cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of A conserved transcriptional fingerprint of multi-neurotransmitter neurons necessary for social behavior
Creators: name: Ncube, Denver
name: Tallafuss, Alexandra
name: Serafin, Jen
name: Bruckner, Joseph
name: Farnsworth, Dylan R.
name: Miller, Adam C.
name: Eisen, Judith S.
name: Washbourne, Philip
Publisher: name: figshare
Year: 2022
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Evolutionary Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Additional file 1: Table 1. LIMTF Gene expression in vTely321 neurons. Key Resource Table 1. Key Resource Table 2. Additional Fig. 1.chatb labelling in vTely321 neurons. Validation of cholinergic identity of vTely321 neurons with chatb ISH probes. White arrows point to selected vTely321 neurons expressing both chatb and GABA. (Scale bars = 20 μm). Additional Fig. 2.gad1b&2 labelling validates GABA immunostaining. gad1b and gad2 transcripts were labelled in vTely321 neurons and validation staining was performed with GABA antibody. White arrows denote GABA and gad1b&2 double-labeling, Yellow arrows label vTely321 neurons which are positive for both GABA and gad1b&2 in the main figure and insert. GABA antibody labelling overlaps extensively with gad1b&2 confirming its specificity. (Scale bars = 20 μm). Additional Fig. 3. GABA antibody labels GABAergic neurons in the larval spinal cord. To test the specificity of the GABA antibody we imaged 24–48 hpf larval spinal cords of the transgenic line Tg (mnx1:GAL4; UAS:GFP) which drives GFP expression (yellow) in cholinergic motor neurons. White arrow denotes KA neurons and Cyan arrow points to DoLA neurons which are known GABAergic neurons in the spinal cord. Yellow arrows denote motor neurons (MN). The absence of overlap between the MN and cyan labelling confirms specificity of the GABA antibody. (Scale bars represent 20 μm).
Finitely constrained groups of maximal Hausdorff dimension
Creators: name: Penland, Andrew
name: Sunic, Zoran
Publisher: name: arXiv
Year: 2014
Subjects: subject: Group Theory (math.GR)
subject: FOS: Mathematics
subject: 20E08, 37B10

description: We prove that if G_P is a finitely constrained group of binary rooted tree automorphisms (a group binary tree subshift of finite type) defined by an essential pattern group P of pattern size d, d>1, and if G_P has maximal Hausdorff dimension (equal to 1-1/2^{d-1}), then G_P is not topologically finitely generated. We describe precisely all essential pattern groups P that yield finitely constrained groups with maximal Haudorff dimension. For a given size d, d>1, there are exactly 2^{d-1} such pattern groups and they are all maximal in the group of automorphisms of the finite rooted regular tree of depth d.
Additional file 1 of Assessment of genotypes, endosymbionts and clinical characteristics of Acanthamoeba recovered from ocular infection
Creators: name: Rayamajhee, Binod
name: Sharma, Savitri
name: Willcox, Mark
name: Henriquez, Fiona L.
name: Rajagopal, Raksheeth Nathan
name: Shrestha, Gauri Shankar
name: Subedi, Dinesh
name: Bagga, Bhupesh
name: Carnt, Nicole
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 1: Table S1: Reference Acanthamoeba strains used in this study for phylogenetic analysis. Table 2: Genotype and species identification of Acanthamoeba isolates recovered from AK patients. Map 1: Map showing the states of the AK patients from different states of India with sample codes and identified genotypes of Acanthamoeba from AK patients. The map was created using ArcGIS (Esri GIS, California, USA). Fig. S1. Monthly distribution of AK cases during study period. Fig. S2. Sequence alignment of Acanthamoeba 18S rDNA DF3 region using ClustalW. Table S3. Overall clinical presentation of the keratitis patients infected with Acanthamoeba spp. Fig S3. Phylogenetic tree inferred from the 18S (ITS1) rDNA sequence of fungi; tree was created using the neighbour-joining approach with the Kimura 2-parameter based on 1000 replicates bootstrap values. Fig. S4. Agarose (1%) gel image of PCR amplicons of 13 Acanthamoeba isolates (18S rRNA), PCR assay was performed using Acanthamoeba genus specific primer pair JDPFw and JDPRv which yielded ~450bp amplicons. Fig. S5: Agarose (1%) gel image of PCR amplicons of 13 Acanthamoeba isolates targeting intracellular bacteria 16S rRNA, primer pair 515Fw and 806Rv (V4, 16S rRNA) was used which yielded ~293bp amplicons.
CMS Trapezoidal GEM Foils Structural Analysis
Creators: name: Raffone, G.
Publisher: name: INFN Open Access Repository
Year: 2010
Subjects: transversely isotropic multilayer, homogenization

