cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Study of the effects of the Cannabinoids Anandamide and Cannabidiol on the feeding processes of Tetrahymena pyriformis
Creators: name: Jaisswar, Charou
Publisher: name: Lancaster University
Year: 2020

description: The regulation and physiological management of feeding behaviour, appetite and fullness in humans, and many other multicellular organisms, is governed by the pathways involved in the Endocannabinoid system (ECS). This complex system comprises lipid endocannabinoids e.g. Anandamide (AEA), that bind to cannabinoid receptors (e.g. CB1 and CB2), together with the enzymes involved in cannabinoid generation and hydrolysis. The ECS can also be stimulated by the plant cannabinoids (phytocannabinoids) such as Δ9-tetrahydrocannabidiol (Δ9-THC) and cannabidiol (CBD) which are found in Cannabis sativa. This study examined the effects exogenous of AEA and CBD on prey ingestion and food vacuole formation in the ciliate Tetrahymena pyriformis when feeding on an indigestible fluorescent cyanobacterium Synechococcus. Both AEA and CBD affected the ciliate feeding by inducing a lag; AEA having a shorter lag (ca. 36 min) in comparison to CBD (ca. 60 min). When ingestion resumed, AEA-treated cells fed at the same rate as the Control cells whereas CBD-treated cells had elevated ingestion rates (hyperphagia). The mechanism behind this is currently unknown but it does not appear to involve a cessation of food vacuole trafficking and defecation. It was also considered unlikely to be due to vacuole membrane recycling and the formation of phagocytic cups as the cellular machinery for this is very similar to that required for vacuole trafficking, which is unaffected by AEA and CBD. The study therefore hypothesised that: AEA and CBD completely stops prey capture but that pre-existing vacuoles are trafficked and defecated as normal and membrane is recycled to the cytostome where it accumulates. A lag of 60 min would allow the accumulation of more membrane than a 30 min lag and is the possible reason as to why ingestion rates after the former are higher. This study provides a basis for future research into the effects of CBD and AEA on the feeding capture processes of protists as well as their potential targets. Since protists do not possess the usual cannabinoid receptors associated with the human ECS future work might elucidate the ancestral targets of these cannabinoids together with their function in single cells.
Supplementary Information to Rutere et al., Ibuprofen degradation and associated bacterial communities in hyporheic zone sediments
Creators: name: Rutere, Cyrus
name: Knoop, Kirsten
name: Posselt, Malte
name: Ho, Adrian
name: Horn, Marcus A.
Publisher: name: Zenodo
Year: 2020

description: Supplementary Information: Supplementary Figures and Tables
title: Исследование листьев манжетки обыкновенной
Creators: name: Карпов, Александр
Publisher: name: Новгородский государственный университет имени Ярослава Мудрого (НовГУ)
Year: 2020

description: Манжетка лекарственная (Alchemilla vulgaris) – перспективное лекарственное растение. Было обнаружено, что сырье содержит большое число органических кислот, и их количественное содержание не зависит от измельченности сырья.
A high-quality chromosome-level genome assembly of the European flat oyster, Ostrea edulis
Creators: name: 白奕天(Yitian Bai)
Publisher: name: CNGB
Year: 2022
Subjects: Assembly
Other
Genome assembly and annotation
Multiisolate
Agricultural

description: Here, we report a high-quality chromosome-level genome assembly of the European flat oyster (Ostrea edulis) utilizing the PacBio single-molecule sequencing and Hi-C technologies. The assembled genome was 946.06 Mb with scaffold N50 length of 94.82 Mb, and a total of 34,495 protein-coding genes were predicted.
Gamma-Ray Burst Prompt Emission
Creators: name: Zhang, Bing
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The origin of gamma-ray burst (GRB) prompt emission, bursts of gamma-rays lasting from shorter than one second to thousands of seconds, remains not fully understood after more than 40 years of observations. The uncertainties lie in several open questions in the GRB physics, including jet composition, energy dissipation mechanism, particle acceleration mechanism, and radiation mechanism. Recent broad-band observations of prompt emission with Fermi sharpen the debates in these areas, which stimulated intense theoretical investigations invoking very different ideas. I will review these debates, and argue that the current data suggest the following picture: A quasi-thermal spectral component originating from the photosphere of the relativistic ejecta has been detected in some GRBs. Even though in some cases (e.g. GRB 090902B) this component dominates the spectrum, in most GRBs, this component either forms a sub-dominant "shoulder" spectral component in the low energy spectral regime of the more dominant "Band" component, or is not detectable at all. The main "Band" spectral component likely originates from the optically thin region due to synchrotron radiation. The diverse magnetization in the GRB central engine is likely the origin of the observed diverse prompt emission properties among bursts.
description: This invited review article is based on invited talks delivered by the author at several conferences, including the 13th Marcel Grossmann Meeting (Stockholm, July 1-7, 2012), "Gamma 2012" (Heidelberg, July 9-13, 2012), the 7th Huntsville GRB Symposium (Nashville, April 14-18, 2013), and SNe and GRBs 2013 (Kyoto, Nov. 11-14, 2013). Published in International Journal of Modern Physics D
High-resolution architecture of human epiphysis formation
Creators: name: 孙亨
Publisher: name: CNGB
Year: 2022
Subjects: Transcriptome or Gene expression
Monoisolate
Medical

