cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 2: of Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils
Creators: name: Zhao, Zhi-Bo
name: Ji-Zheng He
name: Geisen, Stefan
name: Han, Li-Li
name: Wang, Jun-Tao
name: Ju-Pei Shen
name: Wei, Wen-Xue
name: Fang, Yun-Ting
name: Li, Pei-Pei
name: Zhang, Li-Mei
Publisher: name: figshare
Year: 2019
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: Details regarding network analyses to assess seasonal dynamics of soil microbiome associations and SEM to determine the importance abiotic factors and biotic factors on the significant reductions in the alpha diversity of the protist community. (DOCX 39 kb)
Additional file 1: of Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils
Creators: name: Zhao, Zhi-Bo
name: Ji-Zheng He
name: Geisen, Stefan
name: Han, Li-Li
name: Wang, Jun-Tao
name: Ju-Pei Shen
name: Wei, Wen-Xue
name: Fang, Yun-Ting
name: Li, Pei-Pei
name: Zhang, Li-Mei
Publisher: name: figshare
Year: 2019
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology

description: Figure S1. Relative abundance of taxonomic composition of soil bacterial (A), fungal (B), and protist (C) community at phylum level, at class level, and at phylum level, respectively. Figure S2. LEfSe results revealed bacterial biomarkers (from phylum to genus level) sensitive to nitrogen fertilizers (no nitrogen addition (control) or nitrogen addition (N) or nitrogen + straw addition (NS)). Figure S3. LEfSe results revealed fungal biomarkers (from phylum level to genus level) sensitive to nitrogen fertilizers (no nitrogen addition (control) or nitrogen addition (N) or nitrogen + straw addition (NS)). Figure S4. Networks visualizing seasonal changes in co-occurrence patterns among protist, bacterial, and fungal taxa at family level across all soils in black soil, fluvo-aquic soil, and red soil, respectively. Figure S5. Beta-diversity of bacterial, fungal, and protist communities in each soil type under summer and autumn season, visualized by nonmetric multidimensional scaling (NMDS) based on unweighted unifrac phylogenetic distance metrics at OTU level. Figure S6. Putative key hubs in each network identified by betweenness centrality (BC) and closeness centrality (CC) of each node. Figure S7. Geographic location of three field experiment sites in China and diagram of fertilization and sampling arrangements. Table S1. Information of primers used in this study. Table S2. Physicochemical properties of the examined soil. Table S3. Bacterial biomarkers sensitive to nitrogen fertilizer treatments revealed by LEfSe analysis. Table S4. Fungal biomarkers sensitive to nitrogen fertilizer treatments revealed by LEfSe analysis. Table S5. Protist biomarkers sensitive to nitrogen fertilizer treatments revealed by LEfSe analysis. Table S6. Spearman correlations between alpha diversity of microbiomes and physicochemical properties in soils. Table S7. Node information of edges appearing in at least two networks linking protist to bacterial or fungal taxa in Fig.Â 3. Table S8. Topological indices used in this study for each network in Figure S4.Â Table S9. Nodes information of edges appearing in at least two networks linking protist to bacterial or fungal taxa in Figure S4. Table S10. The taxonomic information of protist nodes in TableÂ 5. (DOCX 2031 kb)
Yukawa Unification with light supersymmetric particles consistent with LHC constraints
Creators: name: Hussain, Mureed
name: Khalid, Rizwan
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We investigate supersymmetric models with left-right symmetry based on the group $SU(4)_{c} \times SU(2)_{L} \times SU(2)_{R}$ ($4$-$2$-$2$) with negative sign of bilinear Higgs potential parameter $μ$ in the context of the latest experimental results. In the backdrop of experimental results from the Large Hadron Collider, we investigate the possibility of Yukawa unification in $4$-$2$-$2$ and find out the same is still not ruled out. Furthermore, this scenario also provides a satisfactory dark matter candidate. The current experimental bounds on sparticle masses, mass bounds on Higgs particle, updated phenomenological constraints from the rare decays of B meson and the anomalous magnetic moment of muon with the requirement of a Yukawa unified theory having $10 \%$ or better third family Yukawa unification are utilized to bound the parametric space of these models.
description: 18 pages, 5 sets of figures. Some linguistic paraphrasing. Results are same as in the previous version
Additional file 1 of Further corroboration of distinct functional features in SCN2A variants causing intellectual disability or epileptic phenotypes
Creators: name: Begemann, Anaïs
name: Acuña, Mario
name: Zweier, Markus
name: Vincent, Marie
name: Steindl, Katharina
name: Bachmann-Gagescu, Ruxandra
name: Hackenberg, Annette
name: Abela, Lucia
name: Plecko, Barbara
name: Kroell-Seger, Judith
name: Baumer, Alessandra
name: Yamakawa, Kazuhiro
name: Inoue, Yushi
name: Asadollahi, Reza
name: Sticht, Heinrich
name: Zeilhofer, Hanns
name: Rauch, Anita
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Supplementary Methods. Table S1. Activation and inactivation kinetics of Nav1.2 wild-type and mutants. Table S2. Use-dependent inactivation of Nav1.2 wild-type and mutants. Table S3. Previous electrophysiological studies of disease causing SCN2A variants. Table S4. Previous studies using in-silico modeling of neuronal excitability of disease causing SCN2A variants. (DOCX 46 kb)
Antiferromagnetism, Stripes, and Superconductivity in the t-J Model with Coulomb Interaction
Creators: name: Han, Jung Hoon
name: Wang, Qiang-Hua
name: Lee, Dung-Hai
Publisher: name: arXiv
Year: 2000
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We study mean-field phases of the t-J model with long-range Coulomb interaction. In the order of increasing doping density we find a classical antiferromagnet, charge and spin stripes, and a uniform d-wave superconductor, at the realistic doping parameters. Both in-phase and anti-phase stripes exist as metastable configurations, but the in-phase stripes have a slightly lower energy. The dependence of the stripe width and the inter-stripe spacing on the doping is examined. Effects of fluctuations around the mean-field states are discussed.
