bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistical Properties of Plateau‐Like Turbulence Spectra in the Martian Magnetosheath: MAVEN Observations
Authors: Jiang Wence , Li Hui , Liu Xiaodong , Verscharen Daniel , Wang Chi 
Published: January 2023

AbstractThe Martian magnetosheath provides us with a natural laboratory to study plasma turbulence in the presence of pickup ions and locally generated instabilities. Unlike the typical magnetic‐field spectra with a single spectral scaling at magnetohydrodynamics (MHD) scales in Earth's magnetosheath, the magnetic‐field spectra in the Martian magnetosheath during 4 years of Mars Atmosphere and Volatile EvolutioN observations frequently present an additional spectral break‐point with a shallow slope at MHD scales which we define as a plateau‐like spectral feature. The average occurrence rate of plateau‐like magnetic‐field spectra is 56.6% of our measurement intervals. At moderate pick‐up angles, the occurrence rate increases to a maximum of ∼70.0%. Furthermore, we present a positive correlation with the local ion density and anti‐correlations with the local βi and the solar Extreme Ultra Violet irradiance. A similar occurrence rate in the quasi‐perpendicular and the quasi‐parallel magnetosheath (60.1% vs. 52.9%) indicates that the plateau‐like spectra are more likely formed locally than in the upstream solar wind. Our results suggest that energy injection from pickup ion driven micro‐instabilities, for example, in the form of proton cyclotron waves, has insufficient time to evolve into a fully developed cascade in such a confined space like the Martian magnetosheath.
Martian Meteoric Mg+: Atmospheric Distribution and Variability From MAVEN/IUVS
Authors: Crismani M. M. J. , Tyo R. M. , Schneider N. M. , Plane J. M. C. , Feng W. , Carrillo‐Sánchez J. D. , Villanueva G. L. , Jain S. , Deighan J. , Curry S. 
Published: January 2023

AbstractSince the discovery of atmospheric Mg+ on Mars in 2015 by the Mars Atmosphere and Volatile Evolution mission, there have been almost continuous observations of this meteoric ion layer in a variety of seasons, local times, and latitudes. Here, we present the most comprehensive set of observations of the persistent metal ion layer at Mars, constructing the first grand composite maps from pooled medians of subsamples of a metallic ion species. These maps demonstrate that Mg+ appears in almost all conditions when illuminated, with peak density values varying between 100 and 500 cm−3, dependent on season and local time. There exists significant latitudinal variation within a given season, indicating that Mg+ is not simply an inert tracer, but may instead be influenced by the meteoric input distribution and/or atmospheric dynamics and chemistry. Geographic maps of Mg+ density as a function of latitude and longitude indicate the influence of atmospheric tides, and there is no apparent correlation with remnant crustal magnetic fields. This work also presents counter‐intuitive results, such as a reduction of Mg+ ions in the northern hemisphere during Northern Winter in an apparent correlation with dust aerosols.
Proteins of the XMRV retrovirus implicated in chronic fatigue syndrome and prostate cancer are homologous to human proteins relevant to both diseases.
Authors: Carter Christopher 
Published: January 2023

