cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Salamanadra salamandra Predicted-ORFs
Creators: name: Libro, Pietro
name: Chiocchio, Andrea
name: De Risky, Erika
name: Di Martino, Jessica
name: Bisconti, Roberta
name: Castrignanò, Tiziana
name: Canestrelli, Daniele
Publisher: name: figshare
Year: 2023
Subjects: Bioinformatics and computational biology not elsewhere classified

description: Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Mounting evidence is showing that attitude to disperse is unevenly distributed among individuals within animal populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here, we contribute to the study of the genetic underpinnings of dispersal-related behavioral variation by assembling and annotating the first de novo transcriptome of the head tissues of Salamandra salamandra. Although dispersal occurs mostly during the post-metamorphic terrestrial life stage in this species, variation in dispersal-related personality traits is already evident at the aquatic larval stage, making it an excellent candidate species for studies of carry-over effects. We employed a structured pipeline to de-novo assemble and annotate transcripts from RNA-Seq in a set of individuals representative of distinct behavioral profiles. We obtained 1,153,432,918 reads, which were successfully de novo assembled and annotated. The high-quality assembly was confirmed by comparing BUSCO, DETONATE and TransRate with the S. salamandra dataset. By aligning the contigs against the de novo transcriptome we obtained a percentage of mapping higher than 94%. The homology annotation performed with DIAMOND led to 153,048 (blastx) and 95,942 (blastp) shared contigs, annotated on NCBI nr, Swiss-Prot and TrEMBL. The domain and site protein prediction made with InterProScan led to 9850 GO-annotated contigs. This de-novo transcriptome represents reliable reference for whole transcriptome and proteome studies of other amphibians, for designing primers to clone specific genes or monitor their expression, and for analyzing comparative gene expression profiles between alternative behavioral types.
Spectral and temporal characterization of a fused-quartz microresonator optical frequency comb
Creators: name: Papp, Scott B.
name: Diddams, Scott A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We report on the fabrication of high-Q, fused-quartz microresonators and the parametric generation of a frequency comb with 36 GHz line spacing using them. We have characterized the intrinsic stability of the comb in both the time and frequency domains to assess its suitability for future precision metrology applications. Intensity autocorrelation measurements and line-by-line comb control reveal near-transform-limited picosecond pulse trains that are associated with good relative phase and amplitude stability of the comb lines. The comb's 36 GHz line spacing can be readily photodetected, which enables measurements of its intrinsic and absolute phase fluctuations.
Salamanadra salamandra Predicted-ORF
Creators: name: Libro, Pietro
name: Chiocchio, Andrea
name: De Risky, Erika
name: Di Martino, Jessica
name: Bisconti, Roberta
name: Castrignanò, Tiziana
name: Canestrelli, Daniele
Publisher: name: figshare
Year: 2023
Subjects: Bioinformatics and computational biology not elsewhere classified

description: Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Mounting evidence is showing that attitude to disperse is unevenly distributed among individuals within animal populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here, we contribute to the study of the genetic underpinnings of dispersal-related behavioral variation by assembling and annotating the first de novo transcriptome of the head tissues of Salamandra salamandra. Although dispersal occurs mostly during the post-metamorphic terrestrial life stage in this species, variation in dispersal-related personality traits is already evident at the aquatic larval stage, making it an excellent candidate species for studies of carry-over effects. We employed a structured pipeline to de-novo assemble and annotate transcripts from RNA-Seq in a set of individuals representative of distinct behavioral profiles. We obtained 1,153,432,918 reads, which were successfully de novo assembled and annotated. The high-quality assembly was confirmed by comparing BUSCO, DETONATE and TransRate with the S. salamandra dataset. By aligning the contigs against the de novo transcriptome we obtained a percentage of mapping higher than 94%. The homology annotation performed with DIAMOND led to 153,048 (blastx) and 95,942 (blastp) shared contigs, annotated on NCBI nr, Swiss-Prot and TrEMBL. The domain and site protein prediction made with InterProScan led to 9850 GO-annotated contigs. This de-novo transcriptome represents reliable reference for whole transcriptome and proteome studies of other amphibians, for designing primers to clone specific genes or monitor their expression, and for analyzing comparative gene expression profiles between alternative behavioral types.
Intégralité des coefficients de Taylor de racines d'applications miroir
Creators: name: Delaygue, Eric
Publisher: name: arXiv
Year: 2010
Subjects: subject: Number Theory (math.NT)
subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: We prove the integrality of the Taylor coefficients of roots of mirror maps at the origin. By mirror maps, we mean formal power series z.exp(G(z)/F(z)), where F(z) and G(z)+log(z)F(z) are particular solutions of certain generalized hypergeometric differential equations. This enables us to prove a conjecture stated by Zhou in "Integrality properties of variations of Mahler measures" [arXiv:1006.2428v1 math.AG]. The proof of these results is an adaptation of the techniques used in our article "Critère pour l'intégralité des coefficients de Taylor des applications miroir", [J. Reine Angew. Math. (to appear)].
An analysis of the field theoretic approach to the quasi-continuum method
Creators: name: Gavini, Vikram
name: Liu, Liping
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mathematical Physics (math-ph)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Numerical Analysis (math.NA)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: Using the orbital-free density functional theory as a model theory, we present an analysis of the field theoretic approach to quasi-continuum method. In particular, by perturbation method and multiple scale analysis, we provide a formal justification for the validity of the coarse-graining of various fields, which is central to the quasi-continuum reduction of field theories. Further, we derive the homogenized equations that govern the behavior of electronic fields in regions of smooth deformations. Using Fourier analysis, we determine the far-field solutions for these fields in the presence of local defects, and subsequently estimate cell-size effects in computed defect energies.
description: 26 pages, 1 figure
Analyzing Bias in a Knowledge-Aware News Recommendation System
Creators: name: Greven, Hannah Elisabeth
Publisher: name: Karlsruher Institut für Technologie (KIT)
Year: 2021