RIN4 Interacts with Pseudomonas syringae Type III Effector Molecules and Is Required for RPM1-Mediated Resistance in Arabidopsis
Creators: name: Dangl, Jeffery L.
name: Wiig, Aaron
name: Mackey, David
name: Holt, Ben F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: In Arabidopsis, RPM1 confers resistance against Pseudomonas syringae expressing either of two sequence unrelated type III effectors, AvrRpm1 or AvrB. An RPM1-interacting protein (RIN4) coimmunoprecipitates from plant cell extracts with AvrB, AvrRpm1, or RPM1. Reduction of RIN4 protein levels inhibits both the hypersensitive response and the restriction of pathogen growth controlled by RPM1. RIN4 reduction causes diminution of RPM1. RIN4 reduction results in heightened resistance to virulent Peronospora parasitica and P. syringae, and ectopic defense gene expression. Thus, RIN4 positively regulates RPM1-mediated resistance yet is, formally, a negative regulator of basal defense responses. AvrRpm1 and AvrB induce RIN4 phosphorylation. This may enhance RIN4 activity as a negative regulator of plant defense, facilitating pathogen growth. RPM1 may "guard" against pathogens that use AvrRpm1 and AvrB to manipulate RIN4 activity.
Additional file 14 of Genomic and immunological profiles of small-cell lung cancer between East Asians and Caucasian
Creators: name: Lin, Anqi
name: Zhou, Ningning
name: Zhu, Weiliang
name: Zhang, Jiexia
name: Wei, Ting
name: Guo, Linlang
name: Luo, Peng
name: Zhang, Jian
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Additional file 14: Table S5. Related to Additional file 5: Fig. S5a. The results of the CMap analysis of the East Asian cohort (TP53/RB1 co-mutations vs No alterations in TP53/RB1).
Arabidopsis RIN4 Is a Target of the Type III Virulence Effector AvrRpt2 and Modulates RPS2-Mediated Resistance
Creators: name: Dangl, Jeffery L.
name: Ecker, Joseph R.
name: Alonso, Jose M.
name: Belkhadir, Youssef
name: Mackey, David
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: AbstractType III pili deliver effector proteins (virulence factors) from bacterial pathogens to host cells. Plants express disease resistance (R) proteins that respond specifically to a particular type III effector by activating immune responses. We demonstrated previously that two unrelated type III effectors from Pseudomonas syringae target and modify the Arabidopsis RIN4 protein. Here, we show that AvrRpt2, a third, unrelated type III effector, also targets RIN4 and induces its posttranscriptional disappearance. This effect is independent of the presence of RPS2, the Arabidopsis R protein that senses AvrRpt2. RIN4 overexpression inhibits multiple phenotypes associated with AvrRpt2 function. Conversely, disruption of RIN4 results in RPS2-dependent lethality. RPS2 and RIN4 physically associate in the plant. We suggest that RIN4 is the target of the AvrRpt2 virulence function, and that perturbation of RIN4 activates RPS2. Thus, RIN4 is a point of convergence for the activity of at least three unrelated P. syringae type III effectors.
RIC-8 Is Required for GPR-1/2-Dependent Gα Function during Asymmetric Division of C. elegans Embryos
Creators: name: Johnston, Christopher A.
name: McCudden, Christopher R.
name: Gönczy, Pierre
name: Siderovski, David P.
name: Willard, Francis S.
name: Afshar, Katayoun
name: Colombo, Kelly
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: AbstractHeterotrimeric G proteins are crucial for asymmetric cell division, but the mechanisms of signal activation remain poorly understood. Here, we establish that the evolutionarily conserved protein RIC-8 is required for proper asymmetric division of one-cell stage C. elegans embryos. Spindle severing experiments demonstrate that RIC-8 is required for generation of substantial pulling forces on astral microtubules. RIC-8 physically interacts with GOA-1 and GPA-16, two Gα subunits that act in a partially redundant manner in one-cell stage embryos. RIC-8 preferentially binds to GDP bound GOA-1 and is a guanine nucleotide exchange factor (GEF) for GOA-1. Our analysis suggests that RIC-8 acts before the GoLoco protein GPR-1/2 in the sequence of events leading to Gα activation. Furthermore, coimmunoprecipitation and in vivo epistasis demonstrate that inactivation of the Gβ subunit GPB-1 alleviates the need for RIC-8 in one-cell stage embryos. Our findings suggest a mechanism in which RIC-8 favors generation of Gα free from Gβγ and enables GPR-1/2 to mediate asymmetric cell division.
