cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A covariance kernel for proteins
Creators: name: Cuturi, Marco
name: Vert, Jean-Philippe
Publisher: name: arXiv
Year: 2003
Subjects: subject: Genomics (q-bio.GN)
subject: FOS: Biological sciences

description: We propose a new kernel for biological sequences which borrows ideas and techniques from information theory and data compression. This kernel can be used in combination with any kernel method, in particular Support Vector Machines for protein classification. By incorporating prior biological assumptions on the properties of amino-acid sequences and using a Bayesian averaging framework, we compute the value of this kernel in linear time and space, benefiting from previous achievements proposed in the field of universal coding. Encouraging classification results are reported on a standard protein homology detection experiment.
description: 12 pages, 1 figure
Thermus Brock & Freeze 1969, gen. n.
Creators: name: Brock, Thomas D.
name: Freeze, Hudson
Publisher: name: Zenodo
Year: 1969
Subjects: Biodiversity
Taxonomy
Bacteria
Deinococcus-Thermus
Deinococci
Thermales
Thermaceae
Thermus

description: Thermus gen. n.    Morphology: Rods and filaments, 0.5 to 0.8,um in diameter. Rods 5 to 10 Am in length, filaments of variable length from 20 to greater than 200,um. Rods occurring singly or in aggregates, the latter either side-to-side or end-to-end (rosette-like). Large spheres 10 to 20 Am in diameter usually formed in old cultures. Gram-negative. Flagella and endospores absent. Gliding motility has not been observed.
 DNA base composition: 65.4 to 67.4% GC.
 Colony characteristics: Compact slowly spreading colonies. Yellow to bright orange on 0.1% tryptone plus 0.1% yeast extract plus mineral salts-agar.
Liquid culture: Yellow surface pellicle often formed in unshaken liquid cultures.
 Temperature relations: Optimum, 70 to 72 C, maximum 79 C, minimum around 40 C.
Nutrition: No growth factor requirements (one strain tested). Nitrogen sources, amino acids and NH4+. Carbon sources, sugars, and organic acids. Grows best in complex media such as 0.1 to 0.3% tryptone plus yeast extract.
 Relation to oxygen: Obligately aerobic.
 Relation to pH: Optimum 7.5 to 7.8. No growth below pH 6 or above 9.5.
 Inhibitor sensitivity: Inhibited by 10 Mg or less of streptomycin, penicillin, novobiocin, actinomycin D, or chloramphenicol per ml.
 Inhibited by 100 ug or less of cycloserine, tetracycline, and sodium lauryl sulfate per ml. Inhibited by 500 Mug or less of sodium azide per ml. Inhibited by 2% NaCl. Inhibited by 200 ug or less of oxgall per ml.
Source: Hot springs, hot tap water.
 The name given to this organism is derived from the Greek noun, thermos, meaning hot. One species.
description: Published as part of Brock, Thomas D. & Freeze, Hudson, 1969, Thermus aquaticus gen. n. and sp. n., a Nonsporulating Extreme Thermophile, pp. 289-297 in Journal of Bacteriology 98 (1) on page 295, DOI: 10.1128/jb.98.1.289-297.1969, http://zenodo.org/record/5585059
Does the small CMB quadrupole moment suggest new physics?
Creators: name: Cline, James M.
name: Crotty, Patrick
name: Lesgourgues, Julien
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Motivated by WMAP's confirmation of an anomalously low value of the quadrupole moment of the CMB temperature fluctuations, we investigate the effects on the CMB of cutting off the primordial power spectrum P(k) at low wave numbers. This could arise, for example, from a break in the inflaton potential, a prior period of matter or radiation domination, or an oscillating scalar field which couples to the inflaton. We reanalyze the full WMAP parameter space supplemented by a low-k cutoff for P(k). The temperature correlations by themselves are better fit by a cutoff spectrum, but including the TE temperature-polarization spectrum reduces this preference to a 1.4 sigma effect. Inclusion of large scale structure data does not change the conclusion. If taken seriously, the low-k cutoff is correlated with optical depth so that reionization occurs even earlier than indicated by the WMAP analysis.
description: 10 pages 6 figures; corrected eq. 4.1; clarified discussion explaining apparent discrepancy with WMAP's estimate of low quadrupole significance
High precision detection of change in intermediate range order of amorphous zirconia-doped tantala thin films due to annealing
Creators: name: Prasai, Kiran
name: Jiang, J.
name: Mishkin, A.
name: Shyam, Badri
name: Angelova, S.V.
name: Birney, Ross
name: Drabold, David Alan
name: Fazio, Mariana A.
name: Gustafson, Eric K.
name: Harry, Gregory M.
name: Hoback, S.Y.
name: Hough, James H.
name: Lévesque, C.
name: MacLaren, Ian A.N.
name: Markosyan, Ashot S.
name: Martin, Iain William
name: Menoni, Carmen S.
name: Murray, Peter G.
name: Penn, Steven D.
name: Reid, Stuart
name: Robie, Raymond
name: Rowan, Sheila
name: Schiettekatte, François
name: Shink, R.
name: Turner, A.
name: Vajente, Gabriele
name: Cheng, Haiping
name: Fejer, Martin M.
name: Mehta, Apurva
name: Bassiri, R.
Publisher: name: Physical Review Letters
Year: 2023
Subjects: classificationCode: 51
subject: Physical sciences
subject: FOS: Physical sciences

