cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The associations of circulating common and uncommon polyunsaturated fatty acids and modification effects on dietary quality with all-cause and disease-specific mortality in NHANES 2003–2004 and 2011–2012
Creators: name: Zhang, Yuntao
name: Guo, Xiaoyu
name: Gao, Jian
name: Wei, Chunbo
name: Zhao, Shengnan
name: Liu, Zhipeng
name: Sun, Hu
name: Wang, Jiemei
name: Liu, Lin
name: Li, Ying
name: Han, Tianshu
name: Sun, Changhao
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy
subject: Plant Biology
subject: FOS: Biological sciences

description: Associations of dietary or supplementary intake of several unsaturated fatty acids and mortality have been widely studied but the results were still hitherto inconsistent or limited. It is still need to explore the effects of these fatty acids by using the objective biomarkers. We aimed to investigate the relevancy of several serum n-3 and n-6 fatty acids with all-cause and disease-specific mortality to confirm their health effects and effects on the associations between dietary quality and all-cause mortality. A total of 4132 people from NHANES 2003–2004 and 2011–2012 and the mortality information was confirmed from the NDI. CPH models adjusted for known risk factors were conducted to explore the associations between circulating n-3 and n-6 fatty acids and all-cause or CVD or cancer mortality under complex sampling. We further evaluated their effects on association between dietary quality and all-cause mortality. A total of 437 deaths occurred during the mean follow-up of 83.34 months, including 157 CVD death and 100 cancer death. Serum LA, ALA, EPA and DHA were associated with all-cause mortality (HR in quintile5: LA:0.584, 95%CI: 0.387–0.882, Ptrend = 0.011; ALA:0.626, 95%CI: 0.432–0.907, Ptrend = 0.008; EPA:0.535, 95%CI: 0.375–0.764, Ptrend = 0.001; DHA:0.669, 95%CI: 0.468–0.955, Ptrend = 0.031). Additionally, serum EPA and ALA were respectively related to CVD and cancer mortality (Q5 HR: EPA:0.450, 95%CI: 0.23–0.854, Ptrend = 0.009; ALA:0.387, 95%CI: 0.167–0.900, Ptrend = 0.022). Serum AA, GLA, DGLA and SDA were not associated with any risk of mortality. The effect on all-cause mortality of the lower AHEI scores can be improved by adherence to a higher serum LA, EPA and DHA (in the lowest AHEI strata, LA in tertile3 compared to tertile1 HR:0.596, 95%CI: 0.366–0.970; EPA:0.660, 95%CI: 0.454–0.959; DHA:0.666, 95%CI; 0.444–1.000). Our results support the recent dietary recommendations to increase the intake of plant-derived and marine-derived n-6 and n-3 to improve the ability of primary and secondary prevention.
Low Level Light Therapy (LLLT): Penetration and Photobiomodulation
Creators: name: Young, Cecilia
name: Cheuk Lam Mak
Publisher: name: figshare
Year: 2018
Subjects: subject: 110501 Dental Materials and Equipment
subject: FOS: Clinical medicine
subject: 110502 Dental Therapeutics, Pharmacology and Toxicology
subject: 110599 Dentistry not elsewhere classified
subject: 110505 Oral Medicine and Pathology
subject: 110504 Oral and Maxillofacial Surgery
subject: 110506 Orthodontics and Dentofacial Orthopaedics
subject: 110314 Orthopaedics
subject: 110315 Otorhinolaryngology
subject: 111499 Paediatrics and Reproductive Medicine not elsewhere classified
subject: 110507 Paedodontics
subject: Pathogenesis
subject: 110316 Pathology (excl. Oral Pathology)
subject: 110508 Periodontics

description: Mester et al., stated the laser effects in a review of their studies of 15 various biological systems, they observed the stimulating effect of low energy (in terms of J/cm2) laser and inhibiting effect of high energy laser and later reported the relationship of cumulative energy applied and the effects conforms to the Arndt-Schultz law. They concluded their experience with 875 healed cases and the results of their experiments had convinced them to recommend the use of lasers to stimulate wound healing [1]. Studies on the effects of Low Level Light Therapy reported pain relief [2,3] and promotion of wound healing [2]. These effects are useful in the oro-maxillofacial region and other parts of the body. Ohshiro introduced the concept of photobioactivation [4], he suggested that photobioactivation follows as a result of an exogenous photostimulus, and therefore follows the Arndt-Schultz law (Figure 1) [4].
Analysis of wavepacket tunneling with the method of Laplace transformation
Creators: name: Riahi, Natascha
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We use the method of Laplace transformation to determine the dynamics of a wave packet that passes a barrier by tunneling. We investigate the transmitted wave packet and find that it can be resolved into a sequence of subsequent wave packages. This result sheds new light on the Hartmann effect for the tunneling time and gives a possible explanation for an experimental result obtained by Spielmann et. al.
description: 22 pages; introduction enlarged, example and 1 figure added, Appendix for proof of consistency added
Symbolic powers of monomial ideals and Cohen-Macaulay vertex-weighted digraphs
Creators: name: Gimenez, Philippe
name: Martínez-Bernal, Jose
name: Simis, Aron
name: Villarreal, Rafael H.
name: Vivares, Carlos E.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Commutative Algebra (math.AC)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 13F20, 05C22, 05E40, 13H10