description: News recommendation systems (NRS) are increasingly shaping online news consumption and thus the world perception of many readers. In NRS, state-of-the-art deep learning models are becoming increasingly popular. In these models, unwanted biases in the training data can lead to bias in the model. In recent years, there has been a surge of research on bias in recommendation systems examining bias in word, text, and knowledge graph embeddings. Literature on analyzing biases in research models proposed for news recommendation is still scarce. To translate scientific research models into responsible NRS bias analysis is indispensable. This thesis investigates bias in the KRED NRS, a content-based knowledge-aware NRS that uses a knowledge graph as side information. To analyze KRED’s recommendations regarding political bias in exposure, we create a corpus of news articles on the politically divisive topic of migration in the EU. Using this article corpus, six news reception profiles, and synthetically generated user behavior, we analyze the diversity of recommended articles. The analysis shows that the KRED NRS preferably recommends news from news outlets more frequently contained in the user‘s reading history. Independent from the user‘s news reception profile, the KRED NRS unfairly favors news articles from Breitbart (right-wing political bias) in the article corpus.
Star-Planet Interactions in the Radio Domain: Prospect for Their Detection
Creators: name: Zarka, Philippe
Publisher: name: arXiv
Year: 2024
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: All types of interaction of a magnetized plasma flow with an obstacle (magnetized or not) are considered, and those susceptible to produce a radio signature are identified. The role of the sub-Alfvénic or super-Alfvénic character of the flow is discussed. Known examples in the solar system are given, as well as extrapolations to star-planet plasma interactions. The dissipated power and the fraction that goes into radio waves are evaluated in the frame of the radio-magnetic scaling law, the theoretical bases and validity of which are discussed in the light of recent works. Then it is shown how radio signatures can be interpreted in the frame of the cyclotron-maser theory (developed for explaining the generation of solar system planetary auroral and satellite-induced radio emissions) for deducing many physical parameters of the system studied, including the planetary or stellar magnetic field. Recent detections of such radio signatures with new generation low-frequency radiotelescopes and future prospects are then outlined.
description: 22 pages, 2 figures, 1 table
Additional file 5 of Promoting physical activity in a multi-ethnic population at high risk of diabetes: the 48-month PROPELS randomised controlled trial
Creators: name: Khunti, Kamlesh
name: Griffin, Simon
name: Brennan, Alan
name: Dallosso, Helen
name: Davies, Melanie J.
name: Eborall, Helen C.
name: Edwardson, Charlotte L.
name: Gray, Laura J.
name: Hardeman, Wendy
name: Heathcote, Laura
name: Henson, Joe
name: Pollard, Daniel
name: Sharp, Stephen J.
name: Sutton, Stephen
name: Troughton, Jacqui
name: Yates, Tom
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Science Policy
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Computational Biology

description: Additional file 5:. Sub-group analysis testing whether intervention effect at 48-months for primary outcome is modified by key characteristics.
La publicación desde la perspectiva de un joven investigador
Creators: name: Arroyo-Machado, Wenceslao
Publisher: name: Zenodo
Year: 2022
Subjects: investigación
producción científica
publicación
papers

description: Presentación realizada el miércoles 27 de abril de 2022 en el Máster Interuniversitario en Cultura de Paz, Conflictos, Educación y Derechos. Actualizado a la versión 2, del curso celebrado el 26 de abril de 2023.
Multimodal nonlinear optical polarizing microscopy of long-range molecular order in liquid crystals
Creators: name: Lee, Taewoo
name: Trivedi, Rahul P.
name: Smalyukh, Ivan I.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We demonstrate orientation-sensitive multimodal nonlinear optical polarizing microscopy capable of probing orientational, polar, and biaxial features of mesomorphic ordering in soft matter. This technique achieves simultaneous imaging in broadband coherent anti-Stokes Raman scattering, multi-photon excitation fluorescence, and multi-harmonic generation polarizing microscopy modes and is based on the use of a single femtosecond laser and a photonic crystal fiber as sources of the probing light. We show the viability of this technique for mapping of three dimensional patterns of molecular orientations and that images obtained in different microscopy modes are consistent with each other.
description: Total 12 pages, 4 figures, submitted to Optics Letters on August 2010
La publicación desde la perspectiva de un joven investigador
Creators: name: Arroyo-Machado, Wenceslao
Publisher: name: Zenodo
Year: 2022
Subjects: investigación
producción científica
publicación
papers