description: Understanding the local atomic order in amorphous thin film coatings and how it relates to macroscopic performance factors, such as mechanical loss, provides an important path towards enabling the accelerated discovery and development of improved coatings. High precision x-ray scattering measurements of thin films of amorphous zirconia-doped tantala (ZrO2-Ta2O5) show systematic changes in intermediate range order (IRO) as a function of postdeposition heat treatment (annealing). Atomic modeling captures and explains these changes, and shows that the material has building blocks of metal-centered polyhedra and the effect of annealing is to alter the connections between the polyhedra. The observed changes in IRO are associated with a shift in the ratio of corner-sharing to edge-sharing polyhedra. These changes correlate with changes in mechanical loss upon annealing, and suggest that the mechanical loss can be reduced by developing a material with a designed ratio of corner-sharing to edge-sharing polyhedra.
Tests of the Expectations Hypothesis and Policy Reaction to the Term Spread: some comparative evidence
Creators: name: Boero, Gianna
name: Torricelli, Costanza
name: Boero, Gianna
name: Torricelli, Costanza
Publisher: name: Unknown
Year: 1998
Subjects: subject: Agricultural and Food Policy
subject: Financial Economics
subject: Expectations Hypothesis
subject: interest rates
subject: monetary policy
subject: term structure

description: The aim of this paper is to evaluate the impact of monetary policy in tests of the Expectations Hypothesis of the term structure of interest rates. We apply the model developed by McCallum (1994b), in which the Expectations Hypothesis interacts with a policy reaction function and with a time-varying term premium, to eight countries with different monetary policy stances, within the period 1985 to 1995. The results suggest the importance of the treatment of monetary policy in explaining the empirical performance of the Expectations Hypothesis. Amongst other results, we also find that the model performs better for some countries than others depending upon the monetary policy stance adopted
Additional file 3 of Exploring barriers and facilitators to PrEP use among transgender women in two urban areas: implications for messaging and communication
Creators: name: Bass, Sarah Bauerle
name: Kelly, Patrick J.
name: Brajuha, Jesse
name: Gutierrez-Mock, Luis
name: Koester, Kimberly
name: D’Avanzo, Paul
name: Sevelius, Jae
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: Marine Biology
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology
subject: Cardiology

description: Additional file 3. Demographic characteristics by focus group.
Environmental Pollution: A threat to life in the air
Creators: name: Manju Bissu, Priyanka Bissu
Publisher: name: The Science world a Monthly e magazine
Year: 2024

description: Air pollution is now considered to be the world’s largest environmental health threat, accounting for 7 million deaths around the world every year. Air pollution causes and exacerbates a number of diseases, ranging from asthma to cancer, pulmonary illnesses and heart disease.

Air pollution is contamination of the indoor or outdoor environment by any chemical, physical or biological agent that modifies the natural characteristics of the atmosphere. Air quality is closely linked to the earth’s climate and ecosystems globally. Many of the drivers of air pollution (i.e. combustion of fossil fuels) are also sources of greenhouse gas emissions. Household combustion devices, motor vehicles, industrial facilities and forest fires are common sources of air pollution. Pollutants of major public health concern include particulate matter, carbon monoxide, ozone, nitrogen dioxide and sulfur dioxide.
Out of equilibrium generalized Stokes-Einstein relation: determination of the effective temperature of an aging medium
Creators: name: Pottier, Noelle
Publisher: name: arXiv
Year: 2004
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We analyze in details how the anomalous drift and diffusion properties of a particle evolving in an aging medium can be interpreted in terms of an effective temperature of the medium. From an experimental point of view, independent measurements of the mean-square displacement and of the mobility of a particle immersed in an aging medium such as a colloidal glass give access to an out of equilibrium generalized Stokes-Einstein relation, from which the effective temperature of the medium can eventually be deduced. We illustrate the procedure on a simple model with power-law behaviours.
description: 15 pages
Disordered hyperuniformity in superconducting vortex lattices
Creators: name: Benito-Llorens, Jose
name: Guillamón, Isabel
name: García-Serrano, Ismael
name: Córdoba, Rosa
name: Sesé, Javier
name: De Teresa, José María
name: Ibarra, M. Ricardo
name: Vieira, Sebastián
name: Ortuño, Miguel
name: Suderow, Hermann
Publisher: name: arXiv
Year: 2020
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Particles occupying sites of a random lattice present density fluctuations at all length scales. It has been proposed that increasing interparticle interactions reduces long range density fluctuations, deviating from random behaviour. This leads to power laws in the structure factor and the number variance that can be used to characterize deviations from randomness which eventually lead to disordered hyperuniformity. It is not yet fully clear how to link density fluctuations with interactions in a disordered hyperuniform system. Interactions between superconducting vortices are very sensitive to vortex pinning, to the crystal structure of the superconductor and to the value of the magnetic field. This creates lattices with different degrees of disorder. Here we study disordered vortex lattices in several superconducting compounds (Co-doped NbSe$_2$, LiFeAs and CaKFe$_4$As$_4$) and in two amorphous W-based thin films, one with strong nanostructured pinning (W-film-1) and another one with weak or nearly absent pinning (W-film-2). We calculate for each case the structure factor and number variance and compare to calculations on an interacting set of partially pinned particles. We find that random density fluctuations appear when pinning overcomes interactions and show that the suppression of density fluctuations is indeed correlated to the presence of interactions. Furthermore, we find that we can describe all studied vortex lattices within a single framework consisting of a continous deviation from hyperuniformity towards random distributions when increasing the strength of pinning with respect to the intervortex interaction.
High precision detection of change in intermediate range order of amorphous zirconia-doped tantala thin films due to annealing
Creators: name: Prasai, Kiran
name: Jiang, J.
name: Mishkin, A.
name: Shyam, Badri
name: Angelova, S.V.
name: Birney, Ross
name: Drabold, David Alan
name: Fazio, Mariana A.
name: Gustafson, Eric K.
name: Harry, Gregory M.
name: Hoback, S.Y.
name: Hough, James H.
name: Lévesque, C.
name: MacLaren, Ian A.N.
name: Markosyan, Ashot S.
name: Martin, Iain William
name: Menoni, Carmen S.
name: Murray, Peter G.
name: Penn, Steven D.
name: Reid, Stuart
name: Robie, Raymond
name: Rowan, Sheila
name: Schiettekatte, François
name: Shink, R.
name: Turner, A.
name: Vajente, Gabriele
name: Cheng, Haiping
name: Fejer, Martin M.
name: Mehta, Apurva
name: Bassiri, R.
Publisher: name: American University
Year: 2023

