yvan
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Additional file 1. Sequencing results of the five candidate circRNAs.
Farmers' knowledge and practices on cardamom production in Namor district, Oudoxay province, Lao PDR
Creators: name: Damduan Amphaithip, Panuphan Prapatigul
Publisher: name: Faculty of Agriculture
Year: 2022
Subjects: knowledge
practices
cardamom production
Oudomxay
Lao PDR

description: Khon Kaen Agriculture Journal, 50, 3, 719-730
Additional file 3 of Circular RNAs to predict clinical outcome after cardiac arrest
Creators: name: Stefanizzi, Francesca M.
name: Zhang, Lu
name: Salgado-Somoza, Antonio
name: Dankiewicz, Josef
name: Stammet, Pascal
name: Hassager, Christian
name: Wise, Matthew P.
name: Friberg, Hans
name: Cronberg, Tobias
name: Hundt, Alexander
name: Kjaergaard, Jesper
name: Nielsen, Niklas
name: Devaux, Yvan
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Additional file 3. Supplemental methods and results.
The Cosmic Dance of Negative Ions
Creators: name: Nichols, Miranda
Publisher: name: Zenodo
Year: 2021
Subjects: negative ion
atomic physics
collinear laser spectroscopy
resonance ionization spectroscopy
electron affinity
cesium

description: This poster was presented at EJC in 2021 as a general introduction poster about negative ions and the experimental methods used at The University of Gothenburg.
Advanced battery techno-economics tool - D6.5 INVADE H2020
Creators: name: Hentunen, Ari
name: Forsström, Juha
name: Mukherjee, Victor
Publisher: name: Zenodo
Year: 2018

description: This deliverable presents the advanced battery techno-economic model that will be included in the flexibility management allocation and operation algorithm developed in Task 5.4 Design and program the flexibility management operation algorithm and described in detail in D5.4 Advanced battery operation and control algorithm. The main objective of this deliverable is to provide a tool that optimizes the battery operation in such a way that maximum economic value can be obtained.
H3ABioNet Advanced Systems Administration Workshop 2015 Training Material Archive
Creators: name: Joubert, Fourie
name: Hazelhurst, Scott
name: Alibi, Mohamed
name: Van heusden, Peter
name: Meintjes, Ayton
name: Mulder, Nicola
Publisher: name: University of Cape Town
Year: 2022
Subjects: subject: 80302 Computer System Architecture
subject: FOS: Computer and information sciences
subject: 60102 Bioinformatics

description: This is an archive containing training materials for the H3ABioNet course: “H3ABioNet Advanced Systems Administration Workshop - Bioinformatics and Computational Biology Unit, University of Pretoria 2nd to 11th Feb 2015”.
Brief description of the course: The aim of the workshop was to train newly hired System Administrators and/or their representatives on systems administration of Unix type servers/infrastructure relevant for data management and storage for H3Africa affiliated projects and subsequent bioinformatics research.
Course sponsor/organisers:H3ABioNet and the Bioinformatics and Computational Biology Units, Universities of Pretoria and the Witwatersrand H3ABioNet Nodes
Course level: Advanced
The archive contains the following items:Trainer/creator file containing the names of the person/s responsible for organising and delivering the courseCourse information file - which contains the original information about the course and includes a course scheduleLecture materials which include lecture slides, tutorials and datasetsThis upload was performed by: Verena Ras | H3ABioNet Training and Outreach Coordinator
MOESM12 of Comparative physiological, metabolomic, and transcriptomic analyses reveal developmental stage-dependent effects of cluster bagging on phenolic metabolism in Cabernet Sauvignon grape berries
Creators: name: Sun, Run-Ze
name: Cheng, Guo
name: Li, Qiang
name: Zhu, Yan-Rong
name: Zhang, Xue
name: Wang, Yu
name: He, Yan-Nan
name: Li, Si-Yu
name: He, Lei
name: Chen, Wu
name: Pan, Qiu-Hong
name: Duan, Chang-Qing
name: Wang, Jun
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Computational Biology

description: Additional file 12: Table S7. Transcription profile of light and plant hormone signal transduction related genes among samples.
16S rRNA Microbiome Intermediate Bioinformatics Training Course Material Archive
Creators: name: Botha, Gerrit
name: Lennard, Katie
name: Claassen-Weitz, Shantelle
name: Mwaikono, Kilaza Samson
name: Allali, Imane
name: Ras, Verena
Publisher: name: University of Cape Town
Year: 2022
Subjects: subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 60503 Microbial Genetics
subject: FOS: Biological sciences

