cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Molecular mechanisms of self-mated hydrogel friction
Creators: name: Mees, Jan
name: Simič, Rok
name: O'Connor, Thomas C.
name: Spencer, Nicholas D.
name: Pastewka, Lars
Publisher: name: arXiv
Year: 2022
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Self-mated hydrogel contacts show extremely small friction coefficients at low loads but a distinct velocity dependence. Here we combine mesoscopic simulations and experiments to test the polymer-relaxation hypothesis for this velocity dependence, where a velocity-dependent regime emerges when the perturbation of interfacial polymer chains occurs faster than their relaxation at high velocity. Our simulations reproduce the experimental findings, with speed-independent friction at low velocity, followed by a friction coefficient that rises with velocity to some power of order unity. We show that the velocity-dependent regime is characterized by reorientation and stretching of polymer chains in the direction of shear, leading to an entropic stress that can be quantitatively related to the shear response. The detailed exponent of the power law in the velocity dependent regime depends on how chains interact: We observe a power close to $1/2$ for chains that can stretch, while pure reorientation leads to a power of unity. Our simulations quantitatively match experiments and show that the velocity dependence of hydrogel friction at low loads can be firmly traced back to the morphology of near-surface chains.
description: 18 pages, 6 figures, includes supplementary material
A high performance fingerprint liveness detection method based on quality related features
Creators: name: Galbally, Javier
name: Alonso-Fernandez, Fernando
name: Fierrez, Julian
name: Ortega-Garcia, Javier
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: A new software-based liveness detection approach using a novel fingerprint parameterization based on quality related features is proposed. The system is tested on a highly challenging database comprising over 10,500 real and fake images acquired with five sensors of different technologies and covering a wide range of direct attack scenarios in terms of materials and procedures followed to generate the gummy fingers. The proposed solution proves to be robust to the multi-scenario dataset, and presents an overall rate of 90% correctly classified samples. Furthermore, the liveness detection method presented has the added advantage over previously studied techniques of needing just one image from a finger to decide whether it is real or fake. This last characteristic provides the method with very valuable features as it makes it less intrusive, more user friendly, faster and reduces its implementation costs.
description: Published at Elsevier Future Generation Computer Systems journal
Maternal behaviors during pregnancy impact offspring obesity risk
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: Adult
Birth Weight
Carbonated Beverages
Diet
Dietary Carbohydrates
Energy Intake
Exercise
Female
Fetal Macrosomia
Humans
Infant
Infant, Newborn
Maternal Behavior
Obesity
Overweight
Pregnancy
Pregnancy Complications
Prenatal Exposure Delayed Effects
Risk Factors
Weight Gain

description: This study investigated the effects of maternal changes during pregnancy in diet, exercise, and psychosocial factors on offspring weight parameters at birth and 6 months. In overweight/obese (OW/OB; n = 132) mothers, greater % kcal from sweets early in pregnancy was the strongest, independent predictor of higher weight for age (WFA) (beta = 0. 19; P = 0. 004), higher odds of macrosomia (OR = 1.1 (1.01.2); P = 0. 004) andWFA 90th percentile at birth (OR = 1.2 (1.11.3); P = 0. 002) and higher WFA at 6 months (beta = 0. 30; P = 0. 002). In normal weight (n = 153) mothers, higher intake of soft drinks was the strongest predictor of higher offspring WFA at birth (beta = 0.16; P = 0. 04) but not at 6 months. Prenatal physical activity, depressive symptoms, and sleep-related variables did not significantly predict offspring weight outcomes. Mothers eating behaviors during pregnancy, especially intake of sweets in OW/OB mothers, may have a lasting effect on child weight. Copyright © 2011 Suzanne Phelan et al.
A computer controlled signal averaging spectrometer system
Creators: name: Thewalt, Michael Ludwig Wolfgang
Publisher: name: University of British Columbia
Year: 2010

description: A high sensitivity infrared spectrometer with signal averaging capabilities was constructed for the detection and analysis of luminescent light. The apparatus was interfaced to a Nova- 2 minicomputer which was used to control all aspects of the experiment in progress. Two programs were written for this system: one in machine language through which programs written in a higher level language can communicate with the interface, and one in the Basic language which contols the spectrometer when collecting data. Other programs which have been written for data analysis will not be described here. An example of work currently being performed with the new system has been included. The detection of several heretofore unknown lines in the luminescence spectrum of Si gives evidence of the high sensitivity of this apparatus.
The authority of next-of-kin in explicit and presumed consent systems for deceased organ donation: An analysis of 54 nations
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2012
Subjects: consent
deceased donor
health policy
law
next-of-kin

