cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
SS/SW BASE PAIRS ARE THE ONLY BASE PAIRS INVOLVED IN LONGRANGE RNA TERTIARY MOTIFS
Creators: name: Baulin, Evgeniy
name: Manakov, A.
name: Yakovlev, Viktor
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2020

description: The structure of noncoding RNAs largely determines their functions. With the rapid growth of experimental data on the RNA secondary structures, the task of predicting its spatial structure becomes the most urgent task of RNA bioinformatics. The ability to predict tertiary base pairs from data on the secondary structure could significantly reduce the operating time and improve the quality of the RNA spatial structure prediction algorithms. In this work, we applied the machine learning algorithm for the problem of RNA tertiary base pairs prediction from data on the RNA sequence and secondary structure. A group of local base pairs was identified that can be predicted with high quality (80% precision, 80% recall). It was also shown that more than 70% of all long-range noncanonical base pairs in RNA are the base pairs of geometric classes Sugar-Edge/Sugar-Edge and Sugar-Edge/Watson-Crick-Edge that correspond to ribose zipper and A-minor tertiary motifs.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (13) (2020)
The Aboriginal Mapping Network : a case study in the democratization of mapping
Creators: name: Johnson, Benjamin David
Publisher: name: University of British Columbia
Year: 2009

description: Land claims, increased control over natural resources and movement towards self-government demand that First Nations produce maps that bring local knowledge into planning and governance processes. For their mapping needs, First Nations are turning largely to geographic information systems (GIS), complex and expensive computer-based spatial database systems. They are, however, developing their technical skills independently of each other, rarely experiencing the knowledge-sharing benefits characteristic of an integrated community. To address this problem, and to help build mapping capacities in general, the Aboriginal Mapping Network was created by Ecotrust Canada, an environmental non-governmental organization, and several First Nations. Using the medium of the World Wide Web, the Network seeks to create linkages between First Nations mappers and to provide a space for the sharing of knowledge. This thesis uses a formative program evaluation framework to assess the strengths, weaknesses and potential of the nascent Network. The evaluation draws on interviews with First Nations mappers and network developers. Conclusions are drawn on how effective the Network is in developing communications linkages and facilitating knowledge sharing, and how this might continue in the future. Concurrently, the Network is used as a case study in the democratization of mapping. Capacity building in GIS technology, it is argued, will allow First Nations to produce unconventional maps that articulate local worldviews and perceptions of place. As embodiments of local knowledge, these maps will in turn be used in planning, negotiations and governance to empower First Nations on their own terms.
Detection of Maternal and Fetal Stress from the Electrocardiogram with Self-Supervised Representation Learning
Creators: name: Sarkar, Pritam
name: Lobmaier, Silvia
name: Fabre, Bibiana
name: González, Diego
name: Mueller, Alexander
name: Frasch, Martin G.
name: Antonelli, Marta C.
name: Etemad, Ali
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantitative Methods (q-bio.QM)
subject: Signal Processing (eess.SP)
subject: FOS: Biological sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: In the pregnant mother and her fetus, chronic prenatal stress results in entrainment of the fetal heartbeat by the maternal heartbeat, quantified by the fetal stress index (FSI). Deep learning (DL) is capable of pattern detection in complex medical data with high accuracy in noisy real-life environments, but little is known about DL's utility in non-invasive biometric monitoring during pregnancy. A recently established self-supervised learning (SSL) approach to DL provides emotional recognition from electrocardiogram (ECG). We hypothesized that SSL will identify chronically stressed mother-fetus dyads from the raw maternal abdominal electrocardiograms (aECG), containing fetal and maternal ECG. Chronically stressed mothers and controls matched at enrolment at 32 weeks of gestation were studied. We validated the chronic stress exposure by psychological inventory, maternal hair cortisol and FSI. We tested two variants of SSL architecture, one trained on the generic ECG features for emotional recognition obtained from public datasets and another transfer-learned on a subset of our data. Our DL models accurately detect the chronic stress exposure group (AUROC=0.982+/-0.002), the individual psychological stress score (R2=0.943+/-0.009) and FSI at 34 weeks of gestation (R2=0.946+/-0.013), as well as the maternal hair cortisol at birth reflecting chronic stress exposure (0.931+/-0.006). The best performance was achieved with the DL model trained on the public dataset and using maternal ECG alone. The present DL approach provides a novel source of physiological insights into complex multi-modal relationships between different regulatory systems exposed to chronic stress. The final DL model can be deployed in low-cost regular ECG biosensors as a simple, ubiquitous early stress detection and monitoring tool during pregnancy. This discovery should enable early behavioral interventions.
description: ClinicalTrials.gov registration number: NCT03389178. Code repo: https://code.engineering.queensu.ca/17ps21/ssl-ecg-v2
GBT Multiwavelength Survey of the Galactic Center Region
Creators: name: Law, C. J.
name: Yusef-Zadeh, F.
name: Cotton, W. D.
name: Maddalena, R. J.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We describe the results of a radio continuum survey of the central 4x1deg with the 100 m Green Bank Telescope (GBT) at wavelengths of 3.5, 6, 20, and 90 cm. The 3.5 and 6 cm surveys are the most sensitive and highest resolution single dish surveys made of the central degrees of our Galaxy. We present catalogs of compact and extended sources in the central four degrees of our Galaxy, including detailed spectral index studies of all sources. The analysis covers star-forming regions such as Sgr B and Sgr C where we find evidence of a mixture of thermal and nonthermal emission. The analysis quantifies the relative contribution of thermal and nonthermal processes to the radio continuum flux density toward the GC region. In the central 4x1deg of the GC, the thermal and nonthermal flux fractions for all compact and diffuse sources are 28%/72% at 3.5 cm and 19%/81% at 6 cm. The total flux densities from these sources are 783+-52 Jy and 1063+-93 Jy at 3.5 and 6 cm, respectively, excluding the contribution of Galactic synchrotron emission.
description: Accepted to ApJS. 40 pages, 46 figures, 8 tables (emulate apj style)
DATABASE OF TWO-HELICAL MOTIFS OF PROTEIN MOLECULES AND COMPUTER SERVICES FOR THEIR ANALYSIS
Creators: name: Rudnev, Vladimir
name: Tikhonov, Dmitry
name: Kulikova, Ludmila
name: Gubin, Maxim
name: Efimov, Alexander
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2019

