cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Fragment-based Shape Signatures: A new tool for virtual screening and drug discovery
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: Ligand-based drug design
Fragment-based shape signatures
Scaffold hopping
Shape signatures
Shape similarity
Virtual screening

description: Since its introduction in 2003, the Shape Signatures method has been successfully applied in a number of drug design projects. Because it uses a ray-tracing approach to directly measure molecular shape and properties (as opposed to relying on chemical structure), it excels at scaffold hopping, and is extraordinarily easy to use. Despite its advantages, a significant drawback of the method has hampered its application to certain classes of problems; namely, when the chemical structures considered are large and contain heterogeneous ring-systems, the method produces descriptors that tend to merely measure the overall size of the molecule, and begin to lose selective power. To remedy this, the approach has been reformulated to automatically decompose compounds into fragments using ring systems as anchors, and to likewise partition the ray-trace in accordance with the fragment assignments. Subsequently, descriptors are generated that are fragment-based, and query and target molecules are compared by mapping query fragments onto target fragments in all ways consistent with the underlying chemical connectivity. This has proven to greatly extend the selective power of the method, while maintaining the ease of use and scaffold-hopping capabilities that characterized the original implementation. In this work, we provide a full conceptual description of the next generation Shape Signatures, and we underline the advantages of the method by discussing its practical applications to ligand-based virtual screening. The new approach can also be applied in receptor-based mode, where protein-binding sites (partitioned into subsites) can be matched against the new fragment-based Shape Signatures descriptors of library compounds. © 2013 The Author(s).
Single atom-scale diamond defect allows large Aharonov-Casher phase
Creators: name: Maclaurin, D.
name: Greentree, A. D.
name: Cole, J. H.
name: Hollenberg, L. C. L.
name: Martin, A. M.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: We propose an experiment that would produce and measure a large Aharonov-Casher (A-C) phase in a solid-state system under macroscopic motion. A diamond crystal is mounted on a spinning disk in the presence of a uniform electric field. Internal magnetic states of a single NV defect, replacing interferometer trajectories, are coherently controlled by microwave pulses. The A-C phase shift is manifested as a relative phase, of up to 17 radians, between components of a superposition of magnetic substates, which is two orders of magnitude larger than that measured in any other atom-scale quantum system.
description: 5 pages, 2 figures
Radically open-dialectical behavior therapy for adult anorexia nervosa: Feasibility and outcomes from an inpatient program
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: Anorexia nervosa
DBT
Inpatient
Eating disorders
Overcontrol
Personality disorders
Radical openness

description: Background: Anorexia Nervosa (AN) is a highly life-threatening disorder that is extremely difficult to treat. There is evidence that family-based therapies are effective for adolescent AN, but no treatment has been proven to be clearly effective for adult AN. The methodological challenges associated with studying the disorder have resulted in recommendations that new treatments undergo preliminary testing prior to being evaluated in a randomized clinical trial. The aim of this study was to provide preliminary evidence on the effectiveness of a treatment program based on a novel adaptation of Dialectical Behavior Therapy (DBT) for adult Anorexia Nervosa (Radically Open-DBT; RO-DBT) that conceptualizes AN as a disorder of overcontrol.Methods: Forty-seven individuals diagnosed with Anorexia Nervosa-restrictive type (AN-R; mean admission body mass index = 14.43) received the adapted DBT inpatient program (mean length of treatment = 21.7 weeks).Results: Seventy-two percent completed the treatment program demonstrating substantial increases in body mass index (BMI; mean change in BMI = 3.57) corresponding to a large effect size (d = 1.91). Thirty-five percent of treatment completers were in full remission, and an additional 55% were in partial remission resulting in an overall response rate of 90%. These same individuals demonstrated significant and large improvements in eating-disorder related psychopathology symptoms (d = 1.17), eating disorder-related quality of life (d = 1.03), and reductions in psychological distress (d = 1.34).Conclusions: RO-DBT was associated with significant improvements in weight gain, reductions in eating disorder symptoms, decreases in eating-disorder related psychopathology and increases in eating disorder-related quality of life in a severely underweight sample. These findings provide preliminary support for RO-DBT in treating AN-R suggesting the importance of further evaluation examining long-term outcomes using randomized controlled trial methodology. © 2013 Lynch et al.; licensee BioMed Central Ltd.
Additional file 2 of Knowledge and perceptions of preconception care among health workers and women of reproductive age in Mzuzu City, Malawi: a cross-sectional study
Creators: name: Munthali, Mtondera
name: Chiumia, Isabel Kazanga
name: Mandiwa, Chrispin
name: Mwale, Saul
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Biotechnology
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2. Interview guide for health workers.
Scaling of the thermally induced sign inversion of longitudinal spin Seebeck effect in a compensated ferrimagnet: Role of magnetic anisotropy
Creators: name: Chanda, Amit
name: Schulz, Noah
name: Holzmann, Christian
name: Seyd, Johannes
name: Albrecht, Manfred
name: Phan, Manh-Huong
name: Srikanth, Hari
Publisher: name: arXiv
Year: 2021
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: We report on a systematic investigation of the longitudinal spin Seebeck effect (LSSE) in a GGG(Gd3Ga5O12)/GdIG(Gd3Fe5O12)/Pt film series exhibiting an in-plane magnetic easy axis with a compensation temperature (T_Comp) that decreases from 270 to 220 K when decreasing GdIG film thickness from 272 to 31 nm, respectively. For all the films, the LSSE signal flips its sign below T_Comp. We demonstrate a universal scaling behavior of the temperature dependence of LSSE signal for our GdIG films around their respective T_Comp. Additionally, we demonstrate LSSE in a 31 nm GdIG film grown on a lattice-mismatched GSGG (Gd3Sc2Ga3O12) substrate that exhibits an out-of-plane magnetic easy axis at room temperature. However, this sample reveals a spin reorientation transition where the magnetic easy axis changes its orientation to in-plane at low temperatures. We observed a clear distinction in the LSSE signal for the GSGG/GdIG(31 nm)/Pt heterostructure, relative to GGG/GdIG(31nm)/Pt showing an in-plane magnetic easy axis. Our findings underscore a strong correlation between the LSSE signal and the orientation of magnetic easy axis in compensated ferrimagnets and opens the possibility to tune LSSE through effective anisotropy.
description: Accepted in Advanced Functional Materials
Asymptotic distribution of certain degenerate V- and U-statistics with estimated parameters
Creators: name: Cuparić, Marija
name: Milošević, Bojana
name: Obradović, Marko
Publisher: name: arXiv
Year: 2020
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: 62E20, 62G20

