cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Orchestina shuar Izquierdo 2017, new species
Creators: name: Izquierdo, Matías Andrés
name: Ramírez, Martín J.
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Araneae
Oonopidae
Orchestina
Orchestina shuar

description: Orchestina shuar Izquierdo, new species   Figures 65D–G, 93G–I, 100J–L, map 10
TYPES: Male holotype from Ecuador: Orellana, Tiputini Biodiversity Station, near Yasuní National Park, 250 m, -0.63194°, -76.14416°, July 04, 1998, T. Erwin et al., deposited in USNM, PBI_OON 37647; 1 km S Onkone Gare Camp, Reserva Etnica Waorani, 216 m, -0.65715°, -76.45300°, Oct. 08, 1995, T. Erwin et al., 1 male paratype deposited in USNM, PBI_OON 30217.
 ETYMOLOGY: A noun in apposition; Shuar are indigenous inhabitants of Ecuador and Peru.
 DIAGNOSIS: Males resemble to those of O. mancocapac by having a strong apophysis, covered by short cusps on the copulatory bulb (fig. 93G–I), but in O. shuar this apophysis is longer and cylindrical.
MALE (PBI_OON 37647): Total length 1.13. Habitus as in figure 65A. CEPHALOTHORAX (fig. 65D–G): Carapace orange. Clypeus slightly sinuous in frontal view. Sternum as long as wide. Anterior face of chelicerae with basal anterior blunt projections, promargin with cuticular projections (fig. 65F, G, arrow). Labium rectangular. Endites anteromedian tip with one strong, toothlike projection. ABDOMEN: Pale white. LEGS: Yellow. GENITALIA: Bulb tapering apically, with one strong, huge apophysis covered by short cuticular projections; embolus light, base with one short, spine-shaped apophysis; sperm duct coiled, with many loops (figs. 93G–I, 100J–L).
FEMALE: Unknown; females of morphospecies MI020, MI022–MI023, MI025–MI027, MI029, MI036, and MI038 from the same area are candidates to match this male.
DISTRIBUTION: Known from the province of Orellana in Ecuador (map 10).
 OTHER MATERIAL EXAMINED: ECUADOR: Orellana: 1 km S Onkone Gare Camp, Reserva Etnica Waorani, 216 m, -0.65715°, -76.45300°, June 25, 1996, T. Erwin et al., 13 (USNM PBI _OON 30433); same data, Feb. 13, 1996, T. Erwin et al., 13 (USNM, PBI _ OON 37650); same data, only one palp is in the vial (USNM, PBI _OON 30013); same data, Feb. 08, 1996, T. Erwin et al., 13 (USNM, PBI _OON 37651); same data, Oct. 21, 1998, T. Erwin et al., 13 (USNM, PBI _OON 37648); same data, July 05, 1998, T. Erwin et al., 13 (USNM, PBI _OON 37649).
description: Published as part of Izquierdo, Matías Andrés & Ramírez, Martín J., 2017, Taxonomic Revision Of The Jumping Goblin Spiders Of The Genus Orchestina Simon, 1882, In The Americas (Araneae: Oonopidae), pp. 1 in Bulletin of the American Museum of Natural History 2017 (410) on page 1, DOI: 10.1206/0003-0090-410.1.1, http://zenodo.org/record/5405613
Fluxes of cosmic rays: A delicately balanced stationary state
Creators: name: Tsallis, Constantino
name: Anjos, Joao C.
name: Borges, Ernesto P.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Astrophysics (astro-ph)
subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: The analysis of cosmic rays fluxes as a function of energy reveals a {\it knee} slightly below $10^{16}$ eV and an {\it ankle} close to $10^{19}$ eV. Their physical origins remain up to now quite enigmatic; in particular, no elementary process is known which occurs at energies close to $10^{16}$ eV. We propose a phenomenological approach along the lines of nonextensive statistical mechanics, a formalism which contains Boltzmann-Gibbs statistical mechanics as a particular case. The knee then appears as a crossover between two fractal-like thermal regimes, the crossover being caused by process occurring at energies ten million times lower than that of the knee, in the region of the quark hadron transition ($\simeq 10^{9}$ eV). This opens the door to an unexpected standpoint for further clarifying the phenomenon.
description: RevTeX, 10 pages including 1 eps figure
Signatures of the neutral top-pion in $eγ$ collisions
Creators: name: Yue, Chongxing
name: Li, Hong
name: Wang, Xuelei
Publisher: name: arXiv
Year: 2001
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We calculate the contributions of the neutral top-pion $π_{t}^0$ to the process $e^-γ\to e^-\bar{t}c$ in the framework of topcolor-assisted technicolor(TC2) models and discuss the possible of detecting $π_t^0$ at the high energy linear $e^+e^-$ collider(LC). Our results show that $π_t^0$ can give significant contributions to this process. With reasonable values of the parameters in TC2 models, the cross section $σ$ can reach 0.19 fb which may be detected at the $eγ$ collisions based on the future LC experiments.
description: latex files,11 pages, 3 figures
Additional file 1 of Estimation of renal perfusion based on measurement of rubidium-82 clearance by PET/CT scanning in healthy subjects
Creators: name: Langaa, Stine Sundgaard
name: Lauridsen, Thomas Guldager
name: Mose, Frank Holden
name: Fynbo, Claire Anne
name: Theil, Jørn
name: Bech, Jesper Nørgaard
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology

description: Additional file 1. Appendix: 82Rb-phantom studies for determination of recovery-coefficients.
Additional file 1 of Serial markers of coagulation and inflammation and the occurrence of clinical pulmonary thromboembolism in mechanically ventilated patients with SARS-CoV-2 infection; the prospective Maastricht intensive care COVID cohort
Creators: name: Mulder, Mark M. G.
name: Brandts, LIoyd
name: Brüggemann, Renée A. G.
name: Koelmann, Marcel
name: Streng, Alexander S.
name: Olie, Renske H.
name: Gietema, Hester A.
name: Spronk, Henri M. H.
name: van der Horst, Iwan C. C.
name: Sels, Jan-Willem E. M.
name: Wildberger, Joachim E.
name: van Kuijk, Sander M. J.
name: Schnabel, Ronny M.
name: ten Cate, Hugo
name: Henskens, Yvonne M. C.
name: van Bussel, Bas C. T.
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Physiology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1: Supplemental Table 1. General characteristics of the Maastricht Intensive Care COVID (MaastrICCht) cohort. Supplemental Table 2. The linear mixed-effects models, with step-by-step adjustments, show the difference in fibrinogen, d-dimer, c-reactive protein, and ferritin concentration development over time between mechanically ventilated patients developing a confirmed or suspected pulmonary thrombotic event in comparison with patients lacking this development. Patients who had been discharged to the ICU of another hospital were omitted.
Chiral Extrapolation of Lattice Data for Heavy Baryons
Creators: name: Guo, X. -H.
name: Thomas, A. W.
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The masses of heavy baryons containing a b quark have been calculated numerically in lattice QCD with pion masses which are much larger than its physical value. In the present work we extrapolate these lattice data to the physical mass of the pion by applying the effective chiral Lagrangian for heavy baryons, which is invariant under chiral symmetry when the light quark masses go to zero and heavy quark symmetry when the heavy quark masses go to infinity. A phenomenological functional form with three parameters, which has the correct behavior in the chiral limit and appropriate behavior when the pion mass is large, is proposed to extrapolate the lattice data. It is found that the extrapolation deviates noticably from the naive linear extrapolation when the pion mass is smaller than about 500MeV. The mass differences between Sigma_b and Sigma_b^* and between Sigma_b^{(*)} and Lambda_b are also presented. Uncertainties arising from both lattice data and our model parameters are discussed in detail. We also give a comparision of the results in our model with those obtained in the naive linear extrapolations.
description: 29 pages, 9 figures
Additional file 1 of Ecotoxicity evaluation of polymeric nanoparticles loaded with ascorbic acid for fish nutrition in aquaculture
Creators: name: Luis, Angélica I. S.
name: Campos, Estefânia V. R.
name: Oliveira, Jhones L.
name: Vallim, José Henrique
name: Proença, Patrícia L. F.
name: Castanha, Rodrigo F.
name: de Castro, Vera L. S. S.
name: Fraceto, Leonardo F.
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry

description: Additional file 1: Figure S1. Morphological abnormalities (pericardial edema, skin lesions, undeveloped tail, tail alterations, and bent spine) observed in the zebrafish embryos and larvae exposed to the different treatments at concentrations of 25, 50, and 100 mg/mL: non-encapsulated ascorbic acid (AA), chitosan nanoparticles (NPs_CS), chitosan nanoparticles containing AA (NPs_CS_AA), PCL nanoparticles (NPs_PCL), and PCL nanoparticles containing AA (NPs_PCL_AA). The images were acquired using a stereomicroscope (Model SMZ 2 LED, Optika), at 2x magnification. Figure S2. Morphological abnormalities (yolk sac malformation and edema, pericardial edema, opaque yolk, tail malformation, and bent spine) observed in the zebrafish embryos and larvae exposed to the different treatments: non-encapsulated ascorbic acid (AA), chitosan nanoparticles (NPs_CS), chitosan nanoparticles containing AA (NPs_CS_AA), PCL nanoparticles (NPs_PCL), and PCL nanoparticles containing AA (NPs_PCL_AA). The images were acquired using a stereomicroscope (Model SMZ 2 LED, Optika), at 2x magnification.
Additional file 3: of Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions
Creators: name: Deforges, Jules
name: Reis, Rodrigo
name: Jacquet, Philippe
name: Vuarambon, Dominique
name: Poirier, Yves
Publisher: name: figshare
Year: 2019
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Figure S3. Analysis of co-expression networks by WGCNA clustering. A, The 17 co-expression networks constructed by WGCNA were indicated by arbitrary numbers on the left side of the table. The correlation between expression of the genes of each cluster and the different experimental conditions tested is indicated by a red to green color gradient. Bright red indicates a strong correlation, meaning that most of the genes of the cluster are up-regulated specifically in a given condition. On the opposite, dark green indicates a strong anti-correlation, meaning that most of the genes of the cluster are specifically down-regulated in a given condition. As example, genes from cluster 9 (squared in black) are induced specifically upon Pi starvation while genes associated with the cluster 14 are specifically down-regulated under the same condition. B, Network view of the genes belonging to the cluster 9. Only the TAIR10 genes associated with the GO term â response to Pi starvationâ (blue) are shown, along with the lincRNAs identified by this study (green) or present in the TAIR10 database (red). When a lincRNA was found correlated with a putative target coding gene that was also present in the same cluster, the gene was reported and colored in purple. The nature of the correlation is indicated in legend (upper right box). The size of each octagon indicated the maximum expression level (normalized read count) across the 12 experimental conditions analysis. (PDF 5992 kb)
Additional file 3 of Circular RNA circCCDC9 acts as a miR-6792-3p sponge to suppress the progression of gastric cancer through regulating CAV1 expression
Creators: name: Luo, Zai
name: Rong, Zeyin
name: Zhang, Jianming
name: Zhu, Zhonglin
name: Yu, Zhilong
name: Li, Tengfei
name: Fu, Zhongmao
name: Qiu, Zhengjun
name: Huang, Chen
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 3: Table S3. Correlation between circCCDC9 expression and clinicopathological features in 54 GC tissues from TMA
Acar plicata
Creators: name: Yasser, Amaal Gh.
name: Naser, Murtada D.
name: Abdul-Sahib, Ibtisam M.
name: Abdullah, Dawood S.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Bivalvia
Arcida
Arcidae
Acar
Acar plicata

description: Acar plicata (Dillwyn, 1817)
(Fig. 1A)
Material examined: 6 specimens, length= 28mm, (MSC:500).
Shell description
Often subrectangular and anteriorly decreased. Coarse sculpture composed of lamellae interlaced with radial riblets. Adductor vehicles were lifted somewhat. White to buff with orange or pink undertones.
Habitat: Lower coast and below: adhering to corals and rocks.
Distribution: all (Fig. 2).
description: Published as part of Yasser, Amaal Gh., Naser, Murtada D., Abdul-Sahib, Ibtisam M. & Abdullah, Dawood S., 2023, New records of bivalves from the Iraqi coast, pp. 50-54 in Ecologica Montenegrina 62 on page 51, DOI: 10.37828/em.2023.62.7, http://zenodo.org/record/8044369
DDW Order and its Role in the Phase Diagram of Extended Hubbard Models
Creators: name: Nayak, Chetan
name: Pivovarov, Eugene
Publisher: name: arXiv
Year: 2002
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We show in a mean-field calculation that phase diagrams remarkably similar to those recently proposed for the cuprates arise in simple microscopic models of interacting electrons near half-filling. The models are extended Hubbard models with nearest neighbor interaction and correlated hopping. The underdoped region of the phase diagram features $d_{{x^2}-{y^2}}$ density-wave (DDW) order. In a certain regime of temperature and doping, DDW order coexists with antiferromagnetic (AF) order. For larger doping, it coexists with $d_{{x^2}-{y^2}}$ superconductivity (DSC). While phase diagrams of this form are robust, they are not inevitable. For other reasonable values of the coupling constants, drastically different phase diagrams are obtained. We comment on implications for the cuprates.
description: 7 pages, 3 figures
Additional file 2: of Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions
Creators: name: Deforges, Jules
name: Reis, Rodrigo
name: Jacquet, Philippe
name: Vuarambon, Dominique
name: Poirier, Yves
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Evolutionary 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: 69999 Biological Sciences not elsewhere classified
subject: 60506 Virology
subject: Computational Biology