description: This paper is devoted to the development of structural motifs database of protein molecules consisting of two elements of a secondary structure that have unique spatial stacking of a polypeptide chain. The motives investigated are pairs of any type of helix, connected by a different non-zero length and different conformation of the connection. For each structure, geometric parameters are calculated. The database interface allows you to perform searches, sorting, filtering on all parameters, which makes it possible to obtain samples of structures with given geometric characteristics. Also, the system interface allows for statistical analysis and the construction of histograms for the distribution of various characteristics of structures in the sample. Thus, it is possible to investigate the correlation of the geometry of the spatial structures of the investigated motifs with the amino acid sequences. The system allows uploading of the received samples to the file system in CSV format. The upload format and set of uploaded data is configured in the interface. Downloading can contain both all the geometric characteristics of the structures of interest, and the corresponding amino acid sequences. The database interface also allows you to view 3D models of structural motifs.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 3 (12) (2019)
LSCGAT: LONG SEQUENCES CUSTOMIZABLE GLOBAL ALIGNMENT TOOL
Creators: name: Pankratov, Anton
name: Tetuev, Ruslan
name: Pyatkov, Maxim
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2019

description: The most general model of a pairwise global alignment with the possibility of aligning long sequences is considered. The model features are alignment of sequences in different alphabets including nucleotides and amino acids, alternative alignments with the same score, predefined or fully customazible scoring matrix and gap penalty systems for each sequence including end gap penalties. Developed versatile parallel algorithm for global alignment is based on the Needleman-Wunsch algorithm with an arbitrary scoring matrix and Gotoh algorithm for the affine system of penalties for gaps. The main features of the algorithm include optimal memory consumption and parallel computation. It is proved that algorithm can align two sequences of length in memory space . The algorithm is implemented in the form of a high-performance web application in Javascript programming language with the usage of webworkers and is freely available on http://sbars.impb.ru/aligner.html.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (10) (2019)
Constraining the Circumbinary Disk Tilt in the KH 15D system
Creators: name: Poon, Michael
name: Zanazzi, J. J.
name: Zhu, Wei
Publisher: name: arXiv
Year: 2020
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: KH 15D is a system which consists of a young, eccentric binary, and a circumbinary disk which obscures the binary as the disk precesses. We develop a self-consistent model that provides a reasonable fit to the photometric variability that was observed in the KH 15D system over the past 60 years. Our model suggests that the circumbinary disk has an inner edge $r_{\rm in}\lesssim 1 \ {\rm au}$, an outer edge $r_{\rm out} \sim {\rm a \ few \ au}$, and that the disk is misaligned relative to the stellar binary by $\sim$5-16 degrees, with the inner edge more inclined than the outer edge. The difference between the inclinations (warp) and longitude of ascending nodes (twist) at the inner and outer edges of the disk are of order $\sim$10 degrees and $\sim$15 degrees, respectively. We also provide constraints on other properties of the disk, such as the precession period and surface density profile. Our work demonstrates the power of photometric data in constraining the physical properties of planet-forming circumbinary disks.
description: 17 pages, 9 figures
Continuous window functions for NFFT
Creators: name: Potts, Daniel
name: Tasche, Manfred
Publisher: name: arXiv
Year: 2020
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics
subject: 65T50, 94A12, 42A10