description: The asymptotic distribution of a wide class of V- and U-statistics with estimated parameters is derived in the case when the kernel is not necessarily differentiable along the parameter. The results have their application in goodness-of-fit problems.
description: Revised proof of Theorem 1; other minor changes in text
Hybridization Reveals the Evolving Genomic Architecture of Speciation
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: Animals
Butterflies
Genetic Speciation
Genome, Insect
Hybridization, Genetic
Species Specificity
Wings, Animal

description: The rate at which genomes diverge during speciation is unknown, as are the physical dynamics of the process. Here, we compare full genome sequences of 32 butterflies, representing five species from a hybridizing Heliconius butterfly community, to examine genome-wide patterns of introgression and infer how divergence evolves during the speciation process. Our analyses reveal that initial divergence is restricted to a small fraction of the genome, largely clustered around known wing-patterning genes. Over time, divergence evolves rapidly, due primarily to the origin of new divergent regions. Furthermore, divergent genomic regions display signatures of both selection and adaptive introgression, demonstrating the link between microevolutionary processes acting within species and the origin of species across macroevolutionary timescales. Our results provide a uniquely comprehensive portrait of the evolving species boundary due to the role that hybridization plays in reducing the background accumulation of divergence at neutral sites
Engaging in socially responsible research: exploring scientists' perceived value of online public communication of science
Creators: name: Villares, Rosana
Publisher: name: Zenodo
Year: 2024

description: Communicating science to broad publics using the Internet and social media has become a key social priority on EU scientists’ professional agenda to enhance socially responsible research (Ball 2016). To date, little research has analysed scientists’ values and motivations regarding digital science communication practices targeted at non-specialist audiences. Using a semi-structured interview protocol, I examine Spanish female STEM scientists’ engagement in digital science communication practices. The interview data were analysed using a content thematic approach on the software Atlas.TI. Results confirm that the primary motivation for engaging in digital practices is to make science accessible to broad publics. They also view communicating beyond the scientific community as a valuable practice to improve citizens’ scientific literacy, a finding that echoes the deficit model of science communication as described by Trench (2008). In other words, scientists consider initiatives such as giving online talks, participating in podcasts, creating videos, or sharing events and content on social media (Instagram, TikTok, Twitter, LinkedIn) as an opportunity to democratise science. They also perceive them as socially responsible research, and as a way of raising awareness for scientific topics and careers (Loroño-Leturiondo & Davies 2018; Metcalfe 2019). Interviewees also highlighted the benefits of digital practices, especially after the COVID-19 pandemic, due to their international range, sustainability, and accessibility. The implications derived from the findings point to the need to design LSP training that supports skills development in communicating scientific content to non-specialized audiences on the Internet and the deployment of digital tools and resources supporting online science communication.
Identification of Cichlid Fishes from Lake Malawi Using Computer Vision
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: Animals
Artificial Intelligence
Cichlids
Color
Evolution, Molecular
Fishes
Fresh Water
Humans
Image Processing, Computer-Assisted
Lakes
Malawi