description: The demand of large area GEM detectors requires extreme working conditions of the layered foils from structural point of view; larger area need higher biaxial tensile loads to overcome large deflections and the related stresses may exceed the copper yield limit just around the holes; the present work shows that for a trapezoidal CMS GEM foil (W=1040 mm; L1=530 mm; L2=345 mm) the sag due its own weight is about f =28.6 μm (electrostatic loads not included) for a tensioning of S=1 N/mm; the related stresses are lower than the yield only in a biaxial load. Numerical results are from ANSYS Educational v.10 [1] and their level of accuracy is very good when compared to some theoretical and experimental results.
Nuclear Pasta Matter for Different Proton Fractions
Creators: name: Schuetrumpf, B.
name: Iida, K.
name: Maruhn, J. A.
name: Reinhard, P. -G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Nuclear matter under astrophysical conditions is explored with time-dependent and static Hartree-Fock calculations. The focus is in a regime of densities where matter segregates into liquid and gaseous phases unfolding a rich scenario of geometries, often called nuclear pasta shapes (e.g. spaghetti, lasagna). Particularly the appearance of the different phases depending on the proton fraction and the transition to uniform matter are investigated. In this context the neutron background density is of special interest, because it plays a crucial role for the type of pasta shape which is built. The study is performed in two dynamical ranges, one for hot matter and one at temperature zero to investigate the effect of cooling.
description: 7 pages, 5 figures
Exploratory Proteomic Analysis of Transgenic Alzheimer’s Disease Mouse Model Treated with Young Blood Plasma
Creators: name: Petrie, Allison
Publisher: name: George Mason University
Year: 2023
Subjects: neurodegeneration
Alzheimer's Disease
FORESTRY, AGRICULTURAL SCIENCES and LANDSCAPE PLANNING::Plant production::Plant and forest protection
young blood plasma
liquid chromatography - mass spectrometry
LAW/JURISPRUDENCE::Procedural law

description: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by the accumulation of amyloid plaques and tau tangles. Studies suggest that treatment using young blood plasma in transgenic AD mice is associated with enhanced synaptic activity, increases in neuronal proteins, and behavioral improvements. This exploratory proteomic study used liquid chromatography–mass spectrometry (LCMS) to analyze the composition of blood plasma for the identification of proteins that may contribute to synaptic and behavioral changes. Plasma samples were collected from AD-type (rTg4510 h-Tau P301/CaMKII) and wild-type (WT) mice treated with saline or young blood plasma. A bottom-up approach was used to identify proteins by assessing fragmentation output from LC-MS and cross-referencing values with validated mouse protein databases. 4 proteins were significantly differentiated between AD plasma and AD saline groups including up-regulation of MDH2 and down-regulation of KNG1, KCNB1, and KRT15. Pathway analysis of these results suggest disruptions in brain energy metabolism and blood coagulation may induce chronic immune activation that coincide with AD progression. This study also reveals the need for additional research on blood coagulation mechanisms and its involvement in AD as well as a potential biomarker for diagnosis. By targeting these specific proteins and downstream pathway, future studies may gain a better understanding of the molecular mechanisms that underlie AD.
t-structures are normal torsion theories
Creators: name: Fiorenza, Domenico
name: Loregian, Fosco
Publisher: name: arXiv
Year: 2014
Subjects: subject: Category Theory (math.CT)
subject: Algebraic Topology (math.AT)
subject: FOS: Mathematics
subject: 18E30, 18E35, 18A40

description: We characterize $t$-structures in stable $\infty$-categories as suitable quasicategorical factorization systems. More precisely we show that a $t$-structure $\mathfrak{t}$ on a stable $\infty$-category $\mathbf{C}$ is equivalent to a normal torsion theory $\mathbb{F}$ on $\mathbf{C}$, i.e. to a factorization system $\mathbb{F}=(\mathcal{E},\mathcal{M})$ where both classes satisfy the 3-for-2 cancellation property, and a certain compatibility with pullbacks/pushouts.
description: Minor typographical corrections from v1; 25 pages; to appear in "Applied Categorical Structures"
Development and testing of advanced imaging methods for autonomous robot control
Creators: name: Shepherd, Alan
Publisher: name: Loughborough University
Year: 2023
Subjects: classificationCode: 401799
subject: Mechanical engineering not elsewhere classified
classificationCode: 400899
subject: Electrical engineering not elsewhere classified
classificationCode: 401499
subject: Manufacturing engineering not elsewhere classified

description: The availability of low-cost high-performance computing including General Purpose Graphic Processing units (GPGPU) and low-cost Lidar-based depth cameras offer the potential for the development of an inexpensive Lidar-based tracking system for use in autonomous robot control. Such algorithms can also include development of nonparametric 3D computer models of the robot environment. The 3D model would then enable the robot to physically interact with that environment in a way that would not be possible using alternative robot tracking techniques.This work investigates the practical use and performance of a Lidar-based imaging and tracking algorithm operating at 30Hz and used to create a 3D model of the environment in real-time. The thesis performs a systematic investigation of the practical implementation and performance of such a real-time system using two low-cost test rigs. These test rigs were developed and funded as part of the project by the author to investigate the practical aspects of implementing such systems on real hardware platforms using off-the-shelf Embedded computing and low-cost Depth-cameras, Radio-Control (RC) servos and sensors. From this work a lot of practical experience has been gained and some original contributions made in development of the tracking algorithms and specifically within the GPGPU codes. The test rigs also enabled the systematic development and performance evaluation of the tracking algorithms and the 3D model build process.The performance of several documented Iterative Closest Point (ICP)-based tracking algorithms were evaluated for accuracy and performance and a new system developed here, using image features to improve tracking precision, was also tested.The work also shows that Depth-camera based robot tracking is a very complex problem with no easy solutions and many issues relating to tracking performance were found during the development of this project. These are discussed in detail in the concluding sections of the report.
Emerging Resilience and Patterns of Stress: Microscopic Evaluations of LEH Defects Among Individuals from Colonial Mórrope and Eten
Creators: name: Sellers, Maria
Publisher: name: George Mason University
Year: 2023
Subjects: stress
teeth
Peru
colonialism
bioarchaeology