description: Background. The degree of involvement by the next-of-kin in deceased organ procurement worldwide is unclear. We investigated the next-of-kin's authority in the procurement process in nations with either explicit or presumed consent.Methods.We collected data from 54 nations, 25 with presumed consent and 29 with explicit consent. We characterized the authority of the next-of-kin in the decision to donate deceased organs. Specifically, we examined whether the next-of-kin's consent to procure organs was always required and whether the next-of-kin were able to veto procurement when the deceased had expressed a wish to donate.Results.The next-of-kin are involved in the organ procurement process in most nations regardless of the consent principle and whether the wishes of the deceased to be a donor were expressed or unknown. Nineteen of the 25 nations with presumed consent provide a method for individuals to express a wish to be a donor. However, health professionals in only four of these nations responded that they do not override a deceased's expressed wish because of a family's objection. Similarly, health professionals in only four of the 29 nations with explicit consent proceed with a deceased's pre-existing wish to be a donor and do not require next-of-kin's consent, but caveats still remain for when this is done.Conclusions.The next-of-kin have a considerable influence on the organ procurement process in both presumed and explicit consent nations. © 2012 The Author.
Using HIV Transmission Networks to Investigate Community Effects in HIV Prevention Trials
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: Clinical Trials as Topic
Computer Simulation
HIV
HIV Infections
Humans
Male

description: Effective population screening of HIV and prevention of HIV transmission are only part of the global fight against AIDS. Community-level effects, for example those aimed at thwarting future transmission, are potential outcomes of treatment and may be important in stemming the epidemic. However, current clinical trial designs are incapable of detecting a reduction in future transmission due to treatment. We took advantage of the fact that HIV is an evolving pathogen whose transmission network can be reconstructed using genetic sequence information to address this shortcoming. Here, we use an HIV transmission network inferred from recently infected men who have sex with men (MSM) in San Diego, California. We developed and tested a network-based statistic for measuring treatment effects using simulated clinical trials on our inferred transmission network. We explored the statistical power of this network-based statistic against conventional efficacy measures and find that when future transmission is reduced, the potential for increased statistical power can be realized. Furthermore, our simulations demonstrate that the network statistic is able to detect community-level effects (e.g., reduction in onward transmission) of HIV treatment in a clinical trial setting. This study demonstrates the potential utility of a network-based statistical metric when investigating HIV treatment options as a method to reduce onward transmission in a clinical trial setting. © 2011 Wertheim et al.
Simulatore di interfaccia uomo-macchina per i controllo di UAV
Creators: name: Miranda, Giovanni <1977>
Publisher: name: Alma Mater Studiorum - Università di Bologna
Year: 2008
Subjects: ING-IND/15 Disegno e metodi dell'ingegneria industriale

description: Recent statistics have demonstrated that two of the most important causes of failures of
the UAVs (Uninhabited Aerial Vehicle) missions are related to the low level of
decisional autonomy of vehicles and to the man machine interface. Therefore, a relevant
issue is to design a display/controls architecture which allows the efficient interaction
between the operator and the remote vehicle and to develop a level of automation which
allows the vehicle the decision about change in mission. The research presented in this
paper focuses on a modular man-machine interface simulator for the UAV control,
which simulates UAV missions, developed to experiment solution to this problem. The
main components of the simulator are an advanced interface and a block defined
automation, which comprehend an algorithm that implements the level of automation of
the system. The simulator has been designed and developed following a user-centred
design approach in order to take into account the operator’s needs in the communication
with the vehicle. The level of automation has been developed following the supervisory
control theory which says that the human became a supervisor who sends high level
commands, such as part of mission, target, constraints, in then-rule, while the vehicle
receives, comprehends and translates such commands into detailed action such as routes
or action on the control system. In order to allow the vehicle to calculate and recalculate
the safe and efficient route, in term of distance, time and fuel a 3D planning algorithm
has been developed. It is based on considering UASs representative of real world
systems as objects moving in a virtual environment (terrain, obstacles, and no fly zones)
which replicates the airspace. Original obstacle avoidance strategies have been
conceived in order to generate mission planes which are consistent with flight rules and
with the vehicle performance constraints. The interface is based on a touch screen, used
to send high level commands to the vehicle, and a 3D Virtual Display which provides a
stereoscopic and augmented visualization of the complex scenario in which the vehicle
operates. Furthermore, it is provided with an audio feedback message generator.
Simulation tests have been conducted with pilot trainers to evaluate the reliability of the
algorithm and the effectiveness and efficiency of the interface in supporting the operator
in the supervision of an UAV mission. Results have revealed that the planning
algorithm calculate very efficient routes in few seconds, an adequate level of workload
is required to command the vehicle and that the 3D based interface provides the
operator with a good sense of presence and enhances his awareness of the mission
scenario and of the vehicle under his control.
Global high-order numerical schemes for the time evolution of the general relativistic radiation magneto-hydrodynamics equations
Creators: name: Izquierdo, Manuel R.
name: Pareschi, Lorenzo
name: Miñano, Borja
name: Massó, Joan
name: Palenzuela, Carlos
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Numerical Analysis (math.NA)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: Modeling correctly the transport of neutrinos is crucial in some astrophysical scenarios such as core-collapse supernovae and binary neutron star mergers. In this paper, we focus on the truncated-moment formalism, considering only the first two moments (M1 scheme) within the grey approximation, which reduces Boltzmann seven-dimensional equation to a system of $3+1$ equations closely resembling the hydrodynamic ones. Solving the M1 scheme is still mathematically challenging, since it is necessary to model the radiation-matter interaction in regimes where the evolution equations become stiff and behave as an advection-diffusion problem. Here, we present different global, high-order time integration schemes based on Implicit-Explicit Runge-Kutta (IMEX) methods designed to overcome the time-step restriction caused by such behavior while allowing us to use the explicit RK commonly employed for the MHD and Einstein equations. Finally, we analyze their performance in several numerical tests.
description: 18 + 6. Updated manuscript matching published version + additional appendix "Comparing the convergence order of IMEX and semi-implicit schemes"
Developing a community-based genetic nomenclature for anole lizards
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: Animals
Conserved Sequence
DNA Transposable Elements
Evolution, Molecular
Genetic Markers
Genomics
Lizards
Microsatellite Repeats
Repetitive Sequences, Nucleic Acid
Terminology as Topic