description: Background:The explosively radiating evolution of cichlid fishes of Lake Malawi has yielded an amazing number of haplochromine species estimated as many as 500 to 800 with a surprising degree of diversity not only in color and stripe pattern but also in the shape of jaw and body among them. As these morphological diversities have been a central subject of adaptive speciation and taxonomic classification, such high diversity could serve as a foundation for automation of species identification of cichlids.Methodology/Principal Finding:Here we demonstrate a method for automatic classification of the Lake Malawi cichlids based on computer vision and geometric morphometrics. For this end we developed a pipeline that integrates multiple image processing tools to automatically extract informative features of color and stripe patterns from a large set of photographic images of wild cichlids. The extracted information was evaluated by statistical classifiers Support Vector Machine and Random Forests. Both classifiers performed better when body shape information was added to the feature of color and stripe. Besides the coloration and stripe pattern, body shape variables boosted the accuracy of classification by about 10%. The programs were able to classify 594 live cichlid individuals belonging to 12 different classes (species and sexes) with an average accuracy of 78%, contrasting to a mere 42% success rate by human eyes. The variables that contributed most to the accuracy were body height and the hue of the most frequent color.Conclusions:Computer vision showed a notable performance in extracting information from the color and stripe patterns of Lake Malawi cichlids although the information was not enough for errorless species identification. Our results indicate that there appears an unavoidable difficulty in automatic species identification of cichlid fishes, which may arise from short divergence times and gene flow between closely related species. © 2013 Joo et al.
title: Patrones de captación de la pared intestinal. Semiología y diagnóstico diferencial mediante TC.
Creators: name: Pérez Sánchez, Pablo
Publisher: name: Sociedad Española de Radiología Médica
Year: 2014
Subjects: subject: Conventional radiography
subject: Abdomen
subject: Gastrointestinal tract
subject: CT

description: Objetivo docente
Revisión del tema
Conclusiones
Bibliografía
description: Objetivo docente:
Identificar los patrones de captación de la pared intestinal mediante TC,
que permitan establecer un diagnóstico diferencial...
Search for $B^0 \to K^{*0} \overline{K}{}^{*0}$, $B^0 \to K^{*0} K^{*0}$ and $B^0 \to K^+π^- K^{\mp}π^{\pm}$ Decays
Creators: name: Chiang, C. -C.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We report a search for the decays $B^0\to K^{*0} \overline{K}{}^{*0}$ and $B^0\to K^{*0} K^{*0}$. We also measure other charmless decay modes with $K^+π^-K^-π^+$ and $K^{+}π^{-}K^{+}π^{-}$ final states. The results are obtained from a data sample containing $657 \times 10^6$ $B \overline B$ pairs collected with the Belle detector at the KEKB asymmetric-energy $e^+e^-$ collider. We set upper limits on the branching fractions for $B^0\to K^{*0} \kstarbar$ and $B^0\to K^{*0} K^{*0}$ of $0.81 \times 10^{-6}$ and $0.20\times 10^{-6}$, respectively, at the 90% confidence level.
description: 7 pages, 2 figures. submitted to PRD(R)
Revisiting the Single Cell Protein Application of Cupriavidus necator H16 and Recovering Bioplastic Granules Simultaneously
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: Animals
Bacterial Proteins
Cupriavidus necator
Cytoplasm
Cytoplasmic Granules
Dietary Proteins
Female
Hydroxybutyrates
Male
Models, Animal
Polyesters
Rats
Rats, Sprague-Dawley