description: This is an archive containing training materials for the H3ABioNet course: “16S rRNA Microbiome Intermediate Bioinformatics Training”.
Brief description of the course: The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will provide training to enable participants to gain the knowledge and skills to perform 16S rRNA microbiome data analyses using a variety of bioinformatics methods and tools.
Over a period of 2 months of intensive biweekly contact sessions, the course combines theoretical and practical sessions to allow participants to gain practical experience in using various tools and resources. During contact sessions, classrooms meet virtually to discuss the session’s content with each other and the trainer.
The first iteration of the course ran in 2019.
Course sponsor/organisers:H3ABioNet
Course level: Intermediate
The archive contains the following items:Trainer/creator file containing the names of the person/s responsible for organising and delivering the courseCourse information file - which contains the original information about the course and includes a course scheduleLecture materials which include lecture slides, tutorials and datasetsLecture videosGithub repositoryThis upload was performed by: Verena Ras | H3ABioNet Training and Outreach Coordinator
Sulfur recovery in the sulfide-oxidizing membrane aerated biofilm reactor: experimental investigation and model simulation
Creators: name: Xinyue Jiang
name: Xu, Bin
name: Wu, Jun
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Marine Biology

description: The production of sulfur (S) from the biological oxidization of sulfide (S2−) by SOB (sulfide-oxidizing bacteria) allows for resource recovery. Past researches have indicated that S recovery from S2− oxidation MABR (the membrane aerated biofilm reactor) was feasible. The process was complicated by the requirement of maintaining appropriate oxygen supply to prevent the produced S from being further oxidized into sulfate (SO42−) and by the presence of heterotrophic biomass. In this study, a multispecies biofilm model was developed and experimentally validated to gain insight for the S recovery process in MABR. The developed model was capable of predicting the S recovery performance in the MABR. The optimal conditions involved in maintaining the appropriate oxygen flux and the biofilm thickness according to the hydraulic and S2− loading rate. The low anoxic heterotrophic growth rate using SO42− and S as electron donors could explain why the impact of heterotrophic growth was insignificant.
Sulfur recovery in the sulfide-oxidizing membrane aerated biofilm reactor: experimental investigation and model simulation
Creators: name: Xingyue Jiang
name: Xu, Bin
name: Wu, Jun
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Marine Biology

description: The production of sulfur (S) from the biological oxidization of sulfide (S2−) by SOB (sulfide-oxidizing bacteria) allows for resource recovery. Past researches have indicated that S recovery from S2− oxidation MABR (the membrane aerated biofilm reactor) was feasible. The process was complicated by the requirement of maintaining appropriate oxygen supply to prevent the produced S from being further oxidized into sulfate () and by the presence of heterotrophic biomass. In this study, a multispecies biofilm model was developed and experimentally validated to gain insight for the S recovery process in MABR. The developed model was capable of predicting the S recovery performance in the MABR. The optimal conditions involved in maintaining the appropriate oxygen flux and the biofilm thickness according to the hydraulic and S2− loading rate. The low anoxic heterotrophic growth rate using and S as electron donors could explain why the impact of heterotrophic growth was insignificant.
Additional file 2: Figure S2. of Genome-wide protein phylogenies for four African cichlid species
Creators: name: Varadarajan, Ajay Ramakrishnan
name: Mopuri, Rohini
name: J. Streelman
name: McGrath, Patrick
Publisher: name: figshare
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Subtree from the TF319371 family from a limited number of cichlid species and well-studied model organisms. This family contains a number of Iroquois-family of homeodomain transcription factors involved in patterning and other development processes. (PDF 1170 kb)
title: ADCO, Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome I, Cart. 185 (11 H 70), f. 0130v
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: cartulaire

description: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome I, Archives départementales de la Côte-d'Or, Cart. 185 (11 H 70), f. 0130v, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome I, Archives départementales de la Côte-d'Or, Cart. 185 (11 H 70), f. 0130v, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
The Big Brother’s New Playground: Unmasking the Illusion of Privacy in Web Metaverses from a Malicious User’s Perspective
Creators: name: Mengascini, Andrea
name: Aurelio, Ryan
name: Pellegrino, Giancarlo
Publisher: name: CISPA
Year: 2024

