cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Comparative Anatomy of Chromosomal Domains with Imprinted and Non-Imprinted Allele-Specific DNA Methylation
Creators: name: Paliwal, Anupam
name: Temkin, Alexis M.
name: Kerkel, Kristi
name: Yale, Alexander
name: Yotova, Iveta
name: Drost, Natalia
name: Lax, Simon
name: Nhan-Chang, Chia-Ling
name: Powell, Charles
name: Borczuk, Alain
name: Aviv, Abraham
name: Wapner, Ronald J.
name: Chen, Xiaowei
name: Nagy, Peter L.
name: Schork, Nicholas
name: Do, Catherine
name: Torkamani, Ali
name: Tycko, Benjamin
Publisher: name: Columbia University
Year: 2013
Subjects: subject: Anatomy, Comparative
subject: Genomic imprinting
subject: DNA--Methylation
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular biology

description: Allele-specific DNA methylation (ASM) is well studied in imprinted domains, but this type of epigenetic asymmetry is actually found more commonly at non-imprinted loci, where the ASM is dictated not by parent-of-origin but instead by the local haplotype. We identified loci with strong ASM in human tissues from methylation-sensitive SNP array data. Two index regions (bisulfite PCR amplicons), one between the C3orf27 and RPN1 genes in chromosome band 3q21 and the other near the VTRNA2-1 vault RNA in band 5q31, proved to be new examples of imprinted DMRs (maternal alleles methylated) while a third, between STEAP3 and C2orf76 in chromosome band 2q14, showed non-imprinted haplotype-dependent ASM. Using long-read bisulfite sequencing (bis-seq) in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs), each less than 2kb. The ASM in the C3orf27-RPN1 intergenic region was placenta-specific and associated with allele-specific expression of a long non-coding RNA. Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR. Methylation mapping in two additional genes with non-imprinted haplotype-dependent ASM, ELK3 and CYP2A7, showed that the CYP2A7 DMR also overlaps a CTCF site. Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM. Arguing for biological importance, our analysis of published whole genome bis-seq data from hES cells revealed multiple genome-wide association study (GWAS) peaks near CTCF binding sites with ASM.
Theoretical estimation of metabolic network robustness against multiple reaction knockouts using branching process approximation
Creators: name: Takemoto, Kazuhiro
name: Tamura, Takeyuki
name: Akutsu, Tatsuya
Publisher: name: arXiv
Year: 2013
Subjects: subject: Molecular Networks (q-bio.MN)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: In our previous study, we showed that the branching process approximation is useful for estimating metabolic robustness, measured using the impact degree. By applying a theory of random family forests, we here extend the branching process approximation to consider the knockout of {\it multiple} reactions, inspired by the importance of multiple knockouts reported by recent computational and experimental studies. In addition, we propose a better definition of the number of offspring of each reaction node, allowing for an improved estimation of the impact degree distribution obtained as a result of a single knockout. Importantly, our proposed approach is also applicable to multiple knockouts. The comparisons between theoretical predictions and numerical results using real-world metabolic networks demonstrate the validity of the modeling based on random family forests for estimating the impact degree distributions resulting from the knockout of multiple reactions.
description: 20 pages, 6 figures, 2 tables
An expansion formula with higher-order derivatives for fractional operators of variable order
Creators: name: Almeida, Ricardo
name: Torres, Delfim F. M.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: Numerical Analysis (math.NA)
subject: Optimization and Control (math.OC)
subject: FOS: Mathematics
subject: 26A33, 33F05, 34A08, 49M99

description: We obtain approximation formulas for fractional integrals and derivatives of Riemann-Liouville and Marchaud types with a variable fractional order. The approximations involve integer-order derivatives only. An estimation for the error is given. The efficiency of the approximation method is illustrated with examples. As applications, we show how the obtained results are useful to solve differential equations and problems of the calculus of variations that depend on fractional derivatives of Marchaud type.
description: This is a preprint of a paper whose final and definite form will be published in The Scientific World Journal (http://www.hindawi.com/journals/tswj). Submitted 27-Aug-2013; accepted 19-Sept-2013
Interleukin 15 Primes Natural Killer Cells to Kill via NKG2D and cPLA2 and This Pathway Is Active in Psoriatic Arthritis
Creators: name: Tang, Fangming
name: Sally, Benjamin Andrew
name: Ciszewski, Cezary
name: Abadie, Valerie
name: Curran, Shane A.
name: Groh, Veronika
name: FitzGerald, Oliver
name: Winchester, Robert J.
name: Jabri, Bana
Publisher: name: Columbia University
Year: 2013
Subjects: subject: Killer cells
subject: Interleukins
subject: Psoriatic arthritis
subject: Medicine
subject: Immunology
subject: FOS: Clinical medicine

description: NK cells are large granular lymphocytes that form a critical component of the innate immune system, whose functions include the killing of cells expressing stress-induced molecules. It is increasingly accepted that despite being considered prototypical effector cells, NK cells require signals to reach their full cytotoxic potential. We previously showed that IL-15 is capable of arming CD8 effector T cells to kill independently of their TCR via NKG2D in a cPLA2-dependent process. As NK cells also express NKG2D, we wanted to investigate whether this pathway functioned in an analogous manner and if resting NK cells could be primed to the effector phase by IL-15. Furthermore, to establish relevance to human disease we studied a possible role for this pathway in the pathogenesis of psoriatic arthritis, since there are aspects of this disease that suggest a potential effector role for the innate immune system. We found that PsA patients had upregulated IL-15 and MIC in their affected synovial tissues, and that this unique inflammatory environment enabled NK cell activation and killing via NKG2D and cPLA2. Moreover, we were able to reproduce the phenotype of joint NK cells from blood NK cells by incubating them with IL-15. Altogether, these findings suggest a destructive role for NK cells when activated by environmental stress signals during the pathogenesis of PsA and demonstrate that IL-15 is capable of priming resting NK cells in tissues to the effector phase.
Ctenomys minutus Nehring 1887
Creators: name: Woods, Charles A.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Ctenomyidae
Ctenomys
Ctenomys minutus