Structure of the Cand1-Cul1-Roc1 Complex Reveals Regulatory Mechanisms for the Assembly of the Multisubunit Cullin-Dependent Ubiquitin Ligases
Creators: name: Xiong, Yue
name: Goldenberg, Seth J.
name: Garbutt, Kenneth C.
name: Zheng, Ning
name: Cascio, Thomas C.
name: Shumway, Stuart D.
name: Liu, Jidong
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: AbstractThe SCF ubiquitin ligase complex regulates diverse cellular functions by ubiquitinating numerous protein substrates. Cand1, a 120 kDa HEAT repeat protein, forms a tight complex with the Cul1-Roc1 SCF catalytic core, inhibiting the assembly of the multisubunit E3 complex. The crystal structure of the Cand1-Cul1-Roc1 complex shows that Cand1 adopts a highly sinuous superhelical structure, clamping around the elongated SCF scaffold protein Cul1. At one end, a Cand1 β hairpin protrusion partially occupies the adaptor binding site on Cul1, inhibiting its interactions with the Skp1 adaptor and the substrate-recruiting F box protein subunits. At the other end, two Cand1 HEAT repeats pack against a conserved Cul1 surface cleft and bury a Cul1 lysine residue, whose modification by the ubiquitin-like protein, Nedd8, is able to block Cand1-Cul1 association. Together with biochemical evidence, these structural results elucidate the mechanisms by which Cand1 and Nedd8 regulate the assembly-disassembly cycles of SCF and other cullin-dependent E3 complexes.
Cotranscriptional Set2 Methylation of Histone H3 Lysine 36 Recruits a Repressive Rpd3 Complex
Creators: name: Collins, Sean R.
name: Schuldiner, Maya
name: Buratowski, Stephen
name: Thompson, Natalie J.
name: Weissman, Jonathan S.
name: Ahn, Seong Hoon
name: Chin, Kayu
name: Boone, Charles
name: Podolny, Vladimir
name: Strahl, Brian D.
name: Punna, Thanuja
name: Keogh, Michael-Christopher
name: Grunstein, Michael
name: Morris, Stephanie A.
name: Emili, Andrew
name: Krogan, Nevan J.
name: Hughes, Timothy R.
name: Greenblatt, Jack F.
name: Kurdistani, Siavash K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: SummaryThe yeast histone deacetylase Rpd3 can be recruited to promoters to repress transcription initiation. Biochemical, genetic, and gene-expression analyses show that Rpd3 exists in two distinct complexes. The smaller complex, Rpd3C(S), shares Sin3 and Ume1 with Rpd3C(L) but contains the unique subunits Rco1 and Eaf3. Rpd3C(S) mutants exhibit phenotypes remarkably similar to those of Set2, a histone methyltransferase associated with elongating RNA polymerase II. Chromatin immunoprecipitation and biochemical experiments indicate that the chromodomain of Eaf3 recruits Rpd3C(S) to nucleosomes methylated by Set2 on histone H3 lysine 36, leading to deacetylation of transcribed regions. This pathway apparently acts to negatively regulate transcription because deleting the genes for Set2 or Rpd3C(S) bypasses the requirement for the positive elongation factor Bur1/Bur2.
hDOT1L Links Histone Methylation to Leukemogenesis
Creators: name: Zhang, Yi
name: Coffield, Vernon M.
name: Okada, Yuki
name: Lin, Yihui
name: Su, Lishan
name: Li, Yaqiang
name: Feng, Qin
name: Jiang, Qi
name: Xu, Guoliang
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Epigenetic modifications play an important role in human cancer. One such modification, histone methylation, contributes to human cancer through deregulation of cancer-relevant genes. The yeast Dot1 and its human counterpart, hDOT1L, methylate lysine 79 located within the globular domain of histone H3. Here we report that hDOT1L interacts with AF10, an MLL (mixed lineage leukemia) fusion partner involved in acute myeloid leukemia, through the OM-LZ region of AF10 required for MLL-AF10-mediated leukemogenesis. We demonstrate that direct fusion of hDOT1L to MLL results in leukemic transformation in an hDOT1L methyltransferase activity-dependent manner. Transformation by MLL-hDOT1L and MLL-AF10 results in upregulation of a number of leukemia-relevant genes, such as , concomitant with hypermethylation of H3-K79. Our studies thus establish that mistargeting of hDOT1L to plays an important role in MLL-AF10-mediated leukemogenesis and suggests that the enzymatic activity of hDOT1L may provide a potential target for therapeutic intervention.
Selective Evolution of Stromal Mesenchyme with p53 Loss in Response to Epithelial Tumorigenesis
Creators: name: Hill, Reginald
name: Cardiff, Robert D.
name: Song, Yurong
name: Van Dyke, Terry
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Our understanding of cancer has largely come from the analysis of aberrations within the tumor cell population. Yet it is increasingly clear that the tumor microenvironment can significantly influence tumorigenesis. For example, the mesenchyme can support the growth of tumorigenic epithelium. However, whether fibroblasts are subject to genetic/epigenetic changes as a result of selective pressures conferred by oncogenic stress in the epithelium has not been experimentally assessed. Recent analyses of some human carcinomas have shown tumor-suppressor gene mutations within the stroma, suggesting that the interplay among multiple cell types can select for aberrations nonautonomously during tumor progression. We demonstrate that this indeed occurs in a mouse model of prostate cancer where epithelial cell cycle disruption via cell-specific inhibition of pRb function induces a paracrine p53 response that suppresses fibroblast proliferation in associated stroma. This interaction imposes strong selective pressure yielding a highly proliferative mesenchyme that has undergone p53 loss.