description: Figure S2. Evolutionary conservation of newly identified lincRNAs. Conservation of the nucleotide sequence of newly identified lincRNAs. The conservation index is shown on the top right and is represented has a heatmap with the colors indicating the -log of the E-value of the best blastn hit between each lincRNA and each of the 10 plant species analyzed and listed at the bottom. In the lower panel, lincRNAs were clustered into 4 groups (kmeans) and the average of the -log of the E-value is indicated for each cluster on the lower panel, using the same color code as above. (PDF 5992 kb)
Additional file 1 of Exploring intervention components in association with changes in preschool children’s vegetable intake: the BRA-study
Creators: name: Kristiansen, Anne Lene
name: Himberg-Sundet, Anne
name: Bjelland, Mona
name: Lien, Nanna
name: Holst, René
name: Andersen, Lene Frost
Publisher: name: figshare
Year: 2021
Subjects: subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1: Figure S1. Estimated marginal means of the BRA-study, showing vegetables served in the kindergarten departments (n = 34) at baseline and follow-up 1, in relation to what degree the intervention components (posters, supplementary material and 1-day inspirational course) were perceived useful by the kindergarten staff. (Black box) Baseline data, (Orange dotted box) Follow-up 1 data.
Distortions in the negative energy Dirac sea: violation of the Gottfried sum rule and $Δ\bar{u}$ in proton
Creators: name: Tsushima, K.
name: Thomas, A. W.
name: Dunne, G. V.
Publisher: name: arXiv
Year: 2001
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Theory (hep-th)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We report on recent work concerning the effect which the change in vacuum structure (negative energy Dirac sea), in the presence of a confining scalar field, has on the nucleon structure functions and parton distributions. Using the Dirac equation in 1+1 dimensions, we show that distortions in the Dirac sea are responsible for part of the violation of the Gottfried sum rule -- i.e., part of the flavor asymmetry in the proton sea. Our basic argument is that, even if isospin is an exact symmetry, the presence of a confining potential changes the vacuum structure, and inevitably leads to a violation of SU(2) flavour symmetry in a hadron with a different number of valence $u$ and $d$ quarks. The same mechanism also leads to a prediction for $Δ\bar{u}$ and $Δ\bar{d}$.
description: A sentence was corrected. 8 pages, 2 figures, uses sprocl.sty. Presented at the Joint Workshop of the Special Research Center for the Subatomic Structure of Matter (CSSM) and the National Institute for Theoretical Physics on Lepton Scattering, Hadrons and QCD, March 26 - April 6, 2001, Adelaide, Australia. To be published in the Proceedings
Production of multi-charmed hadrons by recombination in heavy ion collisions
Creators: name: Cho, Sungtae
name: Lee, Su Houng
Publisher: name: arXiv
Year: 2019
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: We study the production of multi-charmed hadrons by recombination in heavy ion collisions by focusing on the production of $Ξ_{cc}$, $Ξ_{cc}^*$, $Ω_{scc}$, $Ω_{scc}^*$, $Ω_{ccc}$ baryons and X(3872) mesons. Starting from the estimation of yields for those hadrons at chemical freeze-out in both the statistical and coalescence model, we evaluate their transverse momentum distributions at mid-rapidity in the coalescence model. We show that yields of multi-charmed hadrons in heavy ion collisions at RHIC and LHC are large enough, and thereby not only multi-charmed hadrons observed so far, e.g., the $Ξ_{cc}$ but also those which have not been observed yet, can be discovered sufficiently in heavy ion collisions. We also find that the transverse momentum distribution ratio between various multi-charmed hadrons sensitively reflects the interplay between quark contents of corresponding hadrons as well as the transverse momentum distribution of charm quarks at the hadronization point, and therefore we insist that studying both the transverse momentum distributions of multi-charmed hadrons themselves and transverse momentum distribution ratios between various multi-charmed hadrons provide us with useful information on hadron production mechanism involving charm quarks in heavy ion collisions.
description: 20 pages, 9 figures
New Constraints on the running-mass inflation model
Creators: name: Covi, Laura
name: Lyth, David H.
name: Melchiorri, Alessandro
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We evaluate new observational constraints on the two-parameter scale-dependent spectral index predicted by the running-mass inflation model by combining the latest Cosmic Microwave Background (CMB) anisotropy measurements with the recent 2dFGRS data on the matter power spectrum, with Lyman $α$ forest data and finally with theoretical constraints on the reionization redshift. We find that present data still allow significant scale-dependence of $n$, which occurs in a physically reasonable regime of parameter space.
description: 9 pages, 7 figures
Additional file 1 of Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper
Creators: name: Kim, Myung-Shin
name: Chae, Geun Young
name: Oh, Soohyun
name: Kim, Jihyun
name: Mang, Hyunggon
name: Kim, Seungill
name: Choi, Doil
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Outline of the genome assembly and annotation workflow. Figure S2. Distribution of 19-mer frequency in two pepper cultivars. Figure S3. Comparison of gene models of five different pepper cultivars. Figure S4. The top 20 highest number of genes containing functional domains shared by CM334, ECW, SF, Zunla-1, and Chiltepin in Capsicum annuum. Figure S5. Gene ontology enrichment analyses of unclustered genes in pepper accessions. Figure S6. The number of genes containing functional domains specific to CM334, Chiltepin, and Zunla-1. Figure S7. PCR and sequencing validation for CNV of NLRs.
Additional file 1 of The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster
Creators: name: Luo, Shiqi
name: Zhang, Hong
name: Duan, Yuange
name: Yao, Xinmin
name: Clark, Andrew
name: Lu, Jian
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: Developmental Biology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1: Figure S1. Tajima’s D in 10 kb bins in each population. Figure S2. Fay and Wu’s H in 10 kb bins in each population. Figure S3. The composite likelihood ratio (CLR) with a grid size of 10 kb in each population. Figure S4. Signatures of natural selection on the novel TE insertion located on chr3R: 15380492–15,380,496 in N population. Figure S5. Multidimensional scaling (MDS) of known (a) or novel (b) TE insertions across GDL strains. Figure S6. Percentages of reads (y-axis) that are mapped to all the sources of TE sequences with different map length and identity. Figure S7. Coverage of weighted piRNAs mapped to the sense (red) and anti-sense (blue) of piRNA cluster flamenco in 10 GDL strains. Figure S8. Coverage of weighted piRNAs mapped to the sense (red) and anti-sense (blue) of piRNA cluster 42AB in 10 GDL strains. Figure S9. Barplots showing the RPKMs of de novo piRNAs generated in the flanking region (2 kb) of novel TE insertions across 10 GDL strains. Figure S10. Barplots showing the RPKMs of de novo siRNAs generated in the flanking region (2 kb) of novel TE insertions. Figure S11. Longer TEs tend to be targeted by higher densities of piRNAs in the 10 GDL strains. Figure S12. The fitness of host organisms (left) and number of TEs carried by one chromosome when selection is weak (s = 0.5, upper) or strong (s = 20, lower). Figure S13. Numbers (y-axis) of TEs (blue), piTEs (pink, these are TEs that are piRNA-repressed), effective TEs (cyan) accumulated in one chromosome along the generations (x-axis) in the simulations. Table S1. Genome features of all novel TE insertions on all chromosomes. Table S2. Candidate hitchhiking events associated with TE insertions in local populations. Table S3. Mapping summary of sequenced small RNAs in the 10 GDL and 16 DGRP strains.
Perturbation theory and renormalisation group equations
Creators: name: Litim, Daniel F.
name: Pawlowski, Jan M.
Publisher: name: arXiv
Year: 2001
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We discuss the perturbative expansion of several one-loop improved renormalisation group equations. It is shown that in general the integrated renormalisation group flows fail to reproduce perturbation theory beyond one loop.
description: 5 pages, 1 figure, revtex, typos corrected, eq. (19) added, discussion extended, to appear in PRD
Additional file 1: of Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions
Creators: name: Deforges, Jules
name: Reis, Rodrigo
name: Jacquet, Philippe
name: Vuarambon, Dominique
name: Poirier, Yves
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Hematology
subject: 60506 Virology