description: Ctenomys minutus Nehring, 1887. Sitzb. Ges. Naturf. Fr. Berlin, p. 47. TYPE LOCALITY: Brazil, Rio Grande do Sul, Campos E of Mondo Novo. DISTRIBUTION: Rio Grande do Sul and Mato Grosso (SW Brazil), Uruguay, NW Argentina. SYNONYMS: bicolor, rionegrensis. COMMENTS: Reviewed by Langguth and Abella (1970). Altuna and Lessa (1985) regarded rionegrensis as a full species. The chromosome no. is 2n=46-55.
description: Published as part of Charles A. Woods, 1993, Order Rodentia - Suborder Hystricognathi, pp. 771-806 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on pages 785-786, DOI: 10.5281/zenodo.7353083
description: {"references": ["Langguth, A., and A. Abella. 1970. Las especies uruguayas del genero Ctenomys. Communiciones Zoologicos Museo Historia Natural de Montevideo, 10 (129): 1 - 20.", "Altuna, C. A., and E. P. Lessa. 1985. Penial morphology in Uruguayan species of Ctenomys (Rodentia: Octodontidae). Journal of Mammalogy, 66: 483 - 488."]}
Deletion of IL-4 Receptor Alpha on Dendritic Cells Renders BALB/c Mice Hypersusceptible to Leishmania major Infection
Creators: name: Hurdayal, Ramona
name: Nieuwenhuizen, Natalie E.
name: Revaz-Breton, Mélanie
name: Smith, Liezel
name: Hoving, Jennifer C.
name: Parihar, Suraj P.
name: Reizis, Boris
name: Brombacher, Frank
Publisher: name: Columbia University
Year: 2013
Subjects: Cell receptors
Immune response--Molecular aspects
Leishmaniasis--Immunological aspects
Cytology

description: In BALB/c mice, susceptibility to infection with the intracellular parasite Leishmania major is driven largely by the development of T helper 2 (Th2) responses and the production of interleukin (IL)-4 and IL-13, which share a common receptor subunit, the IL-4 receptor alpha chain (IL-4Rα). While IL-4 is the main inducer of Th2 responses, paradoxically, it has been shown that exogenously administered IL-4 can promote dendritic cell (DC) IL-12 production and enhance Th1 development if given early during infection. To further investigate the relevance of biological quantities of IL-4 acting on DCs during in vivo infection, DC specific IL-4Rα deficient (CD11ccreIL-4Rα-/lox) BALB/c mice were generated by gene targeting and site-specific recombination using the cre/loxP system under control of the cd11c locus. DNA, protein, and functional characterization showed abrogated IL-4Rα expression on dendritic cells and alveolar macrophages in CD11ccreIL-4Rα-/lox mice. Following infection with L. major, CD11ccreIL-4Rα-/lox mice became hypersusceptible to disease, presenting earlier and increased footpad swelling, necrosis and parasite burdens, upregulated Th2 cytokine responses and increased type 2 antibody production as well as impaired classical activation of macrophages. Hypersusceptibility in CD11ccreIL-4Rα-/lox mice was accompanied by a striking increase in parasite burdens in peripheral organs such as the spleen, liver, and even the brain. DCs showed increased parasite loads in CD11ccreIL-4Rα-/lox mice and reduced iNOS production. IL-4Rα-deficient DCs produced reduced IL-12 but increased IL-10 due to impaired DC instruction, with increased mRNA expression of IL-23p19 and activin A, cytokines previously implicated in promoting Th2 responses. Together, these data demonstrate that abrogation of IL-4Rα signaling on DCs is severely detrimental to the host, leading to rapid disease progression, and increased survival of parasites in infected DCs due to reduced killing effector functions.
New Specimens of the Rare Taeniodont Wortmania (Mammalia: Eutheria) from the San Juan Basin of New Mexico and Comments on the Phylogeny and Functional Morphology of “Archaic” Mammals
Creators: name: Williamson, Thomas E.
name: Brusatte, Stephen L.
Publisher: name: Columbia University
Year: 2013
Subjects: Taeniodonta
Phylogeny
Cladistic analysis
Morphology (Animals)
Morphology
Environmental sciences
Paleontology

description: Background:

Taeniodonta is a clade of Late Cretaceous – Paleogene mammals remarkable for their relatively extreme cranial, dental, and postcranial adaptations and notable for being among the first mammals to achieve relatively large size following the Cretaceous-Paleogene mass extinction. Previous workers have hypothesized that taeniodonts can be divided into two clades: Conoryctidae, a group of small-bodied taeniodonts with supposedly “generalized” postcranial skeletons, and Stylinodontidae, a group of large-bodied, robust animals with massive forelimbs and claws adapted for scratch-digging. However, many taeniodont taxa are poorly known and few are represented by postcranial material, leaving many details about their anatomy, biology, and evolution ambiguous.