description: Cupriavidus necator H16 (formerly known as Hydrogenomonas eutropha) was famous as a potential single cell protein (SCP) in the 1970s. The drawback however was the undesirably efficient accumulation of non-nutritive polyhydroxybutyrate (PHB) storage compound in the cytoplasm of this bacterium. Eventually, competition from soy-based protein resulted in SCP not receiving much attention. Nevertheless, C. necator H16 remained in the limelight as a producer of PHB, which is a material that resembles commodity plastics such as polypropylene. PHB is a 100% biobased and biodegradable polyester. Although tremendous achievements have been attained in the past 3 decades in the efficient production of PHB, this bioplastic is still costly. One of the main problems has been the recovery of PHB from the cell cytoplasm. In this study, we showed for the first time that kilogram quantities of PHB can be easily recovered in the laboratory without the use of any solvents and chemicals, just by using the cells as SCP. In addition, the present study also demonstrated the safety and tolerability of animal model used, Sprague Dawley given lyophilized cells of C. necator H16. The test animals readily produced fecal pellets that were whitish in color, as would be expected of PHB granules. The pellets were determined to contain about 82-97 wt% PHB and possessed molecular mass of around 930 kg/mol. The PHB granules recovered biologically possessed similar molecular mass compared to chloroform extracted PHB [950 kg/mol]. This method now allows the production and purification of substantial quantities of PHB for various experimental trials. The method reported here is easy, does not require expensive instrumentation, scalable and does not involve extensive use of solvents and strong chemicals.
Branes and Quantization for an A-Model Complexification of Einstein Gravity in Almost Kahler Variables
Creators: name: Vacaru, Sergiu I.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Mathematical Physics (math-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Symplectic Geometry (math.SG)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: The general relativity theory is redefined equivalently in almost Kahler variables: symplectic form and canonical symplectic connection (distorted from the Levi-Civita connection by a tensor constructed only from metric coefficients and their derivatives). The fundamental geometric and physical objects are uniquely determined in metric compatible form by a (pseudo) Riemannian metric on a manifold enabled with a necessary type nonholonomic 2+2 distribution. Such nonholonomic symplectic variables allow us to formulate the problem of quantizing Einstein gravity in terms of the A-model complexification of almost complex structures on spacetime manifold, generalizing the Gukov-Witten method, see arXiv:0809.0305. Quantizing the complexified model, we derive a Hilbert space as a space of strings with two A-branes which for the Einstein gravity theory are nonholonomic because of induced nonlinear connection structures. Finally, we speculate on relation of such a method of quantization to curve flows and solitonic hierarchies defined by Einstein metrics on (pseudo) Riemannian spacetimes.
description: latex2e, 45 pages, 11pt, two figures and one table in latex, v3 accepted IJGMMP
Anomalous lack of decoherence of the Macroscopic Quantum Superpositions based on phase-covariant Quantum Cloning
Creators: name: De Martini, Francesco
name: Sciarrino, Fabio
name: Spagnolo, Nicolo'
Publisher: name: arXiv
Year: 2009
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We show that all Macroscopic Quantum Superpositions (MQS) based on phase-covariant quantum cloning are characterized by an anomalous high resilence to the de-coherence processes. The analysis supports the results of recent MQS experiments and leads to conceive a useful conjecture regarding the realization of complex decoherence - free structures for quantum information, such as the quantum computer.
description: 4 pages, 3 figures
Additional file 6 of Cloning and overexpression of PeWRKY31 from Populus × euramericana enhances salt and biological tolerance in transgenic Nicotiana
Creators: name: Yu, Xiaoyue
name: Pan, Yu
name: Dong, Yan
name: Lu, Bin
name: Zhang, Chao
name: Yang, Minsheng
name: Zuo, Lihui
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 6.
Additional file 1 of Cloning and overexpression of PeWRKY31 from Populus × euramericana enhances salt and biological tolerance in transgenic Nicotiana
Creators: name: Yu, Xiaoyue
name: Pan, Yu
name: Dong, Yan
name: Lu, Bin
name: Zhang, Chao
name: Yang, Minsheng
name: Zuo, Lihui
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 1: Table S1. The list of primers.
title: Huéspedes inesperados: imagen de las enfermedades parasitarias.
Creators: name: Hernandez Mateo, Paula
Publisher: name: Sociedad Española de Radiología Médica
Year: 2014
Subjects: subject: CT
subject: MR
subject: Conventional radiography
subject: Musculoskeletal system
subject: Neuroradiology brain
subject: Abdomen

description: Objetivo docente
Revisión del tema
Conclusiones
Bibliografía
description: Objetivo docente:
- Ilustrar los hallazgos por imagen de las enfermedades parasitarias más relevantes. - Resaltar el papel que pueden desempeñar las diferentes técnicas de imagen a la hora de enfrentarnos a este tipo de patología...
Feasibility of a computerized intervention for offenders with substance use disorders: A research note
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2014
Subjects: Computerized intervention
Correctional settings
Offenders
Substance abuse treatment
Substance use

description: Objectives: Despite evidence that treatment is effective in reducing recidivism among inmates with substance use problems, scarce resources mean that few of those in need of treatment actually receive it. Computerized substance abuse interventions could be used to expand access to treatment in prisons without placing an undue burden on resources. The major aim of the study was to compare treatment conditions in terms of their service utilization, skills acquisition, and treatment satisfaction. Methods: The study recruited men and women with substance use disorders from 10 prisons in 4 states. In an open label clinical trial, 494 subjects were randomly assigned either to the Experimental condition, a computerized drug treatment intervention, the Therapeutic Education System (TES; n = 249), or to the Control condition, Standard Care (n = 245). Chi-square tests compared groups on categorical variables and independent samples t tests were used for interval level continuous variables. Results: Initial evidence demonstrated: (1) comparable group rates of session attendance and high rates of TES module completion for experimental subjects; (2) comparable group gains in the development of coping skills; and (3) a more favorable view of TES than of Standard Care. Conclusions: Collectively, these results show that a computerized intervention, such as TES, can be implemented successfully in prison. Given the barriers to the delivery of substance abuse treatment typically encountered in correctional settings, computerized interventions have the potential to fill a significant treatment gap and are particularly well suited to inmates with mild to moderate substance use disorders who often are not treated. © 2013 The Author(s).
Population Differentiation and Species Formation in the Deep Sea: The Potential Role of Environmental Gradients and Depth
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: Animals
Atlantic Ocean
Bayes Theorem
Bivalvia
Cell Nucleus
DNA, Mitochondrial
Ecosystem
Gene Flow
Genetic Speciation
Genetic Variation
Multilocus Sequence Typing
Phylogeny