description: In this project, we mapped differentiation trajectory of human chondrocyte during postnatal finger epiphysis development by using single-cell RNA sequencing. Our results uncovered that chondroprogenitors have two differentiation pathways to hypertrophic chondrocytes during ossification, and one pathway to articular chondrocytes for formation of cartilages. Our study provides a comprehensive roadmap of chondrocyte differentiation in human epiphysis thereby expanding the knowledge of bone and articular cartilage, which could be utilized to design biotherapeutics for bone and articular cartilage regeneration.
O'QUVCHILARNING MUSTAQIL FIKRLASH JARAYONLARINING DINAMIKASI
Creators: name: Dehqanova, Muborakxon
Publisher: name: Zenodo
Year: 2023

description: Maqolada umumiy maktab o'quvchilarida mustaqil fikrlash jarayonlarining dinamikasining ayrim masalalari yoritilgan, bu pedagogik yondashuvga oid muhim uslubiy tavsiyalar berilgan.
A Mining Method to Create Knowledge Map by Analysing the Data Resource
Creators: name: Gupta, Arti
name: Deotale, Prof. N. T
Publisher: name: arXiv
Year: 2014
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: The fundamental step in measuring the robustness of a system is the synthesis of the so called Process Map.This is generally based on the user raw data material.Process Maps are of fundamental importance towards the understanding of the nature of a system in that they indicate which variables are causally related and which are particularly important.This paper represent the system Map or business structure map to understand business criteria studying the various aspects of the company.The business structure map or knowledge map or Process map are used to increase the growth of the company by giving some useful measures according to the business criteria.This paper also deals with the different company strategy to reduce the risk factors.Process Map is helpful for building such knowledge successfully.Making decisions from such map in a highly complex situation requires more knowledge and resources.
description: 6 pages,5 figures, Published with International Journal of Engineering Trends and Technology (IJETT)"
title: Роль дислипидемий в патогенезе атеросклероза
Creators: name: Коржева, М.
name: Кучерина, А.
Publisher: name: Новгородский государственный университет имени Ярослава Мудрого (НовГУ)
Year: 2020

description: В статье представлены результаты изучения основных противоречий холестериновой теории атеросклероза. Произведен разбор её положений, рассмотрены материалы исследований отечественных и иностранных авторов, подтверждающие и опровергающие взаимосвязь явлений атеросклеротического генеза и дислипидемий. Исследованы 16 историй болезни (ИБ) с основным клиническим диагнозом «атеросклероз», проанализированы результаты дуплексного сканирования брахиоцефальных артерий, прижизненного анатомо-морфологического исследования операционного материала и липидограммы.
The NIR structure of the barred galaxy NGC253 from VISTA
Creators: name: Iodice, E.
name: Arnaboldi, M.
name: Rejkuba, M.
name: Neeser, M. J.
name: Greggio, L.
name: Gonzalez, O. A.
name: Irwin, M.
name: Emerson, J. P.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: [abridged] We used J and Ks band images acquired with the VISTA telescope as part of the science verification to quantify the structures in the stellar disk of the barred Sc galaxy NGC253. Moving outward from the galaxy center, we find a nuclear ring within the bright 1 kpc diameter nucleus, then a bar, a ring with 2.9 kpc radius. From the Ks image we obtain a new measure of the deprojected length of the bar of 2.5 kpc. The bar's strength, as derived from the curvature of the dust lanes in the J-Ks image, is typical of weak bars. From the deprojected length of the bar, we establish the corotation radius (R_CR=3 kpc) and bar pattern speed (Omega_b = 61.3 km /s kpc), which provides the connection between the high-frequency structures in the disk and the orbital resonances induced by the bar. The nuclear ring is located at the inner Lindblad resonance. The second ring does not have a resonant origin, but it could be a merger remnant or a transient structure formed during an intermediate stage of the bar formation. The inferred bar pattern speed places the outer Lindblad resonance within the optical disk at 4.9 kpc, in the same radial range as the peak in the HI surface density. The disk of NGC253 has a down-bending profile with a break at R~9.3 kpc, which corresponds to about 3 times the scale length of the inner disk. We discuss the evidence for a threshold in star formation efficiency as a possible explanation of the steep gradient in the surface brightness profile at large radii. The NIR photometry unveils the dynamical response of the NGC253 stellar disk to its central bar. The formation of the bar may be related to the merger event that determined the truncation of stars and gas at large radii and the perturbation of the disk's outer edge.
description: Accepted for publication in Astronomy & Astrphysics. High resolution pdf file is available at the following link: https://www.dropbox.com/s/4o4cofs1lyjrtpv/NGC253.pdf
title: Olfactory host location and host preference of Holepyris sylvanidis (Hymenoptera: Bethylidae) and Cephalonomia waterstoni (Bethylidae), two natural enemies of Tribolium and Cryptolestes species
Creators: name: Amante, Marco
name: Russo, Agatino
name: Schöller, Matthias
name: Steidle, Johannes L.M.
Publisher: name: Julius Kühn-Institut
Year: 2018