Methodology/Principal Findings:

In this paper, we describe three new specimens of the rare taxon Wortmania otariidens from the early Paleocene (Puercan) of New Mexico. Among these specimens is one that includes remarkably complete cranial and dental material, including associated upper and lower teeth, and another that consists of partial forelimbs. These specimens allow for an updated anatomical description of this unusual taxon, supply new data for phylogenetic analyses, and enable a more constrained discussion of taeniodont biology and functional morphology.

Conclusions/Significance:

The new specimen of Wortmania that includes associated upper and lower teeth indicates that previous interpretations of the upper dentition of this taxon were not accurate and the taxon Robertschochia sullivani is a junior synonym of W. otariidens. New specimens that include partial forelimbs indicate that Wortmania is very similar to later, large-bodied taeniodonts, with marked and distinctive adaptations for scratch-digging. Comparisons with other taeniodont taxa that include postcranial material suggest that all taeniodonts may have had scratch-digging adaptations. A phylogenetic analysis shows that Schowalteria and Onychodectes are basal taeniodonts, Stylinodontidae (including Wortmania) is monophyletic, and a monophyletic Conoryctidae (but not including Onychodectes) is only recovered when certain characters are ordered.
Scaling of Magneto-Quantum-Radiative Hydrodynamic Equations: From Laser-produced Plasmas to Astrophysics
Creators: name: Cross, Joseph E.
name: Reville, Brian
name: Gregori, Gianluca
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We introduce here the equations of magneto-quantum-radiative hydrodynamics. By rewriting them in a dimensionless form, we obtain a set of parameters that describe scale-dependent ratios of all the characteristic hydrodynamic quantities. We discuss how these dimensionless parameters relate to the scaling between astrophysical observations and laboratory experiments.
description: 12 pages
The Motion of a Pair of Charged Particles
Creators: name: Franklin, J.
name: LaMont, C.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Classical Physics (physics.class-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We re-visit the problem of two (oppositely) charged particles interacting electromagnetically in one dimension with retarded potentials and no radiation reaction. The specific quantitative result of interest is the time it takes for the particles to fall in towards one another. Starting with the non-relativistic form, we answer this question while adding layers of complexity until we arrive at the full relativistic delay differential equation that governs this problem. That case can be solved using the Synge method, which we describe and discuss.
description: to appear in Brazilian Journal of Physics vol. 43
The nature of the giant diffuse non-thermal source in the A3411-A3412 complex
Creators: name: Giovannini, G.
name: Vacca, V.
name: Girardi, M.
name: Feretti, L.
name: Govoni, F.
name: Murgia, M.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: VLA deep radio images at 1.4 GHz in total intensity and polarization reveal a diffuse non-thermal source in the interacting clusters A3411 - A3412. Moreover a small-size low power radio halo at the center of the merging cluster A3411 is found. We present here new optical and X-ray data and discuss the nature and properties of the diffuse non-thermal source. We suggest that the giant diffuse radio source is related to the presence of a large scale filamentary structure and to multiple mergers in the A3411-A3412 complex.
description: 7 pages, 6 figures, accepted for publication in MNRAS
Polar magnetic fields in black-hole space-times
Creators: name: Kerner, Richard
name: Koekoek, Gideon
name: Schuring, Julia
name: van Holten, Jan-Willem
Publisher: name: arXiv
Year: 2024
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: To model magnetic fields of compact objects we solve the Maxwell equations in the background of the exterior static Schwarzschild and slowly rotating Kerr space-times. We impose the boundary condition that the electromagnetic fields are to vanish at infinity. A full set of solutions is obtained, describing axially symmetric magnetic fields, supplemented by axial electric fields in the case of non-vanishing rotation of the gravitational background. We study the motion of charged test particles in these combined gravitational and electromagnetic fields, in particular considering the conditions for circular equatorial orbits. Such orbits always exist in odd-multipole magnetic fields, and they can exist for particular radii in a combination of two or more even-multipole magnetic fields. Combinations of several odd-multipole fields can give rise to radial variation in the field orientation and the direction of motion of charged particles. Deviations from circularity are described using a perturbative approach. This also allows to study the stability of the parent circular orbits.
Ctenomys nattereri Wagner 1848
Creators: name: Woods, Charles A.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Ctenomyidae
Ctenomys
Ctenomys nattereri