description: Understanding the local atomic order in amorphous thin film coatings and how it relates to macroscopic performance factors, such as mechanical loss, provides an important path towards enabling the accelerated discovery and development of improved coatings. High precision x-ray scattering measurements of thin films of amorphous zirconia-doped tantala (ZrO2-Ta2O5) show systematic changes in intermediate range order (IRO) as a function of postdeposition heat treatment (annealing). Atomic modeling captures and explains these changes, and shows that the material has building blocks of metal-centered polyhedra and the effect of annealing is to alter the connections between the polyhedra. The observed changes in IRO are associated with a shift in the ratio of corner-sharing to edge-sharing polyhedra. These changes correlate with changes in mechanical loss upon annealing, and suggest that the mechanical loss can be reduced by developing a material with a designed ratio of corner-sharing to edge-sharing polyhedra.
Distributive Politics and the Benefits of Decentralisation
Creators: name: Lockwood, Ben
name: Lockwood, Ben
Publisher: name: Unknown
Year: 1998
Subjects: Agricultural and Food Policy
Political Economy

description: This paper integrates the distributive politics literature with the literature on decentralization by incorporating inter-regional project externalities into a standard model of distributive policy. A key …nding is that the degree of uniformity (or “universalism”) of the provision of regional projects is endogenous, and depends on the strength of the externality. The welfare bene…ts of decentralization, and the performance of “constitutional rules” (such as majority voting) which may be used to choose between decentralization and centralization, are then discussed in this framework.
Highly Efficient Salient Object Detection with 100K Parameters
Creators: name: Gao, Shang-Hua
name: Tan, Yong-Qiang
name: Cheng, Ming-Ming
name: Lu, Chengze
name: Chen, Yunpeng
name: Yan, Shuicheng
Publisher: name: arXiv
Year: 2020
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Salient object detection models often demand a considerable amount of computation cost to make precise prediction for each pixel, making them hardly applicable on low-power devices. In this paper, we aim to relieve the contradiction between computation cost and model performance by improving the network efficiency to a higher degree. We propose a flexible convolutional module, namely generalized OctConv (gOctConv), to efficiently utilize both in-stage and cross-stages multi-scale features, while reducing the representation redundancy by a novel dynamic weight decay scheme. The effective dynamic weight decay scheme stably boosts the sparsity of parameters during training, supports learnable number of channels for each scale in gOctConv, allowing 80% of parameters reduce with negligible performance drop. Utilizing gOctConv, we build an extremely light-weighted model, namely CSNet, which achieves comparable performance with about 0.2% parameters (100k) of large models on popular salient object detection benchmarks.
description: Accepted by ECCV 2020. Source code: https://mmcheng.net/sod100k/
Switching of sub-micrometer sized, antiferromagnetically coupled CoFeB/Ru/CoFeB trilayers
Creators: name: Wiese, N.
name: Dimopoulos, T.
name: Ruhrig, M.
name: Wecker, J.
name: Reiss, G.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: This work reports on the magnetic reversal of sub-micrometer sized elements consisting of an CoFeB/Ru/CoFeB artificial ferrimagnet (AFi). The elements were patterned into ellipses having a width of approximately 250 to 270nm and a varying aspect ratio between 1.3 and 8. The coercivity was found to decrease with an increasing imbalance of the magnetic moment of the two antiferromagnetically coupled layers and is therefore strongly affected by an increase of effective anisotropy due to the antiferromagnetic coupling of the two layers. With respect to a single layer of amorphous CoFeB, patterned in comparable elements, the AFi has an increased coercivity. Switching asteroids comparable to single layers were only observed for samples with a high net moment.
description: 5 pages, 6 figures, accepted for publication in J. Appl. Phys
A zoonotic adenoviral human pathogen emerged through genomic recombination among human and nonhuman simian hosts
Creators: name: Dehghan, Shoaleh
name: Seto, Jason
name: Liu, Elizabeth B.
name: Ismail, Ashrafali Mohamed
name: Madupu, Ramana
name: Heim, Albert
name: Jones, Morris Saffold
name: Dyer, David W.
name: Chodosh, James C.
name: Seto, Donald
Publisher: name: American University
Year: 2023

description: Genomics analysis of a historically intriguing and predicted emergent human adenovirus (HAdV) pathogen, which caused pneumonia and death, provides insight into a novel molecular evolution pathway involving “ping-pong” zoonosis and anthroponosis. The genome of this promiscuous pathogen is embedded with evidence of unprecedented multiple, multidirectional, stable, and reciprocal cross-species infections of hosts from three species (human, chimpanzee, and bonobo). This recombinant genome, typed as HAdV-B76, is identical to two recently reported simian AdV (SAdV) genomes isolated from chimpanzees and bonobos. Additionally, the presence of a critical adenoviral replication element found in HAdV genomes, in addition to genes that are highly similar to counterparts in other HAdVs, reinforces its potential as a human pathogen. Reservoirs in nonhuman hosts may explain periods of apparent absence and then reemergence of human adenoviral pathogens, as well as present pathways for the genesis of those thought to be newly emergent. The nature of the HAdV-D76 genome has implications for the use of SAdVs as gene delivery vectors in human gene therapy and vaccines, selected to avoid preexisting and potentially fatal host immune responses to HAdV. IMPORTANCE An emergent adenoviral human pathogen, HAdV-B76, associated with a fatality in 1965, shows a remarkable degree of genome identity with two recently isolated simian adenoviruses that contain cross-species genome recombination events from three hosts: human, chimpanzee, and bonobo. Zoonosis (nonhuman-to-human transmission) and anthroponosis (human to nonhuman transmission) may play significant roles in the emergence of human adenoviral pathogens.
Spatial coverage of protection for terrestrial species under the Canadian Species at Risk Act
Creators: name: Bolliger, Clark S.
name: Calla V. Raymond
name: Schuster, Richard
name: Bennett, Joseph R.
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 20199 Astronomical and Space Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified

description: Canada’s Species at Risk Act (SARA) has been critiqued for only protecting species on federal lands. However, this shortcoming has never been quantitatively assessed in terms of species’ ranges. We assessed the proportion of ranges of federally-listed terrestrial species at risk (SAR) receiving protection via SARA, excluding birds protected by the Migratory Birds Convention Act. Additionally, we assessed species protection provided by provincial and territorial protected areas within the ranges of SARA-listed species. We show that federal land provides protection within only 8.1% of species’ Canadian ranges on average, and 63.1% of 252 terrestrial SAR are protected within less than 5% of their range. The addition of provincial and territorial protected areas increases this average to 14.6% and reduces the percent with less than 5% protection to 34.9% of species. Eighteen species receive 0% protection within their Canadian ranges. We found no significant difference in average protection among taxonomic groups. Canada’s capacity to protect SAR via SARA could be improved by greater coordination among national, provincial and Indigenous governments, the creation of a more effective protected area network, exercising SARA’s provision for emergency protection orders where applicable, and facilitating greater SAR protection on public and private lands.
End-to-End Evaluation of Federated Learning and Split Learning for Internet of Things
Creators: name: Gao, Yansong
name: Kim, Minki
name: Abuadbba, Sharif
name: Kim, Yeonjae
name: Thapa, Chandra
name: Kim, Kyuyeon
name: Camtepe, Seyit A.
name: Kim, Hyoungshick
name: Nepal, Surya
Publisher: name: arXiv
Year: 2020
Subjects: subject: Cryptography and Security (cs.CR)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: This work is the first attempt to evaluate and compare felderated learning (FL) and split neural networks (SplitNN) in real-world IoT settings in terms of learning performance and device implementation overhead. We consider a variety of datasets, different model architectures, multiple clients, and various performance metrics. For learning performance, which is specified by the model accuracy and convergence speed metrics, we empirically evaluate both FL and SplitNN under different types of data distributions such as imbalanced and non-independent and identically distributed (non-IID) data. We show that the learning performance of SplitNN is better than FL under an imbalanced data distribution, but worse than FL under an extreme non-IID data distribution. For implementation overhead, we end-to-end mount both FL and SplitNN on Raspberry Pis, and comprehensively evaluate overheads including training time, communication overhead under the real LAN setting, power consumption and memory usage. Our key observations are that under IoT scenario where the communication traffic is the main concern, the FL appears to perform better over SplitNN because FL has the significantly lower communication overhead compared with SplitNN, which empirically corroborate previous statistical analysis. In addition, we reveal several unrecognized limitations about SplitNN, forming the basis for future research.
description: 10 pages, 12 figures
Additional file 1 of STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families
Creators: name: Zhou, Albert E.
name: Shah, Zalak V.
name: Bradwell, Katie R.
name: Munro, James B.
name: Berry, Andrea A.
name: Serre, David
name: Takala-Harrison, Shannon
name: O’Connor, Timothy D.
name: Silva, Joana C.
name: Travassos, Mark A.
Publisher: name: figshare
Year: 2022
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 1. Word document with information on the creation of STRIDE as well as sequences used for generating, training, and validating each HMM profile.
A zoonotic adenoviral human pathogen emerged through genomic recombination among human and nonhuman simian hosts
Creators: name: Dehghan, Shoaleh
name: Seto, Jason
name: Liu, Elizabeth B.
name: Ismail, Ashrafali Mohamed
name: Madupu, Ramana
name: Heim, Albert
name: Jones, Morris Saffold
name: Dyer, David W.
name: Chodosh, James C.
name: Seto, Donald
Publisher: name: Journal of Virology
Year: 2023
Subjects: classificationCode: 31
subject: Biological sciences
subject: FOS: Biological sciences

description: Genomics analysis of a historically intriguing and predicted emergent human adenovirus (HAdV) pathogen, which caused pneumonia and death, provides insight into a novel molecular evolution pathway involving “ping-pong” zoonosis and anthroponosis. The genome of this promiscuous pathogen is embedded with evidence of unprecedented multiple, multidirectional, stable, and reciprocal cross-species infections of hosts from three species (human, chimpanzee, and bonobo). This recombinant genome, typed as HAdV-B76, is identical to two recently reported simian AdV (SAdV) genomes isolated from chimpanzees and bonobos. Additionally, the presence of a critical adenoviral replication element found in HAdV genomes, in addition to genes that are highly similar to counterparts in other HAdVs, reinforces its potential as a human pathogen. Reservoirs in nonhuman hosts may explain periods of apparent absence and then reemergence of human adenoviral pathogens, as well as present pathways for the genesis of those thought to be newly emergent. The nature of the HAdV-D76 genome has implications for the use of SAdVs as gene delivery vectors in human gene therapy and vaccines, selected to avoid preexisting and potentially fatal host immune responses to HAdV. IMPORTANCE An emergent adenoviral human pathogen, HAdV-B76, associated with a fatality in 1965, shows a remarkable degree of genome identity with two recently isolated simian adenoviruses that contain cross-species genome recombination events from three hosts: human, chimpanzee, and bonobo. Zoonosis (nonhuman-to-human transmission) and anthroponosis (human to nonhuman transmission) may play significant roles in the emergence of human adenoviral pathogens.
Edge-cuts Optimized for Average Weight: a new alternative to Ford and Fulkerson
Creators: name: Payne, Scott
name: Fuller, Edgar
name: Zhang, Cun-Quan
Publisher: name: arXiv
Year: 2020
Subjects: subject: Data Structures and Algorithms (cs.DS)
subject: FOS: Computer and information sciences