description: Background: Comparative studies of amniotes have been hindered by a dearth of reptilian molecular sequences. With the genomic assembly of the green anole, Anolis carolinensis available, non-avian reptilian genes can now be compared to mammalian, avian, and amphibian homologs. Furthermore, with more than 350 extant species in the genus Anolis, anoles are an unparalleled example of tetrapod genetic diversity and divergence. As an important ecological, genetic and now genomic reference, it is imperative to develop a standardized Anolis gene nomenclature alongside associated vocabularies and other useful metrics.Results: Here we report the formation of the Anolis Gene Nomenclature Committee (AGNC) and propose a standardized evolutionary characterization code that will help researchers to define gene orthology and paralogy with tetrapod homologs, provide a system for naming novel genes in Anolis and other reptiles, furnish abbreviations to facilitate comparative studies among the Anolis species and related iguanid squamates, and classify the geographical origins of Anolis subpopulations.Conclusions: This report has been generated in close consultation with members of the Anolis and genomic research communities, and using public database resources including NCBI and Ensembl. Updates will continue to be regularly posted to new research community websites such as lizardbase. We anticipate that this standardized gene nomenclature will facilitate the accessibility of reptilian sequences for comparative studies among tetrapods and will further serve as a template for other communities in their sequencing and annotation initiatives. © 2011 Kusumi et al; licensee BioMed Central Ltd.
The Young Stellar Population, Distance, and Cloud-Cloud Collision Induced Star Formation Scenario of the Trifid Nebula
Creators: name: Kalari, Venu M.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The Trifid Nebula is a young, nearby star-forming region where star formation is proposed to have been triggered by cloud-cloud collision (CCC), based on observations of molecular clouds. It offers a unique opportunity to test whether the CCC hypothesis is supported by the spatial distribution and star formation chronology of young stars. We present the first study of the optically visible pre-main sequence (PMS) population of the region using riH$α$ imaging and Gaia astrometry. Combined with an analysis of young stellar objects (YSOs) using infrared imaging, we capture the spatial distribution and star formation chronology of the young stellar population. From the analysis, 15 Flat/Class I YSOs, 46 Class II YSOs, and 41 accreting PMS stars are identified (diskless/non-accreting sources are not included in the analysis). The distance based on Gaia parallaxes is $\sim$1250 pc, significantly closer than previously reported. The Class II YSOs and PMS stars ($\sim$1.5 Myr old) are spread toward the edge of the molecular clouds. They are slightly younger than the estimated crossing time of $\sim$2.7Myr and closer to the estimated dynamical age $\sim$0.85 Myr. Younger Class I YSOs are more concentrated spatially. There exists a cavity devoid of young stars where the two clouds overlap. This evidence suggests that the current generation of stars formed after the collision of two clouds $\sim$1 Myr ago, and this result can be corroborated using future spectroscopic studies.
description: Published in ApJ. 19 pages, 13 figures. Tables available via CDS
The evolution of protein structures and structural ensembles under functional constraint
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: conformational ensemble
multiscale modeling
structural disorder
sequence-structure-function-evolution relationships