The Polyadenylation Factor CPSF-73 Is Involved in Histone-Pre-mRNA Processing
Creators: name: Yang, Xiao-cui
name: Marzluff, William F.
name: Dominski, Zbigniew
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: During 3' end processing, histone pre-mRNAs are cleaved 5 nucleotides after a conserved stem loop by an endonuclease dependent on the U7 small nuclear ribonucleoprotein (snRNP). The upstream cleavage product corresponds to the mature histone mRNA, while the downstream product is degraded by a 5'-3' exonuclease, also dependent on the U7 snRNP. To identify the two nuclease activities, we carried out UV-crosslinking studies using both the complete RNA substrate and the downstream cleavage product, each containing a single radioactive phosphate and a phosphorothioate modification at the cleavage site. We detected a protein migrating at 85 kDa that crosslinked to each substrate in a U7-dependent manner. Immunoprecipitation experiments identified this protein as CPSF-73, a known component of the cleavage/polyadenylation machinery. These studies suggest that CPSF-73 is both the endonuclease and 5'-3' exonuclease in histone-pre-mRNA processing and reveal an evolutionary link between 3' end formation of histone mRNAs and polyadenylated mRNAs.
Stiefel manifolds and polygons
Creators: name: Shonkwiler, Clayton
Publisher: name: arXiv
Year: 2019
Subjects: subject: History and Overview (math.HO)
subject: FOS: Mathematics
subject: 00A66 (Primary), 53A04, 14M15 (Secondary)

description: Polygons are compound geometric objects, but when trying to understand the expected behavior of a large collection of random polygons -- or even to formalize what a random polygon is -- it is convenient to interpret each polygon as a point in some parameter space, essentially trading the complexity of the object for the complexity of the space. In this paper I describe such an interpretation where the parameter space is a Stiefel manifold and show how to exploit the geometry of the Stiefel manifold both to generate random polygons and to morph one polygon into another.
description: Expanded some explanations, especially in the introduction and about paths in Stiefel and Grassmann manifolds. 8 pages, 8 figures
DEP-Domain-Mediated Regulation of GPCR Signaling Responses
Creators: name: Gladue, Douglas P.
name: Flanary, Paul L.
name: Ballon, Daniel R.
name: Dohlman, Henrik G.
name: Konopka, James B.
name: Thorner, Jeremy
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: G protein-coupled receptors (GPCRs) mediate cellular responses to a variety of stimuli, but how specific responses are regulated has been elusive, as the types of GPCRs vastly outnumber the classes of G protein heterotrimers available to initiate downstream signaling. In our analysis of signaling proteins containing DEP domains ( approximately 90 residue sequence motifs first recognized in fly Dishevelled, worm EGL-10, and mammalian Pleckstrin), we find that DEP domains are responsible for specific recognition of GPCRs. We examined the yeast regulator of G protein signaling (RGS) protein Sst2 and demonstrate that the DEP domains in Sst2 mediate binding to its cognate GPCR (Ste2). DEP-domain-mediated tethering promotes downregulation by placing the RGS protein in proximity to its substrate (receptor-activated Galpha subunit). Sst2 docks to the Ste2 cytosolic tail, but only its unphosphorylated state, allowing for release and recycling of this regulator upon receptor desensitization and internalization. DEP-domain-mediated targeting of effectors and regulators to specific GPCRs provides a means to dictate the nature, duration, and specificity of the response.
Expansion of High Speed Solar Wind Streams from Coronal Holes through the Inner Heliosphere
Creators: name: Garton, Tadhg M.
name: Murray, Sophie A.
name: Gallagher, Peter T.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: Coronal holes (CHs) are regions of open magnetic flux which are the source of high speed solar wind (HSSW) streams. To date, it is not clear which aspects of CHs are of most influence on the properties of the solar wind as it expands through the Heliosphere. Here, we study the relationship between CH properties extracted from AIA (Atmospheric Imaging Assembly) images using CHIMERA (Coronal Hole Identification via Multi-thermal Emission Recognition Algorithm) and HSSW measurements from ACE (Advanced Composition Explorer) at L1. For CH longitudinal widths $Δθ_{CH}$67$^{\circ}$), $v_{max}$ is found to tend to a constant value ($\sim$710~km~s$^{-1}$). Furthermore, we find that the duration of HSSW streams ($Δt$) are directly related to the longitudinal width of CHs ($Δt_{SW}$~$\approx$~0.09$Δθ_{CH}$) and that their longitudinal expansion factor is $f_{SW}~\approx 1.2~\pm 0.1$. We also derive an expression for the coronal hole flux-tube expansion factor, $f_{FT}$, which varies as $f_{SW} \gtrsim f_{FT} \gtrsim 0.8$. These results enable us to estimate the peak speeds and durations of HSSW streams at L1 using the properties of CHs identified in the solar corona.