description: Let $G$ be a directed graph associated with a weight $w: E(G) \rightarrow R^+$. For an edge-cut $Q$ of $G$, the average weight of $Q$ is denoted and defined as $w_{ave}(Q)=\frac{\sum_{e\in Q}w(e)}{|Q|}$. An edge-cut of optimal average weight is an edge-cut $Q$ such that $w_{ave}(Q)$ is maximum among all edge-cuts (or minimum, symmetrically). In this paper, a polynomial algorithm for this problem is proved for finding such an optimal edge-cut in a rooted tree, separating the root and the set of all leafs. This algorithm enables us to develop an automatic clustering method with more accurate detection of communities embedded in a hierarchy tree structure.
Optimal filtering of the LISA data
Creators: name: Krolak, Andrzej
name: Tinto, Massimo
name: Vallisneri, Michele
Publisher: name: arXiv
Year: 2004
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The LISA time-delay-interferometry responses to a gravitational-wave signal are rewritten in a form that accounts for the motion of the LISA constellation around the Sun; the responses are given in closed analytic forms valid for any frequency in the band accessible to LISA. We then present a complete procedure, based on the principle of maximum likelihood, to search for stellar-mass binary systems in the LISA data. We define the required optimal filters, the amplitude-maximized detection statistic (analogous to the F statistic used in pulsar searches with ground-based interferometers), and discuss the false-alarm and detection probabilities. We test the procedure in numerical simulations of gravitational-wave detection.
description: RevTeX4, 28 pages, 9 EPS figures. Minus signs fixed in Eq. (46) and Table II. Corrected discussion of F-statistic distribution in Sec. IV B
Putting all foods on the same table : Achieving sustainable food systems requires full accounting
Creators: name: Halpern, Benjamin S.
name: Cottrell, Richard S.
name: Blanchard, Julia L.
name: Bouwman, Alexander F.
name: Froehlich, Halley E.
name: Gephart, Jessica Ann
name: Jacobsen, Nis Sand
name: Kuempel, Caitlin D.
name: McIntyre, Peter B.
name: Metian, Marc
name: Moran, Daniel Dean
name: Nash, Kirsty L.
name: Többen, Johannes R.
name: Williams, David R.
Publisher: name: Proceedings of the National Academy of Sciences of the United States of America
Year: 2023
Subjects: classificationCode: 41
subject: Environmental sciences

description: Proceedings of the National Academy of Sciences of the United States of America, Volume 116, Issue 37, 10 September 2019, Pages 18152-18156.
Three-dimensional Simulations of Disk Accretion to an Inclined Dipole: II. Hot Spots and Variability
Creators: name: Romanova, Marina M.
name: Ustyugova, Galina V.
name: Koldoba, Alexander V.
name: Lovelace, Richard V. E.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The physics of the "hot spots" on stellar surfaces and the associated variability of accreting magnetized rotating stars is investigated for the first time using fully three-dimensional magnetohydrodynamic simulations. The magnetic moment of the star is inclined relative to its rotation axis by an angle Theta. A sequence of misalignment angles was investigated, between Theta=0 and 90 degrees.Typically at small Theta the spots are observed to have the shape of a bow which is curved around the magnetic axis, while at largest Theta the spots have a shape of a bar, crossing the magnetic pole. The physical parameters (density, temperature, etc.) increase toward the central regions of the spots. At relatively low density and temperature, the spots occupy approximately 10-20 % of the stellar surface, while at the highest values of these parameters this area may be less than 1 % of the area of the star. The light curves were calculated for different Theta and inclination angles of the disk i. They show a range of variability patterns, including one maximum-per-period curves (at most of angles Theta and i), and two maximum-per-period curves (at large Theta and i). At small Theta, the funnel streams may rotate faster/slower than the star, and this may lead to quasi-periodic variability of the star. The results are of interest for understanding the variability and quasi-variability of Classical T Tauri Stars, millisecond pulsars and cataclysmic variables.
description: 15 pages, 13 figures, LaTeX, macros: emulapj.sty, avi simulations are available at http://www.astro.cornell.edu/us-rus/spots.htm
Putting all foods on the same table : Achieving sustainable food systems requires full accounting
Creators: name: Halpern, Benjamin S.
name: Cottrell, Richard S.
name: Blanchard, Julia L.
name: Bouwman, Alexander F.
name: Froehlich, Halley E.
name: Gephart, Jessica Ann
name: Jacobsen, Nis Sand
name: Kuempel, Caitlin D.
name: McIntyre, Peter B.
name: Metian, Marc
name: Moran, Daniel Dean
name: Nash, Kirsty L.
name: Többen, Johannes R.
name: Williams, David R.
Publisher: name: American University
Year: 2023