description: In this paper, we study the error behavior of the nonequispaced fast Fourier transform (NFFT). This approximate algorithm is mainly based on the convenient choice of a compactly supported window function. Here we consider the continuous Kaiser--Bessel, continuous $\exp$-type, $\sinh$-type, and continuous $\cosh$-type window functions with the same support and same shape parameter. We present novel explicit error estimates for NFFT with such a window function and derive rules for the optimal choice of the parameters involved in NFFT. The error constant of a window function depends mainly on the oversampling factor and the truncation parameter. For the considered continuous window functions, the error constants have an exponential decay with respect to the truncation parameter.
MORPHOLOGICAL ANALYSIS OF IMAGES OF DRIED DROPLETS OF SALIVA FOR DETERMINATION THE DEGREE OF ENDOGENOUS INTOXICATION
Creators: name: Lebedev-Stepanov, Peter
name: Buzoverya, Marina
name: Vlasov, Konstantin
name: Potekhina, Yulia
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2018

description: Endogenous intoxication (EI) is an integral pathology which gives the general information about state of health of the patient. There is a correlation of biochemical data (costly, require long-term invasive studies) and morphological indicators based on image analysis of the visual image of a droplet of saliva dried in standard conditions (a simple and cheap non-invasive procedure). It is important to develop cheap, fast, non-invasive, computerized morphological methods for a medical diagnostics of EI based on the unique clinical experience obtained in the past decade to apply for mass rapid screening and monitoring of patients during the clinical examination, and also for individual checkup the health of any patient. The method is proposed and laboratory setup is elaborated for determination of the EI by determination of morphological properties of dried pattern of evaporated saliva droplet. The set of microphotographs of the salivary dried patterns is formed taking into account the degree of EI. Criteria for expert evaluation of the EI degree from images of saliva dried pattern image are proposed. For the first time, computer software was created and tested to determine the EI degree. This makes it possible to process a large number of digital images of saliva patterns, which allows evaluating the monitoring of the patient health. Proposed method is a combination of bioinformatics and biochemistry approaches for obtaining diagnostic information from a morphological analysis of standardized dried patterns of saliva.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 4 (9) (2018)
Nuclear astrophysical plasmas: ion distribution functions and fusion rates
Creators: name: Lissia, Marcello
name: Quarati, Piero
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Nuclear Theory (nucl-th)
subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: This article illustrates how very small deviations from the Maxwellian exponential tail, while leaving unchanged bulk quantities, can yield dramatic effects on fusion reaction rates and discuss several mechanisms that can cause such deviations.
description: 9 ReVTex pages including 2 color figures
NUCLEOLIN AND NUCLEOPHOSMIN AS EXPECTED TARGETS FOR CATIONIC PEPTIDES, INDUCING TUMOR CELL APOPTOSIS
Creators: name: Lushnikova, Anna
name: Ponkratova, Daria
name: Kostarev, Alexander
name: Rudakova, Anna
name: Andreev, Sergey
name: Baryshnikova, Maria
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2018

description: Multifunctional proteins nucleolin (NCL, C23) and nucleophosmin (NPM, B23) are the most abundant nucleolar phosphoproteins with chaperone activities. Nucleolin is over-expressed also on tumor cell surface. The proteins regulate the most of important cell functions, they are considered now as the cell proliferation markers and potential targets for cancer treatment Objective is a screening for some cationic peptides as an expected ligands for NCL/NPM and novel agents with selective cytotoxicity in human cutaneous melanoma cell lines. Three original cell lines mel IS, mel H and mel Ki obtained from the lymph node metastasis of the patients with metastatic cutaneous melanoma were used as a models. To evaluate binding between NCL, NPM and peptides under study molecular docking was used. The data obtained allow to characterize tested cationic peptides as a ligands for NCL and NPM triggered subsequent tumor cell apoptosis.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 3 (8) (2018)
Prop-Based Haptic Interaction with Co-location and Immersion: an Automotive Application
Creators: name: Ortega, Michael
name: Coquillart, Sabine
Publisher: name: arXiv
Year: 2006
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Most research on 3D user interfaces aims at providing only a single sensory modality. One challenge is to integrate several sensory modalities into a seamless system while preserving each modality's immersion and performance factors. This paper concerns manipulation tasks and proposes a visuo-haptic system integrating immersive visualization, tactile force and tactile feedback with co-location. An industrial application is presented.
Thunberg, Lars: Nordisk Ekumenisk Arsbok 1976-77
Creators: name: Deppe, Hans Christoph
Publisher: name: Ökumenische Rundschau
Year: 2025

description: Ökumenische Rundschau, Bd. 27 Nr. 2 (1978): Ökumenische Rundschau, Band 27, Heft 2
Dynamic Modeling of Vapor Compression Systems for Residential Heat Pump Applications with Alternative Low-GWP Refrigerants
Creators: name: Bhanot, Viren
Publisher: name: Digital Repository at the University of Maryland
Year: 2015
Subjects: subject: Mechanical engineering
subject: FOS: Mechanical engineering
subject: Dynamic Simulation
subject: Heat Pump
subject: Low-GWP
subject: Refrigerants
subject: Simulink
subject: Vapor Compression System