description: Ecological speciation probably plays a more prominent role in diversification than previously thought, particularly in marine ecosystems where dispersal potential is great and where few obvious barriers to gene flow exist. This may be especially true in the deep sea where allopatric speciation seems insufficient to account for the rich and largely endemic fauna. Ecologically driven population differentiation and speciation are likely to be most prevalent along environmental gradients, such as those attending changes in depth. We quantified patterns of genetic variation along a depth gradient (1600-3800m) in the western North Atlantic for a protobranch bivalve (Nucula atacellana) to test for population divergence. Multilocus analyses indicated a sharp discontinuity across a narrow depth range, with extremely low gene flow inferred between shallow and deep populations for thousands of generations. Phylogeographical discordance occurred between nuclear and mitochondrial loci as might be expected during the early stages of species formation. Because the geographic distance between divergent populations is small and no obvious dispersal barriers exist in this region, we suggest the divergence might reflect ecologically driven selection mediated by environmental correlates of the depth gradient. As inferred for numerous shallow-water species, environmental gradients that parallel changes in depth may play a key role in the genesis and adaptive radiation of the deep-water fauna. © 2013 Jennings et al.
Bounding the electromagnetic and weak dipole moments of the tau-lepton in a simplest little Higgs model
Creators: name: Gutierrez-Rodriguez, A.
Publisher: name: arXiv
Year: 2009
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: From the total cross section for the reaction $e^+e^-\to τ^+τ^-γ$ at the $Z_1$ pole and in the framework of a simplest little Higgs model (SLHM), we get a limit on the characteristic energy scale of the model $f$, $f \geq 5.4$ $TeV$, which in turn induces bounds on the electromagnetic and weak dipole moments of the tau-lepton. Our bounds on the electromagnetic moments are consistent with the bounds obtained by the L3 and OPAL collaborations for the reaction $e^+e^-\to τ^+τ^-γ$. We also obtained bounds on the tau weak dipole moments which are consistent with the bounds obtained recently by the DELPHI and ALEPH collaborations from the reaction $e^+e^-\to τ^+τ^-$.
description: 14 pages, 5 figures
title: Lesión focal hepática: Guía de supervivencia
Creators: name: Alvarez-Hornia Pérez, Eduardo
Publisher: name: Sociedad Española de Radiología Médica
Year: 2014
Subjects: subject: Metastases
subject: Haemangioma
subject: Neoplasia
subject: Diagnostic procedure
subject: CT
subject: Ultrasound
subject: MR
subject: Contrast agents
subject: Liver
subject: Abdomen

description: Objetivo docente
Revisión del tema
Conclusiones
Bibliografía
description: Objetivo docente:
Describir las características radiológicas y el comportamiento en las diferentes técnicas de imagen y con distintos medios de contrastes de las lesiones hepáticas más características. Permitir un enfoque diagnóstico ante una lesión focal...
On the need for mechanistic models in computational genomics and metagenomics
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: stochastic modeling
computational biology
molecular evolution
gene duplication
transcriptional regulation
bacterial ecology

description: Computational genomics is now generating very large volumes of data that have the potential to be used to address important questions in both basic biology and biomedicine. Addressing these important biological questions becomes possible when mechanistic models rooted in biochemistry and evolutionary/population genetic processes are developed, instead of fitting data to off the-shelf statistical distributions that do not enablemechanistic inference. Three examples are presented, the first involving ecological processes inferred frommetagenomic data, the second involvingmechanisms of gene regulation rooted in protein-DNA interactions with consideration of DNA structure, and the third involving existing models for the retention of duplicate genes that enables prediction of evolutionary mechanisms. This description of mechanistic models is generalized toward future developments in computational genomics and the need for biological mechanisms and processes in biological models. © The Author(s) 2013.
Additional file 6 of Association of ABO blood groups with ovarian reserve, and outcomes after assisted reproductive technology: systematic review and meta-analyses
Creators: name: Zhao, Jing
name: Yao, Zhongyuan
name: Hao, Jie
name: Xu, Bin
name: Wang, Yonggang
name: Li, Yanping
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Marine Biology
subject: Cancer
subject: Science Policy
subject: Hematology