description: Proceedings of the National Academy of Sciences of the United States of America, Volume 116, Issue 37, 10 September 2019, Pages 18152-18156.
title: Ð¡Ð¸ÑÑÐµÐ¼Ð½ÑÐ¹ Ð¿Ð¾Ð´Ñ Ð¾Ð´ Ð² Ð¿ÑÐ¾ÐµÐºÑÐ¸ÑÐ¾Ð²Ð°Ð½Ð¸Ð¸ ÑÐµÑ Ð½Ð¸ÑÐµÑÐºÐ¾Ð³Ð¾ ÐºÐ¾Ð¼Ð¿Ð»ÐµÐºÑÐ° Ð¿ÑÐµÐ´Ð¿ÑÐ¸ÑÑÐ¸Ð¹, ÑÑÐ½ÐºÑÐ¸Ð¾Ð½Ð¸ÑÑÑÑÐ¸Ñ Ð² ÑÑÐ»Ð¾Ð²Ð¸ÑÑ Ð»Ð¾Ð³Ð¸ÑÑÐ¸ÑÐµÑÐºÐ¾Ð¹ Ð½ÐµÐ¾Ð¿ÑÐµÐ´ÐµÐ»ÐµÐ½Ð½Ð¾ÑÑÐ¸
title: A systematic approach to the design of a technical complex of enterprises operating in conditions of logistics uncertainty
Creators: name: Ð¡Ð»Ð°Ð²ÑÐ½Ð¾Ð², ÐÐ½Ð´ÑÐµÐ¹
name: "Ð¡Ð¸ÑÑÐµÐ¼Ð½ÑÐ¹ Ð°Ð½Ð°Ð»Ð¸Ð· Ð² Ð¿ÑÐ¾ÐµÐºÑÐ¸ÑÐ¾Ð²Ð°Ð½Ð¸Ð¸ Ð¸ ÑÐ¿ÑÐ°Ð²Ð»ÐµÐ½Ð¸Ð¸", Ð¼ÐµÐ¶Ð´ÑÐ½Ð°ÑÐ¾Ð´Ð½Ð°Ñ Ð½Ð°ÑÑÐ½Ð¾-Ð¿ÑÐ°ÐºÑÐ¸ÑÐµÑÐºÐ°Ñ ÐºÐ¾Ð½ÑÐµÑÐµÐ½ÑÐ¸Ñ (27; 2023; Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³)
Publisher: name: ÐÐÐÐÐ¢ÐÐ¥-ÐÐ ÐÐ¡Ð¡
Year: 2024
Subjects: ÐÑÐ¾Ð¼ÑÑÐ»ÐµÐ½Ð½ÑÐµ Ð¿ÑÐµÐ´Ð¿ÑÐ¸ÑÑÐ¸Ñ
Ð¡Ð¸ÑÑÐµÐ¼Ð½ÑÐ¹ Ð°Ð½Ð°Ð»Ð¸Ð·
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Ð±Ð»Ð¾ÑÐ½Ð¾-Ð¼Ð¾Ð´ÑÐ»ÑÐ½ÑÐ¹ Ð¿Ð¾Ð´Ñ Ð¾Ð´
Ð»Ð¾Ð³Ð¸ÑÑÐ¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ±Ð¾Ð¹
ÑÐµÑ Ð½Ð¾Ð»Ð¾Ð³Ð¸ÑÐµÑÐºÐ¸Ð¹ ÐºÐ¾Ð¼Ð¿Ð»ÐµÐºÑ
ÑÐµÑ Ð½Ð¸ÑÐµÑÐºÐ°Ñ Ð¸Ð½ÑÑÐ°ÑÑÑÑÐºÑÑÑÐ°
Ð½ÐµÑÑÐ°Ð±Ð¸Ð»ÑÐ½Ð¾ÑÑÑ
Ð¿Ð¾ÑÐ¾ÑÐ½Ð¾Ðµ Ð¿ÑÐ¾Ð¸Ð·Ð²Ð¾Ð´ÑÑÐ²Ð¾
Ð³Ð¸Ð±ÐºÐ¸Ðµ Ð¿ÑÐ¾Ð¸Ð·Ð²Ð¾Ð´ÑÑÐ²ÐµÐ½Ð½ÑÐµ ÑÐ¸ÑÑÐµÐ¼Ñ
production and technical complex
block-modular approach
logistics failure
technological complex
technical infrastructure
instability
continuous production
flexible production systems