description: Parasitoids can suppress populations of their host and thus play a primary role in Integrated Pest Management. In the stored product environment, stimuli deriving from plant products, damaged plant products and hosts might be important for host location by the parasitoids. We studied foraging cues in Holepyris sylvanidis (Hymenoptera: Bethylidae), a larval parasitoid of Tribolium species and Cephalonomia waterstoni (Bethylidae), a natural enemy of the rusty grain beetle Cryptolestes ferrugineus (Coleoptera: Cucujidae). Our studies in a fourchamber olfactometer revealed that the host complexes of both Tribolium species and different living host stages attract naive H. sylvanidis females, whereas no reaction was observed to uninfested substrates. The olfactory response of C. waterstoni was found to be strongly elicited both by chemicals emitted by the dust, adult C. ferrugineus and C. ferrugineus third and fourth instar larvae. Our findings may contribute to the development of biological control strategies of T. castaneum, T. confusum and C. ferrugineus with parasitoids.
description: Julius-Kühn-Archiv, Nr. 463, Vol. 1 (2018): Proceedings of the 12th International Working Conference on Stored Product Protection (IWCSPP) in Berlin, Germany, October 7-11, 2018
title: Superorganism Immunity
title: A Major Transition in Immune System Evolution
titleType: Subtitle
Creators: name: Pull, Christopher D.
name: McMahon, Dino P.
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: superorganism
subject: disease
subject: social evolution
subject: major evolutionary transition
subject: social immunity
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::576 Genetik und Evolution

description: Social insect colonies can express adaptive, organism-like design. In some cases, colonies so resemble a unique, cohesive and integrated “individual” that they are termed superorganisms. The major evolutionary transitions framework explains, via inclusive fitness theory, how new levels of biological individuality, including genes into genomes within cells, cells into multicellular organisms and organisms into superorganisms can emerge. Importantly, it highlights how at each major transition similar challenges arose and why seemingly convergent solutions evolved. One challenge faced at each transition is exploitation, caused internally by social cheaters and externally by parasites and pathogens. To overcome the problem of exploitation transitions in biological individuality required novel immune systems to maintain the integrity of newly emerged individuals. Multicellular organisms evolved an immune system while social insect colonies evolved a social immune system. In this review, we take a major transitions perspective of immunity to highlight the interdependency between the evolution of immune systems and the emergence of biological individuality. We build on the notion that superorganisms have evolved an immune system to promote the fitness of the colony. We draw parallels between the evolution of the metazoan immune system and the social immune system, and their expression as cognitive networks. Moreover, we discuss how research on other group-living species, such as family based cooperative breeders, can inform our understanding of how social immune systems evolve. We conclude that superorganism immunity is an adaptive suite of organismal traits that evolves to maximize the fitness of advanced social insect colonies, fulfilling the same function as the immune system of Metazoa.
title: Accelerating RSA Public Key Cryptography via Hardware Acceleration
Creators: name: Ramesh, Pavithra
Publisher: name: University of Massachusetts Amherst
Year: 2020

description: A large number and a variety of sensors and actuators, also known as edge devices of the Internet of Things, belonging to various industries - health care monitoring, home automation, industrial automation, have become prevalent in today's world. These edge devices need to communicate data collected to the central system occasionally and often in burst mode which is then used for monitoring and control purposes. To ensure secure connections, Asymmetric or Public Key Cryptography (PKC) schemes are used in combination with Symmetric Cryptography schemes. RSA (Rivest - Shamir- Adleman) is one of the most prevalent public key cryptosystems, and has computationally intensive operations which might have a high latency when implemented in resource constrained environments. The objective of this thesis is to design an accelerator capable of increasing the speed of execution of the RSA algorithm in such resource constrained environments. The bottleneck of the algorithm is determined by analyzing the performance of the algorithm in various platforms - Intel Linux Machine, Raspberry Pi, Nios soft core processor. In designing the accelerator to speedup bottleneck function, we realize that the accelerator architecture will need to be changed according to the resources available to the accelerator. We use high level synthesis tools to explore the design space of the accelerator by taking into consideration system level aspects like the number of ports available to transfer inputs to the accelerator, the word size of the processor, etc. We also propose a new accelerator architecture for the bottleneck function and the algorithm it implements and compare the area and latency requirements of it with other designs obtained from design space exploration. The functionality of the design proposed is verified and prototyped in Zynq SoC of Xilinx Zedboard.
title: Вопросы хиральности веществ в фармакологических изысканиях: на примере антигипертензивных средств
Creators: name: Коржева, М.
name: Хруцкий, К.
Publisher: name: Новгородский государственный университет имени Ярослава Мудрого (НовГУ)
Year: 2020