description: Analyses of instances of linear enamel hypoplasia (LEH) using dental enamel microstructures are an underutilized but valuable tool for understanding patterns of stress in the distant and even more recent past. This thesis uses minimally-destructive methods of measuring perikymata, the external manifestations of striae of Retzius, to compare frequencies and timing of LEH at sites on the north coast of Peru. Specifically, this thesis compares individuals from the Early/Middle Colonial (ca. A.D. 1535-1620) Chapel of the Niño Serranito (CNS) and Middle/Late Colonial (ca. A.D. 1620-1750) Church of Santa Maria de Magdalena de Eten (CSMME) at Eten alongside the site of Mórrope, which is contemporaneous with both. Previous studies of Mórrope have found evidence for elevation in the prevalence of nearly every pathological skeletal marker of stress and disease, while the people of Eten have been shown to possess some degree of protection from negative impacts of stress (Klaus and Tam 2009; Thomas, Temple, and Klaus 2018; Klaus and Alvarez-Calderón 2017; Garland, Turner, and Klaus 2016). Results of this work identified more instances of LEH defects than previous macroscopic studies at these sites, particularly those at earlier ages. CNS and Mórrope were found to have the most similar patterns in the distribution of age-at-defect, predicted risk of defect by developmental stage, and generally had more defects at younger ages than CSMME. There was a significant difference in the mean age-at-defect between CNS and CSMME. Taken together, these findings suggest that the systems of buffering against the systemic oppression of colonialism took time to develop and were sometimes unique to specific communities. This thesis provides new data on how mechanisms of resilience emerge in response to large-scale disruption and argues for the continued use of minimally-destructive microscopic methods of examining LEH in future studies.
Quantum Criticality of one-dimensional multicomponent Fermi Gas with Strongly Attractive Interaction
Creators: name: He, Peng
name: Jiang, Yuzhu
name: Guan, Xiwen
name: He, Jinyu
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Quantum criticality of strongly attractive Fermi gas with $SU(3)$ symmetry in one dimension is studied via the thermodynamic Bethe ansatz (TBA) equations.The phase transitions driven by the chemical potential $μ$, effective magnetic field $H_1$, $H_2$ (chemical potential biases) are analyzed at the quantum criticality. The phase diagram and critical fields are analytically determined by the thermodynamic Bethe ansatz equations in zero temperature limit. High accurate equations of state, scaling functions are also obtained analytically for the strong interacting gases. The dynamic exponent $z=2$ and correlation length exponent $ν=1/2$ read off the universal scaling form. It turns out that the quantum criticality of the three-component gases involves a sudden change of density of states of one cluster state, two or three cluster states. In general, this method can be adapted to deal with the quantum criticality of multi-component Fermi gases with $SU(N)$ symmetry.
description: 20 pages, 5 figures, submitted to J.Phys.A, revised version
Enough
Creators: name: Sutton, Asa
Publisher: name: George Mason University
Year: 2023
Subjects: coyote
folklore
storytelling
mythology
relationships
native

description: A collection of Coyote stories, mixed together bits of traditional tales from various Native American cultures and apocryphal original myths, as well as meditations on family, love, addiction, trauma, recovery, responsibility, and growth. The deity/culture-hero/spirit/force of nature, Coyote, is found walking out in the woods, or in the desert, or sitting in the airport waiting for his flight, or teaching a class of second-graders, or trying to get a job as a painter, or working as a grocery delivery-driver. The inherent multiplicity of oral storytelling is explored, along with the sometimes “sideways”-ing of time, situations in which past, present and future conflate, confuse, and commingle. Recurring elements from a variety of traditional tales are centered and examined, inevitably coming again and again: the death of Coyote’s son; the creation of the world; the placement of stars in the sky; Coyote’s loneliness; Coyote’s hunger.
Re-greening Opportunities in Northern Virginia Based on Land Cover Patterns and Social Vulnerability Criteria
Creators: name: Jankowski, Rachel
Publisher: name: George Mason University
Year: 2023
Subjects: re-greening
land suitability
social vulnerability index
Northern Virginia
urban heat island
weighted linear combination