description: Ctenomys nattereri Wagner, 1848. Arch. Naturgesch., 1:72. TYPE LOCALITY: Brazil, Mato Grosso, Caicara. DISTRIBUTION: Mato Grosso. SYNONYMS: brasiliensis Pelzen, 1883; rondoni.
description: Published as part of Charles A. Woods, 1993, Order Rodentia - Suborder Hystricognathi, pp. 771-806 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 786, DOI: 10.5281/zenodo.7353083
Multi-Wavelength Observations of the Spatio-Temporal Evolution of Solar Flares with AIA/SDO: I. Universal Scaling Laws of Space and Time Parameters
Creators: name: Aschwanden, Markus J.
name: Zhang, Jie
name: Liu, Kai
Publisher: name: arXiv
Year: 2013
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We extend a previous statistical solar flare study of 155 GOES M- and X-class flares observed with AIA/SDO (Aschwanden 2012) to all 7 coronal wavelengths (94, 131, 171, 193, 211, 304, 335 \ang) to test the wavelength-dependence of scaling laws and statistical distributions. Except for the 171 and 193 \ang\ wavelengths, which are affected by EUV dimming caused by coronal mass ejections (CMEs), we find near-identical size distributions of geometric (lengths $L$, flare areas $A$, volumes $V$, fractal dimension $D_2$), temporal (flare durations $T$), and spatio-temporal parameters (diffusion coefficient $κ$, spreading exponent $β$, and maximum expansion velocities $v_{max}$) in different wavelengths, which are consistent with the universal predictions of the fractal-diffusive avalanche model of a slowly-driven self-organized criticality (FD-SOC) system, i.e., $N(L) \propto L^{-3}$, $N(A) \propto A^{-2}$, $N(V) \propto V^{-5/3}$, $N(T) \propto T^{-2}$, $D_2=3/2$, for a Euclidean dimension $d=3$. Empirically we find also a new strong correlation $κ\propto L^{0.94\pm0.01}$ and the 3-parameter scaling law $L \propto κ T^{0.1}$, which is more consistent with the logistic-growth model than with classical diffusion. The findings suggest long-range correlation lengths in the FD-SOC system that operate in the vicinity of a critical state, which could be used for predictions of individual extreme events. We find also that eruptive flares (with accompanying CMEs), have larger volumes $V$, longer flare durations $T$, higher EUV and soft X-ray fluxes, and somewhat larger diffusion coefficients $κ$ than confined flares (without CMEs).
description: (2013) The Astrophysical Journal, Vol. 774 (in press)
Bacterial Pathogens Activate a Common Inflammatory Pathway through IFNλ Regulation of PDCD4
Creators: name: Cohen, Taylor S.
name: Prince, Alice S.
Publisher: name: Columbia University
Year: 2013
Subjects: Bacterial diseases--Pathogenesis
Chemokines
Interferon--Physiological effect
Pathology

description: The type III interferon (IFNλ) receptor IL-28R is abundantly expressed in the respiratory tract and has been shown essential for host defense against some viral pathogens, however no data are available concerning its role in the innate immune response to bacterial pathogens. Staphylococcus aureus and Pseudomonas aeruginosa induced significant production of IFNλ in the lung, and clearance of these bacteria from the lung was significantly increased in IL-28R null mice compared to controls. Improved bacterial clearance correlated with reduced lung pathology and a reduced ratio of pro- vs anti-inflammatory cytokines in the airway. In human epithelial cells IFNλ inhibited miR-21 via STAT3 resulting in upregulation of PDCD4, a protein known to promote inflammatory signaling. In vivo 18 hours following infection with either pathogen, miR-21 was significantly reduced and PDCD4 increased in the lungs of wild type compared to IL-28R null mice. Infection of PDCD4 null mice with USA300 resulted in improved clearance, reduced pathology, and reduced inflammatory cytokine production. These data suggest that during bacterial pneumonia IFNλ promotes inflammation by inhibiting miR-21 regulation of PDCD4.
Ctenomys occultus Thomas 1920
Creators: name: Woods, Charles A.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Ctenomyidae
Ctenomys
Ctenomys occultus

description: Ctenomys occultus Thomas, 1920. Ann. Mag. Nat. Hist., ser. 9, 6:243. TYPE LOCALITY: Argentina, Monteagudo, 80 km SE Tucumén City. DISTRIBUTION: NW Argentina in Tucumén and adjacent Provs. COMMENTS: Revised by Reig et al. (1966); also see Cabrera (1961:552) who included this species in mendocinus. The chromosome no. is 2n=22.
description: Published as part of Charles A. Woods, 1993, Order Rodentia - Suborder Hystricognathi, pp. 771-806 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 786, DOI: 10.5281/zenodo.7353083
description: {"references": ["Reig, O. A., J. R. Contreras, and M. J. Piantanida. 1966. Contribucion a la elucidacion de la sistematica de las entidades del genero Ctenomys (Rodentia, Octodontidae). I. Relaciones de parentesco entre muestras de ocho poblaciones de tuco-tucos inferidas del estudio estadistico de variables del fenotipo y su correlacion con las caracteristicas del cariotipo. Contribuciones Cientificas Facultad Ciencias Exactas Naturales, Universidad Buenos Aires (Zoologia), 2: 299 - 352."]}
Alcohol Interacts with Genetic Alteration of the Hippo Tumor Suppressor Pathway to Modulate Tissue Growth in Drosophila
Creators: name: Ilanges, Anoj
name: Jahanshahi, Maryam
name: Balobin, Denis M.
name: Pfleger, Cathie M.
Publisher: name: Columbia University
Year: 2013
Subjects: Cancer--Etiology
Drosophila
Tumor suppressor proteins
Alcohol--Physiological effect
Oncology