description: 8 pages, 4 figures, Accepted for publication in The Astrophysical Journal Letters (APJL) on 25th November 2018
JHDM2A, a JmjC-Containing H3K9 Demethylase, Facilitates Transcription Activation by Androgen Receptor
Creators: name: Erdjument-Bromage, Hediye
name: Toumazou, Charalambos
name: Yamane, Kenichi
name: Zhang, Yi
name: Tempst, Paul
name: Wong, Jiemin
name: Tsukada, Yu-ichi
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Covalent modification of histones plays an important role in regulating chromatin dynamics and transcription. Histone methylation was thought to be an irreversible modification until recently. Using a biochemical assay coupled with chromatography, we have purified a JmjC domain-containing protein, JHDM2A, which specifically demethylates mono- and dimethyl-H3K9. Similar to JHDM1, JHDM2A-mediated histone demethylation requires cofactors Fe(II) and alpha-ketoglutarate. Mutational studies indicate that a JmjC domain and a zinc finger present in JHDM2A are required for its enzymatic activity. Overexpression of JHDM2A greatly reduced the H3K9 methylation level in vivo. Knockdown of JHDM2A results in an increase in the dimethyl-K9 levels at the promoter region of a subset of genes concomitant with decrease in their expression. Finally, JHDM2A exhibits hormone-dependent recruitment to androgen-receptor target genes, resulting in H3K9 demethylation and transcriptional activation. Thus, our work identifies a histone demethylase and links its function to hormone-dependent transcriptional activation.
Kinetochore Microtubule Dynamics and Attachment Stability Are Regulated by Hec1
Creators: name: Salmon, E.D.
name: DeLuca, Jennifer G.
name: Musacchio, Andrea
name: Cimini, Daniela
name: Ciferri, Claudio
name: Gall, Walter E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Mitotic cells face the challenging tasks of linking kinetochores to growing and shortening microtubules and actively regulating these dynamic attachments to produce accurate chromosome segregation. We report here that Ndc80/Hec1 functions in regulating kinetochore microtubule plus-end dynamics and attachment stability. Microinjection of an antibody to the N terminus of Hec1 suppresses both microtubule detachment and microtubule plus-end polymerization and depolymerization at kinetochores of PtK1 cells. Centromeres become hyperstretched, kinetochore fibers shorten from spindle poles, kinetochore microtubule attachment errors increase, and chromosomes severely mis-segregate. The N terminus of Hec1 is phosphorylated by Aurora B kinase in vitro, and cells expressing N-terminal nonphosphorylatable mutants of Hec1 exhibit an increase in merotelic attachments, hyperstretching of centromeres, and errors in chromosome segregation. These findings reveal a key role for the Hec1 N terminus in controlling dynamic behavior of kinetochore microtubules.
Broadband dielectric response of glycerol and propylene carbonate: a comparison
Creators: name: Lunkenheimer, P.
name: Schneider, U.
name: Brand, R.
name: Loidl, A.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Dielectric data on glycerol and propylene carbonate covering 18 decades of frequency are presented and compared to each other. Both materials exhibit qualitatively similar behavior except for marked differences in the high-frequency region just below the boson peak. The results on both materials are consistent with the mode coupling theory of the glass transition.
description: 8 pages including 4 figures
Onthophagus inelegans Balthasar 1935
Creators: name: Bezděk, Aleš
name: Hájek, Jiří
Publisher: name: Zenodo
Year: 2013
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Scarabaeidae
Onthophagus
Onthophagus inelegans

description: Onthophagus inelegans Balthasar, 1935
 Onthophagus inelegans Balthasar, 1935b: 315.
Three syntypes are deposited in NMPC (ex coll. V. Balthasar):
SYNTYPES (3 unsexed specimens): ‘Nitou Tatsienlu / Szechuan China [p] // TYPUS [p, red label, black frame] // O.
inelegans / Typ. m. [hw] / Dr. V. Balthasar det. [p]’.
 Current status. Onthophagus (Altonthophagus) inelegans Balthasar, 1935, see KABAKOV (1990).
description: Published as part of Bezděk, Aleš & Hájek, Jiří, 2013, Catalogue of type specimens of beetles (Coleoptera) deposited in the National Museum, Prague, Czech Republic, pp. 387-442 in Acta Entomologica Musei Nationalis Pragae 53 (1) on page 408, DOI: 10.5281/zenodo.5739743
Physical Mechanism of the d->d+is Transition
Creators: name: Kos, Simon
Publisher: name: arXiv
Year: 2000
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We discuss the basic physical mechanism of the d->d+is transition, which is the currently accepted explanation for the results of tunneling experiments into $ab$ planes. Using the first-order perturbation theory, we show that the zero-bias states drive the transition. We present various order-of-magnitude estimates and consistency checks that support this picture.
description: 7 pages, 2 figures
An Atom Laser with a cw Output Coupler
Creators: name: Bloch, Immanuel
name: Haensch, Theodor W.
name: Esslinger, Tilman
Publisher: name: arXiv
Year: 1998
Subjects: subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: We demonstrate a continuous output coupler for magnetically trapped atoms. Over a period of up to 100 ms a collimated and monoenergetic beam of atoms is continuously extracted from a Bose- Einstein condensate. The intensity and kinetic energy of the output beam of this atom laser are controlled by a weak rf-field that induces spin flips between trapped and untrapped states. Furthermore, the output coupler is used to perform a spectroscopic measurement of the condensate, which reveals the spatial distribution of the magnetically trapped condensate and allows manipulation of the condensate on a micrometer scale.