description: This research reviews a number of socio-demographic and environmental criteria in the interest of identifying suitable areas for re-greening in Northern Virginia. The study area encompasses nine county and county equivalents in Northern Virginia whose sprawling development, demographic characteristics, and historical evolution towards an urban fringe landscape places it at potential risk for adverse effects related to the urban heat island (UHI) effect. Various methods and techniques have been explored to help combat the implications of the UHI, which can result in higher-than-average heat indices, place both the natural and built environment at risk, as well as increase health impacts in local populations with known risk factors. One of the most effective and affordable mitigation techniques is the use of vegetation in the form of grasses, trees, and shrubs that help to cool urban surfaces and reduce ambient temperatures. This premise is the basis of the research question, which asks based on a series of input criteria, where are the most vulnerable, and therefore the best suited areas within the study area for re-greening efforts? This study utilizes an adapted multi-criteria analysis technique and GIS to overlay land surface temperature, land cover change, and socio-demographic characteristics to try and identify such areas. These layers from publicly available sources such as USGS, DOE, and NLCD were pre-processed, scaled and reclassified, weighted, and added together to determine suitability scores per pixel area. Overall, the research found a number of case study areas that scored as high candidates for re-greening, and whose spatial range aligned with expected trends related to the UHI and areas that tend to be hotter such as those that have shifted from forested to development over the course of 18 years (2001 to 2019). The research showed that these areas often exist alongside vulnerable communities as well. Pockets of re-greening suitability include areas in southeastern Prince William, Loudoun County, Manassas and Manassas Park, Alexandria, and parts of eastern Fairfax County. Some areas have major focus on economic development thus resulting in urban and suburban sprawl, while more established neighborhoods that have been developed for quite some time but whose infrastructure tends to leave communities more at risk for heat related issues. The results were highly dependent on the unique status of the region, but this research found that there are many hectares worth of suitable areas that would certainly benefit from additional green space in light of climate change and UHI trends.
Cosmological nonlinear structure formation in full general relativity
Creators: name: Torres, Jose M.
name: Alcubierre, Miguel
name: Diez-Tejedor, Alberto
name: Nunez, Dario
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We perform numerical evolutions of cosmological scenarios using a standard general relativistic code in spherical symmetry. We concentrate on two different situations: initial matter distributions that are homogeneous and isotropic, and perturbations to those that respect the spherical symmetry. As matter models we consider the case of a pressureless perfect fluid, i.e. dust, and the case of a real massive scalar field oscillating around the minimum of the potential. Both types of matter have been considered as possible dark matter candidates in the cosmology literature, dust being closely related to the standard cold dark matter paradigm. We confirm that in the linear regime the perturbations associated with these types of matter grow in essentially the same way, the main difference being that in the case of a scalar field the dynamics introduce a cut-off in the power spectrum of the density perturbations at scales comparable with the Compton wavelength of the field. We also follow the evolutions well beyond the linear regime showing that both models are able to form structure. In particular we find that, once in the nonlinear regime, perturbations collapse faster in a universe dominated by dust. This is expected to delay the formation of the first structures in the scalar field dark matter scenario with respect to the standard cold dark matter one.
description: 16 pages, 14 figures. Matches version in print. To appear in Phys. Rev. D
Additional file 1 of The burden of chronic respiratory disease and attributable risk factors in North Africa and Middle East: findings from global burden of disease study (GBD) 2019
Creators: name: Fallahzadeh, Aida
name: Sharifnejad Tehrani, Yeganeh
name: Sheikhy, Ali
name: Ghamari, Seyyed-Hadi
name: Mohammadi, Esmaeil
name: Saeedi Moghaddam, Sahar
name: Esfahani, Zahra
name: Nasserinejad, Maryam
name: Shobeiri, Parnian
name: Rashidi, Mohammad-Mahdi
name: Rezaei, Nazila
name: Heidari-Foroozan, Mahsa
name: Rezaei, Negar
name: Larijani, Bagher
name: Farzadfar, Farshad
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 1: Table S1. List of ICD-10 mapped codes for CRDs.
Numerical Continuation and SPDE Stability for the 2D Cubic-Quintic Allen-Cahn Equation
Creators: name: Kuehn, Christian
Publisher: name: arXiv
Year: 2014
Subjects: subject: Dynamical Systems (math.DS)
subject: Numerical Analysis (math.NA)
subject: Probability (math.PR)
subject: Pattern Formation and Solitons (nlin.PS)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We study the Allen-Cahn equation with a cubic-quintic nonlinear term and a stochastic $Q$-trace-class stochastic forcing in two spatial dimensions. This stochastic partial differential equation (SPDE) is used as a test case to understand, how numerical continuation methods can be carried over to the SPDE setting. First, we compute the deterministic bifurcation diagram for the PDE, i.e. without stochastic forcing. In this case, two locally asymptotically stable steady state solution branches exist upon variation of the linear damping term. Then we consider the Lyapunov operator equation for the locally linearized system around steady states for the SPDE. We discretize the full SPDE using a combination of finite-differences and spectral noise approximation obtaining a finite-dimensional system of stochastic ordinary differential equations (SODEs). The large system of SODEs is used to approximate the Lyapunov operator equation via covariance matrices. The covariance matrices are numerically continued along the two bifurcation branches. We show that we can quantify the stochastic fluctuations along the branches. We also demonstrate scaling laws near branch and fold bifurcation points. Furthermore, we perform computational tests to show that, even with a sub-optimal computational setup, we can quantify the subexponential-timescale fluctuations near the deterministic steady states upon stochastic forcing on a standard desktop computer setup. Hence, the proposed method for numerical continuation of SPDEs has the potential to allow for rapid parametric uncertainty quantification of spatio-temporal stochastic systems.
description: revised version, 30 pages, 11 figures [movie not included due to arXiv size limitations]
Additional file 2 of The burden of chronic respiratory disease and attributable risk factors in North Africa and Middle East: findings from global burden of disease study (GBD) 2019
Creators: name: Fallahzadeh, Aida
name: Sharifnejad Tehrani, Yeganeh
name: Sheikhy, Ali
name: Ghamari, Seyyed-Hadi
name: Mohammadi, Esmaeil
name: Saeedi Moghaddam, Sahar
name: Esfahani, Zahra
name: Nasserinejad, Maryam
name: Shobeiri, Parnian
name: Rashidi, Mohammad-Mahdi
name: Rezaei, Nazila
name: Heidari-Foroozan, Mahsa
name: Rezaei, Negar
name: Larijani, Bagher
name: Farzadfar, Farshad
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 2: Table S2. SDI Categories for North Africa and Middle East’s countries
Sparticle Mass Hierarchies, Simplified Models from SUGRA Unification, and Benchmarks for LHC Run-II SUSY Searches
Creators: name: Francescone, David
name: Akula, Sujeet
name: Altunkaynak, Baris
name: Nath, Pran
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Sparticle mass hierarchies contain significant information regarding the origin and nature of supersymmetry breaking. The hierarchical patterns are severely constrained by electroweak symmetry breaking as well as by the astrophysical and particle physics data. They are further constrained by the Higgs boson mass measurement. The sparticle mass hierarchies can be used to generate simplified models consistent with the high scale models. In this work we consider supergravity models with universal boundary conditions for soft parameters at the unification scale as well as supergravity models with nonuniversalities and delineate the list of sparticle mass hierarchies for the five lightest sparticles. Simplified models can be obtained by a truncation of these, retaining a smaller set of lightest particles. The mass hierarchies and their truncated versions enlarge significantly the list of simplified models currently being used in the literature. Benchmarks for a variety of supergravity unified models appropriate for SUSY searches at future colliders are also presented. The signature analysis of two benchmark models has been carried out and a discussion of the searches needed for their discovery at LHC RUN-II is given. An analysis of the spin independent neutralino-proton cross section exhibiting the Higgs boson mass dependence and the hierarchical patterns is also carried out. It is seen that a knowledge of the spin independent neutralino-proton cross section and the neutralino mass will narrow down the list of the allowed sparticle mass hierarchies. Thus dark matter experiments along with analyses for the LHC Run-II will provide strong clues to the nature of symmetry breaking at the unification scale.
description: To appear in JHEP; 37 pages, 11 tables, 11 figures
CHE and Related Stresses in GEM Foils
Creators: name: Raffone, G.
Publisher: name: INFN Open Access Repository
Year: 2013
Subjects: hygroscopic expansion, multilayer