description: ÐÐµÑÑÐ°Ð±Ð¸Ð»ÑÐ½Ð¾ÑÑÑ Ð²Ð½ÐµÑÐ½ÐµÐ¹ ÑÑÐµÐ´Ñ ÑÐ¾Ð·Ð´Ð°ÐµÑ ÑÐ³ÑÐ¾Ð·Ñ Ð½Ð¾ÑÐ¼Ð°Ð»ÑÐ½Ð¾Ð¼Ñ ÑÑÐ½ÐºÑÐ¸Ð¾Ð½Ð¸ÑÐ¾Ð²Ð°Ð½Ð¸Ñ ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¾Ð³Ð¾ ÐºÐ¾Ð¼Ð¿Ð»ÐµÐºÑÐ° Ð¿ÑÐµÐ´Ð¿ÑÐ¸ÑÑÐ¸Ñ, ÐºÐ¾ÑÐ¾ÑÑÐ¹ Ð´Ð¾Ð»Ð¶ÐµÐ½ Ð² ÑÐ»Ð¾Ð¶Ð¸Ð²ÑÐ¸ÑÑÑ ÑÑÐ»Ð¾Ð²Ð¸ÑÑ Ð¾Ð±Ð»Ð°Ð´Ð°ÑÑ Ð¼Ð°ÐºÑÐ¸Ð¼Ð°Ð»ÑÐ½Ð¾Ð¹ Ð³Ð¸Ð±ÐºÐ¾ÑÑÑÑ Ð¸ ÑÑÑÐ¾Ð¹ÑÐ¸Ð²Ð¾ÑÑÑÑ. ÐÑÐ¾Ð²ÐµÐ´ÐµÐ½Ð° Ð´ÐµÐºÐ¾Ð¼Ð¿Ð¾Ð·Ð¸ÑÐ¸Ñ ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¾Ð³Ð¾ ÐºÐ¾Ð¼Ð¿Ð»ÐµÐºÑÐ° Ð½Ð° Ð´Ð²Ðµ Ð¿Ð¾Ð´ÑÐ¸ÑÑÐµÐ¼Ñ - ÑÐµÑÐ½Ð¾Ð»Ð¾Ð³Ð¸ÑÐµÑÐºÑÑ Ð¸ Ð¸Ð½ÑÑÐ°ÑÑÑÑÐºÑÑÑÐ½ÑÑ. Ð Ð°Ð·ÑÐ°Ð±Ð¾ÑÐ°Ð½Ñ Ð¿ÑÐµÐ´Ð»Ð¾Ð¶ÐµÐ½Ð¸Ñ Ðº Ð¾Ð¿ÑÐ¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ð¸ ÑÐ¾ÑÑÐ°Ð²Ð° ÑÐ»ÐµÐ¼ÐµÐ½ÑÐ¾Ð² Ð¸Ð½ÑÑÐ°ÑÑÑÑÐºÑÑÑÐ½Ð¾Ð¹ Ð¿Ð¾Ð´ÑÐ¸ÑÑÐµÐ¼Ñ Ð² Ð·Ð°Ð²Ð¸ÑÐ¸Ð¼Ð¾ÑÑÐ¸ Ð¾Ñ ÑÐ¾ÑÑÐ¾ÑÐ½Ð¸Ñ Ð²Ð½ÐµÑÐ½ÐµÐ¹ ÑÑÐµÐ´Ñ. ÐÑÐµÐ´Ð»Ð¾Ð¶ÐµÐ½Ð° Ð¼Ð¾Ð´ÐµÐ»Ñ Ð³Ð¸Ð±ÐºÐ¾Ð³Ð¾ ÑÐµÑÐ½Ð¾Ð»Ð¾Ð³Ð¸ÑÐµÑÐºÐ¾Ð³Ð¾ ÐºÐ¾Ð¼Ð¿Ð»ÐµÐºÑÐ° Ñ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°Ð½Ð¸ÐµÐ¼ ÑÐ¾Ð±Ð¾ÑÐ¸Ð·Ð¸ÑÐ¾Ð²Ð°Ð½Ð½Ð¾Ð¹ ÑÑÐ°Ð½ÑÐ¿Ð¾ÑÑÐ½Ð¾Ð¹ ÑÐ¸ÑÑÐµÐ¼Ñ.
description: The instability of the external environment creates threats to the normal functioning of the technical complex of the enterprise, which in the current conditions must have maximum flexibility and stability. The technical complex was decomposed into two subsystems â technological and infrastructural. Proposals have been developed to optimize the composition of elements of the infrastructure subsystem depending on the state of the external environment. A model of a flexible technological complex using a robotic transport system is proposed.
Supplementary data_PTSD CPT_AJPH_03302020.docx
Creators: name: Jeung-Ki Yoo
Publisher: name: figshare
Year: 2020
Subjects: subject: 110903 Central Nervous System
subject: FOS: Clinical medicine

description: Relationships between peak physiological responses during cold pressor test and post-traumatic stress disorder severity/duration.
Non-adiabatic collapse of a quasi-spherical radiating star
Creators: name: Debnath, Ujjal
name: Nath, Soma
name: Chakraborty, Subenoy
Publisher: name: arXiv
Year: 2003
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: A model is proposed of a collapsing quasi-spherical radiating star with matter content as shear-free isotropic fluid undergoing radial heat-flow with outgoing radiation. To describe the radiation of the system, we have considered both plane symmetric and spherical Vaidya solutions. Physical conditions and thermodynamical relations are studied using local conservation of momentum and surface red-shift. We have found that for existence of radiation on the boundary, pressure on the boundary is not necessary.
description: 8 Latex pages, No figures, Revtex style
Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA
Creators: name: Yerlici, V. Talya
name: Lu, Michael W.
name: Hoge, Carla R.
name: Miller, Richard V.
name: Neme, Rafik
name: Khurana, Jaspreet S.
name: Bracht, John
name: Landweber, Laura F.
Publisher: name: American University
Year: 2023