description: Protein sequence, structure, and function are inherently linked through evolution and population genetics. Our knowledge of protein structure comes from solved structures in the Protein Data Bank (PDB), our knowledge of sequence through sequences found in the NCBI sequence databases (http://www.ncbi.nlm.nih.gov/), and our knowledge of function through a limited set of in-vitro biochemical studies. How these intersect through evolution is described in the first part of the review. In the second part, our understanding of a series of questions is addressed. This includes how sequences evolve within structures, how evolutionary processes enable structural transitions, how the folding process can change through evolution and what the fitness impacts of this might be. Moving beyond static structures, the evolution of protein kinetics (including normal modes) is discussed, as is the evolution of conformational ensembles and structurally disordered proteins. This ties back to a question of the role of neostructuralization and how it relates to selection on sequences for functions. The relationship between metastability, the fitness landscape, sequence divergence, and organismal effective population size is explored. Lastly, a brief discussion of modeling the evolution of sequences of ordered and disordered proteins is entertained. © 2011 by the authors; licensee MDPI, Basel, Switzerland.
Ground state degeneracy on torus in a family of $\mathbb{Z}_N$ toric code
Creators: name: Watanabe, Haruki
name: Cheng, Meng
name: Fuji, Yohei
Publisher: name: arXiv
Year: 2022
Subjects: subject: Other Condensed Matter (cond-mat.other)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Topologically ordered phases in $2+1$ dimensions are generally characterized by three mutually-related features: fractionalized (anyonic) excitations, topological entanglement entropy, and robust ground state degeneracy that does not require symmetry protection or spontaneous symmetry breaking. Such degeneracy is known as topological degeneracy and usually can be seen under the periodic boundary condition regardless of the choice of the system size $L_1$ and $L_2$ in each direction. In this work we introduce a family of extensions of the Kitaev toric code to $N$ level spins ($N\geq2$). The model realizes topologically ordered phases or symmetry-protected topological phases depending on parameters in the model. The most remarkable feature of the topologically ordered phases is that the ground state may be unique, depending on $L_1$ and $L_2$, despite that the translation symmetry of the model remains unbroken. Nonetheless, the topological entanglement entropy takes the nontrivial value. We argue that this behavior originates from the nontrivial action of translations permuting anyon species.
description: 19 pages, 6 figures; v3: Sec VI and Appendix B are added. Minor changes throughout the manuscript
Computational Desire Line Analysis of Cyclists on the Dybbølsbro Intersection in Copenhagen
Creators: name: Breum, Simon Martin
name: Kostic, Bojan
name: Szell, Michael
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computers and Society (cs.CY)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: Contemporary street design prioritizes vehicular traffic flow and assumes compliant road users. However, actual human behavior is typically neglected, especially of cyclists, leading to streets with inadequate wayfinding and protection from vehicular traffic. To improve planning, here we develop a computational method to detect cyclist trajectories from video recordings and apply it to the Dybbølsbro intersection in Copenhagen, Denmark. In one hour of footage we find hundreds of trajectories that contradict the design, explainable by the desire for straightforward, uninterrupted travel largely not provided by the intersection. This neglect and the prioritization of vehicular traffic highlight opportunities for improving Danish intersection design.
description: 7 pages, 3 figures
On the Shuffle Automaton Size for Words
Creators: name: Biegler, Franziska
name: Daley, Mark
name: McQuillan, Ian
Publisher: name: arXiv
Year: 2009
Subjects: subject: Formal Languages and Automata Theory (cs.FL)
subject: Discrete Mathematics (cs.DM)
subject: FOS: Computer and information sciences

description: We investigate the state size of DFAs accepting the shuffle of two words. We provide words u and v, such that the minimal DFA for u shuffled with v requires an exponential number of states. We also show some conditions for the words u and v which ensure a quadratic upper bound on the state size of u shuffled with v. Moreover, switching only two letters within one of u or v is enough to trigger the change from quadratic to exponential.
Regulation of the HIV-1 promoter by HIF-1 and Vpr proteins
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: Gene Expression Regulation, Viral
HIV Long Terminal Repeat
HIV-1
Host-Pathogen Interactions
Humans
Hypoxia-Inducible Factor 1, alpha Subunit
Promoter Regions, Genetic
Protein Binding
Virus Replication
vpr Gene Products, Human Immunodeficiency Virus

description: We previously demonstrated the ability of HIV-1 Vpr protein to activate the oxidative stress pathway, thus leading to the induction of the hypoxia inducible factor 1 alpha (HIF-1). Therefore, we sought to examine the interplay between the two proteins and the impact of HIF-1 activation on HIV-1 transcription. Using transient transfection assays, we identified the optimal concentration of HIF-1 necessary for the activation of the HIV-1 promoter as well as the domain within HIF-1 responsible for this activation. Our findings indicated that activation of the HIV-1 LTR by Vpr is HIF-1 dependent. Furthermore, we showed that both Vpr and HIF-1 activate the HIV-1 promoter through the GC-rich binding domain within the LTR. Taken together, these data shed more light on the mechanisms used by Vpr to activate the HIV-1 promoter and placed HIF-1 as a major participant in this activation. © 2011 Deshmane et al; licensee BioMed Central Ltd.
Unsupervised Integration of Multiple Protein Disorder Predictors: The Method and Evaluation on CASP7, CASP8 and CASP9 Data
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: 0104 Statistics
Generic Health Relevance