description: The “Coefficient of Hygroscopic Expansion” (herein 𝛼CHE) of a GEM foil is simply computed assuming that the expansion is only due to the kapton layer that absorbs and retain the water vapor content of the moisture (or in general of any gas mixture) through the holes; that expansion is highly constrained by the copper layers and the resulting compressive (in kapton) and tensile (in copper) stresses can be easily estimated assuming that no other external loads are applied. It will be shown that the 𝛼CHE-GEM in a GEM foil (2x5 + 50 micron) is 0.135 times lower than the 𝛼CHE-Kapton of the single kapton foil; then the effect of the Relative Humidity (herein RH) on the sag of the GEM foils is substantially negligible if the “kapton-free-to-expand” areas are small.
Olutasidenib: First Approval
Creators: name: Kang, Connie
Publisher: name: Adis Journals
Year: 2023
Subjects: Medicine
Cancer

description: Declarations
 Funding The preparation of this review was not supported by any external funding.
 Authorship and Conflict of interest During the peer review process the manufacturer of the agent under review was offered an opportunity to comment on the article. Changes resulting from any comments received were made by the authors on the basis of scientific completeness and accuracy. Connie Kang is a salaried employee of Adis International Ltd/Springer Nature and declares no relevant conflicts of interest. All authors contributed to the review and are responsible for the article content.
 Ethics approval, Consent to participate, Consent to publish, Availability of data and material, Code availability Not applicable.