AbstractThe XMRV retrovirus has been implicated in chronic fatigue syndrome and prostate cancer. A homology search comparing retroviral with human proteins revealed short contiguous amino acid strings (typically 5-8 aa) matching human proteins whose dysfunction might be expected to cause fatigue, including mitochondrial proteins related to oxidative phosphorylation, glutamate receptors and their synaptic scaffolds, muscular acetylcholine receptor scaffolds and structural proteins, components of the immune system, and phosphatidylinositol signalling inter alia. Viral proteins are also homologous to members of the oestrogen, peroxisome proliferator, and CREB activated receptor networks, all of which are implicated in prostate cancer, and to a protein, SRCAP, that controls the expression of the prostate-specific antigen. These short matches are often predicted to be antigenic, and antibodies to XMRV proteins may target their human homologues. This is supported by the presence of autoantibodies to muscarinic receptors , vimentin and LAMINB1 (all XMRV homologues) in chronic fatigue syndrome sufferers. Homologous XMRV proteins might also interfere with the protein interactomes of their human homologues. Viral mimicry of human proteins is extensive and often relevant to disease. For example Epstein-Barr viral proteins aligns with multiple sclerosis autoantigens, while HIV-1 proteins align with several components of the immune system. Mutant proteins in Huntington&apos;s disease and cystic fibrosis also align with proteins from common phages or viruses. This suggests a common theme of viral derived autoimmunity/network interference in many human disorders, which could radically change the shape of future therapy. Such viral mimicry likely relates to the idea that life evolved from viruses, leaving behind a legacy of viral derived human proteins whose homology to the current virome may be responsible for many human diseases and syndromes. Vaccination programmes or immunosuppression may be beneficial in many of these conditions.
PrOCoil - Advances in predicting two- and three-stranded coiled coils
Authors: Mahrenholz* Carsten , Abfalter* Ingrid , Bodenhofer Ulrich , Volkmer Rudolf , Hochreiter Sepp 
Published: January 2023

Abstract*Overview* ∣ Coiled coils are usually described as consisting of two up to seven α-helices that are wrapped around each other. They can associate as either homomeric or heteromeric structures and bind in parallel or antiparallel topologies. Another characteristic of all coiled coils is the periodic recurrence of a sequence [abcdefg]n called heptad repeat, where n denotes the heptad number. In these repeats, a and d are hydrophobic amino acids at core positions crucial for the tertiary structure. In contrast, the polar positions b, c, and f are hydrophilic and e and g are charged residues.Due to their ability to oligomerize, coiled coils are involved in a variety of important cellular functions, either on their own or as part of larger protein complexes. Hence, they are in the focus of current research, for instance, as potential oncogenes and in the context of viral fusion proteins. Since structure and occurrence are well known, it might stand to reason that we have a clearly drawn picture of coiled coils. Most remarkably, however, the complex rules that govern oligomer formation, and thus the key to biological function, are poorly understood.*Approach* ∣ To find rules that determine oligomerization, we applied support vector machines and statistical methods to classify dimers and trimers on the basis of their amino acid sequences. The data set for this classification task was collected by searching the entire RCSB Protein Data Base for coiled coil structures, extracting the according amino acid sequences, and sorting them into types of oligomers based on properties of their 3D structures. We then extracted important features in the form of specific amino acids at certain key positions or amino acid patterns that are characteristic for each type of oligomer. Amino acid patterns were retrieved from our new coiled coil kernel, which detects amino acid co-occurrences. The relevance of the selected patterns was ensured by statistical tests and the excellent classification results measured by cross-validation.*Results* ∣ We discovered that a complex network of amino acid dependencies and sequence positions previously thought irrelevant to direct coiled coil interaction have an undeniable impact on stoichiometry. Our online-tool PrOCoil, classifies coiled coils with an outstanding accuracy of 86% and is also able to visualize the contribution of each individual amino acid to the overall oligomeric tendency of a given coiled coil sequence. A "web version":http://www.bioinf.jku.at/software/procoil/ and an "R package":http://www.bioinf.jku.at/software/procoil/procoilR.html of our prediction and profiling software (PrOCoil) are available to the scientific community.
Process Makna - A Semantic Wiki for Scientific Workflows
Authors: Paschke Adrian , Zhao Zhili 
Published: January 2023

AbstractVirtual e-Science infrastructures supporting Web-based scientific workflows are an example for knowledge-intensive collaborative and weakly-structured processes where the interaction with the human scientists during process execution plays a central role. In this paper we propose the lightweight dynamic user-friendly interaction with humans during execution of scientific workflows via the low-barrier approach of Semantic Wikis as an intuitive interface for non-technical scientists. Our Process Makna Semantic Wiki system is a novel combination of a business process management system adapted for scientific workflows with a Corporate Semantic Web Wiki user interface supporting knowledge intensive human interaction tasks during scientific workflow execution.
Para-(benzoyl)-phenylalanine as a potential inhibitor against leptospirosis
Authors: Pradhan Dibyabhaba , Priyadarshini Vani , Munikumar Manne , Umamaheswari Amineni 
Published: January 2023