description: В работе изучаются вопросы хирального биологического фактора и стереоспецифичности фармацевтических субстанций: применительно к общим вопросам теории хиральности (главным образом, со ссылкой на достижения
отечественной научной школы, возглавляемой В.А. Твердисловом); и, в частном аспекте, на примере антигипертензивных средств. Обсуждаются перспективы фармакологических изысканий в плане создания новых хиральных фармакологических средств.
Association Between Prolonged Grief and Attitudes Toward Reconciliation in Bereaved Survivors of the Khmer Rouge Regime in Cambodia
Creators: name: Stammel, Nadine
name: Heinzl, Louisa
name: Heeke, Carina
name: Böttche, Maria
name: Knaevelsrud, Christine
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: Cambodia
subject: bereavement
subject: grief
subject: reconciliation
subject: forgiveness
subject: post-conflict
subject: violent death
subject: genocide
subject: 100 Philosophie und Psychologie::150 Psychologie::150 Psychologie

description: Background: During the Khmer Rouge regime in Cambodia, about a quarter of the population died, resulting in many individuals losing close relatives. Still today, many individuals are suffering from the psychological consequences of these losses, which might also affect the process of reconciliation within the Cambodian society. The aim of this paper is therefore to investigate the association between symptoms of prolonged grief and attitudes toward reconciliation. Methods: A sample of 775 survivors of the Khmer Rouge regime who lost relatives during the conflict were interviewed about their losses and traumatic events, prolonged grief (PG; Complicated Grief Assessment Self-Report, CGA-SR), posttraumatic stress disorder (PTSD Checklist - Civilian Version) and attitudes toward reconciliation (Readiness to Reconcile Inventory, RRI). Results: A higher symptom severity of PG was significantly associated with readiness to reconcile even when controlling for other relevant variables (β = −0.22; p
Lacon flavopilosus Vats and Kashyap 1992
Creators: name: Kotru, Akash
name: Chandran, Nithya
name: Dubey, Anil Kumar
name: Prosvirov, Alexander S.
Publisher: name: Zenodo
Year: 2025
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Elateridae
Lacon
Lacon flavopilosus

description: Lacon flavopilosus Vats and Kashyap, 1992
Lacon flavopilosus Vats and Kashyap, 1992: 18.
Type depository. Holotype (NPC-IARI).
Type locality. Uttarakhand (Mohan).
Distribution. India: Uttarakhand.
Literature. Vats and Kashyap (1992: 18): original description; Chakraborty and Chakrabarti (2000: 76): catalogue.
description: Published as part of Kotru, Akash, Chandran, Nithya, Dubey, Anil Kumar & Prosvirov, Alexander S., 2025, A catalogue of Indian Agrypninae Candèze, 1857 (Coleoptera: Elateridae), pp. 1-66 in Zootaxa 5614 (1) on page 31, DOI: 10.11646/zootaxa.5614.1.1, http://zenodo.org/record/15217075
Detection of Class I Methanol (CH3OH) Maser Candidates in Supernova Remnants
Creators: name: Pihlström, Y. M.
name: Sjouwerman, L. O.
name: Frail, D. A.
name: Claussen, M. J.
name: Mesler, R. A.
name: McEwen, B. C.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We have used the Karl G. Jansky Very Large Array (VLA) to search for 36 GHz and 44 GHz methanol (CH3OH) lines in a sample of 21 Galactic supernova remnants (SNRs). Mainly the regions of the SNRs with 1720 MHz OH masers were observed. Despite the limited spatial extent covered in our search, methanol masers were detected in both G1.4-0.1 and W28. Additional masers were found in SgrAEast. More than 40 masers were found in G1.4-0.1 which we deduce are due to interactions between the SNR and at least two separate molecular clouds. The six masers in W28 are associated with the molecular cloud that is also associated with the OH maser excitation. We discuss the possibility that the methanol maser may be more numerous in SNRs than the OH maser, but harder to detect due to observational constraints.
description: 9 pages
Erweiterte Messtechnik und differenzierte Prozessanalyse beim Pressschweißen mit magnetisch bewegtem Lichtbogen: Einblicke in die Schweißdynamik von Stahl und Aluminium
Creators: name: Grünzel, Oliver
Publisher: name: Hannover : Institutionelles Repositorium der Leibniz Universität Hannover
Year: 2024
Subjects: subject: Butt welding
subject: Magnetically impelled arc (MIAB)
subject: Process analysis
subject: Steel-aluminum joints
subject: Pressschweißen
subject: Magnetisch bewegter Lichtbogen (MBP)
subject: Prozessanalyse
subject: Stahl-Aluminium-Verbindungen
subject: Dewey Decimal Classification::600 | Technik::620 | Ingenieurwissenschaften und Maschinenbau