description: In this paper we study irreducible representations and symbolic Rees algebras of monomial ideals. Then we examine edge ideals associated to vertex-weighted oriented graphs. These are digraphs having no oriented cycles of length two with weights on the vertices. For a monomial ideal with no embedded primes we classify the normality of its symbolic Rees algebra in terms of its primary components. If the primary components of a monomial ideal are normal, we present a simple procedure to compute its symbolic Rees algebra using Hilbert bases, and give necessary and sufficient conditions for the equality between its ordinary and symbolic powers. We give an effective characterization of the Cohen--Macaulay vertex-weighted oriented forests. For edge ideals of transitive weighted oriented graphs we show that Alexander duality holds. It is shown that edge ideals of weighted acyclic tournaments are Cohen--Macaulay and satisfy Alexander duality
description: Special volume dedicated to Professor Antonio Campillo, Springer, to appear
Int 2_ITA_Case study 1_24/10/2024
Creators: name: Francesco Bonifacio
Publisher: name: Zenodo
Year: 2024

description: Trascrizione di intervista realizzata da Francesco Bonifacio (Università Cattolica del Sacro Cuore) e Ivana Pais (Università Cattolica del Sacro Cuore) a una lavoratrice di una piattaforma digitale italiana che eroga servizi di pulizie domestiche e assistenza domiciliare. La lavoratrice ha firmato una liberatoria che autorizza a condividere la trascrizione dell'intervista su Zenodo. L'intervista è stata anonimizzata. 

Transcript of an interview conducted by Francesco Bonifacio (Università Cattolica del Sacro Cuore) and Ivana Pais (Università Cattolica del Sacro Cuore) with a worker from an Italian digital platform offering domestic cleaning and care services. The worker signed a release that allows to publish the transcript of the interview on Zenodo. The interview has been anonymised.
MPEC 2024-F57 : 2024 FS1
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2024
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469
subject: 2024 FS1

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
Technical, market codes, and certification strategies
Creators: name: Stomff, Speranta
name: Stancu, Mihaela
Publisher: name: Zenodo
Year: 2024

description: A building code (also building control or building regulations) is a set of rules that specify the standards forconstruction objects such as buildings and non-building structures. Buildings must conform to the code to obtain planning permission, usually from a local council. The main purpose of the building codes is to protect public health, safety and general welfare as they relate to the construction and occupancy of buildings and structures– for example, the building codes in many countries require the engineers to consider the effects of soil liquefaction in the design of new buildings. A building code becomes law of a particular jurisdiction when formally enacted by the appropriate governmental or private authority.Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or REA. Neither the European Union nor the granting authority can be held responsible for them. Grant agreement ID: 101135629
Esthetic recovery of permanent Mandibular Lateral Incisor using biological post after non-surgical healing of Periradicular Lesion: A Case Report
Creators: name: Garg, Amit Kumar
name: Agrawal, Neha
name: Tewari, Rajendra Kumar
name: Surendra Kumar Mishra
Publisher: name: figshare
Year: 2018
Subjects: subject: 110501 Dental Materials and Equipment
subject: FOS: Clinical medicine
subject: 110502 Dental Therapeutics, Pharmacology and Toxicology
subject: 110599 Dentistry not elsewhere classified
subject: 110505 Oral Medicine and Pathology
subject: 110504 Oral and Maxillofacial Surgery
subject: 110506 Orthodontics and Dentofacial Orthopaedics
subject: 110314 Orthopaedics
subject: 110315 Otorhinolaryngology
subject: 111499 Paediatrics and Reproductive Medicine not elsewhere classified
subject: 110507 Paedodontics
subject: Pathogenesis
subject: 110508 Periodontics
subject: 110316 Pathology (excl. Oral Pathology)

description: Statement of the problem: Anterior tooth fracture, as a result of traumatic injuries, frequently occurs in dentistry. This leads to necrosis of pulp and periapical pathology. The goal of endodontic and restorative dentistry is to retain natural teeth with maximum function and pleasing esthetics. Purpose of the study: This study aimed at proper reconstruction of extensively damaged teeth through the procedure known as “Biological Restoration.” Materials and methods: Biological post obtained through natural, extracted teeth from another individual represents a low-cost option and alternative technique for the morphofunctional recovery of damaged anterior teeth that provides highly functional and esthetic outcomes. Conclusions: This case report refers to the esthetics and functional recovery of mandibular left lateral incisor after non-surgical healing of periradicular lesion.
Diagnostic overshadowing negatively influences the treatment of chronic hepatitis C in people with mental disorders who inject drugs: a scoping review
Creators: name: Dr Michael Christmass
name: Preston, Regan
name: Associate Professor Karen Heslop
Publisher: name: Open Science Framework
Year: 2023
Subjects: subject: Medicine and Health Sciences
subject: HCV
subject: scoping review
subject: PWUD
subject: diagnostic overshadowing
subject: hepatitis c
subject: mental health
subject: PWID
subject: people who inject drugs

description: To conduct a scoping review of the literature providing an overview of the current available research evidence on diagnostic overshadowing in hepatitis C assessment and treatment in PWID with mental health and substance-related disorders infected with hepatitis c virus.
Additional file 1: of Rational Design of Ni(OH)2 Hollow Porous Architecture for High-Sensitivity Enzyme-Free Glucose Sensor
Creators: name: Tian, Liangliang
name: He, Gege
name: Chen, Meijing
name: Wang, Jinbiao
name: Yao, Yucen
name: Bai, Xue
Publisher: name: figshare
Year: 2018
Subjects: Biochemistry
Cell Biology
Biotechnology
Chemical Sciences not elsewhere classified
Astronomical and Space Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Science Policy
Hematology