description: Background: Studies of intrinsically disordered proteins that lack a stable tertiary structure but still have important biological functions critically rely on computational methods that predict this property based on sequence information. Although a number of fairly successful models for prediction of protein disorder have been developed over the last decade, the quality of their predictions is limited by available cases of confirmed disorders.Results: To more reliably estimate protein disorder from protein sequences, an iterative algorithm is proposed that integrates predictions of multiple disorder models without relying on any protein sequences with confirmed disorder annotation. The iterative method alternately provides the maximum a posterior (MAP) estimation of disorder prediction and the maximum-likelihood (ML) estimation of quality of multiple disorder predictors. Experiments on data used at CASP7, CASP8, and CASP9 have shown the effectiveness of the proposed algorithm.Conclusions: The proposed algorithm can potentially be used to predict protein disorder and provide helpful suggestions on choosing suitable disorder predictors for unknown protein sequences. © 2011 Zhang and Obradovic; licensee BioMed Central Ltd.
Predicting Cancer Using Supervised Machine Learning: Mesothelioma
Creators: name: Choudhury, Avishek
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Background: Pleural Mesothelioma (PM) is an unusual, belligerent tumor that rapidly develops into cancer in the pleura of the lungs. Pleural Mesothelioma is a common type of Mesothelioma that accounts for about 75% of all Mesothelioma diagnosed yearly in the U.S. Diagnosis of Mesothelioma takes several months and is expensive. Given the risk and constraints associated with PM diagnosis, early identification of this ailment is essential for patient health. Objective: In this study, we use artificial intelligence algorithms recommending the best fit model for early diagnosis and prognosis of MPM. Methods: We retrospectively retrieved patients clinical data collected by Dicle University, Turkey, and applied multilayered perceptron (MLP), voted perceptron (VP), Clojure classifier (CC), kernel logistic regression (KLR), stochastic gradient decent SGD), adaptive boosting (AdaBoost), Hoeffding tree (VFDT), and primal estimated sub-gradient solver for support vector machine (s-Pegasos). We evaluated the models, compared and tested using paired T-test (corrected) at 0.05 significance based on their respective classification accuracy, f-measure, precision, recall, root mean squared error, receivers characteristic curve (ROC), and precision-recall curve (PRC). Results: In phase-1, SGD, AdaBoost. M1, KLR, MLP, VFDT generate optimal results with the highest possible performance measures. In phase 2, AdaBoost, with a classification accuracy of 71.29%, outperformed all other algorithms. C-reactive protein, platelet count, duration of symptoms, gender, and pleural protein were found to be the most relevant predictors that can prognosticate Mesothelioma. Conclusion: This study confirms that data obtained from Biopsy and imagining tests are strong predictors of Mesothelioma but are associated with a high cost; however, they can identify Mesothelioma with optimal accuracy.
Timing the origin of human malarias: The lemur puzzle
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: Animals
Biological Evolution
Genome, Mitochondrial
Humans
Lemuridae
Madagascar
Malaria
Phylogeny
Plasmodium

description: Background: Timing the origin of human malarias has been a focus of great interest. Previous studies on the mitochondrial genome concluded that Plasmodium in primates, including those parasitic to humans, radiated relatively recently during a process where host switches were common. Those investigations, however, assumed constant rate of evolution and tightly bound (fixed) calibration points based on host fossils or host distribution. We investigate the effect of such assumptions using different molecular dating methods. We include parasites from Lemuroidea since their distribution provides an external validation to time estimates allowing us to disregard scenarios that cannot explain their introduction in Madagascar. Results: We reject the assumption that the Plasmodium mitochondrial genome, as a unit or each gene separately, evolves at a constant rate. Our analyses show that Lemuroidea parasites are a monophyletic group that shares a common ancestor with all Catarrhini malarias except those related to P. falciparum. However, we found no evidence that this group of parasites branched with their hosts early in the evolution of primates. We applied relaxed clock methods and different calibrations points to explore the origin of primate malarias including those found in African apes. We showed that previous studies likely underestimated the origin of malarial parasites in primates. Conclusions: The use of fossils from the host as absolute calibration and the assumption of a strict clock likely underestimate time when performing molecular dating analyses on malarial parasites. Indeed, by exploring different calibration points, we found that the time for the radiation of primate parasites may have taken place in the Eocene, a time consistent with the radiation of African anthropoids. The radiation of the four human parasite lineages was part of such events. The time frame estimated in this investigation, together with our phylogenetic analyses, made plausible a scenario where gorillas and humans acquired malaria from a Pan lineage. © 2011 Pacheco et al; licensee BioMed Central Ltd.
MicroRNAs in rhabdomyosarcoma: Pathogenetic implications and translational potentiality
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: Animals
Base Sequence
Cell Differentiation
Gene Expression Regulation, Neoplastic
Humans
MicroRNAs
Muscle Development
Muscle, Skeletal
Polycomb-Group Proteins
Repressor Proteins
Rhabdomyosarcoma