description: With the increased focus on reducing greenhouse gas emissions, low-GWP refrigerants, R32 and D2Y60, have been proposed as drop-in replacements for R410A in residential heat pumps. This thesis presents the development of a modeling framework in Simulink® for the dynamic simulations of such residential heat pumps. The framework is component-based, allowing arbitrary cycle configurations, and includes most of the relevant components. Finite-volume method has been applied to the heat exchanger. Compression and expansion processes are treated as quasi-steady state.  The framework has been used to study the performance of the system using the baseline refrigerant and charge-optimized alternatives at ASHRAE test conditions, and the results have been compared against experimental data. Steady-state COP values fall within ±8% of experimental data. For the cyclic tests, the pressure and temperature behaviors compare well and accumulated capacity and power consumption errors are found to be within ±9%. Relative differences between the refrigerants are consistent between simulations and measurements. The framework shows potential for being used to simulate the operation of residential heat pumps under dynamic conditions.
How Discrete Spectrum and Resonances Influence the Asymptotics of the Toda Shock Wave
Creators: name: Egorova, Iryna
name: Michor, Johanna
Publisher: name: arXiv
Year: 2020
Subjects: subject: Mathematical Physics (math-ph)
subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences
subject: 37K40, 35Q53, 37K45, 35Q15

description: We rigorously derive the long-time asymptotics of the Toda shock wave in a middle region where the solution is asymptotically finite gap. In particular, we describe the influence of the discrete spectrum in the spectral gap on the shift of the phase in the theta-function representation for this solution. We also study the effect of possible resonances at the endpoints of the gap on this phase. This paper is a continuation of research started in [arXiv:2001.05184].
Contesting modernism : communities and the pacific salmon revitalization plan
Creators: name: Robertson, Stephen
Publisher: name: University of British Columbia
Year: 2009

description: This thesis explores the role for social work in addressing government policies that threaten the sustainability of small coastal communities. The response of government and industry to the globalization of trade and resource degradation is at odds with the needs of people. Utilizing a case study methodology the development and implementation of the Pacific Salmon Revitalization Plan is explored. This department of fisheries plan to rationalize the fishery was highly contested on the grounds that it took jobs out of small coastal communities. It was accused of benefiting the large fishing corporations and the urban based fishing fleet, which had the capital to profit from the plan. Concentrated opposition from coastal communities, fishers, advocacy groups and academics was unsuccessful in changing the plan. The assumptions of modernism - expert knowledge, scientific rationality and orthodox economics - as well as distorted communications, were postulated to be behind this lack of success. A post modern analysis suggests that a successful challenge to the plan would have incorporated the local knowledge of fishers and coastal communities within a process of fair and equitable public discourse aimed at reaching intersubjectively mediated understanding. For social work this demonstrates the need to work conjointly with communities and affected groups to identify the modernist assumptions on which policy decisions are based and develop locally derived alternatives to these assumptions. And most importantly, that the focus of social change efforts be on demanding a process for discussion and decision-making that ensures that the concerns of effected individuals will be fairly addressed.
AJAE Appendix: De-regulation as (Welfare Reducing) Trade Reform: The Case of the Australian Wheat Board
Creators: name: McCorriston, Steve
name: MacLaren, Donald
name: McCorriston, Steve
name: MacLaren, Donald
Publisher: name: Unknown
Year: 2007
Subjects: International Relations/Trade