description: Alcohol-mediated cancers represent more than 3.5% of cancer-related deaths, yet how alcohol promotes cancer is a major open question. Using Drosophila, we identified novel interactions between dietary ethanol and loss of tumor suppressor components of the Hippo Pathway. The Hippo Pathway suppresses tumors in flies and mammals by inactivating transcriptional co-activator Yorkie, and the spectrum of cancers associated with impaired Hippo signaling overlaps strikingly with those associated with alcohol. Therefore, our findings may implicate loss of Hippo Pathway tumor suppression in alcohol-mediated cancers. Ethanol enhanced overgrowth from loss of the expanded, hippo, or warts tumor suppressors but, surprisingly, not from over-expressing the yorkie oncogene. We propose that in parallel to Yorkie-dependent overgrowth, impairing Hippo signaling in the presence of alcohol may promote overgrowth via additional alcohol-relevant targets. We also identified interactions between alcohol and Hippo Pathway over-activation. We propose that exceeding certain thresholds of alcohol exposure activates Hippo signaling to maintain proper growth control and prevent alcohol-mediated mis-patterning and tissue overgrowth.
Characterizing Immunoglobulin Repertoire from Whole Blood by a Personal Genome Sequencer
Creators: name: Gao, Fan
name: Lin, Edwin
name: Feng, Yaping
name: Mack, William J.
name: Shen, Yufeng
name: Wang, Kai
Publisher: name: Columbia University
Year: 2013
Subjects: subject: Immunoglobulins
subject: Nucleotide sequence
subject: Meningioma
subject: Blood--Analysis
subject: Bioinformatics
subject: FOS: Computer and information sciences
subject: Immunology
subject: FOS: Clinical medicine

description: In human immune system, V(D)J recombination produces an enormously large repertoire of immunoglobulins (Ig) so that they can tackle different antigens from bacteria, viruses and tumor cells. Several studies have demonstrated the utility of next-generation sequencers such as Roche 454 and Illumina Genome Analyzer to characterize the repertoire of immunoglobulins. However, these techniques typically require separation of B cell population from whole blood and require a few weeks for running the sequencers, so it may not be practical to implement them in clinical settings. Recently, the Ion Torrent personal genome sequencer has emerged as a tabletop personal genome sequencer that can be operated in a time-efficient and cost-effective manner. In this study, we explored the technical feasibility to use multiplex PCR for amplifying V(D)J recombination for IgH, directly from whole blood, then sequence the amplicons by the Ion Torrent sequencer. The whole process including data generation and analysis can be completed in one day. We tested the method in a pilot study on patients with benign, atypical and malignant meningiomas. Despite the noisy data, we were able to compare the samples by their usage frequencies of the V segment, as well as their somatic hypermutation rates. In summary, our study suggested that it is technically feasible to perform clinical monitoring of V(D)J recombination within a day by personal genome sequencers.
Ctenomys opimus Wagner 1848
Creators: name: Woods, Charles A.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Ctenomyidae
Ctenomys
Ctenomys opimus

description: Ctenomys opimus Wagner, 1848. Arch. Naturgesch., 1:75. TYPE LOCALITY: Bolivia, Oruro Dept., Monte Sajama. DISTRIBUTION: NW Argentina, SW Bolivia, S Peru, N Chile between 2,000 and 5,000 m elevation on the high Andean steppe (= Puna). STATUS: Common. SYNONYMS: luteolus. COMMENTS: May be conspecific with fulvus; opimus and fulvus cannot be separated on the basis of karyotypes; see Gallardo (1979:80) and Cook et al. (1990). The chromosome no. is 2n=26; FN=48.
description: Published as part of Charles A. Woods, 1993, Order Rodentia - Suborder Hystricognathi, pp. 771-806 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 786, DOI: 10.5281/zenodo.7353083
description: {"references": ["Gallardo, M. 1979. Las especies chilenas de Ctenomys (Rodentia, Octodontidae). I. Estabilidad cariotipica. Archivos de Biologia y Medicina Experimentales (Santiago), 12: 71 - 82.", "Cook, J. A., S. Anderson, and T. L. Yates. 1990. Notes on Bolivian mammals. 6. The genus Ctenomys (Rodentia, Ctenomyidae) in the highlands. American Museum Novitates, 2980: 1 - 27."]}
Ctenomys pearsoni Lessa and Langguth 1983
Creators: name: Woods, Charles A.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Ctenomyidae
Ctenomys
Ctenomys pearsoni

description: Ctenomys pearsoni Lessa and Langguth, 1983. Res. Com. Jour. Cienc. Nat. Montevideo (Uruguay) 3:86. TYPE LOCALITY: Uruguay, Dept. Colonia, 25 km SE of Carmelo, Arroyo Limetas. DISTRIBUTION: Soriana, San José, and Colonia Depts. (Uruguay). COMMENTS: The chromosome no. is 2n=56-70.
description: Published as part of Charles A. Woods, 1993, Order Rodentia - Suborder Hystricognathi, pp. 771-806 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 786, DOI: 10.5281/zenodo.7353083
Acute Decompensated Heart Failure Is Routinely Treated as a Cardiopulmonary Syndrome
Creators: name: Dharmarajan, Kumar
name: Strait, Kelly M.
name: Lagu, Tara
name: Lindenauer, Peter K.
name: Tinetti, Mary E.
name: Lynn, Joanne
name: Li, Shu-Xia
name: Krumholz, Harlan M.
Publisher: name: Columbia University
Year: 2013
Subjects: Diagnostic errors
Heart--Diseases--Diagnosis
Heart failure--Treatment
Medical sciences

description: Background:
Heart failure as recognized and treated in typical practice may represent a complex condition that defies discrete categorizations. To illuminate this complexity, we examined treatment strategies for patients hospitalized and treated for decompensated heart failure. We focused on the receipt of medications appropriate for other acute conditions associated with shortness of breath including acute asthma, pneumonia, and exacerbated chronic obstructive pulmonary disease.