description: Figure S1. Analysis of the degree of overlap in lincRNAs identified in distinct studies. Venn diagram showing the number of lincRNAs identified in our study (blue area) that overlap at least partially, on the same strand, to a noncoding RNA reported in Yuan et al. (BMC Genomics 17, 655, 2016) (green area), in Li et al. (Dev. Cell 39, 508, 2016) (pink) or in Bazin et al. (Proc. Natl. Acad. Sci. USA 114, E10018, 2017) (red). (PDF 5992 kb)
Additional file 3 of Predicting breast cancer drug response using a multiple-layer cell line drug response network model
Creators: name: Huang, Shujun
name: Hu, Pingzhao
name: Lakowski, Ted M.
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Hematology
subject: 110309 Infectious Diseases
subject: Computational Biology

description: Additional file 3: Figure S1. Correlations of cell line pairs, tumor pairs and cell line-tumor pairs. (a) The pairwise Pearson correlation of the 49 BC cell lines from GDSC was calculated based on their gene expression profiles. (b) The pairwise Pearson correlation of the 1100 BC samples from TCGA was calculated based their gene expression profiles. (c) The pairwise Pearson correlation between the 49 BC cell lines and the 1100 BC samples was calculated based their gene expression profiles. (d) The pairwise Pearson correlation of the 49 BC cell lines was calculated based on their pathway activity profiles. (e) The pairwise Pearson correlation of the 1100 BC samples from TCGA was calculated based their pathway activity profiles. (f) The pairwise Pearson correlation between the 49 BC cell lines and the 1100 BC samples was calculated based their pathway activity profiles.
Dark Matter through the Higgs portal
Creators: name: Arcadi, Giorgio
name: Djouadi, Abdelhak
name: Raidal, Martti
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We review scenarios in which the particles that account for the Dark Matter (DM) in the Universe interact only through their couplings with the Higgs sector of the theory, the so-called Higgs-portal models. In a first step, we use a general and model-independent approach in which the DM particles are singlets with spin $0,\frac12$ or $1$, and assume a minimal Higgs sector with the presence of only the Standard Model (SM) Higgs particle observed at the LHC. In a second step, we discuss non-minimal scenarios in which the spin-$\frac12$ DM particle is accompanied by additional lepton partners and consider several possibilities like sequential, singlet-doublet and vector-like leptons. In a third step, we examine the case in which it is the Higgs sector of the theory which is enlarged either by a singlet scalar or pseudoscalar field, an additional two Higgs doublet field or by both; in this case, the matter content is also extended in several ways. Finally, we investigate the case of supersymmetric extensions of the SM with neutralino DM, focusing on the possibility that the latter couples mainly to the neutral Higgs particles of the model which then serve as the main portals for DM phenomenology. In all these scenarios, we summarize and update the present constraints and future prospects from the collider physics perspective, namely from the determination of the SM Higgs properties at the LHC and the search for its invisible decays into DM, and the search for heavier Higgs bosons and the DM companion particles at high-energy colliders. We then compare these results with the constraints and prospects obtained from the cosmological relic abundance as well as from direct and indirect DM searches in astroparticle physics experiments. The complementarity of collider and astroparticle DM searches is investigated in all the considered models.
description: 260 pages, 105 figures. The review is open to comments and suggestions
A Variational Bayes Approach to Clustered Latent Preference Models for Directed Network Data
Creators: name: Lee, Jaron Jia Rong
Publisher: name: The Australian National University
Year: 2016