description: The material contained herein is supplementary to the article named in the title and published in the American Journal of Agricultural Economics,Volume 89, Number 3, August 2007.
Superconductivity, charge ordering and structural properties of alpha and beta-NaxCoO2.y(H2O, D2O)
Creators: name: Shi, Y. G.
name: Yang, H. X.
name: Huang, H.
name: Liu, X.
name: Li, J. Q.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Two series of alpha and beta-NaxCoO2 materials have been prepared by means of Na deintercalation from the parent alpha-NaCoO2 and beta-Na0.6CoO2 phases, respectively. The alpha-NaxCoO2 materials undergo a clear phase transition from the hexagonal to the beta-phase like monoclinic structure along with Na deintercalation. Measurements of resistivity and magnetization demonstrated the presence notable charge ordering transitions in both alpha and beta-NaxCoO2 with 0.4 < x < 0.5 below 100K. Bulk Superconductivity has been observed in the hydrated alpha-NaxCoO2.1.3H2O at ~4.5K and in beta-NaxCoO2.1.3H2O at \~4.3K. Intercalation of D2O in alpha and beta-Na0.33CoO2 also yields superconductivity at slightly lower temperatures. It is worthy to note that, despite of the structural difference, the alpha-, beta- and gamma-NaxCoO2 .yH2O materials show up notable commonalities in their essential physical properties, e.g. superconductivity and charge ordering transitions.
description: 18 pages, 4 figures
Controlled Analyses of Social Biases in Wikipedia Bios
Creators: name: Field, Anjalie
name: Park, Chan Young
name: Lin, Kevin Z.
name: Tsvetkov, Yulia
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: Social biases on Wikipedia, a widely-read global platform, could greatly influence public opinion. While prior research has examined man/woman gender bias in biography articles, possible influences of other demographic attributes limit conclusions. In this work, we present a methodology for analyzing Wikipedia pages about people that isolates dimensions of interest (e.g., gender), from other attributes (e.g., occupation). Given a target corpus for analysis (e.g.~biographies about women), we present a method for constructing a comparison corpus that matches the target corpus in as many attributes as possible, except the target one. We develop evaluation metrics to measure how well the comparison corpus aligns with the target corpus and then examine how articles about gender and racial minorities (cis. women, non-binary people, transgender women, and transgender men; African American, Asian American, and Hispanic/Latinx American people) differ from other articles. In addition to identifying suspect social biases, our results show that failing to control for covariates can result in different conclusions and veil biases. Our contributions include methodology that facilitates further analyses of bias in Wikipedia articles, findings that can aid Wikipedia editors in reducing biases, and a framework and evaluation metrics to guide future work in this area.
description: Accepted to the Web Conference 2022 (WWW '22)
Optical and Transport Studies of Single Molecule Tunnel junctions based on Self-Assembled Monolayers
Creators: name: Burtman, Vladimir
name: Ndobe, Alexander S.
name: Vardeny, Valy Z.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: We have fabricated a variety of novel molecular tunnel junctions based on self-assembled-monolayers (SAM) of two-component solid-state mixtures of molecular wires (1,4 methane benzene-dithiol; Me-BDT with two thiol anchoring groups), and molecular insulator spacers (1-pentanethiol; PT with one thiol anchoring group) at different concentration ratios, r of wires/spacers, which were sandwiched between two metallic electrodes such as gold and cobalt. FTIR spectroscopy and surface titration were used, respectively to verify the formation of covalent bonds with the electrodes, and obtain the number of active molecular wires in the device. The electrical transport properties of the SAM devices were studied as a function of (i) r-value, (ii) temperatures, and (iii) different electrodes, via the conductance and differential conductance spectra. The measurements were used to analyze the Me-BDT density of states near the electrode Fermi level, and the properties of the interface barriers. We measured the Me-BDT single molecule resistance at low bias and gold electrodes to be 6x10^9 Ohm. We also determine the energy difference, D between the Me-BDT HOMO level and the gold Fermi level to be about 1.8 eV. In addition we also found that the temperature dependence of the SAM devices with r < 10^-4 is much weaker than that of the pure PT device (or r = 0), showing a small interface barrier.
description: 32 pages 10 fugures
COMPARATIVE CONSERVATION OF MEIOTIC PROTEINS IN DIFFERENT PHYLOGENETIC LINES OF EUKARYOTES
Creators: name: Grishaeva, Tatiana
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2018

description: Motivation: Meiosis — a two-stage process of sex cell division — is served by several hundreds of proteins. A part of them went to eukaryotes from prokaryotes, others appeared in first eukaryotes, and some proteins appeared de novo in multicellular eukaryotes. We compared the conservation of proteins involved in various processes occurring in meiosis. Results: The conservations of five meiotic enzymes (MLH1, MRE11, MSH4, BRCA1, BRCA2) and three silencing markers (histone H2AX, SUMO1, ATR) were compared using a set of bioinformatics methods. Orthologs of these proteins from the proteomes of model species were compared, representing different lines of development of eukaryotes. Among the enzymes, the most conserved is MLH1, which provide correction of mismatch bases, and the least conserved are BRCA1 and BRCA2 repair enzymes which are present only in vertebrates. Among silencing proteins, histone H2AX is the most conserved one, playing the central part in the regulation of the transcription, in the repair and replication of DNA. The small protein SUMO1, which is involved in many cellular processes, is less conserved. ATR kinase in different species is similar only in the C-terminal part of the molecule.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 2 (7) (2018)
Reversing the training effect in exchange biased CoO/Co bilayers
Creators: name: Brems, Steven
name: Buntinx, Dieter
name: Temst, Kristiaan
name: Van Haesendonck, Chris
name: Radu, Florin
name: Zabel, Hartmut
Publisher: name: arXiv
Year: 2005
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We performed a detailed study of the training effect in exchange biased CoO/Co bilayers. High-resolution measurements of the anisotropic magnetoresistance (AMR) are consistent with nucleation of magnetic domains in the antiferromagnetic CoO layer during the first magnetization reversal. This accounts for the enhanced spin rotation observed in the ferromagnetic Co layer for all subsequent reversals. Surprisingly, the AMR measurements as well as magnetization measurements reveal that it is possible to partially reinduce the untrained state by performing a hysteresis measurement with an in plane external field perpendicular to the cooling field. Indeed, the next hysteresis loop obtained in a field parallel to the cooling field resembles the initial asymmetric hysteresis loop, but with a reduced amount of spin rotation occurring at the first coercive field. This implies that the antiferromagnetic domains, which are created during the first reversal after cooling, can be partially erased.
description: 4 pages, 4 figures
Source Code Reduction to Summarize False Positives
Creators: name: Marenchino, Matias
Publisher: name: Digital Repository at the University of Maryland
Year: 2015
Subjects: subject: Computer science
subject: False Positives
subject: Software Engineering
subject: Source Code Reduction
subject: Static Code Analysis