description: Figure S1. (a) SEM and (b) XRD pattern of the prepared Cu2O. Figure S2 The SEM image of Ni(OH)2 BHPA. Figure S3 The detection limit of Ni(OH)2 HPA and Ni(OH)2 BHPA. Table S1 Comparison of researched Ni(OH)2 HPA electrode with Ni(OH)2 BHPA about EIS. (DOCX 1575 kb)
GDI: D1.10 - Initial reports documenting the situation of and support provided to the NMGs
Creators: name: Doménech Cruz, Elena María
name: Ponce Polo, Ángela
name: Kubota, Kirina
Publisher: name: Zenodo
Year: 2024
Subjects: GDI
European Genomic Data Infrastructure
1+MG
1+Millions Genomes Initiative
B1MG
National Mirror Group
NMG
Genomic data sharing
Health data infrastructure
Capacity building
National genomic plans
ELIXIR collaboration
Implementation framework

description: The European Genomic Data Infrastructure (GDI) is a deployment and implementation project, co-funded by the Digital Europe programme. GDI's main objective is to realise the data infrastructure required by the 1+Million Genome Initiative (1+MG) to share high-quality genomic  and health data across borders; the 1+MG Virtual Cohort. Countries participating have committed to establish an operational National Mirror Group (NMG) that promotes and supports the national implementation of 1+MG Initiative guide via the 1+MG Framework that brings together all the guidelines and recommendations as well as National resources that will support the implementation.

This deliverable presents the results of the first activities carried out within task 1.6. National Mirror Group (NMG) support of the GDI project. The activities would be classified as follows:

Analysis of the NMG status in collaboration with ELIXIR. (Quarterly reports) 

Foster participation and capacity building actions. Following identification of gaps via the Quarterly Reports a workshop took place on June 25th “Towards the Implementation of National Genomic Plans in EU countries”. Representatives from Belgium, Denmark, France and Italy gave updates on the implementation of their national genomic plans. 

The data we worked with was collected from the Member States’ answers of two of the non-technical steps of the Quarterly reports of GDI nodes operational readiness. 

1.1.3. Have developed the 1+MG NMG or equivalent structure to contribute to the 1+MG Initiative.

1.1.4. Have developed a national genomic plan or similar that secures long-term funding that matches the target implementation level.

In addition, this deliverable includes a summary of the current national genomics plan of Belgium, Denmark, France and Italy.

Finally, common elements in the development process of the plan, and actors involved in the decision-making process were identified in order to help other countries develop their own National Genomics Plan.
Phenotypic proteomic profiling identifies a landscape of targets for circadian clock-modulating compounds.
Creators: name: Sandipan Ray
name: Radoslaw Lach
name: Heesom, Kate J
name: Utham K Valekunja
name: Encheva, Vesela
name: Snijders, Ambrosius P
name: Akhilesh B Reddy
Publisher: name: The Francis Crick Institute
Year: 2020
Subjects: Chemical Biology & High Throughput
Biochemistry & Proteomics
Computational & Systems Biology

description: Determining the exact targets and mechanisms of action of drug molecules that modulate circadian rhythms is critical to develop novel compounds to treat clock-related disorders. Here, we have used phenotypic proteomic profiling (PPP) to systematically determine molecular targets of four circadian period-lengthening compounds in human cells. We demonstrate that the compounds cause similar changes in phosphorylation and activity of several proteins and kinases involved in vital pathways, including MAPK, NGF, B-cell receptor, AMP-activated protein kinases (AMPKs), and mTOR signaling. Kinome profiling further indicated inhibition of CKId, ERK1/2, CDK2/7, TNIK, and MST4 kinases as a common mechanism of action for these clock-modulating compounds. Pharmacological or genetic inhibition of several convergent kinases lengthened circadian period, establishing them as novel circadian targets. Finally, thermal stability profiling revealed binding of the compounds to clock regulatory kinases, signaling molecules, and ubiquitination proteins. Thus, phenotypic proteomic profiling defines novel clock effectors that could directly inform precise therapeutic targeting of the circadian system in humans.
Bruxism: Its multiple causes and its effects on Dental Implants: A Review
Creators: name: Sameera Singh Deo
name: Singh, Devinder Preet
name: Nitya Dogra
Publisher: name: figshare
Year: 2018
Subjects: subject: 110502 Dental Therapeutics, Pharmacology and Toxicology
subject: FOS: Clinical medicine
subject: 110501 Dental Materials and Equipment
subject: 110599 Dentistry not elsewhere classified
subject: 110505 Oral Medicine and Pathology
subject: 110504 Oral and Maxillofacial Surgery
subject: 110314 Orthopaedics
subject: 110506 Orthodontics and Dentofacial Orthopaedics
subject: 110315 Otorhinolaryngology
subject: 111499 Paediatrics and Reproductive Medicine not elsewhere classified
subject: 110507 Paedodontics
subject: Pathogenesis
subject: 110508 Periodontics
subject: 110316 Pathology (excl. Oral Pathology)