description: Additional file 6: Fig. S5.1 Funnel plot of analysis for the association of blood group non-O/O and MR, showing the results of Eggers to assess publication bias.
On Differential Rotation and Convection in the Sun
Creators: name: Balbus, S. A.
name: Bonart, J.
name: Latter, H. N.
name: Weiss, N. O.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We show that the differential rotation profile of the solar convection zone, apart from inner and outer boundary layers, can be reproduced with great accu- racy if the isorotation contours correspond to characteristics of the thermal wind equation. This requires that there be a formal quantitative relationship involving the entropy and the angular velocity. Earlier work has suggested that this could arise from magnetohydrodynamic stability constraints; here we argue that purely hydrodynamical processes could also lead to such a result. Of special importance to the hydrodynamical solution is the fact that the thermal wind equation is insensitive to radial entropy gradients. This allows a much more general class of solutions to fit the solar isorotation contours, beyond just those in which the entropy itself must be a function of the angular velocity. In particular, for this expanded class, the thermal wind solution of the solar rotation profile remains valid even when large radial entropy gradients are present. A clear and explicit example of this class of solution appears to be present in published numerical simulations of the solar convective zone. Though hydrodynamical in character, the theory is not sensitive to the presence of weak magnetic fields. Thus, the identification of solar isorotation contours with the characteristics of the thermal wind equation appears to be robust, accommodating, but by no means requiring, magnetic field dynamics.
description: 16 pages, 2 figures. Accepted for publication in MNRAS
Gene trapping using Gal4 in zebrafish
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: subject: Developmental Biology
subject: Issue 79
subject: Zebrafish
subject: Mutagenesis
subject: Genetics
subject: FOS: Biological sciences
subject: genetics (animal and plant)
subject: Gal4
subject: transposon
subject: gene trap
subject: insertional mutagenesis

description: Large clutch size and external development of optically transparent embryos make zebrafish an exceptional vertebrate model system for in vivo insertional mutagenesis using fluorescent reporters to tag expression of mutated genes. Several laboratories have constructed and tested enhancer- and gene-trap vectors in zebrafish, using fluorescent proteins, Gal4- and lexA- based transcriptional activators as reporters 1-7. These vectors had two potential drawbacks: suboptimal stringency (e.g. lack of ability to differentiate between enhancer- and gene-trap events) and low mutagenicity (e.g. integrations into genes rarely produced null alleles). Gene Breaking Transposon (GBTs) were developed to address these drawbacks 8-10. We have modified one of the first GBT vectors, GBT-R15, for use with Gal4-VP16 as the primary gene trap reporter and added UAS:eGFP as the secondary reporter for direct detection of gene trap events. Application of Gal4-VP16 as the primary gene trap reporter provides two main advantages. First, it increases sensitivity for genes expressed at low expression levels. Second, it enables researchers to use gene trap lines as Gal4 drivers to direct expression of other transgenes in very specific tissues. This is especially pertinent for genes with non-essential or redundant functions, where gene trap integration may not result in overt phenotypes. The disadvantage of using Gal4-VP16 as the primary gene trap reporter is that genes coding for proteins with N-terminal signal sequences are not amenable to trapping, as the resulting Gal4-VP16 fusion proteins are unlikely to be able to enter the nucleus and activate transcription. Importantly, the use of Gal4-VP16 does not pre-select for nuclear proteins: we recovered gene trap mutations in genes encoding proteins which function in the nucleus, the cytoplasm and the plasma membrane.
Quantifying Condition-Dependent Intracellular Protein Levels Enables High-Precision Fitness Estimates
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: Fungal Proteins
Genetic Fitness
Likelihood Functions
Proteomics
Saccharomycetales
Selection, Genetic
Transcriptome