description: In der vorliegenden Dissertation wird das Pressschweißen mit magne-tisch bewegtem Lichtbogen (MBP) mit einem Fokus auf messtechnischen Erweiterungen, insbesondere der Erfassung von Lichtbogenstrom und Lichtbogenspannung, untersucht. Untersuchungen wurden an verschie-denen Materialverbindungen wie Stahl-Stahl, Aluminium-Aluminium und Stahl-Aluminium durchgeführt. Während sich die Analyse der Lichtbo-genparameter als reproduzierbar für Stahlverbindungen erwies, traten Herausforderungen bei Aluminium- und Mischverbindungen hinsichtlich Prozessstabilität und auch in den erreichten Festigkeiten auf. Die Integration neuer Messtechniken ermöglichte detaillierte Einblicke in den Verlauf von Lichtbogenstrom und Lichtbogenspannung während des Schweißprozesses. Diese Forschungsarbeit trägt dazu bei, das Ver-ständnis des MBP-Prozesses zu vertiefen und bietet Ansätze zur Optimie-rung der Prozessstabilität und Schweißqualität bei verschiedenen Mate-rialkombinationen. Durch die Fokussierung auf Lichtbogenstrom und -spannung eröffnen sich neue Möglichkeiten zur präzisen Steuerung und Regelung des Schweißprozesses, was potenziell zu verbesserten Eigen-schaften der Schweißverbindungen führt.
description: This dissertation explores the magnetically impelled arc butt welding (MIAB) process with a focus on metrological extensions, particularly the measurement of arc current and voltage. Investigations were conducted on various material combinations such as steel-steel, aluminum-aluminum, and steel-aluminum. While the analysis of arc parameters proved to be reproducible for steel joints, challenges arose in aluminum and hybrid joints regarding process stability and strength. The integration of novel measurement techniques provided detailed in-sights into the evolution of arc current and voltage during the welding process. This research contributes to deepening the understanding of the MIAB process and offers approaches to optimize process stability and weld quality for different material combinations. By focusing on arc current and voltage, new opportunities emerge for precise control and regulation of the welding process, potentially leading to improved prop-erties of the welded joints.
Creating Emordle: Animating Word Cloud for Emotion Expression
Creators: name: Xie, Liwenhan
name: Shu, Xinhuan
name: Su, Jeon Cheol
name: Wang, Yun
name: Chen, Siming
name: Qu, Huamin
Publisher: name: arXiv
Year: 2023
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: We propose emordle, a conceptual design that animates wordles (compact word clouds) to deliver their emotional context to the audiences. To inform the design, we first reviewed online examples of animated texts and animated wordles, and summarized strategies for injecting emotion into the animations. We introduced a composite approach that extends an existing animation scheme for one word to multiple words in a wordle with two global factors: the randomness of text animation (entropy) and the animation speed (speed). To create an emordle, general users can choose one predefined animated scheme that matches the intended emotion class and fine-tune the emotion intensity with the two parameters. We designed proof-of-concept emordle examples for four basic emotion classes, namely happiness, sadness, anger, and fear. We conducted two controlled crowdsourcing studies to evaluate our approach. The first study confirmed that people generally agreed on the conveyed emotions from well-crafted animations, and the second one demonstrated that our identified factors helped fine-tune the delivered emotion extent. We also invited general users to create emordles on their own based on our proposed framework. Through this user study, we confirmed the effectiveness of the approach. We concluded with implications for future research opportunities of supporting emotion expression in visualizations.
description: Accepted in IEEE Transactions on Visualization and Computer Graphics
Protein production, kinetic and biophysical characterization of three human dihydroorotate dehydrogenase mutants associated with Miller syndrome
Creators: name: Rodriguez, Juan Manuel Orozco
name: Krupinska, Ewa
name: Wacklin-Knecht, Hanna
name: Knecht, Wolfgang
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Miller syndrome is a rare Mendelian disorder caused by mutations in the gene encoding human dihydroorotate dehydrogenase (DHODH). Human DHODH, a Class II DHODH, is an integral protein of the inner mitochondrial membrane (IMM) catalyzing the fourth step of the de novo pyrimidine biosynthesis pathway. Here we present a summary of the state of knowledge regarding Miller syndrome in the absence of any current review on the topic. We then describe the production and characterization of three distinct DHODH missense mutations (G19E, E52G, R135C) associated with Miller syndrome by means of enzyme kinetics and biophysical techniques. These human DHODH mutants were produced both in E. coli and in insect cells using the baculovirus expression vector system. We can show that the effects of these mutations differ from each other and the wild-type enzyme with respect to decreased enzymatic activity, decreased protein stability and probably disturbance of the correct import into the IMM. In addition, our results show that the N-terminus of human DHODH is not only a structural element necessary for correct mitochondrial import and location of DHODH on the outer side of the IMM, but also influences thermal stability, enzymatic activity and affects the kinetic parameters. Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2021.2023749 .
Constant time encryption as a countermeasure against remote cache timing attacks
Creators: name: Jayasinghe, D.
name: Ragel, R. G.
name: Elkaduwe, D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: Rijndael was standardized in 2001 by National Institute of Standard and Technology as the Advanced Encryption Standard (AES). AES is still being used to encrypt financial, military and even government confidential data. In 2005, Bernstein illustrated a remote cache timing attack on AES using the client-server architecture and therefore proved a side channel in its software implementation. Over the years, a number of countermeasures have been proposed against cache timing attacks both using hardware and software. Although the software based countermeasures are flexible and easy to deploy, most of such countermeasures are vulnerable to statistical analysis. In this paper, we propose a novel software based countermeasure against cache timing attacks, known as constant time encryption, which we believe is secure against statistical analysis. The countermeasure we proposed performs rescheduling of instructions such that the encryption rounds will consume constant time independent of the cache hits and misses. Through experiments, we prove that our countermeasure is secure against Bernstein's cache timing attack.
Protein production, kinetic and biophysical characterization of three human dihydroorotate dehydrogenase mutants associated with Miller syndrome
Creators: name: Rodriguez, Juan Manuel Orozco
name: Krupinska, Ewa
name: Wacklin-Knecht, Hanna
name: Knecht, Wolfgang
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Miller syndrome is a rare Mendelian disorder caused by mutations in the gene encoding human dihydroorotate dehydrogenase (DHODH). Human DHODH, a Class II DHODH, is an integral protein of the inner mitochondrial membrane (IMM) catalyzing the fourth step of the de novo pyrimidine biosynthesis pathway. Here we present a summary of the state of knowledge regarding Miller syndrome in the absence of any current review on the topic. We then describe the production and characterization of three distinct DHODH missense mutations (G19E, E52G, R135C) associated with Miller syndrome by means of enzyme kinetics and biophysical techniques. These human DHODH mutants were produced both in E. coli and in insect cells using the baculovirus expression vector system. We can show that the effects of these mutations differ from each other and the wild-type enzyme with respect to decreased enzymatic activity, decreased protein stability and probably disturbance of the correct import into the IMM. In addition, our results show that the N-terminus of human DHODH is not only a structural element necessary for correct mitochondrial import and location of DHODH on the outer side of the IMM, but also influences thermal stability, enzymatic activity and affects the kinetic parameters. Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2021.2023749 .
Microbial and human transcriptional profiling of coronavirus disease 2019 patients: Potential predictors of disease severity
Creators: name: 庞鹏飞(Pengfei Pang)
Publisher: name: CNGB
Year: 2022
Subjects: Metagenome
Multiisolate
Medical