description: The main disadvantage of static code analysis tools is the high

rates of false positives they produce. Users may need to manually analyze a

large number of warnings, to determine if these are false or legitimate

warnings, reducing the benefits of automatic static analysis. Our long term

goal is to significantly reduce the number of false positives that these

tools report. A learning system could classify the warnings into true

positives and false positives by means of features extracted from the

program source code. This work implements and evaluates a technique to

reduce the source code producing false positives into code snippets that are

simpler to analyze. Results indicate that the method considerably reduces

the source code size and it is feasible to use it to characterize false

positives.
Relativistic reflection in NGC 4151
Creators: name: Szanecki, Michal
name: Niedzwiecki, Andrzej
name: Zdziarski, Andrzej A.
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We investigate the X-ray spectrum of the Seyfert galaxy NGC 4151 using the simultaneous Suzaku/NuSTAR observation and flux-resolved INTEGRAL spectra supplemented by Suzaku and XMM observations. Our best spectral solution indicates that the narrow Fe Kalpha line is produced in Compton-thin matter at the distance of several hundred gravitational radii. In such a model, we find a weak but significant relativistic reflection from a disk truncated at about ten gravitational radii when the source is in bright X-ray states. We do not find evidence either for or against the presence of relativistic reflection in the dim X-ray state. We also rule out models with X-ray emission dominated by a source located very close to the black hole horizon, which was proposed in previous works implementing the lamp-post geometry for this source. We point out that accurate computation of the thermal Comptonization spectrum and its distortion by strong gravity is crucial in applications of the lamp-post geometry to the NuSTAR data.
description: ApJ, in press
Insight into Delay Based Reservoir Computing via Eigenvalue Analysis
Creators: name: Köster, Felix
name: Yanchuk, Serhiy
name: Lüdge, Kathy
Publisher: name: arXiv
Year: 2020
Subjects: subject: Machine Learning (cs.LG)
subject: Dynamical Systems (math.DS)
subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: In this paper we give a profound insight into the computation capability of delay-based reservoir computing via an eigenvalue analysis. We concentrate on the task-independent memory capacity to quantify the reservoir performance and compare these with the eigenvalue spectrum of the dynamical system. We show that these two quantities are deeply connected, and thus the reservoir computing performance is predictable by analyzing the small signal response of the reservoir. Our results suggest that any dynamical system used as a reservoir can be analyzed in this way. We apply our method exemplarily to a photonic laser system with feedback and compare the numerically computed recall capabilities with the eigenvalue spectrum. Optimal performance is found for a system with the eigenvalues having real parts close to zero and off-resonant imaginary parts.
description: New Journal Submission
AJAE Appendix: Stochastic Rangeland Use Under Capital Constraints
Creators: name: Kobayashi, Mimako
name: Howitt, Richard E.
name: Jarvis, Lovell S.
name: Laca, Emilio A.
name: Kobayashi, Mimako
name: Howitt, Richard E.
name: Jarvis, Lovell S.
name: Laca, Emilio A.
Publisher: name: Unknown
Year: 2007
Subjects: Land Economics/Use

description: The material contained herein is supplementary to the article named in the title and published in the American Journal of Agricultural Economics, Volume 89, Number 2, August 2007.
D1.1 Project Management Plan
Creators: name: Fielding Pollard, Sarah
Publisher: name: SteamBioAfrica
Year: 2022
Subjects: subject: Innovation management