description: There is growing evidence that interconnections among molecular pathways governing tissue differentiation are nodal points for malignant transformation. In this scenario, microRNAs appear as crucial players. This class of non-coding small regulatory RNA molecules controls developmental programs by modulating gene expression through post-transcriptional silencing of target mRNAs. During myogenesis, muscle-specific and ubiquitously-expressed microRNAs tightly control muscle tissue differentiation. In recent years, microRNAs have emerged as prominent players in cancer as well. Rhabdomyosarcoma is a pediatric skeletal muscle-derived soft-tissue sarcoma that originates from myogenic precursors arrested at different stages of differentiation and that continue to proliferate indefinitely. MicroRNAs involved in muscle cell fate determination appear down-regulated in rhabdomyosarcoma primary tumors and cell lines compared to their normal counterparts. More importantly, they behave as tumor suppressors in this malignancy, as their re-expression is sufficient to restore the differentiation capability of tumor cells and to prevent tumor growth in vivo. In addition, up-regulation of pro-oncogenic microRNAs has also been recently detected in rhabdomyosarcoma.In this review, we provide an overview of current knowledge on microRNAs de-regulation in rhabdomyosarcoma. Additionally, we examine the potential of microRNAs as prognostic and diagnostic markers in this soft-tissue sarcoma, and discuss possible therapeutic applications and challenges of a "microRNA therapy". © 2011 Rota et al; licensee BioMed Central Ltd.
Material Named Entity Recognition (MNER) for Knowledge-driven Materials Using Deep Learning Approach
Creators: name: Miah, M. Saef Ullah
name: Sulaiman, Junaida
Publisher: name: arXiv
Year: 2022
Subjects: subject: Information Retrieval (cs.IR)
subject: FOS: Computer and information sciences

description: The scientific literature contains a wealth of cutting-edge knowledge in the field of materials science, as well as useful data (e.g., numerical data from experimental results, material properties and structure). These data are critical for data-driven machine learning (ML) and deep learning (DL) methods to accelerate material discovery. Due to the large and growing number of publications, it is difficult for humans to manually retrieve and retain this knowledge. In this context, we investigate a deep neural network model based on Bi-LSTM to retrieve knowledge from published scientific articles. The proposed deep neural network-based model achieves an f-1 score of \~97\% for the Material Named Entity Recognition (MNER) task. The study addresses motivation, relevant work, methodology, hyperparameters, and overall performance evaluation. The analysis provides insight into the results of the experiment and points to future directions for current research.
description: 10 pages
Pattern recognition analysis on heavy ion reaction data
Creators: name: De Sanctis, Jacopo <1977>
Publisher: name: Alma Mater Studiorum - Università di Bologna
Year: 2008
Subjects: FIS/04 Fisica nucleare e subnucleare

description: One of the problems in the analysis of nucleus-nucleus collisions is
to get information on the value of the impact parameter b. This work
consists in the application of pattern recognition techniques aimed at
associating values of b to groups of events. To this end, a support vec-
tor machine (SVM) classifier is adopted to analyze multifragmentation
reactions. This method allows to backtracing the values of b through
a particular multidimensional analysis. The SVM classification con-
sists of two main phase. In the first one, known as training phase,
the classifier learns to discriminate the events that are generated by
two different model:Classical Molecular Dynamics (CMD) and Heavy-
Ion Phase-Space Exploration (HIPSE) for the reaction: 58Ni +48 Ca
at 25 AMeV. To check the classification of events in the second one,
known as test phase, what has been learned is tested on new events
generated by the same models. These new results have been com-
pared to the ones obtained through others techniques of backtracing
the impact parameter. Our tests show that, following this approach,
the central collisions and peripheral collisions, for the CMD events,
are always better classified with respect to the classification by the
others techniques of backtracing. We have finally performed the SVM
classification on the experimental data measured by NUCL-EX col-
laboration with CHIMERA apparatus for the previous reaction.
Stimulant Reduction Intervention using Dosed Exercise (STRIDE) - CTN 0037: Study protocol for a randomized controlled trial
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: stimulant abuse
stimulant dependence
exercise
health education
behavioral intervention