description: The high morbidity of patients with coronavirus disease 2019 (COVID-19) brings on a panic around the world. COVID-19 is associated with sex bias, immune system, and preexisting chronic diseases. We analyzed the gene expression in patients with COVID-19 and in their microbiota in order to identify potential biomarkers to aid in disease management. A total of 129 RNA samples from nasopharyngeal, oropharyngeal, and anal swabs were collected and sequenced in a high-throughput manner. Several microbial strains differed in abundance between patients with mild or severe COVID-19. Microbial genera were more abundant in oropharyngeal swabs than in nasopharyngeal or anal swabs. Oropharyngeal swabs allowed more sensitive detection of the causative SARS-CoV-2. Microbial and human transcriptomes in swabs from patients with mild disease showed enrichment of genes involved in amino acid metabolism, or protein modification via small protein removal, antibacterial defense responses, respectively, whereas swabs from patients with severe disease showed enrichment of genes involved in drug metabolism, or negative regulation of apoptosis execution, spermatogenesis, immune system, respectively. Microbial abundance and diversity did not differ significantly between males and females. The expression of several host genes on the X chromosome correlated negatively with disease severity. In this way, our analyses identify host genes whose differential expression could aid in the diagnosis of COVID-19 and prediction of its severity via non-invasive assay.
title: Особенности паттерна ЭЭГ при различной степени обогащения акцептора результата действия для успешного завершения целенаправленной деятельности
Creators: name: Кучерина, А.
name: Коржева, М.
name: Плотников, И
name: Шабаев, В.
name: Бойцов, С.
Publisher: name: Новгородский государственный университет имени Ярослава Мудрого (НовГУ)
Year: 2020

description: В работе рассматривается функционирование высшей нервной деятельности с позиций системного подхода, а также влияние обогащения акцептора результата действия на достижение успешного результата целенаправленной деятельности. Теоретические предпосылки повышения качества целенаправленной
деятельности при предварительном инструктировании были успешно применены в прикладном аспекте. В ходе исследования были получены ЭЭГ-корреляты и показаны паттерны активности нейронов головного мозга при достижении цели у испытуемых трех групп, разделенных по степени предварительного инструктирования.
A semi-parametric Bayesian model of inter- and intra-examiner agreement for periodontal probing depth
Creators: name: Hill, E. G.
name: Slate, E. H.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Applications (stat.AP)
subject: FOS: Computer and information sciences

description: Periodontal probing depth is a measure of periodontitis severity. We develop a Bayesian hierarchical model linking true pocket depth to both observed and recorded values of periodontal probing depth, while permitting correlation among measures obtained from the same mouth and between duplicate examiners' measures obtained at the same periodontal site. Periodontal site-specific examiner effects are modeled as arising from a Dirichlet process mixture, facilitating identification of classes of sites that are measured with similar bias. Using simulated data, we demonstrate the model's ability to recover examiner site-specific bias and variance heterogeneity and to provide cluster-adjusted point and interval agreement estimates. We conclude with an analysis of data from a probing depth calibration training exercise.
description: Published in at http://dx.doi.org/10.1214/13-AOAS688 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org)
title: Цифровые подходы в диагностике ранних признаков поверхностно распространяющихся меланом
Creators: name: Науменко, Е.
name: Рисс, М.
Publisher: name: Новгородский государственный университет имени Ярослава Мудрого (НовГУ)
Year: 2020