description: Presentación realizada el miércoles 27 de abril de 2022 en el Máster Interuniversitario en Cultura de Paz, Conflictos, Educación y Derechos.
Additional file 7 of Promoting physical activity in a multi-ethnic population at high risk of diabetes: the 48-month PROPELS randomised controlled trial
Creators: name: Khunti, Kamlesh
name: Griffin, Simon
name: Brennan, Alan
name: Dallosso, Helen
name: Davies, Melanie J.
name: Eborall, Helen C.
name: Edwardson, Charlotte L.
name: Gray, Laura J.
name: Hardeman, Wendy
name: Heathcote, Laura
name: Henson, Joe
name: Pollard, Daniel
name: Sharp, Stephen J.
name: Sutton, Stephen
name: Troughton, Jacqui
name: Yates, Tom
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Science Policy
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Computational Biology

description: Additional file 7:. Serious and non-serious adverse events.
Looking for flares and CME signatures in the spectra of several cool stars
Creators: name: Avramova-Boncheva, Antoaneta
name: Korhonen, Heidi
name: Stateva, Ivanka
name: Antonova, Antoaneta
Publisher: name: Zenodo
Year: 2022
Subjects: cool stars
coronal mass ejection
magnetic activity

description: It is critical to look for and estimate CME and flare signatures from late-type stars in order to understand stellar activity and its
 impact on space weather and planetary atmospheres. Spectroscopic observations of the Hα Balmer line is one of the methods.
 We present spectroscopic observations of four stars of spectral types G, K, and M. The observations were made over a number of epochs using the NOT/ALFOSC on La Palma and the 2-m RCC telescope/ESPERO at the National Astronomical Observatory of Rozhen. In April, July, and September of 2021, we collected 303 spectra over six nights. With the ALFOSC instrument, we obtained 168 spectra, and the ESPERO instrument, we obtained 135 spectra. The results do not show the events we are looking for, which raises concerns.
description: This research is based on activities supported by the Bulgarian National Science Fund under contract DN 06-Н58/3 – 16.11.2021.
Non linear equation of state and effective phantom divide in brane models
Creators: name: Dutta, Jibitesh
name: Chakraborty, Subenoy
name: Ansari, M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Here, DGP model of brane-gravity is analyzed and compared with the standard general relativity and Randall-Sundrum cases using non-linear equation of state. Phantom fluid is known to violate the weak energy condition. In this paper, it is found that this characteristic of phantom energy is affected drastically by the negative brane-tension $λ$ of the RS-II model. It is found that in DGP model strong energy condition(SEC) is always violated and the universe accelerates only where as in RS-II model even SEC is not violated for $1 < ρ/λ< 2$ and the universe decelerates.
A general wavelet-based profile decomposition in the critical embedding of function spaces
Creators: name: Bahouri, Hajer
name: Cohen, Albert
name: Koch, Gabriel
Publisher: name: arXiv
Year: 2011
Subjects: subject: Functional Analysis (math.FA)
subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: We characterize the lack of compactness in the critical embedding of functions spaces $X\subset Y$ having similar scaling properties in the following terms : a sequence $(u_n)_{n\geq 0}$ bounded in $X$ has a subsequence that can be expressed as a finite sum of translations and dilations of functions $(ϕ_l)_{l>0}$ such that the remainder converges to zero in $Y$ as the number of functions in the sum and $n$ tend to $+\infty$. Such a decomposition was established by Gérard for the embedding of the homogeneous Sobolev space $X=\dot H^s$ into the $Y=L^p$ in $d$ dimensions with $0
description: 24 pages
Characterization of two tomato ringspot virus replication proteins : the NTB protein and the RNA-dependent RNA polymerase
Creators: name: Wei, Ting
Publisher: name: University of British Columbia
Year: 2015