Methods and Results:
Using Premier Perspective®, we studied adults hospitalized with a principal discharge diagnosis of heart failure and evidence of acute heart failure treatment from 2009-2010 at 370 US hospitals. We determined treatment with acute respiratory therapies during the initial 2 days of hospitalization and daily during hospital days 3-5. We also calculated adjusted odds of in-hospital death, admission to the intensive care unit, and late intubation (intubation after hospital day 2). Among 164,494 heart failure hospitalizations, 53% received acute respiratory therapies during the first 2 hospital days: 37% received short-acting inhaled bronchodilators, 33% received antibiotics, and 10% received high-dose corticosteroids. Of these 87,319 hospitalizations, over 60% continued receiving respiratory therapies after hospital day 2. Respiratory treatment was more frequent among the 60,690 hospitalizations with chronic lung disease. Treatment with acute respiratory therapy during the first 2 hospital days was associated with higher adjusted odds of all adverse outcomes.

Conclusions:
Acute respiratory therapy is administered to more than half of patients hospitalized with and treated for decompensated heart failure. Heart failure is therefore regularly treated as a broader cardiopulmonary syndrome rather than as a singular cardiac condition.
Ctenomys perrensis Thomas 1898
Creators: name: Woods, Charles A.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Ctenomyidae
Ctenomys
Ctenomys perrensis

description: Ctenomys perrensis Thomas, 1898. Ann. Mag. Nat. Hist., ser. 6, 18:311. TYPE LOCALITY: Argentina, Corrientes Prov., Goya. DISTRIBUTION: Corrientes, Entre Rios, and Misiones Provs. (NE Argentina). COMMENTS: The chromosome no. is 2n=50-56.
description: Published as part of Charles A. Woods, 1993, Order Rodentia - Suborder Hystricognathi, pp. 771-806 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 786, DOI: 10.5281/zenodo.7353083
On the Stability of Quantum Hall Kagome-ice Insulator
Creators: name: Ishizuka, Hiroaki
name: Motome, Yukitoshi
Publisher: name: arXiv
Year: 2013
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The stability of the kagome-ice insulator against the three dimensionality and the canting angle of the spin anisotropy axes is studied numerically using the exact diagonalization method. The kagome-ice insulator, which was recently found at 2/3 electron filling in the double-exchange model on a kagome lattice, is a Chern insulator showing a quantized Hall response despite the absence of magnetic long-range order. We find that this peculiar state remains stable when the lattice is extended to three dimensions in an anisotropic pyrochlore lattice in the weak interlayer coupling region. On the other hand, we show that the kagome-ice insulator is also stable against the change of the canting angle. Furthermore, we find another kagome-ice insulator at 1/3 filling in a different range of the canting angle. Our results indicate that the quantum anomalous Hall response is widely observed in the variants of the kagome-ice double-exchange systems.
description: 6 pages, 3 figures
Differential Joint-Specific Corticospinal Tract Projections within the Cervical Enlargement
Creators: name: Asante, Curtis O.
name: Martin, John H.
Publisher: name: Columbia University
Year: 2013
Subjects: subject: Spinal cord
subject: Pyramidal tract
subject: Motor cortex
subject: Interneurons
subject: Medical sciences
subject: Physiology
subject: FOS: Biological sciences
subject: Neurosciences
subject: FOS: Clinical medicine

description: The motor cortex represents muscle and joint control and projects to spinal cord interneurons and–in many primates, including humans–motoneurons, via the corticospinal tract (CST). To examine these spinal CST anatomical mechanisms, we determined if motor cortex sites controlling individual forelimb joints project differentially to distinct cervical spinal cord territories, defined regionally and by the locations of putative last-order interneurons that were transneuronally labeled by intramuscular injection of pseudorabies virus. Motor cortex joint-specific sites were identified using intracortical-microstimulation. CST segmental termination fields from joint-specific sites, determined using anterograde tracers, comprised a high density core of terminations that was consistent between animals and a surrounding lower density projection that was more variable. Core terminations from shoulder, elbow, and wrist control sites overlapped in the medial dorsal horn and intermediate zone at C5/C6 but were separated at C7/C8. Shoulder sites preferentially terminated dorsally, in the dorsal horn; wrist/digit sites, more ventrally in the intermediate zone; and elbow sites, medially in the dorsal horn and intermediate zone. Pseudorabies virus injected in shoulder, elbow, or wrist muscles labeled overlapping populations of predominantly muscle-specific putative premotor interneurons, at a survival time for disynaptic transfer from muscle. At C5/C6, CST core projections from all joint zones were located medial to regions of densely labeled last-order interneurons, irrespective of injected muscle. At C7/C8 wrist CST core projections overlapped the densest interneuron territory, which was located in the lateral intermediate zone. In contrast, elbow CST core projections were located medial to the densest interneuron territories, and shoulder CST core projections were located dorsally and only partially overlapped the densest interneuron territory. Our findings show a surprising fractionation of CST terminations in the caudal cervical enlargement that may be organized to engage different spinal premotor circuits for distal and proximal joint control.
Ankyrin-G Participates in INa Remodeling in Myocytes from the Border Zones of Infarcted Canine Heart
Creators: name: Dun, Wen
name: Lowe, John S.
name: Wright, Patrick
name: Hund, Thomas J.
name: Mohler, Peter J.
name: Boyden, Penelope A.
Publisher: name: Columbia University
Year: 2013
Subjects: Myocardial infarction--Animal models
Purkinje cells
Sodium channels
Medical sciences