description: В исследовании проведено изучение возможности применения метода USB микроскопической диагностики для выявления поверхностных меланом в ранней стадии малигнизации. Нами использован портативный USB микроскоп со встроенной подсветкой, подключаемый к компьютеру. Также проведена предварительная
обработка образования специальным красителем. В процессе исследования удалось установить наличие у пациентов пограничных и потенциально злокачественных невусов. Данный способ может быть использован для ранней диагностики меланом с целью предотвращения развития онкологического процесса.
ASReview Software Documentation 0.14
Creators: name: De Bruin, Jonathan
name: Ferdinands, Gerbrich
name: Harkema, Albert
name: De Boer, Jan
name: Van den Brand, Sofie
name: Ma, Yongchao
name: Van de Schoot, Rens
Publisher: name: Zenodo
Year: 2020
Subjects: systematic review
asreview
machine learning

description: This document contains detailed information for version 0.14 of the ASReview software. For more information, see https://github.com/asreview/asreview.
ASReview LAB Software Documentation
Creators: name: ASReview LAB Developers
Publisher: name: Zenodo
Year: 2022
Subjects: systematic review
asreview
machine learning
documentation
active learning

description: This document contains detailed information on the ASReview LAB software. The latest version of the documentation can also be found on the web page https://asreview.readthedocs.io/en/latest/index.html. For more information, see https://github.com/asreview/asreview or https://asreview.ai.
The gut microbiome in people with Parkinson's disease
Creators: name: 聂世清(Shiqing Nie)
Publisher: name: CNGB
Year: 2022
Subjects: Raw sequence reads
Metagenome
Metagenomic assembly
Other
Gut microbes from fecal samples
Medical

description: To investigate the relationship between gut microbes and Parkinson's disease, 90 fecal samples were analyzed. All samples (90) were used of 16S rRNA amplicon sequencing. 16 of 90 samples were used of shotgun sequencing and 250 metagenome-assembled genomes (MAGs) were obtained.
Energy transfer efficiency in the FMO complex strongly coupled to a vibronic mode
Creators: name: Mourokh, Lev
name: Nori, Franco
Publisher: name: arXiv
Year: 2014
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Chemical Physics (physics.chem-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Using methods of condensed matter and statistical physics, we examine the transport of excitons through the Fenna-Matthews-Olson (FMO) complex from a receiving antenna to a reaction center. Writing the equations of motion for the exciton creation/annihilation operators, we are able to describe the exciton dynamics, even in the regime when the reorganization energy is of the order of the intra-system couplings. In particular, we obtain the well-known quantum oscillations of the site populations. We determine the exciton transfer efficiency in the presence of a quenching field and protein environment. While the majority of the protein vibronic modes are treated as a heat bath, we address the situation when specific modes are strongly coupled to excitons and examine the effects of these modes on the quantum oscillations and the energy transfer efficiency. We find that, for the vibronic frequencies below 16 meV, the exciton transfer is drastically suppressed. We attribute this effect to the formation of "polaronic states" where the exciton is transferred back and forth between the two pigments with the absorption/emission of the vibronic quanta, instead of proceeding to the reaction center. The same effect suppresses the quantum beating at the vibronic frequency of 25 meV. We also show that the efficiency of the energy transfer can be enhanced when the vibronic mode strongly couples to the third pigment only, instead of coupling to the entire system.
ASReview LAB Software Documentation
Creators: name: ASReview LAB developers
Publisher: name: Zenodo
Year: 2023
Subjects: systematic review
asreview
machine learning
documentation
active learning

description: This document contains detailed information on the ASReview LAB software. The latest version of the documentation can also be found on the web page https://asreview.readthedocs.io/en/latest/index.html. 

For more information, see https://github.com/asreview/asreview or https://asreview.ai.
Three-dimensional chromatin organisation in human pancreatic islets
Creators: name: Ponsa, Joan
Publisher: name: Imperial College London
Year: 2017

description: Diabetes is a group of metabolic diseases that affects millions of people. Despite this, little is known about the underlying molecular mechanisms. Diabetes is characterised by an impaired blood-glucose regulation that can lead to severe consequences, such as kidney failure, and premature death. Pancreatic islets are one of the major tissues to understand diabetes pathogenesis as they produce insulin, a hormone central for blood-glucose homeostasis. Our previous work showed that studying epigenomic regulation is key to giving insight into the molecular mechanisms underlying diabetes, as risk-associated genomic variants are enriched at transcriptional regulatory regions named enhancers. To give further insight in pancreatic islet transcriptional regulation, I aimed to decipher the 3D chromatin organisation, an aspect of epigenomic regulation in human pancreatic islets that remained largely unexplored until now. As part of my PhD project I have studied high-resolution chromatin interaction maps that characterise 3D chromatin organisation at different levels, from single interactions between specific pair of genomic loci to large genomic topological domains known as TADs. These high-resolution chromatin interaction maps, integrated with a large collection of epigenomic datasets, allowed me to describe several aspects of islet 3D chromatin organisation, such as the identification of islet-selective chromatin structures associated to islet-specific gene expression. Moreover, I identified groups of enhancers that gather in 3D space. These 3D enhancer clusters were frequently found in loci key for islet function and highly enriched in diabetes associated variants. The results of this thesis allow us to have a more accurate picture of the epigenomic regulation in human pancreatic islets and how non-coding diabetes risk variants could be impairing enhancer-promoter communication.
Multi-omics analysis reveals the host-microbe interactions in aged rhesus macaques
Creators: name: 唐瑞祥(Ruixiang Tang)
Publisher: name: CNGB
Year: 2022
Subjects: Raw sequence reads
Metagenome
Transcriptome or Gene expression
Metabolome
Multiisolate
Model organism