AbstractLeptospirosis is a zoonotic disease of global concern caused by Leptospira interrogans. Subtractive genomic approach, metabolic pathway analysis and multi strain genome comparisons of Leptospira interrogans serovars had proposed 88 common drug targets from 5,124 genes of serovar Copenhageni and 4,727 genes of serovar Lai. Three potential drug targets (lpxC, lpxD and lpxB) were identified from Lipid A biosynthesis process of lipopolysaccharide (LPS) biosynthesis pathway. Lipid A is one of the three components of LPS that contains multiple hydrophobic fatty acid chains which anchor the LPS into the bacterial membrane. Designing inhibitory drug molecules targeting Lipid A biosynthesis would dissolve the structural integrity of membrane structure leading to cell lysis and death of Leptospira. LpxC being the first enzyme among the three drug targets of Lipid A biosynthesis pathway; blocking the enzyme with suitable inhibitor would stop synthesizing substrates for lpxD and lpxB. Also, there is no alternative mechanism in Leptospira to replace the catalytic activity rendered by lpxC; hence, the drug target was selected herein for rational drug design. The lpxC tertiary structure was modeled incorporating inhibitor BB-78485 using Modeller9v8. The lpxC 3D structure reliability was assessed through various model validation techniques. Ligand based virtual screening was performed from one million entries of ligand.Info metadatabase. The leads were ranked using computational docking technique of Glidev5.5. Twelve leads with better binding affinity than BB-78485 (XPGscore -7.98 Kcal/mol) were proposed as potential inhibitors of lpxC. Para-(benzoyl)-phenylalanine, the best ranked inhibitor (XPGscore -10.34Kcal/mol), would be intriguing for rational drug design against leptospirosis.
Use of Semantic Technologies - Semantic Chemistry
Authors: Todor Alexandru , Paschke Adrian , Heineke Stephan 
Published: January 2023

AbstractOur Chemical e-Science Information Cloud (ChemCloud) – a Semantic Web based eScience infrastructure – integrates and automates a multitude of databases, tools and services in the domain of chemistry, pharmacy and bio-chemistry available at the Fachinformationszentrum Chemie (FIZ Chemie), at the Freie Universitaet Berlin (FUB), and on the public Web. Based on the approach of the W3C Linked Open Data initiative and the W3C Semantic Web technologies for ontologies and rules it semantically links and integrates knowledge from our W3C HCLS knowledge base hosted at the FUB, our multi-domain knowledge base DBpedia (Deutschland) implemented at FUB, which is extracted from Wikipedia (De) providing a public semantic resource for chemistry, and our well-established databases at FIZ Chemie such as ChemInform for organic reaction data, InfoTherm the leading source for thermophysical data, Chemisches Zentralblatt, the complete chemistry knowledge from 1830 to 1969, and ChemgaPedia the largest and most frequented e-Learning platform for Chemistry and related sciences in German language.
Cu2+ uptake by Chlorococcum hemicolum - A Xeric Chlorophycean Alga
Authors: Harish Mr. , Sundaramoorthy S. , Kumar Devendra , Vaijapurkar S.G. 
Published: January 2023

AbstractBioremediation of copper by xeric chlorophycean bioremediator, Chlorococcum hemicolum was investigated. The growth rates at various concentrations of Cu2+ were assessed in terms of protein level and 8 mg L-1 (37.67 % level in growth kinetics) is the tolerance limit. Absorption/adsorption kinetics was estimated after 240 hrs of Cu2+ treatments. Absorptions were higher than adsorption with maximum accumulation factor (AF) of 1.40. The Cu2+ concentration and absorption were linearly related (r = 0.99; p>0.01). Other biochemical parameters like total sugar, chlorophyll and carotenoids were also quantified to correlate the state of metabolism and these exhibited reduction due to heavy metal stress.
Bio-resources for sharing: which communities and what specific needs
Authors: Metspalu Andres 
Published: January 2023