 Additional information about this Adis Drug Review can be found here.
 Abstract Olutasidenib (REZLIDHIATM), an isocitrate dehydrogenase-1 (IDH1) inhibitor, is being developed by Rigel Pharmaceuticals for the treatment of relapsed or refractory (R/R) acute myeloid leukaemia (AML). Olutasidenib was recently approved in the USA for the treatment of adults with R/R AML with a susceptible IDH1 mutation as detected by a US Food and Drug Administration-approved test. This article summarizes the milestones in the development of olutasidenib leading to this first approval for R/R AML.
 © Springer Nature Switzerland AG 2023
Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
Creators: name: Faircloth, Brant C.
name: Branstetter, Michael G.
name: White, Noor D.
name: Brady, Seán G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Genomics (q-bio.GN)
subject: Populations and Evolution (q-bio.PE)
subject: FOS: Biological sciences

description: Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci collected across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g., exons). However, molecular techniques requiring RNA as a template are limited to using very high quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n$=$1510) of ultraconserved elements (UCE) shared among the insect order Hymenoptera. We use in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled Hymenoptera, and we design a set of baits for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We use our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we use these UCE loci to reconstruct phylogenetic relationships spanning very old ($\geq$220 MYA) to very young ($\leq$1 MYA) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support.
JULIE Lab GNormPlus Resources
Creators: name: Faessler, Erik
Publisher: name: Zenodo
Year: 2022
Subjects: gene recognition, gene normalization

description: The gene recognition and normalization software GNormPlus[1] is published at https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/gnormplus/ and includes resources like a gene dictionary, gene ID scoring files and more, required to run the GNormPlus program. Updates to the code or resources have not been indicated on the GNormPlus Web site since its release and a changelog is not available. Previous versions of code and resources are not publicly accessible. This hinders reproducibility or evaluation results achieved with specific versions of GNormPlus. This repository includes the resources - but not the code - of the GNormPlus release in September 2022. From this release, the JULIE Lab version of GNormPlus is derived. The JULIE Lab GNormPlus code can be found at https://github.com/JULIELab/gnormplus. The JULIE Lab code and the resources in this repository are used to create tools and applications. In the respective papers, evaluation numbers of experiments are reported that require these resource for reproduction. The resources herein are not product of work in the JULIE Lab but from the authors of GNormPlus. [1] Wei, C. H., Kao, H. Y., & Lu, Z. (2015). GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains. BioMed Research International, 2015. https://doi.org/10.1155/2015/918710
Additional file 3 of The burden of chronic respiratory disease and attributable risk factors in North Africa and Middle East: findings from global burden of disease study (GBD) 2019
Creators: name: Fallahzadeh, Aida
name: Sharifnejad Tehrani, Yeganeh
name: Sheikhy, Ali
name: Ghamari, Seyyed-Hadi
name: Mohammadi, Esmaeil
name: Saeedi Moghaddam, Sahar
name: Esfahani, Zahra
name: Nasserinejad, Maryam
name: Shobeiri, Parnian
name: Rashidi, Mohammad-Mahdi
name: Rezaei, Nazila
name: Heidari-Foroozan, Mahsa
name: Rezaei, Negar
name: Larijani, Bagher
name: Farzadfar, Farshad
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 3: Table S3. Age-standardized rate of incidence, prevalence, deaths, DALYs, YLLs, and YLDs due to CRDs in North Africa and Middle East countries between 1990 and 2019, with percentage change by sex.
Decays $D^+_{(s)}\to π(K)^{+}\ell^+\ell^-$ and $D^0\to \ell^+\ell^-$ in the MSSM with and without R-parity
Creators: name: Wang, Ru-Min
name: Sheng, Jin-Huan
name: Zhu, Jie
name: Fan, Ying-Ying
name: Yang, Ya-Dong
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study the rare decays $D^+\to π^{+}\ell^+\ell^-$, $D^+_s\to K^{+}\ell^+\ell^-$ and $D^0\to \ell^+\ell^-(\ell=e,μ)$ in the minimal supersymmetic standard model with and without R-parity. Using the strong constraints on relevant supersymmetric parameters from $D^0-\bar{D}^0$ mixing and $K^+\to π^+ν\barν$ decay, we examine constrained supersymmetry contributions to relevant branching ratios, direct CP violations and ratios of $D^+_{(s)}\to π(K)^{+}μ^+μ^-$ and $D^+_{(s)}\to π(K)^{+}e^+e^-$ decay rates. We find that both R-parity conserving LR as well as RL mass insertions and R-parity violating squark exchange couplings have huge effects on the direct CP violations of $D^+_{(s)}\to π(K)^{+}\ell^+\ell^-$, moreover, the constrained LR and RL mass insertions still have obvious effects on the ratios of $D^+_{(s)}\to π(K)^{+}μ^+μ^-$ and $D^+_{(s)}\to π(K)^{+}e^+e^-$ decay rates. The direct CP asymmetries and the ratios of $D^+_{(s)}\to π(K)^{+}μ^+μ^-$ and $D^+_{(s)}\to π(K)^{+}e^+e^-$ decay rates are very sensitive to both moduli and phases of relevant supersymmetric parameters. In addition, the differential direct CP asymmetries of $D^+_{(s)}\to π(K)^{+}\ell^+\ell^-$ are studied in detail.
description: 18 pages, 9 figures
Свързани партньорства: Наръчник
Creators: name: Aldis, Helen
name: Allamand, Ana
name: Osborn, Simone
Publisher: name: Zenodo
Year: 2022