description: Multi-omics analysis reveals the host-microbe interactions in aged rhesus macaques
Accelerating string matching for bio-computing applications on multi-core CPUs
Creators: name: Herath, D.
name: Lakmali, C.
name: Ragel, R. G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: Huge amount of data in the form of strings are being handled in bio-computing applications and searching algorithms are quite frequently used in them. Many methods utilizing on both software and hardware are being proposed to accelerate processing of such data. The typical hardware-based acceleration techniques either require special hardware such as general purpose graphics processing units (GPGPUs) or need building a new hardware such as an FPGA based design. On the other hard, software-based acceleration techniques are easier since they only require some changes in the software code or the software architecture. Typical software-based techniques make use of computers connected over a network, also known as a network grid to accelerate the processing. In this paper, we test the hypothesis that multi-core architectures should provide better performance in this kind of computation, but still it would depend on the algorithm selected as well as the programming model being utilized. We present the acceleration of a string-searching algorithm on a multi-core CPU via a POSIX thread based implementation. Our implementation on an 8-core processor (that supports 16-threads) resulted in 9x throughput improvement compared to a single thread implementation.
纹带棒杆菌耐药基因
Creators: name: 李玉串(Li Yuchuan)
Publisher: name: CNGB
Year: 2022
Subjects: Raw sequence reads
Monoisolate
Medical

description: 2021年1月-4月引起山西白求恩医院院内感染暴发纹带棒杆菌耐药基因。样本总数为64份基因组数据。64份样本均分离于临床患者痰、尿液以及静脉导管等，并通过北京诺禾致源基因测序平台进行了全基因测序，现将全基因测序的原始基因数据公开上传。
Structural, elastic, optical properties and quasiparticle band structure of solid cyanuric triazide
Creators: name: Appalakondaiah, S.
name: Vaitheeswaran, G.
name: Lebègue, S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: In this letter, we report the structural, elastic, and quasiparticle band structure of cynauric triazide. The structural properties using a dispersion corrected method to treat van der Waals (vdW) forces offers a significant improvement in the description of the ground state properties. The predicted bulk modulus from the equation of state and the elastic constants are consistent and the magnitude lies in the order of secondary explosives. Then, the G$_0$W$_0$ approximation is used to study the band structure and an indirect band gap of 6.33 eV is obtained. Finally, we have calculated the optical and detonation characteristics at ambient pressure.
description: 5 figures
Development of novel untargeted SPE-NMR protocols for metabolite annotation
Creators: name: McGill, Daniel George
Publisher: name: Imperial College London
Year: 2019

description: Metabolite identification and annotation procedures are necessary for the discovery of biomarkers indicative of diet, lifestyle, and disease. NMR spectroscopy remains a powerful tool in metabolic profiling — however, despite its reproducibility, ease of use, and quantitative data generation, its relatively limited sensitivity remains a bottleneck; low-concentration compounds become indistinguishable from noise, and the signals of more concentrated compounds regularly obscure those of less concentrated compounds. The aim of the project was to develop SPE-NMR protocols utilising different cartridge chemistries, using both natural and artificial urine mixtures, to produce unique retention profiles useful for metabolic profiling. These methods can then be incorporated as part of an analyst’s ‘toolbox’ for metabolite identification and structural elucidation. Different cartridge sorbents and conditions were utilised in order to produce unique retention profiles for different compound classes. Each elution demonstrated differing retention profiles for each method — replicates of the same method, however, had little difference between spectra, guaranteeing the reproducibility of the spectra. We found that application of the developed SPE methods to biofluids (such as urine) can be used to selectively retain metabolites based on compound taxonomy or other key functional groups, reducing peak overlap through concentration and fractionation of unknowns, and hence promising greater control over the metabolite annotation/identification process. Several NMR peaks demonstrating the presence of 3-hydroxyhippurate, unreported in literature or databases, were revealed through the use of the developed methods on human urine — a range of analytical methods were subsequently utilised in order to annotate the revealed peaks. Finally, standard operating procedures were written and validated for an automated SPE system, such that the SPE methods can be more generally used by researchers; this automated procedure was used to attempt to selectively retain specific glucuronide metabolites found in human urine, with retention being demonstrated where the moiety contains aromatic or otherwise significantly hydrophobic functional groups.