description: This Project Management Plan builds on the Work Plan included in the project proposal to the EU submission deadline (26th January 2021) and approved for funding. It includes amendments from the grant preparation phase made at the request of the European Commission Project Officers. It also addresses identified typographical errors.This plan includes a Gantt Chart and a Work Breakdown Structure (WBS). This plan will be employed as a project management tool to ensure that the project keeps on schedule. It will therefore be inherently dynamic and responsive to the challenges faced in project delivery. This plan will be updated and revised at Month 17 and Month 35. These revisions will be uploaded along with this deliverable onto the EU portal.Following a review and feedback by the EC this report was updated with a record of “History of Changes” being presented in a table. This updated report provides a “Handbook” with all relevant information concerning project management, participation, and obligations of individual partners. This Handbook report will be uploaded onto the EUI portal and onto the shared project Google Drive and accessible to all project participants.This plan will be used to monitor progress and identify deviation from plan. As it is by its nature dynamic it will upgraded through the project life with updates and revisions uploaded along with this deliverable onto the EU portal at Month 17 and Month 35.
The Aladin2 experiment: status and perspectives
Creators: name: Bimonte, Giuseppe
name: Born, Detlef
name: Calloni, Enrico
name: Esposito, Giampiero
name: Hubner, Uve
name: Il'ichev, Evgeni
name: Rosa, Luigi
name: Scaldaferri, Ornella
name: Tafuri, Francesco
name: Vaglio, Ruggero
Publisher: name: arXiv
Year: 2005
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Aladin2 is an experiment devoted to the first measurement of variations of Casimir energy in a rigid cavity. The main scientific motivation relies on the possibility of the first demonstration of a phase transition influenced by vacuum fluctuations. The guiding principle of the measurement, based on the behaviour of the critical field for an in-cavity superconducting film, will be only briefly recalled. In this paper, after an introduction to the long term motivations, the experimental apparatus and the results of the first measurement of sensitivity will be presented in detail, particularly in comparison with the expected signal. Last, the most important steps towards the final measurement will be discussed.
description: Talk given by Calloni at QFEXT05 Conference in Barcelona: Quantum Field Theory Under the Influence of External Conditions
AJAE Appendix: Modeling Farm Households' Price Responses in the Presence of Transaction Costs and Heterogeneity in Labor Markets
Creators: name: Henning, Christian H.C.A.
name: Henningsen, Arne
name: Henning, Christian H.C.A.
name: Henningsen, Arne
Publisher: name: Unknown
Year: 2007
Subjects: Labor and Human Capital

description: The material contained herein is supplementary to the article named in the title and published in the American Journal of Agricultural Economics, Volume 89, Number 2, August 2007.
Influence of tamoxifen on hormonally regulated cytochrome P450 enzyme expression in rats
Creators: name: Ickenstein, Ludger Markus
Publisher: name: University of British Columbia
Year: 2009

description: Tamoxifen, a partial estrogen antagonist in humans, is used widely in the treatment of breast cancer and suppresses growth hormone plasma levels in rats up to seven weeks after treatment. The purpose of the present study was to determine if tamoxifen treatment results in long-term alterations of hormonally regulated cytochrome P450 enzymes. Female rats were injected subcutaneously with tamoxifen at 0.5, 5, 20, 50, 100, or 200 mg/kg for two consecutive days. Male rats were injected subcutaneously with tamoxifen at 200 mg/kg for two consecutive days. Blood samples were taken at regular time intervals. Rats were killed 36 days after treatment and hepatic microsomes were prepared. Administration of tamoxifen decreased body weight gain in male and female rats. Testosterone 7α-hydroxylase activity and cytochrome P450 2A1 content were decreased in hepatic microsomes from tamoxifen treated female rats by 40% and 35%, respectively. In hepatic microsomes from tamoxifen treated male rats, testosterone 7α-hydroxylase activity was increased by 70% and testosterone 2a- and 16oc-hydroxylase activities and cytochrome P450 2C11 content was decreased by approximately 44% and 30%, respectively. Administration of tamoxifen decreased peak growth hormone plasma levels in male and female rats, but did not affect the average and nadir growth hormone plasma levels. In plasma of rats treated at 50 mg/kg, tamoxifen was detected at one day and at twelve days after treatment but not at 24 or 36 days after treatment. 4-Hydroxytamoxifen was detected at one and twelve days after treatment. In plasma of rats treated with tamoxifen at a dosage of 200 mg/kg, 4-hydroxytamoxifen was detected up to 36 days after treatment. The results of the present study indicate that tamoxifen treatment suppressed body weight gain, blunted peak growth hormone plasma levels, and resulted in long-term alterations of specific hepatic cytochrome P450 enzymes in male and female rats. These effects are different from the previously reported direct, short-term effects of tamoxifen on hepatic cytochrome P450 2B and 3A enzymes. The effects of tamoxifen on cytochrome P450 enzymes are not believed to be mediated solely by the effects of tamoxifen on growth hormone plasma levels. More likely, the effects of tamoxifen on cytochrome P450 enzymes were caused by its estrogenic or antiestrogenic effects. Alternatively, the effects could have been caused by a residual tamoxifen metabolite that remained in rat tissues at concentrations below the limits of quantitation of the HPLC assay.
ATROF-MUHITNI MUHOFAZA QILISHDA XALQARO STANDARTLAR TAHLILI
Creators: name: Shermatov, Elyor
Publisher: name: Zenodo
Year: 2024