description: The rehabilitation of partially or completely edentulous patients with implant supported prostheses has been widely used, achieving high success rates. However, many studies consider the presence of bruxism as a contraindication for this treatment modality. The purpose of this study was to review the literature and identify risk factors in implant supported rehabilitation planning in subjects with bruxism. The rehabilitation of bruxers using implant supported prostheses, using implants with adequate length and diameter, as well as proper positioning, seems to be a reliable treatment with reduced risks of failure. Bruxism control through the use of a night guard by rigid occlusal stabilization appliance, relieved in the region of implants, is highly indicated. Although it is clear that implant supported rehabilitation of patients with bruxism requires adequate planning and follow-up, well-designed randomized controlled trials are needed to provide reliable evidence on the long-term success of this treatment modality.
Renewal sequences and record chains related to multiple zeta sums
Creators: name: Duchamps, Jean-Jil
name: Pitman, Jim
name: Tang, Wenpin
Publisher: name: arXiv
Year: 2017
Subjects: subject: Probability (math.PR)
subject: Combinatorics (math.CO)
subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 11M06, 60C05, 60E05

description: For the random interval partition of $[0,1]$ generated by the uniform stick-breaking scheme known as GEM$(1)$, let $u_k$ be the probability that the first $k$ intervals created by the stick-breaking scheme are also the first $k$ intervals to be discovered in a process of uniform random sampling of points from $[0,1]$. Then $u_k$ is a renewal sequence. We prove that $u_k$ is a rational linear combination of the real numbers $1, ζ(2), \ldots, ζ(k)$ where $ζ$ is the Riemann zeta function, and show that $u_k$ has limit $1/3$ as $k \to \infty$. Related results provide probabilistic interpretations of some multiple zeta values in terms of a Markov chain derived from the interval partition. This Markov chain has the structure of a weak record chain. Similar results are given for the GEM$(θ)$ model, with beta$(1,θ)$ instead of uniform stick-breaking factors, and for another more algebraic derivation of renewal sequences from the Riemann zeta function.
description: 25 pages. This paper is published by https://www.ams.org/journals/tran/2019-371-08/S0002-9947-2018-07516-X/
PEGylated surfaces for the study of DNA-protein interactions by atomic force microscopy.
Creators: name: Akpinar, Bernice
name: Haynes, Philip J
name: Bell, Nicholas AW
name: Brunner, Katharina
name: Pyne, Alice LB
name: Hoogenboom, Bart W
Publisher: name: The Francis Crick Institute
Year: 2020
Subjects: Imaging
Structural Biology & Biophysics
Cell Biology

description: DNA-protein interactions are vital to cellular function, with key roles in the regulation of gene expression and genome maintenance. Atomic force microscopy (AFM) offers the ability to visualize DNA-protein interactions at nanometre resolution in near-physiological buffers, but it requires that the DNA be adhered to the surface of a solid substrate. This presents a problem when working in biologically relevant protein concentrations, where proteins may be present in large excess in solution; much of the biophysically relevant information can therefore be occluded by non-specific protein binding to the underlying substrate. Here we explore the use of PLLx-b-PEGy block copolymers to achieve selective adsorption of DNA on a mica surface for AFM studies. Through varying both the number of lysine and ethylene glycol residues in the block copolymers, we show selective adsorption of DNA on mica that is functionalized with a PLL10-b-PEG113/PLL1000-2000 mixture as viewed by AFM imaging in a solution containing high concentrations of streptavidin. We show - through the use of biotinylated DNA and streptavidin - that this selective adsorption extends to DNA-protein complexes and that DNA-bound streptavidin can be unambiguously distinguished in spite of an excess of unbound streptavidin in solution. Finally, we apply this to the nuclear enzyme PARP1, resolving the binding of individual PARP1 molecules to DNA by in-liquid AFM.
title: ADCO, Cartulaire de Cîteaux pour les possessions de Beaune et du Beaunois (XVe siècle), Cart. 174 (11 H 79), 56 pages, f. 0006
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/2015
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: Chartes de la Bourgogne du Moyen Âge
subject: cartulaire
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: Corpus Burgundiae Medii Aevi

description: Cartulaire de Cîteaux pour les possessions de Beaune et du Beaunois (XVe siècle), Archives départementales de la Côte-d'Or, Cart. 174 (11 H 79), 56 pages, f. 0006, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire de Cîteaux pour les possessions de Beaune et du Beaunois (XVe siècle), Archives départementales de la Côte-d'Or, Cart. 174 (11 H 79), 56 pages, f. 0006, 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
Controlling the coherence of a diamond spin qubit through strain engineering
Creators: name: Sohn, Young-Ik
name: Meesala, Srujan
name: Pingault, Benjamin
name: Atikian, Haig A.
name: Holzgrafe, Jeffrey
name: Gundogan, Mustafa
name: Stavrakas, Camille
name: Stanley, Megan J.
name: Sipahigil, Alp
name: Choi, Joonhee
name: Zhang, Mian
name: Pacheco, Jose L.
name: Abraham, John
name: Bielejec, Edward
name: Lukin, Mikhail D.
name: Atature, Mete
name: Loncar, Marko
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The uncontrolled interaction of a quantum system with its environment is detrimental for quantum coherence. In the context of solid-state qubits, techniques to mitigate the impact of fluctuating electric and magnetic fields from the environment are well-developed. In contrast, suppression of decoherence from thermal lattice vibrations is typically achieved only by lowering the temperature of operation. Here, we use a nano-electro-mechanical system (NEMS) to mitigate the effect of thermal phonons on a solid-state quantum emitter without changing the system temperature. We study the silicon-vacancy (SiV) colour centre in diamond which has optical and spin transitions that are highly sensitive to phonons. First, we show that its electronic orbitals are highly susceptible to local strain, leading to its high sensitivity to phonons. By controlling the strain environment, we manipulate the electronic levels of the emitter to probe, control, and eventually, suppress its interaction with the thermal phonon bath. Strain control allows for both an impressive range of optical tunability and significantly improved spin coherence. Finally, our findings indicate that it may be possible to achieve strong coupling between the SiV spin and single phonons, which can lead to the realisation of phonon-mediated quantum gates and nonlinear quantum phononics.
description: 11 pages, 3 figures
การออกแบบบรรจุภัณฑ์และการสื่อสารการตลาดออนไลน์ที่ส่งผลต่อการตัดสินใจซื้อผลิตภัณฑ์บราวนี่ภายใต้แบรนด์
Creators: name: พิชญาวีร์ ธิติจรัสชัย
Publisher: name: มหาวิทยาลัยนราธิวาสราชนครินทร์
Year: 2567
Subjects: การออกแบบบรรจุภัณฑ์
การสื่อสารการตลาดออนไลน์
การตัดสินใจซื้อ
บราวนี่