description: Variational Bayes (VB) refers to a framework used to make fast deterministic approximations to the posterior density for Bayesian statistical inference. Traditionally, it has competed with Markov Chain Monte Carlo (MCMC) methods, a stochastic method which is asymptotically correct but computationally expensive. We derive the VB approximation to the Directed Clustered Latent Preference Network Model, which is inspired by ideas from Hoff et al. (2002); Handcock et al. (2007); Ward and Hoff (2007); Salter-Townshend and Murphy (2013); Krivitsky and Handcock (2008). The model handles binary-valued or continuous directed network data, and incorporates Gaussian mixture models over the separate latent sending and receiving preference spaces of each actor. We apply the model to simulated and real datasets to evaluate its performance against ex- isting MCMC methods such as the Gibbs sampler. We discover new insights in the well-studied Sampson’s Monks dataset (Sampson, 1968), as well as confirm existing results with the Correlates of War International Trade dataset (Barbieri and Keshk, 2012). We conclude by discussing unresolved issues, potential solutions, and areas of future work.
Excitons and Excitonic Molecules in Mixed $Zn(P_{1-x}As_{x})_{2}$ Crystals
Creators: name: Yeshchenko, O. A.
name: Biliy, M. M.
name: Yanchuk, Z. Z.
Publisher: name: arXiv
Year: 2001
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Low-temperature (1.8 K) excitonic absorption, reflection and photoluminescence spectra of mixed $Zn(P_{1 - x}As_{x})_{2}$ crystals were studied at $x = $0.01, 0.02, 0.03 and 0.05. Energy gap and rydbergs of excitonic B, C and A-series decrease monotonically at the increase of $x$. Spectral half-widths of absorption $n = 1$ lines of B and A-series increase monotonically at the increase of $x$ due to fluctuations of crystal potential. Emission lines of excitonic molecules were observed in photoluminescence spectra of $Zn(P_{1 - x}As_{x})_{2}$ crystals. Binding energy of molecule increases at the increase of $x$ that is due to the decrease of the electron-hole mass ratio.
description: 10 pages, 7 figures, paper submitted to Physica B: Condensed Matter
Anisotropic Tensor Renormalization Group
Creators: name: Adachi, Daiki
name: Okubo, Tsuyoshi
name: Todo, Synge
Publisher: name: arXiv
Year: 2019
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Computational Physics (physics.comp-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We propose a new tensor renormalization group algorithm, Anisotropic Tensor Renormalization Group (ATRG), for lattice models in arbitrary dimensions. The proposed method shares the same versatility with the Higher-Order Tensor Renormalization Group (HOTRG) algorithm, i.e., it preserves the lattice topology after the renormalization. In comparison with HOTRG, both of the computation cost and the memory footprint of our method are drastically reduced, especially in higher dimensions, by renormalizing tensors in an anisotropic way after the singular value decomposition. We demonstrate the ability of ATRG for the square lattice and the simple cubic lattice Ising models. Although the accuracy of the present method degrades when compared with HOTRG of the same bond dimension, the accuracy with fixed computation time is improved greatly due to the drastic reduction of the computation cost.
description: 6 pages, 9 figures
Orchestina predator Izquierdo 2017, new species
Creators: name: Izquierdo, Matías Andrés
name: Ramírez, Martín J.
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Araneae
Oonopidae
Orchestina
Orchestina predator