description: 4 pages, 4 figures
Sequential Quality-Control Checkpoints Triage Misfolded Cystic Fibrosis Transmembrane Conductance Regulator
Creators: name: Fan, Chun-Yang
name: Patterson, Cam
name: Turnbull, Emma L.
name: Chen, Liling
name: Cyr, Douglas M.
name: Rosser, Meredith F.N.
name: Younger, J. Michael
name: Ren, Hong-Yu
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Cystic fibrosis arises from the misfolding and premature degradation of CFTR Delta F508, a Cl- ion channel with a single amino acid deletion. Yet, the quality-control machinery that selects CFTR Delta F508 for degradation and the mechanism for its misfolding are not well defined. We identified an ER membrane-associated ubiquitin ligase complex containing the E3 RMA1, the E2 Ubc6e, and Derlin-1 that cooperates with the cytosolic Hsc70/CHIP E3 complex to triage CFTR and CFTR Delta F508. Derlin-1 serves to retain CFTR in the ER membrane and interacts with RMA1 and Ubc6e to promote CFTR's proteasomal degradation. RMA1 is capable of recognizing folding defects in CFTR Delta F508 coincident with translation, whereas the CHIP E3 appears to act posttranslationally. A folding defect in CFTR Delta F508 detected by RMA1 involves the inability of CFTR's second membrane-spanning domain to productively interact with amino-terminal domains. Thus, the RMA1 and CHIP E3 ubiquitin ligases act sequentially in ER membrane and cytosol to monitor the folding status of CFTR and CFTR Delta F508.
The Regulation of INK4/ARF in Cancer and Aging
Creators: name: Sharpless, Norman E.
name: Kim, William Y.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Loss of the // locus on chromosome 9p21 is among the most frequent cytogenetic events in human cancer. The products of the locus—p15, p16, and ARF—play widespread and independent roles in tumor suppression. Recent data also suggest that expression of p16 induces an age-dependent decrease in the proliferative capacity of certain tissue-specific stem cells and unipotent progenitors. Here, we discuss the regulation and role of p16, ARF, and p15 in cancer and aging.
The Renormalization Group and its Finite Lattice Approximations
Creators: name: Cacciuto, A.
name: Gregory, E. B.
name: Travesset, A.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We investigate finite lattice approximations to the Wilson Renormalization Group in models of unconstrained spins. We discuss first the properties of the Renormalization Group Transformation (RGT) that control the accuracy of this type of approximations and explain different methods and techniques to practically identify them. We also discuss how to determine the anomalous dimension of the field. We apply our considerations to a linear sigma model in two dimensions in the domain of attraction of the Ising Fixed Point using a Bell-Wilson RGT. We are able to identify optimal RGTs which allow accurate computations of quantities such as critical exponents, fixed point couplings and eigenvectors with modest statistics. We finally discuss the advantages and limitations of this type of approach.
description: LaTeX file, 38 pages, 21 eps figures, uses epsfig
Symmetry Breaking in Coupled SYK or Tensor Models
Creators: name: Kim, Jaewon
name: Klebanov, Igor R.
name: Tarnopolsky, Grigory
name: Zhao, Wenli
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We study a large $N$ tensor model with $O(N)^3$ symmetry containing two flavors of Majorana fermions, $ψ_1^{abc}$ and $ψ_2^{abc}$. We also study its random counterpart consisting of two coupled Sachdev-Ye-Kitaev models, each one containing $N_{\rm SYK}$ Majorana fermions. In these models we assume tetrahedral quartic Hamiltonians which depend on a real coupling parameter $α$. We find a duality relation between two Hamiltonians with different values of $α$, which allows us to restrict the model to the range of $-1\leq α\leq 1/3$. The scaling dimension of the fermion number operator $Q=iψ_1^{abc} ψ_2^{abc}$ is complex and of the form $1/2 +i f(α)$ in the range $-1\leq α<0$, indicating an instability of the conformal phase. Using Schwinger-Dyson equations to solve for the Green functions, we show that in the true low-temperature phase this operator acquires an expectation value. This demonstrates the breaking of an anti-unitary particle-hole symmetry and other discrete symmetries. We also calculate spectra of the coupled SYK models for values of $N_{\rm SYK}$ where exact diagonalizations are possible. For negative $α$ we find a gap separating the two lowest energy states from the rest of the spectrum; this leads to exponential decay of the zero-temperature correlation functions. For $N_{\rm SYK}$ divisible by $4$, the two lowest states have a small splitting. They become degenerate in the large $N_{\rm SYK}$ limit, as expected from the spontaneous breaking of a $\mathbb{Z}_2$ symmetry.
description: 37 pages, v2: some improvements, references added. v3: added a discussion of separation of spectra into sectors and an Appendix on zero-energy states. The version to appear in Physical Review X
Edge electron states for quasi-one-dimensional organic conductors in the magnetic-field-induced spin-density-wave phases
Creators: name: Sengupta, K.
name: Kwon, Hyok-Jon
name: Yakovenko, Victor M.