description: LIAISON (По-добри иновации в селските райони: свързване в мрежи на субекти, инструменти и поли­тики) е проект с множество участници, финансиран в рамките на ЕПИ-АГРИ, инициатива, стартирана от Европейската комисия през 2012 г. с цел насърчава­не на конкурентоспособно и устойчиво земеделие и горско стопанство, което „постига повече и по-добри резултати с по-малко ресурси“. Интерактивният иновационен подход обединява разнообразна гама от публични и частни участници в иновациите (земеделски стопани, консултанти, из­следователи, предприятия, НПО и др.) с допълващи се знания и опит за оценяване, събиране, съвместно създаване и разпространение на практически реше­ния за реалните нужди на фермери и лесовъди. Тези нужди се обуславят и произтичат от реалните въз­можности и ежедневните предизвикателства, пред които са изправени земеделските стопани, горските и селските предприятия. Иновациите, генерирани
The tropical shadow-vertex algorithm solves mean payoff games in polynomial time on average
Creators: name: Allamigeon, Xavier
name: Benchimol, Pascal
name: Gaubert, Stéphane
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computer Science and Game Theory (cs.GT)
subject: Data Structures and Algorithms (cs.DS)
subject: Optimization and Control (math.OC)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: We introduce an algorithm which solves mean payoff games in polynomial time on average, assuming the distribution of the games satisfies a flip invariance property on the set of actions associated with every state. The algorithm is a tropical analogue of the shadow-vertex simplex algorithm, which solves mean payoff games via linear feasibility problems over the tropical semiring $(\mathbb{R} \cup \{-\infty\}, \max, +)$. The key ingredient in our approach is that the shadow-vertex pivoting rule can be transferred to tropical polyhedra, and that its computation reduces to optimal assignment problems through Plücker relations.
description: 17 pages, 7 figures, appears in 41st International Colloquium, ICALP 2014, Copenhagen, Denmark, July 8-11, 2014, Proceedings, Part I
Polarized Fermi gases at finite temperature in the BCS-BEC crossover
Creators: name: Pantel, Pierre-Alexandre
name: Davesne, Dany
name: Urban, Michael
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We consider a polarized Fermi gas in the BCS-BEC crossover region above the critical temperature within a T matrix formalism. By treating the mean-field like shift of the quasiparticle energies in a self-consistent manner, we avoid the known pathological behavior of the standard Nozieres-Schmitt-Rink approach in the polarized case, i.e., the polarization has the right sign and the spin polarizability is positive. The momentum distributions of the correlated system are computed and it is shown that, in the zero-temperature limit, they satisfy the Luttinger theorem. Results for the phase diagram, the spin susceptibility, and the compressibility are discussed.
description: 9 pages; v2: references and comparison with more recent experimental data added; v3: reference added and minor corrections
Expression, Purification, and Characterization of the SIAA M79A Protein
Creators: name: Basden, Brian
Publisher: name: Georgia State University
Year: 2007

description:
Some pathogenic bacteria derive significant amounts of iron heme from their hosts. In this study we investigated SiaA, a heme binding protein from Streptococcus pyogenes. The wildtype methionine79 putative axial ligand was mutated to alanine. SiaA M79A was expressed in E. coli in three production runs, lysed by sonication or French press, and purified by fast protein liquid chromatography (FPLC). Nickel affinity FPLC was found to give much purer SiaA when 30 mM imidazole was added to the binding buffer. The protocol using extensive sonication resulted in SiaA weighing 30464 Da. The protocol using French press resulted in SiaA weighting 33358 Da. Despite the difference in masses, the two forms of SiaA interacted with heme similarly.
Additional file 4 of The burden of chronic respiratory disease and attributable risk factors in North Africa and Middle East: findings from global burden of disease study (GBD) 2019
Creators: name: Fallahzadeh, Aida
name: Sharifnejad Tehrani, Yeganeh
name: Sheikhy, Ali
name: Ghamari, Seyyed-Hadi
name: Mohammadi, Esmaeil
name: Saeedi Moghaddam, Sahar
name: Esfahani, Zahra
name: Nasserinejad, Maryam
name: Shobeiri, Parnian
name: Rashidi, Mohammad-Mahdi
name: Rezaei, Nazila
name: Heidari-Foroozan, Mahsa
name: Rezaei, Negar
name: Larijani, Bagher
name: Farzadfar, Farshad
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 4: Table S4. Decomposition analysis of CRDs new cases between 1990 and 2019 by sex, in North Africa and Middle East region and its countries.
SiaA: A Heme Protein
Creators: name: Libkind, Marianna
Publisher: name: Georgia State University
Year: 2007

description:
The protein SiaA (Streptococcal iron acquisition) is involved in heme uptake in the bacterium Streptococcus pyogenes. It is difficult to obtain this protein in its fully holo form (completely loaded with heme). To increase the concentration of heme in the growing cell, we added -aminolevulinic acid (ALA) and ferrous sulfate (FeSO4), precursors of heme, to the growth media. Neither increasing the concentration of heme in vivo, nor growth at lower temperature for longer times, increased the production of holoprotein. The classical method of measuring the concentration of heme in a newly discovered heme protein is cumbersome. We have developed an improved method, which gives a solution that is more stable and has a cleaner spectrum. With further development, this new technique may replace the classical assay. Background information on S. pyogenes, SiaA, ABC transporters, heme biosynthesis, and the pyridine hemochrome assay are described.
Sorption of 137Cs onto Weathered Micaceous Minerals from Georgia Kaolin Deposits
Creators: name: Kwong-Moses, Dominique
Publisher: name: Georgia State University
Year: 2017