description: วารสารมหาวิทยาลัยนราธิวาสราชนครินทร์ สาขามนุษยศาสตร์และสังคมศาสตร์, 11, 1, 1-24
A combined structural and biochemical approach reveals translocation and stalling of UvrB on the DNA lesion as a mechanism of damage verification in bacterial nucleotide excision repair.
Creators: name: Jaciuk, Marcin
name: Swuec, Paolo
name: Gaur, Vineet
name: Kasprzak, Joanna M
name: Renault, Ludovic
name: Dobrychłop, Mateusz
name: Shivlee Nirwal
name: Bujnicki, Janusz M
name: Costa, Alessandro
name: Nowotny, Marcin
Publisher: name: The Francis Crick Institute
Year: 2020
Subjects: Structural Biology & Biophysics
Biochemistry & Proteomics
Imaging
Genome Integrity & Repair
Cell Cycle & Chromosomes

description: Nucleotide excision repair (NER) is a DNA repair pathway present in all domains of life. In bacteria, UvrA protein localizes the DNA lesion, followed by verification by UvrB helicase and excision by UvrC double nuclease. UvrA senses deformations and flexibility of the DNA duplex without precisely localizing the lesion in the damaged strand, an element essential for proper NER. Using a combination of techniques, we elucidate the mechanism of the damage verification step in bacterial NER. UvrA dimer recruits two UvrB molecules to its two sides. Each of the two UvrB molecules clamps a different DNA strand using its β-hairpin element. Both UvrB molecules then translocate to the lesion, and UvrA dissociates. The UvrB molecule that clamps the damaged strand gets stalled at the lesion to recruit UvrC. This mechanism allows UvrB to verify the DNA damage and identify its precise location triggering subsequent steps in the NER pathway.
Supplementary material from Overcoming clofazimine intrinsic toxicity: statistical modelling and characterization of solid lipid nanoparticles
Creators: name: Luíse L. Chaves
name: Lima, Sofia
name: Vieira, Alexandre C. C.
name: Ferreira, Domingos
name: Sarmento, Bruno
name: Salette Reis
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: 90301 Biomaterials
subject: FOS: Medical engineering
subject: 100799 Nanotechnology not elsewhere classified
subject: FOS: Nanotechnology

description: The aim of this work was to develop solid lipid nanoparticles (SLNs) loaded with clofazimine (CLZ) (SLNs-CLZ) to overcome its intrinsic toxicity and low water solubility, for oral drug delivery. A Box–Behnken design was constructed to unravel the relations between the independent variables in the selected responses. The optimized SLNs-CLZ exhibited the following properties: particle size ca 230 nm, zeta potential of −34.28 mV, association efficiency of 72% and drug loading of 2.4%, which are suitable for oral delivery. Further characterization included Fourier transformed infrared spectroscopy that confirmed the presence of the drug and the absence of chemical interactions. By differential scanning calorimetry was verified the amorphous state of CLZ. The storage stability studies ensured the stability of the systems over a period of 12 weeks at 4°C. In vitro cytotoxicity studies evidenced no effect of both drug-loaded and unloaded SLNs on MKN-28 gastric cells and on intestinal cells, namely Caco-2 and HT29-MTX cells up to 25 µg ml−1 in CLZ. Free CLZ solutions exhibited IC50 values of 16 and 20 µg ml−1 for Caco-2 and HT29-MTX cells, respectively. It can be concluded that the optimized system, designed considering important variables for the formulation of poorly soluble drugs, represents a promising platform for oral CLZ delivery.
Local cohomology and stratification
Creators: name: Nanda, Vidit
Publisher: name: arXiv
Year: 2017
Subjects: subject: Algebraic Topology (math.AT)
subject: FOS: Mathematics
subject: 57N80, 18F20