description: Tomato ringspot virus (ToRSV) replicates in large protein complexes that are associated with modified endoplasmic reticulum membranes. The ToRSV RNA-dependent RNA polymerase (Pol) and integral membrane protein NTB-VPg are essential components of these complexes. Membrane-associated modifications of NTB-VPg (N-glycosylation and a putative signal peptidase cleavage) were previously observed in vitro but were not well characterized. Two forms of the polymerase were detected in infected plants: the full-length Pol, which accumulates at low concentration and the VPg-Pro-Pol' polyprotein, which includes a 15kDa C-terminal truncation of Pol and accumulates to higher levels. My specific objectives were to characterize the signal peptidase cleavage in NTB-VPg and investigate the stability and function of various forms of the polymerase. Using in vitro translation assays and plant transient expression assays, I detected signal peptidase processing in the NTB-VPg of three ToRSV isolates. Using site-directed mutagenesis, I mapped a suboptimal GAAGG cleavage site (Rasp2 isolate) and identified key amino acids that regulate the efficiency of cleavage. Compared to typical signal peptides, the NTB-VPg sequence has an unusually long distance between the end of the hydrophobic region and the cleavage site, indicating that it adopts a unique topology in the membrane. This is the first detailed characterization of signal peptidase cleavage of a plant virus replication protein. This cleavage may alter the conformation of NTB-VPg in the membrane and influence the architecture of the replication complexes. Using agroinfiltration assays, I show that the full-length Pol and VPg-Pro-Pol are unstable when ectopically expressed in N. benthamiana. Truncation of the C-terminal 15 kDa from Pol or VPg-Pro-Pol increased their stability in plants, which is consistent with the accumulation of VPg-Pro-Pol' in infected plants. In spite of repeated attempts, I was unable to establish an in vitro assays to compare the activity of Pol and VPg-Pro-Pol', possibly because an essential plant factor is missing. The instability of VPg-Pro-Pol and Pol may regulate the rate of virus replication, allowing the virus to keep its genome integrity and reducing the chance of being recognized by host defense responses.
Conformal Holography of Bulk Elliptic Flow and Heavy Quark Quenching in Relativistic Heavy Ion Collisions
Creators: name: Noronha, Jorge
name: Gyulassy, Miklos
name: Torrieri, Giorgio
Publisher: name: arXiv
Year: 2010
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We show that the ``perfect fluid'' elliptic flow of the bulk hadrons and the unexpectedly strong quenching of heavy quark jet fragments in Au+Au reactions at 200 AGeV can be simultaneously accounted for within leading order AdS/CFT holography with a common large t'Hooft coupling $λ=g^2_{YM} N_c \sim 30$. In contrast, weakly coupled quark-gluon plasma models have so far failed to describe the observed correlation between these soft and hard observables even for couplings extrapolated to $α_s\sim 0.5$. We show that phenomenological applications of the classical trailing string AdS/CFT holographic solution are furthermore remarkably robust to higher order curvature corrections $\mathcal{O}(1/λ^{3/2})$ in type IIB supergravity theories, as well as to worldsheet fluctuation corrections $\mathcal{O}(1/λ^{1/2})$ that were not considered previously. We emphasize the importance of future measurements at RHIC and LHC of the correlation between {\em identified} charm and beauty quark hard ($p_T > 10-30$ GeV) jet quenching observables and low transverse momenta ($p_T\le 1$ GeV) bulk elliptic flow observables to further tests the limits of applicability of conformal holography to strongly coupled quark-gluon plasma.
description: 6 pages, 2 figures
Modeling of Magnetic Properties of NiCl$_2$ Nanostripes, Nanotubes and Fullerenes
Creators: name: Enyashin, Andrey N.
name: Ivanovskii, Alexander L.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We show that the magnetic properties of antiferromagnetic layered NiCl$_{2}$ can be altered under nano-sizing depending on dimensionality and morphology type of the corresponding nano-forms. By means of Monte-Carlo simulations within classical Heisenberg model, the spin ordering, magnetic part of heat capacity C$_{v}$ and Néel temperatures T$_{N}$ for multi-walled NiCl$_{2}$ nanotubes and a fullerene were calculated and analyzed in comparison with the bulk NiCl$_{2}$ and multilayered two-dimensional NiCl$_{2}$ crystals and nanostripes. We have found that the nano-structuring of NiCl$_{2}$ at the size reducing and at the formation of the closed structures can influence propitiously on the preservation of antiferromagnetic properties.
description: 13 pages, 3 figures, 1 Table
Recent advances in the application of the heck reaction in the synthesis of heterocyclic compounds: An update
Creators: name: Mommahed Heravi, Majid
name: Moradi, Razieh
name: Malmir, Masoumeh
Publisher: name: figshare
Year: 2022
Subjects: subject: 30302 Nanochemistry and Supramolecular Chemistry
subject: FOS: Chemical sciences
subject: 30502 Natural Products Chemistry
subject: 30205 Non-metal Chemistry
subject: 39904 Organometallic Chemistry
subject: Organic Chemistry
subject: 30599 Organic Chemistry not elsewhere classified
subject: Nuclear Chemistry
subject: 30504 Organic Green Chemistry
subject: 30303 Optical Properties of Materials

description: Background: The reaction of aryl halides or vinyl halides with activated alkenes in the presence of Palladium-catalyst along with a base for the formation of the C-C bond is called the Heck reaction. This reaction has been employed extensively in the synthesis of heterocyclic compounds. Methodology: We have highlighted these applications in 2010. Conclusion: This review aims to cover the recent application of the Heck reaction in the synthesis of heterocyclic compounds during a period from 2010 to 2017. Dedicated to my dearest “ TEEDA” on the occasion of her third birthday.
Reconocimiento y Garantías para la Protección y la Participación de los Pueblos Étnicos en la Construcción de Paz: Informe Especial Sobre el Estado Efectivo de la implementación del enfoque transversal étnico del Acuerdo Final de Paz de Colombia
Creators: name: Matriz De Acuerdos De Paz, Instituto Kroc De Estudios Internacionales
Publisher: name: University of Notre Dame
Year: 2021