description: Countless studies monitor the growth rate of microbial populations as a measure of fitness. However, an enormous gap separates growth-rate differences measurable in the laboratory from those that natural selection can distinguish efficiently. Taking advantage of the recent discovery that transcript and protein levels in budding yeast closely track growth rate, we explore the possibility that growth rate can be more sensitively inferred by monitoring the proteomic response to growth, rather than growth itself. We find a set of proteins whose levels, in aggregate, enable prediction of growth rate to a higher precision than direct measurements. However, we find little overlap between these proteins and those that closely track growth rate in other studies. These results suggest that, in yeast, the pathways that set the pace of cell division can differ depending on the growth-altering stimulus. Still, with proper validation, protein measurements can provide high-precision growth estimates that allow extension of phenotypic growth-based assays closer to the limits of evolutionary selection. © 2013 Geiler-Samerotte et al.
Solid on Solid Model for Surface Growth in 2+1 Dimensions
Creators: name: Hosseinabadi, S.
name: Masoudi, A. A.
name: Movahed, M. Sadegh
Publisher: name: arXiv
Year: 2010
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: We analyze in detail the Solid-On-Solid model (SOS) for growth processes on a square substrate in 2+1 dimensions. By using the Markovian surface properties, we introduce an alternative approach for determining the roughness exponent of a special type of SOS model-the Restricted-Solid-On-Solid model (RSOS)- in 2+1 dimensions. This model is the SOS model with the additional restriction that the height difference must be S=1. Our numerical results show that the behaviour of the SOS model in 2+1 dimensions for approximately $S\geq S_{\times}\sim 8$ belongs to the two different universality classes: during the initial time stage, $t< t_{\times}$ it belongs to the Random-Deposition (RD) class, while for $t_{\times}
description: 13 pages, 7 figures and 1 table, Accepted for publication in Physica B: Condensed Matter
Broadband Non-Geostationary Satellite Communication Systems: Research Challenges and Key Opportunities
Creators: name: Al-Hraishawi, Hayder
name: Chatzinotas, Symeon
name: Ottersten, Björn
Publisher: name: arXiv
Year: 2021
Subjects: subject: Signal Processing (eess.SP)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Besides conventional geostationary (GSO) satellite broadband communication services, non-geostationary (NGSO) satellites are envisioned to support various new communication use cases from countless industries. These new scenarios bring many unprecedented challenges that will be discussed in this paper alongside with several potential future research opportunities. NGSO systems are known for various advantages, including their important features of low cost, lower propagation delay, smaller size, and lower losses in comparison to GSO satellites. However, there are still many deployment challenges to be tackled to ensure seamless integration not only with GSO systems but also with terrestrial networks. In this paper, we discuss several key challenges including satellite constellation and architecture designs, coexistence with GSO systems in terms of spectrum access and regulatory issues, resource management algorithms, and NGSO networking requirements. Additionally, the latest progress in provisioning secure communication via NGSO systems is discussed. Finally, this paper identifies multiple important open issues and research directions to inspire further studies towards the next generation of satellite networks.
State mapping and discontinuous entanglement transfer in a multipartite open system
Creators: name: Bina, M.
name: Casagrande, F.
name: Genoni, M.
name: Lulli, A.
name: Paris, M. G. A.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We describe the transfer of quantum information and correlations from an entangled tripartite bosonic system to three separate qubits through their local environments also in the presence of various dissipative effects. Optimal state mapping and entanglement transfer are shown in the framework of optical cavity quantum electrodynamics involving qubit-like radiation states and two-level atoms via the mediation of cavity modes. For an input GHZ state mixed with white noise we show the occurrence of sudden death and birth of entanglement that is discontinuously exchanged among the tripartite subsystems.
description: revised and enlarged, title changed
Malarial parasite diversity in chimpanzees: The value of comparative approaches to ascertain the evolution of Plasmodium falciparum antigens
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: Antigen
Chimpanzee
Co-evolution
Circumsporozoite protein
Dihydrofolate reductase-thymidylate synthase
Malaria
Merozoite surface protein 2
Mitochondrion genome
Pan troglodytes
Parasite evolution
Plasmodium phylogeny
Plasmodium
Plasmodium falciparum
Var2CSA

description: Background: Plasmodium falciparum shares its most recent common ancestor with parasites found in African apes; these species constitute the so-called Laverania clade. In this investigation, the evolutionary history of Plasmodium lineages found in chimpanzees (Pan troglodytes) was explored. Methods. Here, the remainders of 74 blood samples collected as part of the chimpanzees' routine health examinations were studied. For all positive samples with parasite lineages belonging to the Laverania clade, the complete mitochondrial genome (mtDNA), the gene encoding dihydrofolate reductase-thymidylate synthase (dhfr-ts), the chloroquine resistance transporter (Pfcrt), the circumsporozoite protein (csp), merozoite surface protein 2 (msp2), and the DBL-1 domain from var2CSA were amplified, cloned, and sequenced. Other Plasmodium species were included in the mtDNA, dhfr-ts, and csp analyses. Phylogenetic and evolutionary genetic analyses were performed, including molecular clock analyses on the mtDNA. Results/Conclusions. Nine chimpanzees were malaria positive (12.2%); four of those infections were identified as P. falciparum, two as a Plasmodium reichenowi-like parasite or Plasmodium sp., one as Plasmodium gaboni, and two as Plasmodium malariae. All P. falciparum isolates were resistant to chloroquine indicating that the chimpanzees acquired such infections from humans in recent times. Such findings, however, are not sufficient for implicating chimpanzees as an animal reservoir for P. falciparum. Timing estimates support that the Laverania clade has co-existed with hominids for a long-period of time. The proposed species P. gaboni, Plasmodium billbrayi, and Plasmodium billcollinsi are monophyletic groups supporting that they are indeed different species. An expanded CSP phylogeny is presented, including all the Laverania species and other malarial parasites. Contrasting with other Plasmodium, the Laverania csp exhibits great conservation at the central tandem repeat region. Msp2 and var2CSA, however, show extended recent polymorphism in P. falciparum that likely originated after the P. reichenowi-P. falciparum split. The accumulation of such diversity may indicate adaptation to the human host. These examples support the notion that comparative approaches among P. falciparum and its related species will be of great value in understanding the evolution of proteins that are important in parasite invasion of the human red blood cell, as well as those involved in malaria pathogenesis. © 2013 Pacheco et al.; licensee BioMed Central Ltd.
List of NIH-supported repositories under review
Creators: name: Arènes, Cécile
Publisher: name: Zenodo
Year: 2025
Subjects: research data
repository

description: The table is a download from the list of repositories supported by the NIH, available here https://sharing.nih.gov/data-management-and-sharing-policy/sharing-scientific-data/repositories-for-sharing-scientific-data

Each repository was visited between 6 and 10 April 2025. If "under review" appears on the repository's website, it is included in the table.