description: Cardiac Na channel remodeling provides a critical substrate for generation of reentrant arrhythmias in border zones of the infarcted canine heart. Recent studies show that Nav1.5 assembly and function are linked to ankyrin-G, gap, and mechanical junction proteins. In this study our objective is to expound the status of the cardiac Na channel, its interacting protein ankyrinG and the mechanical and gap junction proteins at two different times post infarction when arrhythmias are known to occur; that is, 48 hr and 5 day post coronary occlusion. Previous studies have shown the origins of arrhythmic events come from the subendocardial Purkinje and epicardial border zone. Our Purkinje cell (Pcell) voltage clamp study shows that INa and its kinetic parameters do not differ between Pcells from the subendocardium of the 48hr infarcted heart (IZPCs) and control non-infarcted Pcells (NZPCs). Immunostaining studies revealed that disturbances of Nav1.5 protein location with ankyrin-G are modest in 48 hr IZPCs. Therefore, Na current remodeling does not contribute to the abnormal conduction in the subendocardial border zone 48 hr post myocardial infarction as previously defined. In addition, immunohistochemical data show that Cx40/Cx43 co-localize at the intercalated disc (IDs) of control NZPCs but separate in IZPCs. At the same time, Purkinje cell desmoplakin and desmoglein2 immunostaining become diffuse while plakophilin2 and plakoglobin increase in abundance at IDs. In the epicardial border zone 5 days post myocardial infarction, immunoblot and immunocytochemical analyses showed that ankyrin-G protein expression is increased and re-localized to submembrane cell regions at a time when Nav1.5 function is decreased. Thus, Nav1.5 and ankyrin-G remodeling occur later after myocardial infarction compared to that of gap and mechanical junctional proteins. Gap and mechanical junctional proteins remodel in IZPCs early, perhaps to help maintain Nav1.5 subcellular location position and preserve its function soon after myocardial infarction.
Quantitative characterization of the spin orbit torque using harmonic Hall voltage measurements
Creators: name: Hayashi, Masamitsu
name: Kim, Junyeon
name: Yamanouchi, Michihiko
name: Ohno, Hideo
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Solid understanding of current induced torques is key to the development of current and voltage controlled magnetization dynamics in ultrathin magnetic heterostructures. To evaluate the size and direction of such torques, or effective fields, a number of methods have been employed. Here we examine the adiabatic (low frequency) harmonic Hall voltage measurement that has been used to study the effective field. We derive an analytical formula for the harmonic Hall voltages to evaluate the effective field for both out of plane and in-plane magnetized systems. The formula agrees with numerical calculations based on a macrospin model. Two different in-plane magnetized films, Pt|CoFeB|MgO and CuIr|CoFeB|MgO are studied using the formula developed. The effective field obtained for the latter system shows relatively good agreement with that estimated using a spin torque switching phase diagram measurements reported previously. Our results illustrate the versatile applicability of harmonic Hall voltage measurement for studying current induced torques in magnetic heterostructures.
description: Extended version of arXiv:1307.5603
Ctenomys peruanus Sanborn and Pearson 1947
Creators: name: Woods, Charles A.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Ctenomyidae
Ctenomys
Ctenomys peruanus

description: Ctenomys peruanus Sanborn and Pearson, 1947. Proc. Biol. Soc. Washington, 60:13. TYPE LOCALITY: Peru, Puno Dept., Pisacoma. DISTRIBUTION: Altipiano of extreme S Peru.
description: Published as part of Charles A. Woods, 1993, Order Rodentia - Suborder Hystricognathi, pp. 771-806 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 786, DOI: 10.5281/zenodo.7353083
Approximate Bayesian Computation (ABC) in Retrievals of Exoplanet Atmospheres
Creators: name: Davey, Jack
name: Waldmann, Ingo
name: Al-Refaie, Ahmed
Publisher: name: Zenodo
Year: 2023