Abstract
Physics-based control-oriented modelling for floating offshore wind turbines
Creators: name: Homer, Jeffrey R.
Publisher: name: University of British Columbia
Year: 2017

description: As offshore wind technology advances, floating wind turbines are becoming larger and moving further offshore, where wind is stronger and more consistent. Despite the increased potential for energy capture, wind turbines in these environments are susceptible to large platform motions, which in turn can lead to fatigue loading and shortened life, as well as harmful power fluctuations. To minimize these ill effects, it is possible to use advanced, multi-objective control schemes to minimize harmful motions, reject disturbances, and maximize power capture. Synthesis of such controllers requires simple but accurate models that reflect all of the pertinent dynamics of the system, while maintaining a reasonably low degree of complexity. In this thesis, we present a simplified, control-oriented model for floating offshore wind turbines that contains as many as six platform degrees of freedom, and two drivetrain degrees of freedom. The model is derived from first principles and, as such, can be manipulated by its real physical parameters while maintaining accuracy across the highly non-linear operating range of floating wind turbine systems. We validate the proposed model against advanced simulation software FAST, and show that it is extremely accurate at predicting major dynamics of the floating wind turbine system. Furthermore, the proposed model can be used to generate equilibrium points and linear state-space models at any operating point. Included in the linear model is the wave disturbance matrix, which can be used to accommodate for wave disturbance in advanced control schemes either through disturbance rejection or feedforward techniques. The linear model is compared to other available linear models and shows drastically improved accuracy, due to the presence of the wave disturbance matrix. Finally, using the linear model, we develop four different controllers of increasing complexity, including a multi-objective PID controller, an LQR controller, a disturbance-rejecting H∞ controller, and a feedforward H∞ controller. We show through simulation that the controllers that use the wave disturbance information reduce harmful motions and regulate power better than those that do not, and reinforce the notion that multi-objective control is necessary for the success of floating offshore wind turbines.
Taeao: ʻO māfaufauga o faʻāliga ata ma o sāuniga mo o tātou lumanaʻi
Creators: name: LEULI ESHRAGHI
Publisher: name: Monash University
Year: 2019
Subjects: Art

description: In bringing archipelagic and diasporic Sāmoan aesthetic practices, sensual and textual languages, and ceremonial-political structures into clearer constellation with those of our Indigenous relations near and far across the Vasalaolao (Great Ocean) and beyond, we can surpass faigamālō faʻakolone (colonial impacts) and continue becoming. This suʻesuʻega situates the recuperation of Indigenous knowledges, bodies and territories in sovereign futures within genealogical time and generational shifts today. Beyond Western curating, tautuanaga ʻo faʻāliga ata (images/likenesses/shadows/pictures serving collective wellbeing) is proposed, amongst associated innovations in language terms, to lead changes in the structures and outcomes of galleries, exhibitions, texts and works today.
Ketoreductases as biocatalysts in the synthesis of chiral diketides
Creators: name: Luna Robles, Mireya
Publisher: name: The University of Texas at Austin
Year: 2020
Subjects: Ketoreductase
Stereocontrol
Diketides

description: Ketoreductases (KRs) are capable of setting different combinations of stereocenters at the α and β position, resulting in complex polyketides with multiple chiral centers. In order to increase the stereocontrol of KRs a structure–activity relationship study was performed using four diketides of various lengths. The stereocontrol of KRs was increased with a longer hydrophobic chain or a pantetheine handle
Salamandra salamandra interproscan results
Creators: name: Libro, Pietro
name: Chiocchio, Andrea
name: De Risky, Erika
name: Di Martino, Jessica
name: Bisconti, Roberta
name: Castrignanò, Tiziana
name: Canestrelli, Daniele
Publisher: name: figshare
Year: 2023
Subjects: Bioinformatic methods development