description: We outline an algorithm to recover the canonical (or, coarsest) stratification of a given finite-dimensional regular CW complex into cohomology manifolds, each of which is a union of cells. The construction proceeds by iteratively localizing the poset of cells about a family of subposets; these subposets are in turn determined by a collection of cosheaves which capture variations in cohomology of cellular neighborhoods across the underlying complex. The result is a nested sequence of categories, each containing all the cells as its set of objects, with the property that two cells are isomorphic in the last category if and only if they lie in the same canonical stratum. The entire process is amenable to efficient distributed computation.
description: Final version, published in Foundations of Computational Mathematics
Survival impact of achieving minimal residual negativity by multi-parametric flow cytometry in AL amyloidosis
Creators: name: Muchtar, Eli
name: Dispenzieri, Angela
name: Jevremovic, Dragan
name: Dingli, David
name: Buadi, Francis K.
name: Lacy, Martha Q.
name: Gonsalves, Wilson
name: Warsame, Rahma
name: Kourelis, Taxiarchis V.
name: Hayman, Suzanne R.
name: Kapoor, Prashant
name: Leung, Nelson
name: Russell, Stephen
name: Lust, John A.
name: Lin, Yi
name: Go, Ronald S.
name: Zeldenrust, Steven
name: Kyle, Robert A.
name: Rajkumar, S. Vincent
name: Kumar, Shaji K.
name: Gertz, Morie A.
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biotechnology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences

description: Response assessment in light chain (AL) amyloidosis is challenging given the low level of circulating free light chains usually seen. Multi-parametric flow cytometry (MFC) from a marrow aspirate was demonstrated to retain a prognostic significance in several recent studies. In this work, 82 AL patients who had MFC study at end of therapy were analysed based on whether clonal plasma cells were detected or not. Among patients who achieved deep response (i.e. very good partial response or complete response) to first-line therapy, lack of clonal marrow plasma cells as measured by MFC was associated with improved progression-free survival (PFS) compared to patients with residual clonal plasma cells (3-year PFS 88% vs. 46%, p = .003), particularly among patients who achieved a complete response (3-year PFS 100% vs. 33%, p = .001). Absence of clonal plasma cells by MFC compared with patients with detectable clonal plasma cells among deep responders was associated with lower level of involved light chain (involved free light chain (iFLC), median 1.1 vs. 1.7 mg/dL; p = .02) and higher frequency of renal response (100% vs. 68%; p = .005). Further studies are needed to determine if MFC should be incorporated into response criteria in AL amyloidosis.
Brauer groups of schemes associated to symmetric powers of smooth projective curves in arbitrary characteristics
Creators: name: Iyer, Jaya NN
name: Joshua, Roy
Publisher: name: arXiv
Year: 2017
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14C25, 14F20, 14F22, 14D05, 14D20, 14D21

description: In this paper we show that the l^n-torsion part of the cohomological Brauer groups of certain schemes associated to symmetric powers of a projective smooth curve over a separably closed field k are isomorphic, when `l is invertible in k. The schemes considered are the Symmetric powers themselves, then the corresponding Picard schemes and also certain Quot-schemes. We also obtain similar results for Prym varieties associated to certain finite covers of such curves: we prove such results only for curves defined over the field of complex numbers.
External Root Resorption associated with Impacted Third Molars: A Case Report
Creators: name: Mayrink, Gabriela
name: Ballista, Paula Ramos
name: Laisa Kinderlly
name: Araujo, Stella
name: Marano, Renato
Publisher: name: figshare
Year: 2018
Subjects: subject: 110501 Dental Materials and Equipment
subject: FOS: Clinical medicine
subject: 110502 Dental Therapeutics, Pharmacology and Toxicology
subject: 110599 Dentistry not elsewhere classified
subject: 110505 Oral Medicine and Pathology
subject: 110504 Oral and Maxillofacial Surgery
subject: 110506 Orthodontics and Dentofacial Orthopaedics
subject: 110314 Orthopaedics
subject: 110315 Otorhinolaryngology
subject: 111499 Paediatrics and Reproductive Medicine not elsewhere classified
subject: 110507 Paedodontics
subject: Pathogenesis
subject: 110316 Pathology (excl. Oral Pathology)
subject: 110508 Periodontics

description: The indications for impacted third molar extraction include the prevention of dental reabsorption on the adjacent tooth. Resorption can be classified as physiological (when deciduous teeth are exfoliated) or pathological (when caused by injury or irritation to the periodontal ligament). Many causes can trigger external root resorption (ERR), the most common cause of which is orthodontic forces. The most common cases of ERR involve impacted third molars which, due to the lack of space for their eruption, generate a greater chance of ERR on the distal portion of the second molar. This pathology is becoming progressively more frequent in clinical dental care. Periapical and panoramic radiographs are used to aid in diagnosis, as is cone beam computed tomography. In cone beam computed tomography scans, radiolucent areas with irregular gaps are detected; these gaps represent a significant loss of dental material. The objectives of this article were to report a case of second molar resorption triggered by an impacted third molar and to perform a review of the literature on the causes of external root resorption. Ideally, this information will aid dental clinicians (and orthodontists in particular) in understanding the features of this pathology so that they may recommend preventive third molar extraction when necessary.
Enhancing data security in GA4GH task execution services with confidential computing
Creators: name: Nikonorov, Pavel
name: Vakhitov, Ruslan
name: Senf, Alexander
name: Guennewig, Boris
name: Kanitz, Alex
Publisher: name: F1000 Research Limited
Year: 2024