Where statistics or number of datasets are available, they have been added, but not systematically.

This is a work in progress and may contain errors.
Metric aspects of noncommutative homogeneous spaces
Creators: name: Li, Hanfeng
Publisher: name: arXiv
Year: 2008
Subjects: subject: Operator Algebras (math.OA)
subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: 46L87

description: For a closed cocompact subgroup $Γ$ of a locally compact group $G$, given a compact abelian subgroup $K$ of $G$ and a homomorphism $ρ:\hat{K}\to G$ satisfying certain conditions, Landstad and Raeburn constructed equivariant noncommutative deformations $C^*(\hat{G}/Γ, ρ)$ of the homogeneous space $G/Γ$, generalizing Rieffel's construction of quantum Heisenberg manifolds. We show that when $G$ is a Lie group and $G/Γ$ is connected, given any norm on the Lie algebra of $G$, the seminorm on $C^*(\hat{G}/Γ, ρ)$ induced by the derivation map of the canonical $G$-action defines a compact quantum metric. Furthermore, it is shown that this compact quantum metric space depends on $ρ$ continuously, with respect to quantum Gromov-Hausdorff distances.
description: Minor change
Efficient disruption of Zebrafish genes using a Gal4-containing gene trap
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: Zebrafish
Insertional mutagenesis
Gene trap
Gal4
Tol2
nsfa
Fleer
atp1a3a
bbs7

description: Background: External development and optical transparency of embryos make zebrafish exceptionally suitable for in vivo insertional mutagenesis using fluorescent proteins to visualize expression patterns of mutated genes. Recently developed Gene Breaking Transposon (GBT) vectors greatly improve the fidelity and mutagenicity of transposon-based gene trap vectors.Results: We constructed and tested a bipartite GBT vector with Gal4-VP16 as the primary gene trap reporter. Our vector also contains a UAS:eGFP cassette for direct detection of gene trap events by fluorescence. To confirm gene trap events, we generated a UAS:mRFP tester line. We screened 270 potential founders and established 41 gene trap lines. Three of our gene trap alleles display homozygous lethal phenotypes ranging from embryonic to late larval: nsf tpl6, atp1a3atpl10 and flrtpl19. Our gene trap cassette is flanked by direct loxP sites, which enabled us to successfully revert nsf tpl6, atp1a3atpl10 and flrtpl19 gene trap alleles by injection of Cre mRNA. The UAS:eGFP cassette is flanked by direct FRT sites. It can be readily removed by injection of Flp mRNA for use of our gene trap alleles with other tissue-specific GFP-marked lines. The Gal4-VP16 component of our vector provides two important advantages over other GBT vectors. The first is increased sensitivity, which enabled us to detect previously unnoticed expression of nsf in the pancreas. The second advantage is that all our gene trap lines, including integrations into non-essential genes, can be used as highly specific Gal4 drivers for expression of other transgenes under the control of Gal4 UAS.Conclusions: The Gal4-containing bipartite Gene Breaking Transposon vector presented here retains high specificity for integrations into genes, high mutagenicity and revertibility by Cre. These features, together with utility as highly specific Gal4 drivers, make gene trap mutants presented here especially useful to the research community. © 2013 Balciuniene et al.; licensee BioMed Central Ltd.
YOHKOH remnants: partially occulted flares in hard X-rays
Creators: name: Tomczak, M.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Flares being partially occulted by the solar limb, are the best reservoir of our knowledge about hard X-ray loop-top sources. Recently, the survey of partially occulted flares observed by the RHESSI has been published (Krucker & Lin 2008). The extensive YOHKOH database still awaits such activities. This work is an attempt to fill this gap. Among from 1286 flares in the YOHKOH Hard X-ray Telescope Flare Catalogue, for which the hard X-ray images had been enclosed, we identified 98 events that occurred behind the solar limb. We investigated their hard X-ray spectra and spatial structure. We found that in most cases the hard X-ray spectrum of partially occulted flares consists of two components, non-thermal and thermal, which are co-spatial. The photon energy spectra of the partially occulted flares are systematically steeper than spectra of the non-occulted flares. Such a difference we explain as a consequence of intrinsically dissimilar conditions ruling in coronal parts of flares, in comparison with the footpoints which usually dominate the hard X-ray emission of disk flares. At least two reasons of the difference should be taken into consideration: (1) stronger contamination of hard X-rays with emission of thermal plasma, (2) different mechanism in which non-thermal electrons radiate their energy. A schematic picture, in which thin-target mechanism is responsible for hard X-ray emission of loop-top sources and thick-target mechanism -- for emission of footpoint sources, can be modified by the presence of some coronal thick-target sources. At least a part of them suggests a magnetic trapping. Investigated flares do not respond the global magnetic configuration of the solar corona. For their characteristics conclusive is rather the local magnetic configuration in which they were developed.
description: 16 pages, 12 figures, 7 tables, submitted to A&A