description: While Approximate Bayesian Computation (ABC) and other likelihood free (LF) methods for Bayesian inference have been adopted in many areas of scientific research including cosmology, they have seen limited application in exoplanetary science. Cosmologists have been dealing with the problem of intractable likelihoods for a number of years and have implemented these techniques in order to bypass the need to define a likelihood function. With the launch and first observations of the James Webb Space Telescope (JWST), there is a strong expectation that assumptions in the likelihood could bias results of atmospheric retrievals on exoplanet transmission spectra so the need for LF methods is evident now more than ever. Here, we implement ABC with the atmospheric retrieval code TauREx3 (using the PyMC library) with the aims of revealing and mitigating the effects of non-gaussianity in spectral data sets. To this end we will study effects due to non-gaussian noise in simulated data sets of hot Jupiter spectra. This will allow us to identify any biases on specific parameters and we will then go on to perform a reanalysis of Hubble and JWST early release science observations to identify any non-gaussian bias in retrievals performed with these data.
Zero-modes and global antiferromagnetism in strained graphene
Creators: name: Roy, Bitan
name: Assaad, Fakher F.
name: Herbut, Igor F.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: A novel magnetic ground state is reported for the Hubbard Hamiltonian in strained graphene. When the chemical potential lies close to the Dirac point, the ground state exhibits locally both the Néel and ferromagnetic orders, even for weak Hubbard interaction. Whereas the Néel order parameter remains of the same sign in the entire system, the magnetization at the boundary takes the opposite sign from the bulk. The total magnetization this way vanishes, and the magnetic ground state is globally only an antiferromagnet. This peculiar ordering stems from the nature of the strain-induced single particle zero-energy states, which have support on one sublattice of the honeycomb lattice in the bulk, and on the other sublattice near the boundary of a finite system. We support our claim with the self-consistent numerical calculation of the order parameters, as well as by the Monte Carlo simulations of the Hubbard model in both uniformly and non-uniformly strained honeycomb lattice. The present result is contrasted with the magnetic ground state of the same Hubbard model in the presence of a true magnetic field (and for vanishing Zeeman coupling), which is exclusively Néel ordered, with zero local magnetization everywhere in the system.
description: Published version, 11+epsilon pages, 7 figures, added discussion on experimental detection of Global Antiferromagnet
Long range rapidity correlations in soft interaction at high energies
Creators: name: Gotsman, E.
name: Levin, E.
name: Maor, U.
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: In this paper we take the next step (following the successful description of inclusive hadron production) in describing the structure of the bias events without the aid of Monte Carlo codes. Two new results are presented :(i) a method for calculating the two particle correlation functions in the BFKLPomeron calculus in zero transverse dimension;and (ii) an estimation of the values of these correlations in a model of soft interactions. Comparison with the multiplicity data at the LHC is given.
description: 23pp. 13 figures in eps.files
Inhibition of Caveolin-1 Restores Myeloid Cell Function in Human Glioblastoma
Creators: name: Shimato, Shinji
name: Anderson, Lisa M.
name: Asslaber, Martin
name: Bruce, Jeffrey N.
name: Canoll, Peter D.
name: Anderson, David E.
name: Anderson, Richard C. E.
Publisher: name: Columbia University
Year: 2013
Subjects: Monocytes
Microglia
Cancer--Immunotherapy
Glioblastoma multiforme
Cytology

description: Background:

Gliomas are the most common primary brain tumor in both children and adults. The prognosis for glioblastoma (GBM), the most common type of malignant glioma, has remained dismal, with median survival a little over one year despite maximal therapy with surgery, chemotherapy, and radiation. Although immunotherapy has become increasingly successful against many systemic tumors, clinical efficacy against brain tumors has been limited. One reason for this is an incomplete understanding of the local immunologic tumor microenvironment, particularly the function of large numbers of infiltrating myeloid derived cells. Monocytes/microglia are myeloid derived immunomodulatory cells, and they represent the predominant infiltrating immune cell population in gliomas. Our group has previously demonstrated using complementary in vitro and in vivo approaches that GBM tumor cells polarize tumor-associated myeloid cells (TAMs) and suppress their immunostimulatory function.

Methods and Results:

To better understand the mechanisms responsible for this immunosuppression, we used gene expression profiling of stimulated monocytes in the presence or absence of GBM tumor cells. Our analysis identified caveolin-1 (CAV1), a plasma membrane molecule with pleiotropic functions, as significantly up-regulated in monocytes in the presence of GBMs. We validated these findings ex vivo by confirming up-regulation of CAV1 in TAMs isolated from GBMs immediately after surgical resection. Finally, we demonstrate that siRNA inhibition of CAV1 restores myeloid cell function, as measured by TNF-alpha secretion, in the presence of GBMs.

Conclusions:

Restoration of TAM function through pharmacologic blockage of CAV1 may facilitate more successful immunotherapeutic strategies directed against a variety of solid human tumors infiltrated by TAMs.
Generation of 3D Skin Equivalents Fully Reconstituted from Human Induced Pluripotent Stem Cells (iPSCs)
Creators: name: Itoh, Munenari
name: Umegaki-Arao, Noriko
name: Guo, Zongyou
name: Liu, Liang
name: Christiano, Angela M.
name: Higgins, Claire A.
Publisher: name: Columbia University
Year: 2013
Subjects: Fibroblasts
Keratinocytes
Skin--Diseases--Treatment
Stem cells
Medical sciences

description: Recent generation of patient-specific induced pluripotent stem cells (PS-iPSCs) provides significant advantages for cell- and gene-based therapy. Establishment of iPSC-based therapy for skin diseases requires efficient methodology for differentiating iPSCs into both keratinocytes and fibroblasts, the major cellular components of the skin, as well as the reconstruction of skin structures using these iPSC-derived skin components. We previously reported generation of keratinocytes from human iPSCs for use in the treatment of recessive dystrophic epidermolysis bullosa (RDEB) caused by mutations in the COL7A1 gene. Here, we developed a protocol for differentiating iPSCs into dermal fibroblasts, which also produce type VII collagen and therefore also have the potential to treat RDEB. Moreover, we generated in vitro 3D skin equivalents composed exclusively human iPSC-derived keratinocytes and fibroblasts for disease models and regenerative therapies for skin diseases, first demonstrating that iPSCs can provide the basis for modeling a human organ derived entirely from two different types of iPSC-derived cells.
Ctenomys pontifex Thomas 1918
Creators: name: Woods, Charles A.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Ctenomyidae
Ctenomys
Ctenomys pontifex

description: Ctenomys pontifex Thomas, 1918. Ann. Mag. Nat. Hist., ser. 9, 1:39. TYPE LOCALITY: Argentina, Mendoza Prov., San Rafael. DISTRIBUTION: W Argentina, east of the Andes in San Luis and Mendoza Provs.
description: Published as part of Charles A. Woods, 1993, Order Rodentia - Suborder Hystricognathi, pp. 771-806 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 786, DOI: 10.5281/zenodo.7353083