description: In conventional computing systems, the sharing of data with another party implies its disclosure and the inability to control its further usage. Confidential Computing is a CPU-based technology that addresses these issues by enabling hardware-enforced trust establishment between remote computing devices and allowing them to exchange data that cannot be accessed outside one’s environment. The technology provides a new security feature for the protection of data in use by performing computations in a hardware-based, isolated and attested Trusted Execution Environment (TEE). Pioneered by Intel, Confidential Computing marks an evolutionary leap, transitioning from TEE in mobile devices to high-performance general-purpose CPUs, and now to GPUs.
Poincaré profiles of groups and spaces
Creators: name: Hume, David
name: Mackay, John M.
name: Tessera, Romain
Publisher: name: arXiv
Year: 2017
Subjects: subject: Group Theory (math.GR)
subject: Geometric Topology (math.GT)
subject: Metric Geometry (math.MG)
subject: FOS: Mathematics
subject: 20F65, 20F67, 20F18

description: We introduce a spectrum of monotone coarse invariants for metric measure spaces called Poincaré profiles. The two extremes of this spectrum determine the growth of the space, and the separation profile as defined by Benjamini--Schramm--Timár. In this paper we focus on properties of the Poincaré profiles of groups with polynomial growth, and of hyperbolic spaces, where we deduce a connection between these profiles and conformal dimension. As applications, we use these invariants to show the non-existence of coarse embeddings in a variety of examples.
description: 55 pages. To appear in Revista Matem\'atica Iberoamericana
Dynamics of a planar Coulomb gas
Creators: name: Bolley, François
name: Chafai, Djalil
name: Fontbona, Joaquín
Publisher: name: arXiv
Year: 2017
Subjects: subject: Mathematical Physics (math-ph)
subject: Functional Analysis (math.FA)
subject: Probability (math.PR)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We study the long-time behavior of the dynamics of interacting planar Brow-nian particles, confined by an external field and subject to a singular pair repulsion. The invariant law is an exchangeable Boltzmann -- Gibbs measure. For a special inverse temperature, it matches the Coulomb gas known as the complex Ginibre ensemble. The difficulty comes from the interaction which is not convex, in contrast with the case of one-dimensional log-gases associated with the Dyson Brownian Motion. Despite the fact that the invariant law is neither product nor log-concave, we show that the system is well-posed for any inverse temperature and that Poincar{é} inequalities are available. Moreover the second moment dynamics turns out to be a nice Cox -- Ingersoll -- Ross process in which the dependency over the number of particles leads to identify two natural regimes related to the behavior of the noise and the speed of the dynamics.
description: Minor revision for Annals of Applied Probability
Achieving the Heisenberg limit in quantum metrology using quantum error correction
Creators: name: Zhou, Sisi
name: Zhang, Mengzhen
name: Preskill, John
name: Jiang, Liang
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum metrology has many important applications in science and technology, ranging from frequency spectroscopy to gravitational wave detection. Quantum mechanics imposes a fundamental limit on measurement precision, called the Heisenberg limit, which can be achieved for noiseless quantum systems, but is not achievable in general for systems subject to noise. Here we study how measurement precision can be enhanced through quantum error correction, a general method for protecting a quantum system from the damaging effects of noise. We find a necessary and sufficient condition for achieving the Heisenberg limit using quantum probes subject to Markovian noise, assuming that noiseless ancilla systems are available, and that fast, accurate quantum processing can be performed. When the sufficient condition is satisfied, a quantum error-correcting code can be constructed which suppresses the noise without obscuring the signal; the optimal code, achieving the best possible precision, can be found by solving a semidefinite program.
description: 16 pages, 2 figures, see also arXiv:1704.06280
Evaluating Ising Processing Units with Integer Programming
Creators: name: Coffrin, Carleton
name: Nagarajan, Harsha
name: Bent, Russell
Publisher: name: arXiv
Year: 2017
Subjects: subject: Optimization and Control (math.OC)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: The recent emergence of novel computational devices, such as adiabatic quantum computers, CMOS annealers, and optical parametric oscillators, present new opportunities for hybrid-optimization algorithms that are hardware accelerated by these devices. In this work, we propose the idea of an Ising processing unit as a computational abstraction for reasoning about these emerging devices. The challenges involved in using and benchmarking these devices are presented and commercial mixed integer programming solvers are proposed as a valuable tool for the validation of these disparate hardware platforms. The proposed validation methodology is demonstrated on a D-Wave 2X adiabatic quantum computer, one example of an Ising processing unit. The computational results demonstrate that the D-Wave hardware consistently produces high-quality solutions and suggests that as IPU technology matures it could become a valuable co-processor in hybrid-optimization algorithms.
Additional file 1: of Bacterial microbiomes of Ixodes scapularis ticks collected from Massachusetts and Texas, USA
Creators: name: Thapa, Santosh
name: Zhang, Yan
name: Allen, Michael
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Figure S1. Rarefaction curves of the number of OTUs observed in male and female I. scapularis. Figure S2. Relative abundance of bacterial phyla in I. scapularis ticks from Texas and Massachusetts, USA. Figure S3. Bacterial richness (ACE and Chao1 estimators) in I. scapularis ticks. Figure S4. PCoA plot of weighted UniFrac distance metrics in male and female I. scapularis ticks collected from Texas and Massachusetts, USA. Figure S5. Unweighted PCoA plot of Borrelia-positive and Borrelia-negative I. scapularis males and females collected from Massachusetts, USA. Figure S6. Comparison of the bacterial microbiomes in colony-reared and field-collected I. scapularis ticks. (DOCX 1633 kb)
Rv2617c and P36 are virulence factors of pathogenic mycobacteria involved in resistance to oxidative stress.
Creators: name: Forrellad, Marina A
name: Vázquez, Cristina L
name: Blanco, Federico C
name: Klepp, Laura I
name: García, Elizabeth A
name: Rocha, Rosana V
name: Villafañe Luciana
name: Bigi, María M
name: Gutierrez, Maximiliano G
name: Bigi, Fabiana
Publisher: name: The Francis Crick Institute
Year: 2020
Subjects: Model organisms
Infectious Disease
Cell Biology