description: Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Mounting evidence is showing that attitude to disperse is unevenly distributed among individuals within animal populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here, we contribute to the study of the genetic underpinnings of dispersal-related behavioral variation by assembling and annotating the first de novo transcriptome of the head tissues of Salamandra salamandra. Although dispersal occurs mostly during the post-metamorphic terrestrial life stage in this species, variation in dispersal-related personality traits is already evident at the aquatic larval stage, making it an excellent candidate species for studies of carry-over effects. We employed a structured pipeline to de-novo assemble and annotate transcripts from RNA-Seq in a set of individuals representative of distinct behavioral profiles. We obtained 1,153,432,918 reads, which were successfully de novo assembled and annotated. The high-quality assembly was confirmed by comparing BUSCO, DETONATE and TransRate with the S. salamandra dataset. By aligning the contigs against the de novo transcriptome we obtained a percentage of mapping higher than 94%. The homology annotation performed with DIAMOND led to 153,048 (blastx) and 95,942 (blastp) shared contigs, annotated on NCBI nr, Swiss-Prot and TrEMBL. The domain and site protein prediction made with InterProScan led to 9850 GO-annotated contigs. This de-novo transcriptome represents reliable reference for whole transcriptome and proteome studies of other amphibians, for designing primers to clone specific genes or monitor their expression, and for analyzing comparative gene expression profiles between alternative behavioral types.
Decision rules based on hypothesis tests and effect sizes for logistic regression differential item functioning
Creators: name: Gesicki, Adam
Publisher: name: University of British Columbia
Year: 2015

description: Logistic Regression (LR) has been a technique used for the detection of items exhibiting differential item functioning (DIF). When it was introduced in 1990, the LR was conceptualized as strictly a test of statistical significance. This led to the over-identification of items as DIF, generally not exhibiting practically (psychometrically) significant differences. The use of blended decision rules – where effect sizes are used in addition to statistical significance in the decision-making process – was proposed to address this issue. Previous work in the literature attempted to align a decision rule grounded in the Mantel-Haenszel (M-H) technique to LR. However, this work is unable to replicate previously recommended cut-offs, through the use of the same methodology on a different data set. It is possible that cut-off values may be dataset specific, which also opens the question of whether universal cut-off values for effect sizes for DIF are a realistic expectation.
Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic
Creators: name: Privman, Vladimir
name: Halamek, Jan
name: Arugula, Mary A.
name: Melnikov, Dmitriy
name: Bocharova, Vera
name: Katz, Evgeny
Publisher: name: arXiv
Year: 2010
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Other Computer Science (cs.OH)
subject: Chemical Physics (physics.chem-ph)
subject: Molecular Networks (q-bio.MN)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by hydrogen peroxide, was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved capabilities for design of scalable biomolecular information processing systems.
description: 24 pages, PDF
Salamandra salamandra interproscan result
Creators: name: Libro, Pietro
name: Chiocchio, Andrea
name: De Risky, Erika
name: Di Martino, Jessica
name: Bisconti, Roberta
name: Castrignanò, Tiziana
name: Canestrelli, Daniele
Publisher: name: figshare
Year: 2023
Subjects: Bioinformatic methods development

description: Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Mounting evidence is showing that attitude to disperse is unevenly distributed among individuals within animal populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here, we contribute to the study of the genetic underpinnings of dispersal-related behavioral variation by assembling and annotating the first de novo transcriptome of the head tissues of Salamandra salamandra. Although dispersal occurs mostly during the post-metamorphic terrestrial life stage in this species, variation in dispersal-related personality traits is already evident at the aquatic larval stage, making it an excellent candidate species for studies of carry-over effects. We employed a structured pipeline to de-novo assemble and annotate transcripts from RNA-Seq in a set of individuals representative of distinct behavioral profiles. We obtained 1,153,432,918 reads, which were successfully de novo assembled and annotated. The high-quality assembly was confirmed by comparing BUSCO, DETONATE and TransRate with the S. salamandra dataset. By aligning the contigs against the de novo transcriptome we obtained a percentage of mapping higher than 94%. The homology annotation performed with DIAMOND led to 153,048 (blastx) and 95,942 (blastp) shared contigs, annotated on NCBI nr, Swiss-Prot and TrEMBL. The domain and site protein prediction made with InterProScan led to 9850 GO-annotated contigs. This de-novo transcriptome represents reliable reference for whole transcriptome and proteome studies of other amphibians, for designing primers to clone specific genes or monitor their expression, and for analyzing comparative gene expression profiles between alternative behavioral types.
Variability in Quasar Broad Absorption Line Outflows I. Trends in the Short-Term versus Long-Term Data
Creators: name: Capellupo, Daniel M.
name: Hamann, Fred
name: Shields, Joseph C.
name: Hidalgo, Paola Rodríguez
name: Barlow, Tom A.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Broad absorption lines (BALs) in quasar spectra identify high velocity outflows that likely exist in all quasars and could play a major role in feedback to galaxy evolution. The variability of BALs can help us understand the structure, evolution, and basic physical properties of the outflows. Here we report on our first results from an ongoing BAL monitoring campaign of a sample of 24 luminous quasars at redshifts 1.2
description: 14 pages, 7 figures, accepted for publication in MNRAS
TIBBIYOTDA NANOTEXNOLOGIYALAR HAQIDA
Creators: name: Eshmamatova Ruxshona Tulqin qizi, Maxmudova Intizor Abdurauf qizi
Publisher: name: Zenodo
Year: 2024

description: Annotatsiya: Ushbu maqolada tibbiyotda nanoo‘lchamli strukturaga ega texnologiyalarning qo‘llanilishi hamda istiqbollari, hozirgi zamon ilg‘or texnologiyalarining tibbiyotdagi ahamiyati to‘g‘risida ma’lumotlar berilgan.