description: Mazkur maqolada atrof-muhitni muhofaza qilishda xalqaro standartlar tahliliga doir masalalar bayon etilgan. Shuningdek, maqolada xalqaro kelishuvlar atrof-muhitni muhofaza qilish masalalarini hal etishga xizmat qilganligi borasida fikirlar ham ilgari surilgan.
Polarization of 21cm Radiation from the Epoch of Reionization
Creators: name: Babich, Daniel
name: Loeb, Abraham
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We consider the polarization of 21cm line radiation from the epoch of reionization due to both intrinsically polarized emission and secondary mechanisms. We argue that Thomson scattering of the 21cm quadrupole by the reionized universe is likely to produce the largest effect. The 21cm quadrupole is sourced by baryonic density fluctuations and the fluctuations in the ionization fraction due to discrete \ion{H}{2} regions. Since Thomson scattering produces only E-type polarization and is achromatic, its unique fingerprint can in principle be separated from foregrounds associated with polarized synchrotron emission which should not be correlated with the cosmic signal. We estimate that Poisson fluctuations of \ion{H}{2} regions at the end of reionization ($z_R \sim 6$--20) produce a brightness temperature-polarization cross-correlation signal of $\sim 0.1 - 0.3 {mK}$ on angular scales of tens of arcminutes. This cross-correlation signal is within the instrument sensitivities of the future {\it Square Kilometer Array} (SKA) and close to the sensitivities of the forthcoming {\it Mileura Widefield Array} (MWA) and {\it Low Frequency Array} (LOFAR).
description: 10 pages, 6 figures, replaced to match version accepted by ApJ
Engineering Geognosy of Boyd County
Creators: name: Hopkins, Tommy C.
name: Pigman, Jerry G.
Publisher: name: Kentucky Transportation Center, University of Kentucky
Year: 1969
Subjects: subject: Transportation Engineering

description: Engineering soils and geologic maps are proving to be invaluable tools of engineers, industrial leaders, community planners, and administrators during tbe preliminary stages of planning and site selection for major construction projects and the development of plans to use nature's basic resource--the land. Quantitative engineering data for soils and geological formations, and the interpretation of tbese data, are important factors to consider in the best land-use plans and in providing stable foundations and proper usage of earth materials for highways, buildings, and other earth structures. Engineering soils and geologic maps can be used to great advantage by planners and engineers to 1) make soil and geological reconnaissance surveys, 2) organize and check field surveys, 3) correlate and predict performances of soil and geological materials, and 4) locate construction material and resource deposits.  Recognizing the need and demand for this type of information, the Research Division of the Kentucky Department of Highways has undertaken a pilot study to report tbe engineering geognosy of a selected area in Kentucky. The area reported herein is located in the vicinity of Ashland.  This report discusses the engineering properties and behavior of unconsolidated surficial deposits and consolidated bedrock materials in Boyd County, Kentucky. It is based mainly on an interpretation of engineering test data retrieved and summarized from Kentucky Department of Highways' design and construction plans for routes I 64, KY 3, and US 60, which pass tbrough the area; a soils report (1) prepared by the Soil Conservation Service for the city of Ashland; and published geologic reports and maps (2, 4, 5). Engineering soils and geologic maps and interpretations presented in this report should be viewed from a standpoint of rapidly providing generalized engineering information of the different soil and rock materials in the subject area. For important earthwork and foundation engineering purposes and for detailed and specific data, it is recommended that the soil and rock materials at a particular site be explored and tested thoroughly.
AN ALGORITHM FOR DERIVING COMBINATORIAL BIOMARKERS BASED ON RIDGE REGRESSION
Creators: name: Terpilowski, Maxim
name: Korf, Ekaterina
name: Jenkins, Richard
name: Goncharov, Nikolay
Publisher: name: JOURNAL OF BIOINFORMATICS AND GENOMICS
Year: 2018

description: Motivation: Combinatorial biomarkers are considered more specific and sensitive than single markers in medical diagnostics and prediction, yet even detection of such these combinatorial biomarkers requires deep computational analysis. The principles of analytic combinatorics, linear and kernel ridge regression, and machine learning were applied to derive new combinatorial biomarkers of muscle damage. Results: Lactate, phosphate, and middle-chain fatty acids were most often included into biochemical combinatorial markers, while the following physiological parameters were found to be prevalent: muscle isometric strength, H-reflex length, and contraction tone. Several strongly correlated combinatorial biomarkers of muscle damage with high prediction accuracy scores were identified. The approach — based on computational methods, regression algorithms and machine learning — provides a flexible, platform independent and highly extendable means of discovery and evaluation of combinatorial biomarkers alongside current diagnostic tools. Availability: The developed algorithm was implemented in Python programming language on a quantitative dataset comprising 23 biochemical parameters, 37 physiological parameters and 3,903 observations. The algorithm and our dataset are available free of charge on GitHub. Supplementary information: Supplementary data are available at Journal of Bioinformatics and Genomics online.
description: JOURNAL OF BIOINFORMATICS AND GENOMICS, No. 1 (6) (2018)