AbstractBiobanks are an important source to obtain samples and data for research purposes for a wide array of communities. In fact, sharing of bio-resources and data is an integral part of a biobank's role. For an effective partnership a list of requirements or needs have to be met, assuring quality of the resources shared as well as quality of the collaboration in general. Tracking and documenting bio-resource sharing and collaborations of a biobank can be seen as one indicator of the "impact" a biobank has to the field. As an example, the practice of the Estonian Genome Center of the University of Tartu is presented.
Models of Multifunctional Central Pattern Generators: Polyrhythmic Bursting
Authors: Shilnikov Andrey 
Published: January 2023

AbstractWe demonstrate a motif of three reciprocally inhibitory cells that is able to produce multiple patterns of bursting rhythms. Through the examination of the qualitative geometric structure of two-dimensional maps for phase lag between the cells we reveal the organizing centers of emergent polyrhythmic patterns and their bifurcations, as the asymmetry of the synaptic coupling is varied. The presence of multistability and the types of attractors in the network are shown to be determined by the duty cycle of bursting. This analysis does not require knowledge of the equations that model the system, and so provides a powerful new approach to studying regulatory networks. Thus, the approach is applicable to a variety of biological phenomena beyond motor control.
A simulation study on different STDP models concerning localized gamma oscillations
Authors: Hauser Florian , Knoblauch Andreas , Palm Günther 
Published: January 2023

AbstractGamma oscillations are a prominent feature in experimental as well as theoretical descriptions of brain activity. One of the network models which has the capability to generate such oscillations is what we call a local cell assembly (CA), i.e. a group of neighboring neurons which are strongly interconnected in an excitatory manner. Postulated by experimenters and extensively used in theoretical studies, these local networks seem to be a good candidate for investigating the impact of biological constraints given by models of spike-timing-dependent plasticity (STDP) on local gamma oscillating structures in the mammalian brain. Therefore we fi*tted a two-compartment neuron model with AMPA- and NMDA-receptor mediated synaptic currents to desired properties of a local CA, meaning pattern completion and after-activity. We simulated 100 recurrently connected neurons with fi*xed axonal transmission delays. In addition, every neuron receives Poissonian spikes from 1000 input cells *firing at low background rate. During simulation the network is stimulated every second by increasing the input rate 10-fold for 35 msec. As a quality measure for keeping or even enhancing the properties of the network, we counted the relative amount of synapses with increased synaptic strengths with reference to the initial values. Three phenomenological STDP models (Song et al., Nature Neuroscience, 3, 2000; Pfi*ster and Gerstner, The J. of Neuroscience, 26, 2006; Clopath et al., Nature Neuroscience, 13, 2010) were implemented. Model-specifi*c parameters were varied in ranges determined by experimental measurements. We conclude that more recent STDP models which take into account frequency-dependent terms lead to a higher probability of strengthening synapses in a local CA (larger LTP region). This corresponds to experimental observations that long-term potentiation (LTP) outweighs long-term depression (LTD) in high-frequency pairing protocols. Furthermore, our simulations show that short axonal transmission delays clearly enlarge the LTP region of STDP parameter space.
The Army of One (Sample): the Characteristics of Sampling-based Probabilistic Neural Representations
Authors: Berkes Pietro , Turner Richard , Fiser Jozsef 
Published: January 2023