description: Metaverses are virtual worlds where users can engage in social exchanges, collaborate, or play games. Their clients now are JavaScript programs that run inside modern web browsers. They implement functionalities typical of multiplayer video games, like 3D and physics engines, requiring them to maintain complex data structures of objects in the browser’s memory. Unfortunately, these objects can be accessed and manipulated by malicious users, allowing them to learn about events beyond the ones rendered on screen or to hijack the physics of the metaverse to spy on other users.
In this paper, we propose one of the first comprehensive security assessments for web clients of metaverse platforms. We begin with a survey and selection of three metaverse platforms — FrameVR, Mozilla Hubs, and Somnium Space — and introduce a softwarecentric threat modeling approach designed to identify the securityrelevant entities. Then, we propose a JavaScript global object snapshot diffing technique to identify in-memory objects correlated with the attribute and design 10 attacks, of which eight successfully executed against at least one of the metaverses, enabling a malicious user to perform audio/video surveillance or continuous
user position tracking — to mention a few — who could exacerbate current threats posed by stalkers and online abusers. Finally, we discuss the implications of our attacks should the metaverse become a business tool and possible solutions.
title: Beleidsinformerende Nota: Overzicht van het onderzoekslandschap en de wetenschappelijke informatie inzake (marien) zwerfvuil en microplastics in België
Creators: name: Devriese, Lisa
name: Janssen, Colin
Publisher: name: Flanders Marine Institute
Year: 2022

description: Title : VLIZ Beleidsinformerende Nota's. Vlaams Instituut voor de Zee (VLIZ): Oostende. ISSN 2295-7464 Volume : 2022_001 Issue : Pagination : 56
Beam developments for actinides at ISOLDE
Creators: name: Au, Mia
name: Atanasov, Dinko
name: Athanasakis-Kaklamanakis, Michail
name: Ballof, Jochen
name: Barbero, Ermanno
name: Berger, Robert
name: Bovigny, Mathieu
name: Chrysalidis, Katerina
name: Crepieux, Bernard
name: Cruikshank, James
name: Düllmann, Christoph
name: Geldhof, Sarina
name: Heinke, Reinhard
name: Johnson, Jake
name: Leimbach, David
name: Mamis, Edgars
name: Marsh, Bruce
name: Mougeot, Maxime
name: Nies, Lukas
name: Reich, Bianca
name: Stegemann, Simon
name: Nel Vila Gracia, Yago
name: Wessolek, Julius
name: Wilkins, Shane
name: Rothe, Sebastian
Publisher: name: Zenodo
Year: 2022

description: Contribution ID: 57 Type: Invited Tuesday, December 14, 2021 2:40 PM (15 minutes)
A computational study to probe the binding aspects of potent polyphenolic inhibitors of pancreatic lipase
Creators: name: Kottekad, Sanjay
name: Roy, Sudip
name: Dandamudi, Usharani
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Physical Sciences not elsewhere classified
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified

description: Pancreatic lipase (PL) is a keen target for anti-obesity therapy that reduces dietary fat absorption. Here, we investigated the binding patterns of 220 PL inhibitors having experimental IC50 values, using molecular docking and binding energy calculations. Screening of these compounds illustrated most of them bound at the catalytic site (S1-S2 channel) and a few compounds are at the non-catalytic site (S2-S3 channel/S1-S3 channel) of PL. This binding pattern could be due to structural uniqueness or bias in conformational search. A strong correlation of pIC50 values with SP/XP docking scores, binding energies (ΔGMMGBSA) assured the binding poses are more true positives. Further, understanding of each class and subclasses of polyphenols indicated tannins preferred non-catalytic site wherein binding energies are underestimated due to huge desolvation energy. In contrast, most of the flavonoids and furan-flavonoids have good binding energies due to strong interactions with catalytic residues. While scoring functions limited the understanding of sub-classes of flavonoids. Hence, focused on 55 potent PL inhibitors of IC50 < 5 µM for better in vivo efficacy. The prediction of bioactivity, drug-likeness properties, led to 14 bioactive compounds. The low root mean square deviation (0.1-0.2 nm) of these potent flavonoids and non-flavonoid/non-polyphenols PL-inhibitor complexes during 100 ns molecular dynamics runs (MD) as well as binding energies obtained from both MD and well-tempered metadynamics, support strong binding to catalytic site. Based on the bioactivity, ADMET properties, and binding affinity data of MD and wt-metaD of potent PL-inhibitors suggests Epiafzelechin 3-O-gallate, Sanggenon C, and Sanggenofuran A shall be promising inhibitors at in vivo conditions. Communicated by Ramaswamy H. Sarma Binding aspects of natural compounds reveal the crucial factors of bioactivity towards pancreatic lipase.
Additional file 3: Table S3. of Molecular profiling of lung cancer specimens and liquid biopsies using MALDI-TOF mass spectrometry
Creators: name: Bonaparte, Eleonora
name: Pesenti, Chiara
name: Fontana, Laura
name: Falcone, Rossella
name: Paganini, Leda
name: Marzorati, Anna
name: Ferrero, Stefano
name: Nosotti, Mario
name: Mendogni, Paolo
name: Bareggi, Claudia
name: Sirchia, Silvia
name: Tabano, Silvia
name: Bosari, Silvano
name: Miozzo, Monica
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Molecular profile of NSCLC mutated cases. For each detected mutation, the number of positive cases and the diagnosis are reported. (DOCX 14 kb)
Caroline Petit
Creators: name: Leibowitch, Jacques (1942-2020)
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020