Publisher: name: arXiv
Year: 2000
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We develop a microscopic picture of the electron states localized at the edges perpendicular to the chains in the Bechgaard salts in the quantum Hall regime. In a magnetic-field-induced spin-density-wave state (FISDW) characterized by an integer N, there exist N branches of chiral gapless edge excitations. Localization length is much longer and velocity much lower for these states than for the edge states parallel to the chains. We calculate the contribution of these states to the specific heat and propose a time-of-flight experiment to probe the propagating edge modes directly.
description: 4 pages, 2 figures. V.2: Minor changes to the final version published in PRL
C. elegans Telomeres Contain G-Strand and C-Strand Overhangs that Are Bound by Distinct Proteins
Creators: name: Karlseder, Jan
name: Dillin, Andrew
name: Raices, Marcela
name: Griffith, Jack D.
name: Compton, Sarah A.
name: Haggblom, Candy I.
name: Verdun, Ramiro E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Single-strand extensions of the G strand of telomeres are known to be critical for chromosome-end protection and length regulation. Here, we report that in , chromosome termini possess 3′ G-strand overhangs as well as 5′ C-strand overhangs. C tails are as abundant as G tails and are generated by a well-regulated process. These two classes of overhangs are bound by two single-stranded DNA binding proteins, CeOB1 and CeOB2, which exhibit specificity for G-rich or C-rich telomeric DNA. Strains of worms deleted for CeOB1 have elongated telomeres as well as extended G tails, whereas CeOB2 deficiency leads to telomere-length heterogeneity. Both CeOB1 and CeOB2 contain OB (oligo-saccharide/oligo-nucleotide binding) folds, which exhibit structural similarity to the second and first OB folds of the mammalian telomere binding protein hPOT1, respectively. Our results suggest that telomere homeostasis relies on a novel mechanism that involves 5′ and 3′ single-stranded termini.
Markov chain approach to anomalous diffusion on Newman-Watts networks
Creators: name: Allen-Perkins, Alfonso
name: Serrano, Alfredo Blanco
name: de Assis, Thiago Albuquerque
name: Pastor, Juan Manuel
name: Andrade, Roberto F. S.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences

description: A Markov chain (MC) formalism is used to investigate the mean-square displacement (MSD) of a random walker on Newman-Watts (NW) networks. It leads to a precise analysis of the conditions for the emergence of anomalous sub- or super-diffusive regimes in such random media. Whereas results provided by most numerical approaches used so far base their results on the computation of a large number of independent runs over many equivalent substrates, the MC framework is applied only once to each equivalent sample. Starting from the simple cycle graph with $2k$ nearest neighbor connections, for which exact MSD expressions within the MC formalism can be derived, the randomness and complexity of the substrate is easily controlled by the number $x$ of added links. Results for different values of $k$, $x$, and the number $N$ of nodes make it possible to distinguish actual anomalous regimes from transient behavior and finite size effects. Albeit the high computing cost restricts the size of our networks to $N\leq1500$ nodes, our very precise results justify a new and more comprehensive scaling ansatz for walker dynamics, from which the behavior for very large networks can be derived.
description: 24 pages, 13 figures
Cooperation of B Cell Lineages in Induction of HIV-1-Broadly Neutralizing Antibodies
Creators: name: Haynes, Barton F.
name: Lynch, Rebecca M.
name: Lu, Xiaozhi
name: Hraber, Peter
name: Kamanga, Gift
name: Montefiori, David C.
name: Alam, S. Munir
name: Song, Hongshuo
name: Hahn, Beatrice H.
name: Gao, Feng
name: Kelsoe, Garnett
name: Korber, Bette T.
name: Liao, Hua-Xin
name: Kwong, Peter D.
name: Ferrari, Guido
name: Bonsignori, Mattia
name: Xia, Shi-Mao
name: Hwang, Kwan-Ki
name: Moody, M. Anthony
name: Mascola, John R.
name: Shaw, George M.
name: Kumar, Amit
name: Berrong, Mark
name: Zhou, Tongqing
name: Kepler, Thomas B.
name: Cai, Fangping
name: Cohen, Myron S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Development of strategies for induction of HIV-1 broadly neutralizing antibodies (bnAbs) by vaccines is a priority. Determining the steps of bnAb induction in HIV-1-infected individuals who make bnAbs is a key strategy for immunogen design. Here we study the B cell response in a bnAb-producing individual, and report cooperation between two B cell lineages to drive bnAb development. We isolated an autologous virus-neutralizing antibody lineage that targeted an envelope region (loop D) and selected virus escape mutants that resulted in both enhanced bnAb lineage envelope binding and escape mutant neutralization—traits associated with increased B cell antigen drive. Thus, in this individual, two B cell lineages cooperated to induce the development of bnAbs. Design of vaccine immunogens that simultaneously drive both autologous and broadly neutralizing B cell lineages may be important for vaccine-induced recapitulation of events that transpire during the maturation of neutralizing antibodies in HIV-1-infected individuals.