AbstractThere is growing evidence that humans and animals represent the uncertainty associated with sensory stimuli and utilize this uncertainty during planning and decision making in a statistically optimal way. Recently, a nonparametric framework for representing probabilistic information has been proposed whereby neural activity encodes samples from the distribution over external variables. Although such sample-based probabilistic representations have strong empirical and theoretical support, two major issues need to be clarified before they can be considered as viable candidate theories of cortical computation. First, in a fluctuating natural environment, can neural dynamics provide sufficient samples to accurately estimate a stimulus? Second, can such a code support accurate learning over biologically plausible time-scales? Although it is well known that sampling is statistically optimal if the number of samples is unlimited, biological constraints mean that estimation and learning in the cortex must be supported by a relatively small number of possibly dependent samples. We explored these issues in a cue combination task by comparing a neural circuit that employed a sampling-based representation to an optimal estimator. For static stimuli, we found that a single sample is sufficient to obtain an estimator with less than twice the optimal variance, and that performance improves with the inverse square root of the number of samples. For dynamic stimuli, with linear-Gaussian evolution, we found that the efficiency of the estimation improves significantly as temporal information stabilizes the estimate, and because sampling does not require a burn-in phase. Finally, we found that using a single sample, the dynamic model can accurately learn the parameters of the input neural populations up to a general scaling factor, which disappears for modest sample size. These results suggest that sample-based representations can support estimation and learning using a relatively small number of samples and are therefore highly feasible alternatives for performing probabilistic cortical computations.
The Attentional Routing Circuit: Receptive Field Modulation Through Nonlinear Dendritic Interactions
Authors: Bobier Bruce , Stewart Terrence , Eliasmith Chris 
Published: January 2023

AbstractWe present a model of attentional routing called the Attentional Routing Circuit (ARC) that extends an existing model of spiking neurons with dendritic nonlinearities. Specifically, we employ the Poirazi et al. (2003) pyramidal neuron in a population coding framework. ARC demonstrates that the dendritic nonlinearities can be exploited to result in selective routing, with a decrease in the number of cells needed by a factor of ~5 as compared with a linear dendrite model.Routing of attended information occurs through the modulation of feedforward visual signals by a cortical control signal specifying the location and size of the attended target. The model is fully specified in spiking single cells. Our approach differs from past work on shifter circuits by having more efficient control, and using a more biologically detailed substrate. Our approach differs from existing models that use gain fields by providing precise hypotheses about how the control signals are generated and distributed in a hierarchical model in spiking neurons. Further, the model accounts for numerous experimental findings regarding the timing, strength and extent of attentional modulation in ventral stream areas, and the perceived contrast enhancement of attended stimuli.To further demonstrate the plausibility of ARC, it is applied to the attention experiments of Womelsdorf et al. (2008) and tested in detail. For the simulations, the model has only two free parameters that influence its ability to match the experimental data, and without fitting, we show that it can account for the experimental observations of changes in receptive field (RF) gain and position with attention in macaques. In sum, the model provides an explanation of RF modulation as well as testable predictions about nonlinear cortical dendrites and attentional changes of receptive field properties.
Hierarchical inference of disparity
Authors: Tosic Ivana , Olshausen Bruno 
Published: January 2023

AbstractDisparity selective cells in V1 respond to the correlated receptive fields of the left and right retinae, which do not necessarily correspond to the same object in the 3D scene, i.e., these cells respond equally to both false and correct stereo matches. On the other hand, neurons in the extrastriate visual area V2 show much stronger responses to correct visual matches [Bakin et al, 2000]. This indicates that a part of the stereo correspondence problem is solved during disparity processing in these two areas. However, the mechanisms employed by the brain to accomplish this task are not yet understood. Existing computational models are mostly based on cooperative computations in V1 [Marr and Poggio 1976, Read and Cumming 2007], without exploiting the potential benefits of the hierarchical structure between V1 and V2. Here we propose a two-layer graphical model for disparity estimation from stereo. The lower layer matches the linear responses of neurons with Gabor receptive fields across images. Nodes in the upper layer infer a sparse code of the disparity map and act as priors that help disambiguate false from correct matches. When learned on natural disparity maps, the receptive fields of the sparse code converge to oriented depth edges, which is consistent with the electrophysiological studies in macaque [von der Heydt et al, 2000]. Moreover, when such a code is used for depth inference in our two layer model, the resulting disparity map for the Tsukuba stereo pair [middlebury database] has 40% less false matches than the solution given by the first layer. Our model offers a demonstration of the hierarchical disparity computation, leading to testable predictions about V1-V2 interactions.