description: Orchestina predator Izquierdo, new species   Figures 86, 97A–C, 102A–C, map 10
TYPE: Male holotype from Ecuador: Orellana: 1 km S Onkone Gare Camp, Reserva Etnica Waorani, 216 m, -0.65715°, -76.45300°, July 06, 1995, T. Erwin et al., deposited in USNM, PBI_ OON 30229.
 ETYMOLOGY: A noun in apposition; the name is a reference to the modifications of chelicerae reminiscent of those of the genus Predatoroonops Brescovit et al. (2012).
DIAGNOSIS: Males can be distinguished by the following combination of characters: carapace with two sclerotized stripes on both sides (fig. 86D), clypeus sinuous (fig. 86C), chelicerae strong, modified, with swollen median part and a projection on the promargin (fig. 86C, D), cheliceral fangs slightly sinuous with bifid tips, copulatory bulb with short embolus and a short, strong, prolateral spinelike apophysis (figs. 97A– C, 102A–C).
MALE (PBI_OON 30229): Total length 1.11. CEPHALOTHORAX (fig. 86): Carapace with sclerotized stripes along margin of cephalic area, wide in dorsal view (fig. 86A), anteriorly narrowed to 0.49× its maximum width or less. Clyp- eus sinuous in front view, vertical in lateral view (fig. 86C, D). Sternum wider than long (fig. 86B). Chelicerae, endites, labium orange-brown. Chelicerae anterior face with swollen median part, promargin with cuticular projections, fang tips bifurcated (fig. 86C, D). Labium rectangular.
LEGS: Yellow. GENITALIA: Palp proximal segments yellow; cymbium yellow; bulb with one short, spine-shaped apophysis near base of embolus; embolus light, short; sperm duct slightly coiled (figs. 97A–C, 102A–C).
FEMALE: Unknown; females of morphospecies MI020–MI027, MI029, MI036, and MI038 from the same area are candidates to match this male.
DISTRIBUTION: Known only from the type locality in Ecuador (Orellana, map 10).
OTHER MATERIAL EXAMINED: Same data as holotype, Oct. 08, 1995, T. Erwin et al., 13 (USNM, PBI_ OON 43278).
description: Published as part of Izquierdo, Matías Andrés & Ramírez, Martín J., 2017, Taxonomic Revision Of The Jumping Goblin Spiders Of The Genus Orchestina Simon, 1882, In The Americas (Araneae: Oonopidae), pp. 1 in Bulletin of the American Museum of Natural History 2017 (410) on page 1, DOI: 10.1206/0003-0090-410.1.1, http://zenodo.org/record/5405613
t -> c H^0 decay in the general two Higgs doublet model
Creators: name: Iltan, E. O.
Publisher: name: arXiv
Year: 2001
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study the flavor changing t -> c H^0 decay in the framework of the general two Higgs doublet model, so called model III. Here, we take the Yukawa couplings complex and switch on the CP violating effects. We predict the branching ratio six orders larger compared to the one calculated in the SM, namely BR ~ 10^{-7}, and observe a measurable CP asymmetry, at the order of 10^{-2}.
description: 7 pages, 6 figures
Additional file 1: of Two decades of variable retention in British Columbia: a review of its implementation and effectiveness for biodiversity conservation
Creators: name: Beese, William
name: Deal, John
name: B. Dunsworth
name: Mitchell, Stephen
name: Philpott, Timothy
Publisher: name: figshare
Year: 2019
Subjects: subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Science Policy

description: Supplementary materials, Appendices A - D. (PDF 809 kb)
Additional file 2 of Exploring the mechanisms of collaboration between the Tuberculosis and Diabetes Programs for the control of TB-DM Comorbidity in Ghana
Creators: name: Salifu, Rita Suhuyini
name: Hlongwana, Khumbulani W.
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: Computational Biology

description: Additional file 2. Interview guide 2- Policy Makers.
Connecting Learning Analytics and Problem-Based Learning – Potentials and Challenges
Creators: name: Kilińska, Daria
name: Ryberg, Thomas
Publisher: name: Journal of Problem Based Learning in Higher Education
Year: 2019

description: Learning analytics (LA) are a young but fast-growing field, which, according to some authors, holds big promises for education. Some claim that LA solutions can help measure and support constructivist classrooms and 21st century skills, thus creating a potential of making an alignment between LA and PBL principles and practices. Despite this argument, LA have not yet gained much interest among the Problem-Based Learning (PBL) practitioners and researchers and the possible connections between PBL and LA have not yet been properly explored. The purpose of this paper is, therefore, to investigate how LA can potentially be used to support and inform PBL practice. We do this by identifying central themes that remain constant across various orchestrations of PBL (collaboration, self-directed learning, and reflection) and present examples of LA tools and concepts that have been developed within LA and neighbouring fields (e.g. CSCL) in connection to those themes. This selection of LA solutions is later used as a basis for discussing wider potentials, challenges and recommendations for making connections between PBL and LA.
description: Journal of Problem Based Learning in Higher Education, Early view
The direction of time and Boltzmann's time hypothesis
Creators: name: Klimenko, A. Y.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: This work explores Boltzmann's time hypothesis, which associates the perceived direction of "time flow" with the second law of thermodynamics. We discuss mechanisms that can be responsible for the action of the second law, for directional properties of time and, ultimately, for the perception that past events cause future events. Special attention is paid to possibility of testing these mechanisms in experiments. It is argued that CP-violations known in particle physics may offer such an opportunity. A time-symmetric version of Everett's many-worlds interpretation (which is based on a thermodynamic interpretation of quantum collapses) is given in the Appendix.
description: 22 pages, 6 figures, appendix
Orchestina yanayacu Izquierdo 2017, new species
Creators: name: Izquierdo, Matías Andrés
name: Ramírez, Martín J.
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Araneae
Oonopidae
Orchestina
Orchestina yanayacu