description: 1 fichier (1 page)
description: Autre destinataire : Olivier Delelis
All-atoms molecular dynamics study to screen potent efflux pump inhibitors against KpnE protein of Klebsiella pneumoniae
Creators: name: Dey, Suchanda
name: Rout, Madhusmita
name: Pati, Sanghamitra
name: Singh, Mahender Kumar
name: Dehury, Budheswar
name: Subudhi, Enketeswara
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences

description: The Small Multidrug Resistance efflux pump protein KpnE, plays a pivotal role in multi-drug resistance in Klebsiella pneumoniae. Despite well-documented study of its close homolog, EmrE, from Escherichia coli, the mechanism of drug binding to KpnE remains obscure due to the absence of a high-resolution experimental structure. Herein, we exclusively elucidate its structure-function mechanism and report some of the potent inhibitors through drug repurposing. We used molecular dynamics simulation to develop a dimeric structure of KpnE and explore its dynamics in lipid-mimetic bilayers. Our study identified both semi-open and open conformations of KpnE, highlighting its importance in transport process. Electrostatic surface potential map suggests a considerable degree of similarity between KpnE and EmrE at the binding cleft, mostly occupied by negatively charged residues. We identify key amino acids Glu14, Trp63 and Tyr44, indispensable for ligand recognition. Molecular docking and binding free energy calculations recognizes potential inhibitors like acarbose, rutin and labetalol. Further validations are needed to confirm the therapeutic role of these compounds. Altogether, our membrane dynamics study uncovers the crucial charged patches, lipid-binding sites and flexible loop that could potentiate substrate recognition, transport mechanism and pave the way for development of novel inhibitors against K. pneumoniae. Communicated by Ramaswamy H. Sarma
Computational screening of natural MtbDXR inhibitors for novel anti-tuberculosis compound discovery
Creators: name: Islam, Sabrina
name: Salekeen, Rahagir
name: Ashraf, Ayesha
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: DXR (1-deoxy-d-xylulose-5-phosphate reductoisomerase) is an essential enzyme in the Methylerythritol 4-phosphate (MEP) pathway, which is used by M. tuberculosis and a few other pathogens. This essential enzyme in the isoprenoid synthesis pathway has been previously reported as an important target for antibiotic drug design. However, till now, there is no record of any drug-like safe molecule to inhibit MtbDXR. Numerous plant species have been traditionally used for tuberculosis therapies. In this study, we selected six plant species with anti-tubercular properties. The chemoinformatic screening was performed on 352 phytochemicals from those plants against the MtbDXR protein. After molecular docking analysis, we filtered the top five compounds, CID: 5280443 (Apigenin), CID: 3220 (Emodin), CID: 5280863 (Kaempferol), CID: 5280445 (Luteolin), and CID: 6101979 (beta-Hydroxychalcone), based on binding affinity. Molecular dynamics simulations disclosed the stability of the compounds at the active site of the proteins. Finally, in silico ADME and toxicity evaluations confirmed the compounds to be effective and safe for oral administration. Thus, our findings identified three drug-like safe molecules- Apigenin, Kaempferol, and beta-Hydroxychalcone, that showed good stability in the protein’s active site. The results of this computational approach may act as an initial instruction for future in vitro and in vivo testing to identify natural drug-like compounds to treat tuberculosis. Communicated by Ramaswamy H. Sarma
H3Africa Genotyping Chip Data Analysis and GWAS workshop 2018 Training Videos
Creators: name: Hazelhurst, Scott
name: Botha, Gerrit
name: Aron, Shaun
name: Meintjes, Ayton
name: Maslamoney, Suresh
name: Panji, Sumir
name: Mbiyavanga, Mamana
Publisher: name: University of Cape Town
Year: 2022
Subjects: subject: 60405 Gene Expression (incl. Microarray and other genome-wide approaches)
subject: FOS: Biological sciences
subject: 60408 Genomics
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences

description: This is an archive containing training materials for the H3ABioNet course: “H3Africa Genotyping Chip Data Analysis and GWAS workshop, 2018”.
Brief description of the course: The H3Africa chip is being used by the H3Africa projects to generate data that will need to be analysed.
The course consisted of two components; a series of online lectures provided by experts in that specific domain. These are to introduce the main concepts and theory behind population genetics and GWAS. The second part of the course for selected participants was a practical Bring Your Own Data (BYOD) workshop on the analysis of H3Africa genotyping data using the H3ABioNet GWAS and Imputation workflows.
Intended Audience: People who would like to learn more about genotyping, calling, QC and running a GWAS study for the online lectures. H3Africa project members who will be undertaking the analysis of the genotype data from the H3Africa chip, and who had data available for the practical course.
Course trainers/authors: Mamana Mbiyavanga | H3ABioNet, University of Cape TownAyton Meintjes | H3ABioNet, University of Cape TownSuresh Maslamoney | H3ABioNet, University of Cape TownGerrit Botha | H3ABioNet, University of Cape TownShaun Aron | H3ABioNet, University of WitwatersrandSumir Panji | H3ABioNet, University of Cape TownScott Hazelhurst | H3ABioNet, University of Witwatersrand
Course level: Advanced
The archive contains the following items:Trainer/creator file containing the names of the person/s responsible for organising and delivering the courseCourse information file - which contains the original information about the course and includes a course scheduleLecture videos - slides loaded separately
Additional file 1: Figure S1. of Genome-wide protein phylogenies for four African cichlid species
Creators: name: Varadarajan, Ajay Ramakrishnan
name: Mopuri, Rohini
name: J. Streelman
name: McGrath, Patrick
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Full tree for the TF351789 family from all 109 species included in the Treefam database. This family contains a number of BMP growth factors belonging to the transforming growth factor beta family. (PDF 3001 kb)
MOESM13 of Comparative physiological, metabolomic, and transcriptomic analyses reveal developmental stage-dependent effects of cluster bagging on phenolic metabolism in Cabernet Sauvignon grape berries
Creators: name: Sun, Run-Ze
name: Cheng, Guo
name: Li, Qiang
name: Zhu, Yan-Rong
name: Zhang, Xue
name: Wang, Yu
name: He, Yan-Nan
name: Li, Si-Yu
name: He, Lei
name: Chen, Wu
name: Pan, Qiu-Hong
name: Duan, Chang-Qing
name: Wang, Jun
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Space Science
subject: Genetics
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Computational Biology

description: Additional file 13: Table S8. Co-expression analysis of genes encoding transcription factors and key enzymes required for sunlight-regulated phenolic biosynthesis.
Risk Factors for Targeted Violence: A Systematic Review [PROTOCOL]
Creators: name: Rotter, Merrill
name: Gonzales, Jay M. L.
name: Rosenfeld, Barry
name: Callahan, Perry A.
Publisher: name: Open Science Framework
Year: 2023
Subjects: subject: Criminology and Criminal Justice
subject: Legal Studies
subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology
subject: systematic literature review
subject: risk assessment
subject: targeted violence
subject: terrorism
subject: forensic psychology

description: This registration describes the protocol for a systematic literature review concerning risk factors for targeted violence. The review, which is currently underway, will critically examine the existing body of research on individual risk assessment for both ideological and non-ideological targeted violence.
Additional file 1: of Evaluation of the Preschool Situational Self-Regulation Toolkit (PRSIST) Program for Supporting childrenâ s early self-regulation development: study protocol for a cluster randomized controlled trial
Creators: name: Howard, Steven
name: Vasseleu, Elena
name: Neilsen-Hewett, Cathrine
name: Cliff, Ken
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Science Policy
subject: Computational Biology

description: SPIRIT checklist. (DOC 124 kb)