description: Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular DNA molecules across the genome to gain insight into its processes of programmed genome rearrangement. We recovered thousands of circularly excised Tc1/mariner-type transposable elements and high confidence non-repetitive germline-limited loci. We verified their bona fide circular topology using circular DNA deep-sequencing, 2D gel electrophoresis and inverse polymerase chain reaction. In contrast to the precise circular excision of transposable elements, we report widespread heterogeneity in the circular excision of non-repetitive germline-limited loci. We also demonstrate that circular DNAs are transcribed in Oxytricha, producing rearrangement-specific long non-coding RNAs. The programmed formation of thousands of eccDNA molecules makes Oxytricha a model system for studying nucleic acid topology. It also suggests involvement of eccDNA in programmed genome rearrangement.
Thermalization and dynamical spectral properties in the quark-meson model
Creators: name: Shen, Linda
name: Berges, Jürgen
name: Pawlowski, Jan M.
name: Rothkopf, Alexander
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We investigate the nonequilibrium evolution of the quark-meson model using two-particle irreducible effective action techniques. Our numerical simulations, which include the full dynamics of the order parameter of chiral symmetry, show how the model thermalizes into different regions of its phase diagram. In particular, by studying quark and meson spectral functions, we shed light on the real-time dynamics approaching the crossover transition, revealing e.g. the emergence of light effective fermionic degrees of freedom in the infrared. At late times in the evolution, the fluctuation-dissipation relation emerges naturally among both meson and quark degrees of freedom, confirming that the simulation successfully reaches thermal equilibrium.
High-dimensional Angular Two-Photon Interference and Angular Qudit States
Creators: name: Puentes, Graciana
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Physics (quant-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Using angular position-orbital angular momentum entangled photons, we propose an experiment to generate maximally entangled states of $D$-dimensional quantum systems, the so called qudits, by exploiting correlations of parametric down-converted photons. Angular diffraction masks containing $N$-slits in the arms of each twin photon define a qudit space of dimension $N^2$, spanned by the alternative pathways of the photons. Due to phase-matching conditions, the twin photons will pass only by symmetrically opposite angular slits, generating maximally entangled states between these different paths, which can be detected by high-order two-photon interference fringes via coincidence counts. Numerical results for $N$ angular slits with $N = 2, 4, 5, 6, 10$ are reported, corresponding to qudit Hilbert spaces of dimension $D=N^2=4,16,25, 36,100$, respectively. We discuss relevant experimental parameters for an experimental implementation of the proposed scheme using Spatial Light Modulators (SLMs), and twin-photons produced by Spontaneouos Parametric Down Conversion (SPDC). The entanglement of the qudit state can be quantified in terms of the Concurrence, which can be expressed in terms of the visibility of the interference fringes, or by using Entanglement Witnesses. These results provide an additional means for preparing entangled quantum states in high-dimensions, a fundamental resource for quantum simulation and quantum information protocols.
description: 10 pages, 8 figures
High Thermoelectric Performance and Defect Energetics of Multi-pocketed Full-Heusler Compounds
Creators: name: Park, Junsoo
name: Xia, Yi
name: Ganose, Alex
name: Jain, Anubhav
name: Ozolins, Vidvuds
Publisher: name: arXiv
Year: 2020
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report first-principles density-functional study of electron-phonon interactions and thermoelectric transport properties of full-Heusler compounds Sr$_{2}$BiAu and Sr$_{2}$SbAu. Our results show that ultrahigh intrinsic bulk thermoelectric performance across a wide range of temperatures is physically possible and point to the presence of multiply degenerate and highly dispersive carrier pockets as the key factor for achieving it. Sr$_{2}$BiAu, which features ten energy-aligned low effective mass pockets (six along $Γ-X$ and four at $L$), is predicted to deliver $n$-type $zT=0.4-4.9$ at $T=100-700$~K. Comparison with the previously investigated Ba$_{2}$BiAu compound shows that the additional $L$-pockets in Sr$_{2}$BiAu significantly increase its low-temperature power factor to a maximum value of $12$~mW~m$^{-1}$~K$^{-2}$ near $T=300$~K. However, at high temperatures the power factor of Sr$_{2}$BiAu drops below that of Ba$_{2}$BiAu because the $L$ states are heavier and subject to strong scattering by phonon deformation as opposed to the lighter $Γ-X$ states that are limited by polar-optical scattering. Sr$_{2}$SbAu is predicted to deliver lower $n$-type of $zT=3.4$ at $T=750$~K due to appreciable misalignment between the $L$ and $Γ-X$ carrier pockets, generally heavier scattering, and slightly higher lattice thermal conductivity. Soft acoustic modes, responsible for low lattice thermal conductivity, also increase vibrational entropies and high-temperature stability of the Heusler compounds, suggesting that their experimental synthesis may be feasible. The dominant intrinsic defects are found to be Au vacancies, which drive the Fermi level towards the conduction band and work in favor of $n$-doping.
F.F. Bosworth’s Surprising Connection to 'The Battle Hymn of the Republic': His wife, reportedly, was related to the person who wrote the lyrics for the song
Creators: name: Barnes, Roscoe
Publisher: name: figshare
Year: 2020
Subjects: subject: 210304 Biography
subject: FOS: History and archaeology
subject: 220401 Christian Studies (incl. Biblical Studies and Church History)
subject: FOS: Philosophy, ethics and religion
subject: History
subject: Religious Studies
subject: 220499 Religion and Religious Studies not elsewhere classified

description: This is a blog post about F.F. Bosworth's possible connection to Julia Ward Howe, who wrote the words of “The Battle Hymn of the Republic.” #FFBosworth
Slepton production from gauge boson fusion
Creators: name: Choudhury, Debajyoti
name: Datta, Anindya
name: Huitu, Katri
name: Konar, Partha
name: Moretti, Stefano
name: Mukhopadhyaya, Biswarup
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We emphasise that charged slepton pairs produced via vector-boson fusion along with two high-mass, high-$p_T$ forward/backward jets (in two opposite hemispheres) can have a higher production cross-section for heavy slepton masses than that from conventional Drell-Yan production at a hadronic collider like the LHC. We analyse the signal and leading backgrounds in detail in the minimal supersymmetric standard model with conserved baryon and lepton numbers. Our investigation reveals that the mass reach of the vector-boson fusion channel is certainly an improvement over the scope of the Drell-Yan mode.
description: 17 pages, Latex, version to appear in Physical Review D
Physical models of streaming instabilities in protoplanetary disks
Creators: name: Squire, Jonathan
name: Hopkins, Philip F.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We develop simple, physically motivated models for drag-induced dust-gas streaming instabilities, which are thought to be crucial for clumping grains to form planetesimals in protoplanetary disks. The models explain, based on the physics of gaseous epicyclic motion and dust-gas drag forces, the most important features of the streaming instability and its simple generalisation, the disk settling instability. Some of the key properties explained by our models include the sudden change in the growth rate of the streaming instability when the dust-to-gas-mass ratio surpasses one, the slow growth rate of the streaming instability compared to the settling instability for smaller grains, and the main physical processes underlying the growth of the most unstable modes in different regimes. As well as providing helpful simplified pictures for understanding the operation of an interesting and fundamental astrophysical fluid instability, our models may prove useful for analysing simulations and developing nonlinear theories of planetesimal growth in disks.
description: Accepted for publication in MNRAS
H.R. MacMillan : University of British Columbia
Creators: name: Velarde, Jericho
Publisher: name: The University of British Columbia
Year: 2015

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