description: Orchestina yanayacu Izquierdo, new species   Figures 99C, 111A, map 10
TYPE: Female holotype from Ecuador: Napo: Yanayacu Biological Station, Rio Perdido trail, 2085 m, -0.60826°, -77.88245°, Nov. 26, 2009, Niarchos Expedition, deposited in QCAZ, PBI_ OON 30745.
ETYMOLOGY: The specific name is a noun in apposition taken from the type locality.
DIAGNOSIS: Females can be distinguished by having two external pockets, widely separated on the epigastric region (figs. 99C, 111A).
MALE: Unknown.
FEMALE (PBI_OON 30745): CEPHALOTHO- RAX (separated from abdomen): Carapace length 0.64; orange. Sternum as long as wide. Labium rectangular. ABDOMEN: Pale orange.
LEGS: Missing. GENITALIA: Epigastric region with two external pockets widely separated, internal pockets absent; anterior receptaculum with wide anterior tip; posterior receptaculum present, posterior apodeme formed by entire plate (figs. 99C, 111A).
DISTRIBUTION: Known only from the type locality in Ecuador (Napo, map 10).
OTHER MATERIAL EXAMINED: None.
description: Published as part of Izquierdo, Matías Andrés & Ramírez, Martín J., 2017, Taxonomic Revision Of The Jumping Goblin Spiders Of The Genus Orchestina Simon, 1882, In The Americas (Araneae: Oonopidae), pp. 1 in Bulletin of the American Museum of Natural History 2017 (410) on page 1, DOI: 10.1206/0003-0090-410.1.1, http://zenodo.org/record/5405613
Additional file 1 of Exploring the mechanisms of collaboration between the Tuberculosis and Diabetes Programs for the control of TB-DM Comorbidity in Ghana
Creators: name: Salifu, Rita Suhuyini
name: Hlongwana, Khumbulani W.
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: Computational Biology

description: Additional file 1. Interview guide 1-Health Managers.
Additional file 1: of How does feedback shared with interprofessional health care teams shape nursing performance improvement systems? A rapid realist review protocol
Creators: name: Rapin, Joachim
name: Pellet, Joanie
name: Mabire, Cedric
name: Gendron, Sylvie
name: Carl-Ardy Dubois
Publisher: name: figshare
Year: 2019
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology

description: The PRISMA-P 2015 checklist. (DOCX 30 kb)
Spatial Organization of Active Particles with Field Mediated Interactions
Creators: name: Zakine, Ruben
name: Fournier, Jean-Baptiste
name: van Wijland, Frédéric
Publisher: name: arXiv
Year: 2019
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We consider a system of independent point-like particles performing a Brownian motion while interacting with a Gaussian fluctuating background. These particles are in addition endowed with a discrete two-state internal degree of freedom that is subjected to a nonequilibrium source of noise, which affects their coupling with the background field. We explore the phase diagram of the system and pinpoint the role of the nonequilibrium drive in producing a nontrivial patterned spatial organization. We are able, by means of a weakly nonlinear analysis, to account for the parameter-dependence of the boundaries of the phase and pattern diagram in the stationary state.
description: 17 pages, 17 figures
Single Transverse-Spin Asymmetry in $pp^\uparrow \to πX$ and $ep^\uparrow \to πX$
Creators: name: Koike, Yuji
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Cross section formulas for the single spin asymmetry in $p^\uparrow p\to π(\ell_T)X$ and $e p^\uparrow \to π(\ell_T)X$ are derived and its characteristic features are discussed.
description: 5 pages in LaTex. Talk presented at SPIN'02 held at BNL from Sep. 9 to 14, 2002. Typos corrected
Additional file 4 of Care pathway and prioritization of rapid testing for COVID-19 in UK hospitals: a qualitative evaluation
Creators: name: Hicks, Timothy
name: Winter, Amanda
name: Green, Kile
name: Kierkegaard, Patrick
name: Price, D. Ashley
name: Body, Richard
name: Allen, A. Joy
name: Graziadio, Sara
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Biotechnology
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Additional file 4. Members of the CONDOR Steering Group