The Chalker-Coddington Network Model is Quantum Critical
Creators: name: Marston, J. B.
name: Tsai, Shan-Wen
Publisher: name: arXiv
Year: 1998
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We show that the localization transition in the integer quantum Hall effect as described by the Chalker-Coddington network model is quantum critical. We first map the anisotropic network model to the problem of diagonalizing a one-dimensional non-Hermitian non-compact supersymmetric lattice Hamiltonian of interacting bosons and fermions. Its behavior is investigated numerically using the density matrix renormalization group method, and critical behavior is found at the plateau transition. This result is confirmed by an exact, analytic, generalization of the Lieb-Schultz-Mattis theorem.
description: Version accepted for publication in PRL. 4 pages, 2 eps figures
Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications
Creators: name: Ringel, Yehuda
name: Bäckhed, Fredrik
name: Fraser, Claire M.
name: Young, Vincent
name: Sanders, Mary Ellen
name: Sherman, Philip M.
name: Sartor, R. Balfour
name: Versalovic, James
name: Finlay, B. Brett
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Indigenous microbiota are an essential component in the modern concept of human health, but the composition and functional characteristics of a healthy microbiome remain to be precisely defined. Patterns of microbial colonization associated with disease states have been documented, but the health-associated microbial patterns and their functional characteristics are less clear. A healthy microbiome, considered in the context of body habitat or body site, could be described in terms of ecologic stability (i.e., ability to resist community structure change under stress or to rapidly return to baseline following a stress-related change), by an idealized (presumably health-associated) composition or by a desirable functional profile (including metabolic and trophic provisions to the host). Elucidation of the properties of healthy microbiota would provide a target for dietary interventions and/or microbial modifications aimed at sustaining health in generally healthy populations and improving the health of individuals exhibiting disrupted microbiota and associated diseases.
Molecular motor that never steps backwards
Creators: name: Porto, Markus
name: Urbakh, Michael
name: Klafter, Joseph
Publisher: name: arXiv
Year: 2000
Subjects: subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: We investigate the dynamics of a classical particle in a one-dimensional two-wave potential composed of two periodic potentials, that are time-independent and of the same amplitude and periodicity. One of the periodic potentials is externally driven and performs a translational motion with respect to the other. It is shown that if one of the potentials is of the ratchet type, translation of the potential in a given direction leads to motion of the particle in the same direction, whereas translation in the opposite direction leaves the particle localized at its original location. Moreover, even if the translation is random, but still has a finite velocity, an efficient directed transport of the particle occurs.
description: 4 pages, 5 figures, Phys. Rev. Lett. (in print)
Microbiota and Host Nutrition across Plant and Animal Kingdoms
Creators: name: Ackermann, Gail
name: González, Antonio
name: Schulze-Lefert, Paul
name: Lebeis, Sarah
name: Dangl, Jeffrey L.
name: Spaepen, Stijn
name: McHardy, Alice C.
name: Hacquard, Stéphane
name: Garrido-Oter, Ruben
name: Knight, Rob
name: Ley, Ruth
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Plants and animals each have evolved specialized organs dedicated to nutrient acquisition, and these harbor specific bacterial communities that extend the host's metabolic repertoire. Similar forces driving microbial community establishment in the gut and plant roots include diet/soil-type, host genotype, and immune system as well as microbe-microbe interactions. Here we show that there is no overlap of abundant bacterial taxa between the microbiotas of the mammalian gut and plant roots, whereas taxa overlap does exist between fish gut and plant root communities. A comparison of root and gut microbiota composition in multiple host species belonging to the same evolutionary lineage reveals host phylogenetic signals in both eukaryotic kingdoms. The reasons underlying striking differences in microbiota composition in independently evolved, yet functionally related, organs in plants and animals remain unclear but might include differences in start inoculum and niche-specific factors such as oxygen levels, temperature, pH, and organic carbon availability.
Phase diagram for a class of spin-half Heisenberg models interpolating between the square-lattice, the triangular-lattice and the linear chain limits
Creators: name: Weihong, Zheng
name: McKenzie, Ross H.
name: Singh, Rajiv R. P
Publisher: name: arXiv
Year: 1998
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We study the spin-half Heisenberg models on an anisotropic two-dimensional lattice which interpolates between the square-lattice at one end, a set of decoupled spin-chains on the other end, and the triangular-lattice Heisenberg model in between. By series expansions around two different dimer ground states and around various commensurate and incommensurate magnetically ordered states, we establish the phase diagram for this model of a frustrated antiferromagnet. We find a particularly rich phase diagram due to the interplay of magnetic frustration, quantum fluctuations and varying dimensionality. There is a large region of the usual 2-sublattice Neél phase, a 3-sublattice phase for the triangular-lattice model, a region of incommensurate magnetic order around the triangular-lattice model, and regions in parameter space where there is no magnetic order. We find that the incommensurate ordering wavevector is in general altered from its classical value by quantum fluctuations. The regime of weakly coupled chains is particularly interesting and appears to be nearly critical.
description: RevTeX, 15 figures
Additional file 2 of Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response
Creators: name: Zhang, Zhen
name: Wang, Zi-Xian
name: Chen, Yan-Xing
name: Wu, Hao-Xiang
name: Yin, Ling
name: Zhao, Qi
name: Luo, Hui-Yan
name: Zeng, Zhao-Lei
name: Qiu, Miao-Zhen
name: Xu, Rui-Hua
Publisher: name: figshare
Year: 2022
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 2: Figure S1. Boxplots depicting the correlation of immune cells infiltration with Stem.Sig and TMB. Figure S2. Subgroup analysis of testing set. Figure S3. Correlation plot of Stem.Sig and other stemness signatures. Figure S4. Association Stem.Sig and expression level of TLS-related genes.