description: Background: There is a need for novel approaches to the treatment of stimulant abuse and dependence. Clinical data examining the use of exercise as a treatment for the abuse of nicotine, alcohol, and other substances suggest that exercise may be a beneficial treatment for stimulant abuse, with direct effects on decreased use and craving. In addition, exercise has the potential to improve other health domains that may be adversely affected by stimulant use or its treatment, such as sleep disturbance, cognitive function, mood, weight gain, quality of life, and anhedonia, since it has been shown to improve many of these domains in a number of other clinical disorders. Furthermore, neurobiological evidence provides plausible mechanisms by which exercise could positively affect treatment outcomes. The current manuscript presents the rationale, design considerations, and study design of the National Institute on Drug Abuse (NIDA) Clinical Trials Network (CTN) CTN-0037 Stimulant Reduction Intervention using Dosed Exercise (STRIDE) study.Methods/Design: STRIDE is a multisite randomized clinical trial that compares exercise to health education as potential treatments for stimulant abuse or dependence. This study will evaluate individuals diagnosed with stimulant abuse or dependence who are receiving treatment in a residential setting. Three hundred and thirty eligible and interested participants who provide informed consent will be randomized to one of two treatment arms: Vigorous Intensity High Dose Exercise Augmentation (DEI) or Health Education Intervention Augmentation (HEI). Both groups will receive TAU (i.e., usual care). The treatment arms are structured such that the quantity of visits is similar to allow for equivalent contact between groups. In both arms, participants will begin with supervised sessions 3 times per week during the 12-week acute phase of the study. Supervised sessions will be conducted as one-on-one (i.e., individual) sessions, although other participants may be exercising at the same time. Following the 12-week acute phase, participants will begin a 6-month continuation phase during which time they will attend one weekly supervised DEI or HEI session. Clinical Trials Registry: ClinicalTrials.gov, NCT01141608. http://clinicaltrials.gov/ct2/show/NCT01141608?term=Stimulant+Reduction+Intervention+using+Dosed+Exercise&rank=1. © 2011 Trivedi et al; licensee BioMed Central Ltd.
South American plasmodium falciparum after the malaria eradication era: Clonal population expansion and survival of the fittest hybrids
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: Antimalarials
Dihydropteroate Synthase
Drug Resistance
Epidemics
Gene Frequency
Genotype
Geography
Haplotypes
Humans
Linkage Disequilibrium
Malaria, Falciparum
Membrane Transport Proteins
Microsatellite Repeats
Multidrug Resistance-Associated Proteins
Peru
Phylogeny
Plasmodium falciparum
Population Growth
Protozoan Proteins
Tetrahydrofolate Dehydrogenase

description: Malaria has reemerged in many regions where once it was nearly eliminated. Yet the source of these parasites, the process of repopulation, their population structure, and dynamics are ill defined. Peru was one of malaria eradication's successes, where Plasmodium falciparum was nearly eliminated for two decades. It reemerged in the 1990s. In the new era of malaria elimination, Peruvian P. falciparum is a model of malaria reinvasion. We investigated its population structure and drug resistance profiles. We hypothesized that only populations adapted to local ecological niches could expand and repopulate and originated as vestigial populations or recent introductions. We investigated the genetic structure (using microsatellites) and drug resistant genotypes of 220 parasites collected from patients immediately after peak epidemic expansion (1999-2000) from seven sites across the country. The majority of parasites could be grouped into five clonal lineages by networks and AMOVA. The distribution of clonal lineages and their drug sensitivity profiles suggested geographic structure. In 2001, artesunate combination therapy was introduced in Peru. We tested 62 parasites collected in 2006-2007 for changes in genetic structure. Clonal lineages had recombined under selection for the fittest parasites. Our findings illustrate that local adaptations in the post-eradication era have contributed to clonal lineage expansion. Within the shifting confluence of drug policy and malaria incidence, populations continue to evolve through genetic outcrossing influenced by antimalarial selection pressure. Understanding the population substructure of P. falciparum has implications for vaccine, drug, and epidemiologic studies, including monitoring malaria during and after the elimination phase.
gtfs2vec -- Learning GTFS Embeddings for comparing Public Transport Offer in Microregions
Creators: name: Gramacki, Piotr
name: Woźniak, Szymon
name: Szymański, Piotr
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: We selected 48 European cities and gathered their public transport timetables in the GTFS format. We utilized Uber's H3 spatial index to divide each city into hexagonal micro-regions. Based on the timetables data we created certain features describing the quantity and variety of public transport availability in each region. Next, we trained an auto-associative deep neural network to embed each of the regions. Having such prepared representations, we then used a hierarchical clustering approach to identify similar regions. To do so, we utilized an agglomerative clustering algorithm with a euclidean distance between regions and Ward's method to minimize in-cluster variance. Finally, we analyzed the obtained clusters at different levels to identify some number of clusters that qualitatively describe public transport availability. We showed that our typology matches the characteristics of analyzed cities and allows succesful searching for areas with similar public transport schedule characteristics.
description: Accepted at 1st ACM SIGSPATIAL International Workshop on Searching and Mining Large Collections of Geospatial Data (GeoSearch 2021)
Chiral low-energy constants from lattice QCD
Creators: name: Necco, Silvia
Publisher: name: arXiv
Year: 2009
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Different strategies for the computation of QCD low-energy couplings by matching lattice results with the chiral effective theory are reviewed. After recalling some relevant predictions from the effective theory, the current status of leading order (Σ,F, Sigma_0,F_0) and next-to-leading order (l_i, L_i) low-energy constants is summarized, focusing on recent results obtained with N_f=2 and N_f=2+1 lattice simulations.
description: Plenary talk at 8th Conference Quark Confinement and the Hadron Spectrum, September 1-6 2008, Mainz (Germany)
Toward a general model for the evolutionary dynamics of gene duplicates
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: dosage balance
gene duplication
neofunctionalization
subfunctionalization
protein-protein interaction network
stochastic model