Tayanch so‘zlar: nanoamper, nanometr, elektrodlar, yupqa platforma, nanotranzistor, attoo‘lcham, robotlashtirish, telemeditsina, nanostruktura, DNK, nanosensorlar, mutatsiyalar, virus, diognostika, biochiplar, fermentlar, antitelolalar, fluoressent nur, nanochip, hujayra regeneratsiyasi, implantatsiya.
Generalised second law of thermodynamics for interacting dark energy in the DGP brane world
Creators: name: Dutta, Jibitesh
name: Chakraborty, Subenoy
Publisher: name: arXiv
Year: 2010
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: In this paper, we investigate the validity of the generalized second law of thermodynamics (GSLT) in the DGP brane world when universe is filled with interacting two fluid system: one in the form of cold dark matter and other is holographic dark energy. The boundary of the universe is assumed to be enclosed by the dynamical apparent horizon or the event horizon. The universe is chosen to be homogeneous and isotropic FRW model and the validity of the first law has been assumed here.
Deep determinism and the assessment of mechanistic interaction between categorical and continuous variables
Creators: name: Berzuini, Carlo
name: Dawid, A. Philip
Publisher: name: arXiv
Year: 2010
Subjects: subject: Methodology (stat.ME)
subject: Genomics (q-bio.GN)
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: Our aim is to detect mechanistic interaction between the effects of two causal factors on a binary response, as an aid to identifying situations where the effects are mediated by a common mechanism. We propose a formalization of mechanistic interaction which acknowledges asymmetries of the kind "factor A interferes with factor B, but not viceversa". A class of tests for mechanistic interaction is proposed, which works on discrete or continuous causal variables, in any combination. Conditions under which these tests can be applied under a generic regime of data collection, be it interventional or observational, are discussed in terms of conditional independence assumptions within the framework of Augmented Directed Graphs. The scientific relevance of the method and the practicality of the graphical framework are illustrated with the aid of two studies in coronary artery disease. Our analysis relies on the "deep determinism" assumption that there exists some relevant set V - possibly unobserved - of "context variables", such that the response Y is a deterministic function of the values of V and of the causal factors of interest. Caveats regarding this assumption in real studies are discussed.
description: 20 pages including the four figures, plus two tables. Submitted to "Biostatistics" on November 24, 2010
Edge and bulk components of lowest-Landau-level orbitals, correlated fractional quantum Hall effect incompressible states, and insulating behavior in finite graphene samples
Creators: name: Yannouleas, Constantine
name: Romanovsky, Igor
name: Landman, Uzi
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Nuclear Theory (nucl-th)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Many-body calculations of the total energy of interacting Dirac electrons in finite graphene samples exhibit joint occurrence of cusps at angular momenta corresponding to fractional fillings characteristic of formation of incompressible (gapped) correlated states (nu=1/3 in particular) and opening of an insulating energy gap (that increases with the magnetic field) at the Dirac point, in correspondence with experiments. Single-particle basis functions obeying the zigzag boundary condition at the sample edge are employed in exact diagonalization of the interelectron Coulomb interaction, showing, at all sizes, mixed equal-weight bulk and edge components. The consequent depletion of the bulk electron density attenuates the fractional-quantum-Hall-effect excitation energies and the edge charge accumulation results in a gap in the many-body spectrum.
description: 8 pages with 7 figures. REVTEX4. For related publications, see http://www.prism.gatech.edu/~ph274cy
B to J/Psi measurements in p+p and Cu+Au collisions by the PHENIX experiment
Creators: name: Li, Xuan
Publisher: name: Zenodo
Year: 2021
Subjects: sfjhf17
phenix
fvtx
b-meson
J/Ψ
p+p
cu+au
heavy flavor
au+au
raa
nuclear
modification
elliptic
flow
energy loss
vtx
dimuon
dca
charm
bottom

description: Talk presented at the Santa Fe Jets and Heavy Flavor workshop 2017
Bijections from weighted Dyck paths to Schroeder paths
Creators: name: Drake, Dan
Publisher: name: arXiv
Year: 2010
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: Primary: 05A19, Secondary: 05A15, 05A05