description: In this study, we characterized the role of Rv2617c in the virulence of Mycobacterium tuberculosis. Rv2617c is a protein of unknown function unique to M. tuberculosis complex (MTC) and Mycobacterium leprae. In vitro, this protein interacts with the virulence factor P36 (also named Erp) and KdpF, a protein linked to nitrosative stress. Here, we showed that knockout of the Rv2617c gene in M. tuberculosis CDC1551 reduced the replication of the pathogen in a mouse model of infection and favored the trafficking of mycobacteria to phagolysosomes. We also demonstrated that Rv2617c and P36 are required for resistance to in vitro hydrogen peroxide treatment in M. tuberculosis and Mycobacterium bovis, respectively. These findings indicate Rv2617c and P36 act in concert to prevent bacterial damage upon oxidative stress.
RCW 36 in the Vela Molecular Ridge: Evidence for a high-mass star cluster formation triggered by Cloud-Cloud Collision
Creators: name: Sano, Hidetoshi
name: Enokiya, Rei
name: Hayashi, Katsuhiro
name: Yamagishi, Mitsuyoshi
name: Saeki, Shun
name: Okawa, Kazuki
name: Tsuge, Kisetsu
name: Tsutsumi, Daichi
name: Kohno, Mikito
name: Hattori, Yusuke
name: Yoshiike, Satoshi
name: Fujita, Shinji
name: Nishimura, Atsushi
name: Ohama, Akio
name: Tachihara, Kengo
name: Torii, Kazufumi
name: Hasegawa, Yutaka
name: Kimura, Kimihiro
name: Ogawa, Hideo
name: Wong, Graeme F.
name: Braiding, Catherine
name: Rowell, Gavin
name: Burton, Michael G.
name: Fukui, Yasuo
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: A collision between two molecular clouds is one possible candidate for high-mass star formation. The HII region RCW 36, located in the Vela molecular ridge, contains a young star cluster with two O-type stars. We present new CO observations of RCW 36 with NANTEN2, Mopra, and ASTE using $^{12}$CO($J$ = 1-0, 2-1, 3-2) and $^{13}$CO($J$ = 2-1) line emissions. We have discovered two molecular clouds lying at the velocities $V_\mathrm{LSR} \sim$5.5 and 9 km s$^{-1}$. Both clouds are likely to be physically associated with the star cluster, as verified by the good spatial correspondence among the two clouds, infrared filaments, and the star cluster. We also found a high intensity ratio of $\sim$0.6-1.2 for CO $J$ = 3-2 / 1-0 toward both clouds, indicating that the gas temperature has been increased due to heating by the O-type stars. We propose that the O-type stars in RCW 36 were formed by a collision between the two clouds, with a relative velocity separation of 5 km s$^{-1}$. The complementary spatial distributions and the velocity separation of the two clouds are in good agreement with observational signatures expected for O-type star formation triggered by a cloud-cloud collision. We also found a displacement between the complementary spatial distributions of the two clouds, which we estimate to be 0.3 pc assuming the collision angle to be 45$^{\circ}$ relative to the line-of-sight. We estimate the collision timescale to be $\sim$10$^5$ yr. It is probable that the cluster age by Ellerbroek et al. (2013b) is dominated by the low-mass members which were not formed under the triggering by cloud-cloud collision, and that the O-type stars in the center of the cluster are explained by the collisional triggering independently from the low-mass star formation.
description: 13 pages, 9 figures, and 2 tables, accepted for publication in PASJ
B cells extract antigens at Arp2/3-generated actin foci interspersed with linear filaments.
Creators: name: Roper, Sophie I
name: Laabiah Wasim
name: Malinova, Dessislava
name: Way, Michael
name: Cox, Susan
name: Tolar, Pavel
Publisher: name: The Francis Crick Institute
Year: 2020
Subjects: subject: Model organisms
subject: Biochemistry & Proteomics
subject: Imaging
subject: Signalling & Oncogenes
subject: Structural Biology & Biophysics
subject: Cell Biology
subject: Infectious Disease
subject: Immunology
subject: FOS: Clinical medicine

description: Antibody production depends on B cell internalization and presentation of antigens to helper T cells. To acquire antigens displayed by antigen-presenting cells, B cells form immune synapses and extract antigens by the mechanical activity of the acto-myosin cytoskeleton. While cytoskeleton organization driving the initial formation of the B cell synapse has been studied, how the cytoskeleton supports antigen extraction remains poorly understood. Here we show that after initial cell spreading, F-actin in synapses of primary mouse B cells and human B cell lines forms a highly dynamic pattern composed of actin foci interspersed with linear filaments and myosin IIa. The foci are generated by Arp2/3-mediated branched-actin polymerization and stochastically associate with antigen clusters to mediate internalization. However, antigen extraction also requires the activity of formins, which reside near the foci and produce the interspersed filaments. Thus, a cooperation of branched-actin foci supported by linear filaments underlies B cell mechanics during antigen extraction.