description: Gene duplication is an important process in the functional divergence of genes and genomes. Several processes have been described that lead to duplicate gene retention over different timescales after both smaller-scale events and whole-genome duplication, including neofunctionalization, subfunctionalization, and dosage balance. Two common modes of duplicate gene loss include nonfunctionalization and loss due to population dynamics (failed fixation). Previous work has characterized expectations of duplicate gene retention under the neofunctionalization and subfunctionalization models. Here, that work is extended to dosage balance using simulations. A general model for duplicate gene loss/retention is then presented that is capable of fitting expectations under the different models, is defined at t = 0, and decays to an orthologous asymptotic rate rather than zero, based upon a modified Weibull hazard function. The model in a maximum likelihood framework shows the property of identifiability, recovering the evolutionary mechanism and parameters of simulation. This model is also capable of recovering the evolutionary mechanism of simulation from data generated using an unrelated network population genetic model. Lastly, the general model is applied as part of a mixture model to recent gene duplicates from the Oikopleura dioica genome, suggesting that neofunctionalization may be an important process leading to duplicate gene retention in that organism. © The Author(s) 2010.
Analysis of ACE and EACE Protocols in Underwater Wireless Sensor Networks
Creators: name: S, Rajini
name: Ramakrishna, Dr. M
Publisher: name: figshare
Year: 2021
Subjects: subject: 80503 Networking and Communications
subject: FOS: Computer and information sciences
subject: 100507 Optical Networks and Systems
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: 100503 Computer Communications Networks

description: Underwater Wireless Sensor Networks (UWSNs) are extremely significant in running every type of duties underwater. Dependable and effective communication among sensor nodes is extremely stimulating. Initially, since radio waves can’t function fine in such atmosphere, so we utilize acoustic communication. Secondly, acoustic communication is extremely slower compared to radio communication. Furthermore, atmosphere is extremely dynamic, that transforms topology of network. Because of these motives information can’t spread to destination timely or dependably. This generates necessity of method that can advance functioning of network in terms of dependability and quantity. Cooperation among nodules is one of main methods that can significantly improve dependability of network at price of extra energy ingesting. In this paper, we are focusing on ACE (Adaptive Cooperative Retransmission in EEDBR) Protocol and EACE (Enhanced Adaptive Cooperative Retransmission in EEDBR) protocols for improving the functioning regarding network lifetime, energy efficiency, throughput, relay, packets delay compared to other cooperative routing protocols.
Why does Rhinopithecus bieti prefer the highest elevation range in winter? a test of the sunshine hypothesis
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: Altitude
Animals
Colobinae
Ecosystem
Geographic Information Systems
Seasons
Sunlight

description: Environmental factors that affect spatiotemporal distribution patterns of animals usually include resource availability, temperature, and the risk of predation. However, they do not explain the counterintuitive preference of high elevation range in winter by the black-and-white snub-nosed monkey (Rhinopithecus bieti). We asked whether variation of sunshine along with elevations is the key driving force. To test this hypothesis, we conducted field surveys to demonstrate that there was a statistically significant pattern of high elevation use during winter. We then asked whether this pattern can be explained by certain environmental factors, namely temperature, sunshine duration and solar radiation. Finally, we concluded with a possible ecological mechanism for this pattern. In this study, we employed GIS technology to quantify solar radiation and sunshine duration across the monkey's range. Our results showed that: 1) R. bieti used the high altitude range between 4100-4400 m in winter although the yearly home range spanned from 3500-4500 m; 2) both solar radiation and sunshine duration increased with elevation while temperature decreased with elevation; 3) within the winter range, the use of range was significantly correlated with solar radiation and sunshine duration; 4) monkeys moved to the areas with high solar radiation and duration following a snowfall, where the snow melts faster and food is exposed earlier. We concluded that sunshine was the main factor that influences selection of high elevation habitat for R. bieti in winter. Since some other endotherms in the area exhibit similar winter distributional patterns, we developed a sunshine hypothesis to explain this phenomenon. In addition, our work also represented a new method of integrating GIS models into traditional field ecology research to study spatiotemporal distribution pattern of wildlife. We suggest that further theoretical and empirical studies are necessary for better understanding of sunshine influence on wildlife range use. © 2011 Quan et al.