description:
This study examined the propensity for a weathered muscovite-rich test material to sorb 137Cs in a dilute NaCl solution (1 mmol/L, pH 5) across a range of added stable Cs and Rb concentrations for 130 days at room temperature. This muscovite test material, slaked from processed kaolin ore, was composed of 76% muscovite, 21% kaolinite and 3% quartz. Sorption experiments in the absence of stable Cs and Rb yielded increasing Kd values (1.49 x 103 mL/g to 1.18 x 104 mL/g) over 130 days for 137Cs sorbed onto muscovite. Sorption experiments with stable Cs and Rb displayed linear decreases in Kd values as functions of the concentrations of stable Cs and Rb. These findings are consistent with a Freundlich isotherm. After 130 days, the addition of NaCl (1 mM and 10 mM) caused the desorption of only a small fraction (0.011% - 1.476%) of the sorbed 137Cs from this muscovite test material. The Kd values calculated after the desorption of 137Cs were still generally large 6.93 x 103 mL/g to 1.40 x 106 mL/g. 137Cs was interpreted to be fixed at high affinity sites within the muscovite. This test material showed promise for being a sorbent for radiocesium contaminated waste solutions.
Landau-Zener transitions in a two-level system coupled to a finite-temperature harmonic oscillator
Creators: name: Ashhab, S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: We analyze the dynamics and final populations in a Landau-Zener problem for a two level system (or qubit) when this system interacts with one harmonic oscillator mode that is initially set to a finite-temperature thermal equilibrium state. The harmonic oscillator could represent an external mode that is strongly coupled to the qubit, e.g. an ionic oscillation mode in a molecule, or it could represent a prototypical uncontrolled environment. We analyze the qubit's occupation probabilities at the final time in a number of different regimes, varying the qubit and oscillator frequencies, their coupling strength and the temperature. In particular we find some surprising non-monotonic dependence on the coupling strength and temperature.
description: 7 pages (two-column), 6 figures
Full three-body problem in effective-field-theory models of gravity
Creators: name: Battista, Emmanuele
name: Esposito, Giampiero
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Recent work in the literature has studied the restricted three-body problem within the framework of effective-field-theory models of gravity. This paper extends such a program by considering the full three-body problem, when the Newtonian potential is replaced by a more general central potential which depends on the mutual separations of the three bodies. The general form of the equations of motion is written down, and they are studied when the interaction potential reduces to the quantum-corrected central potential considered recently in the literature. A recursive algorithm is found for solving the associated variational equations, which describe small departures from given periodic solutions of the equations of motion. Our scheme involves repeated application of a 2 x 2 matrix of first-order linear differential operators.
description: 23 pages, 1 figure, Revtex4. In the final version, Section VII is much longer, the misprints have been amended, and new References have been included
Characterization of the Proline-78-Glycine Mutant of PA1024 from Pseudomonas aeruginosa
Creators: name: Dratch, Benjamin
Publisher: name: Georgia State University
Year: 2019

description:
NAD(P)H:quinone oxidoreductases (NQOs) are flavin-dependent enzymes that catalyze the two-electron reduction of quinones and the oxidation of NAD(P)H. NQOs play a role in cellular detoxification by preventing the formation of radical quinones thus avoiding the generation of reactive oxygen species. The NQO from Pseudomonas aeruginosa PAO1 (PA1024) is proposed to serve a dual function in the cell by detoxifying quinones and balancing the [NAD+]/[NADH] ratio. Crystal structures of wild-type PA1024 were previously solved in free form and in complex with NAD+ (PDB: 2GJN & 6E2A). Comparison of the ligand-free and ligand-bound structures of the enzyme reveals a loop (residues 75-86) in two conformations, suggesting the mobile loop may play a role in NADH binding and selectivity. P78 is located on the mobile loop and is hypothesized to provide internal rigidity to the mobile loop to help carry out its functions. In the present study, site-directed mutagenesis was utilized to replace P78 with glycine and increase mobile loop flexibility. The mutant (NQO-P78G) was expressed and purified as previously described for wild-type PA1024. Apparent steady-state kinetics of NQO-P78G, at varying concentrations of benzoquinone and a fixed [NADH] of 0.1 mM, showed a 20-fold reduction in the kcat value with respect to the wild-type enzyme, i.e., 1.3 s-1 vs. 27 s-1. When the concentration of NADH was varied with a fixed [benzoquinone] at 21 ?M, NQO-P78G could not be saturated and only a kcat/KNADH value of 11,000  700 M-1 s-1 could be determined. On the basis of kinetic results presented here, we propose that P78 does not play a role in substrate specificity but rather it is important in assisting with catalysis in PA1024.