description: Kim and Drake used generating functions to prove that the number of 2-distant noncrossing matchings, which are in bijection with little Schroeder paths, is the same as the weight of Dyck paths in which downsteps from even height have weight 2. This work presents bijections from those Dyck paths to little Schroeder paths, and from a similar set of Dyck paths to big Schroeder paths. We show the effect of these bijections on the corresponding matchings, find generating functions for two new classes of lattice paths, and demonstrate a relationship with 231-avoiding permutations.
description: 16 pages, TikZ figures, includes Sage code
Mapping Large-Scale CO Depletion in a Filamentary Infrared Dark Cloud
Creators: name: Hernandez, Audra K.
name: Tan, Jonathan C.
name: Caselli, Paola
name: Butler, Michael J.
name: Jimenez-Serra, Izaskun
name: Fontani, Francesco
name: Barnes, Peter
Publisher: name: arXiv
Year: 2011
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Infrared Dark Clouds (IRDCs) are cold, high mass surface density and high density structures, likely to be representative of the initial conditions for massive star and star cluster formation. CO emission from IRDCs has the potential to be useful for tracing their dynamics, but may be affected by depleted gas phase abundances due to freeze-out onto dust grains. Here we analyze C18O J=1-0 and J=2-1 emission line data, taken with the IRAM 30m telescope, of the highly filamentary IRDC G035.39.-0033. We derive the excitation temperature as a function of position and velocity, with typical values of ~7K, and thus derive total mass surface densities, Sigma_C18O, assuming standard gas phase abundances and accounting for optical depth in the line, which can reach values of ~1. The mass surface densities reach values of ~0.07 g/cm^2. We compare these results to the mass surface densities derived from mid-infrared (MIR) extinction mapping, Sigma_SMF, by Butler & Tan, which are expected to be insensitive to the dust temperatures in the cloud. With a significance of >10sigma, we find Sigma_C18O/Sigma_SMF decreases by about a factor of 5 as Sigma increases from ~0.02 to ~0.2 g/cm^2, which we interpret as evidence for CO depletion. Several hundred solar masses are being affected, making this one of the most massive clouds in which CO depletion has been observed directly. We present a map of the depletion factor in the filament and discuss implications for the formation of the IRDC.
description: 9 pages, accepted to ApJ, Mac users: Figure 1 is best viewed with Adobe acroread rather than preview
Balkan Revisions to the Myth of Central Europe
Creators: name: Labov, Jessie
Publisher: name: Zenodo
Year: 1999

description: This paper was presented at the Sokrates Kokkalis Graduate Student Workshop at Harvard University. It takes up the challenge presented by Maria Todorova at the end of her chapter on Central Europe in Imagining the Balkans, to address the question of how the Balkans are related to the mythical project of Central Europe.
Ionized Gas in the Irr Galaxy IC 10: The Emission Spectrum and Ionization Sources
Creators: name: Arkhipova, V. P.
name: Egorov, O. V.
name: Lozinskaya, T. A.
name: Moiseev, A. V.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present the results of observations of the Irr galaxy IC 10 at the 6-m SAO telescope with the panoramic Multi-Pupil Fiber Spectrograph (MPFS). Based on the results of these observations and our long-slit spectroscopy performed previously, we have investigated the ionized-gas emission spectrum in the region of intense star formation and refined the gas metallicity estimates. We show that the "diagnostic diagrams" constructed from our observations agree best with the new improved ionization models by Martin-Manjon et al. Using these models, we have determined the electron density and gas ionization parameter and ionizing-cluster characteristics, the age and mass, from the spectra of the investigated HII regions. The cluster age and mass are shown to be within the ranges 2.5 - 5 Myr and (0.2 - 1)*10^5 M(sun), respectively.
description: 22 pages, 8 figures, 5 tables; the extended version of the paper accepted for publication in Astronomy Letters, Vol. 37, No. 2 (2011)
A Minimal Model of Signaling Network Elucidates Cell-to-Cell Stochastic Variability in Apoptosis
Creators: name: Raychaudhuri, Subhadip
Publisher: name: arXiv
Year: 2010
Subjects: subject: Molecular Networks (q-bio.MN)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: Signaling networks are designed to sense an environmental stimulus and adapt to it. We propose and study a minimal model of signaling network that can sense and respond to external stimuli of varying strength in an adaptive manner. The structure of this minimal network is derived based on some simple assumptions on its differential response to external stimuli. We employ stochastic differential equations and probability distributions obtained from stochastic simulations to characterize differential signaling response in our minimal network model. We show that the proposed minimal signaling network displays two distinct types of response as the strength of the stimulus is decreased. The signaling network has a deterministic part that undergoes rapid activation by a strong stimulus in which case cell-to-cell fluctuations can be ignored. As the strength of the stimulus decreases, the stochastic part of the network begins dominating the signaling response where slow activation is observed with characteristic large cell-to-cell stochastic variability. Interestingly, this proposed stochastic signaling network can capture some of the essential signaling behaviors of a complex apoptotic cell death signaling network that has been studied through experiments and large-scale computer simulations. Thus we claim that the proposed signaling network is an appropriate minimal model of apoptosis signaling. Elucidating the fundamental design principles of complex cellular signaling pathways such as apoptosis signaling remains a challenging task. We demonstrate how our proposed minimal model can help elucidate the effect of a specific apoptotic inhibitor Bcl-2 on apoptotic signaling in a cell-type independent manner. We also discuss the implications of our study in elucidating the adaptive strategy of cell death signaling pathways.
description: 9 pages, 6 figures