cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Differential contribution of cis -regulatory elements to higher order chromatin structure and expression of the CFTR locus
Creators: name: Kerschner, Jenny L.
name: Crawford, Gregory E.
name: Gorsic, Lidija K.
name: Safi, Alexias
name: Harris, Ann
name: Neems, Daniel
name: Kosak, Steven T.
name: Yang, Rui
name: Gosalia, Nehal
name: Leir, Shih-Hsing
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Higher order chromatin structure establishes domains that organize the genome and coordinate gene expression. However, the molecular mechanisms controlling transcription of individual loci within a topological domain (TAD) are not fully understood. The cystic fibrosis transmembrane conductance regulator (CFTR) gene provides a paradigm for investigating these mechanisms. CFTR occupies a TAD bordered by CTCF/cohesin binding sites within which are cell-type-selective cis-regulatory elements for the locus. We showed previously that intronic and extragenic enhancers, when occupied by specific transcription factors, are recruited to the CFTR promoter by a looping mechanism to drive gene expression. Here we use a combination of CRISPR/Cas9 editing of cis-regulatory elements and siRNA-mediated depletion of architectural proteins to determine the relative contribution of structural elements and enhancers to the higher order structure and expression of the CFTR locus. We found the boundaries of the CFTR TAD are conserved among diverse cell types and are dependent on CTCF and cohesin complex. Removal of an upstream CTCF-binding insulator alters the interaction profile, but has little effect on CFTR expression. Within the TAD, intronic enhancers recruit cell-type selective transcription factors and deletion of a pivotal enhancer element dramatically decreases CFTR expression, but has minor effect on its 3D structure.
Soil surface profile with a diagram of Sonderend, Waboomberg, Langeberg, site 3320CA/3
Creators: name: Jonkershoek Forestry Research Center
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: Jonkershoek Forestry Research Centre
soil surface profile
Sonderend
Langeberg
Waboomberg

description: This is a scanned copy of a soil surface profile of Sonderend, Waboomberg,  Langeberg, site 3320CA/3. The Jonkershoek Forestry Research Center (part of the former South African Forestry Research Institute) was established in 1935 at Jonkershoek, near Stellenbosch, under the directorship of Dr C. L. Wicht. The initial aim was to determine how forestry activities in state plantations would affect climate, water conservation and erosion, and was later expanded to include studies of fynbos ecology, fire and alien species. Studies from the 1930s to the early 1990s saw the accumulation of a large amount of data dealing with fire experiments, detailed vegetation plot surveys, rare plant surveys and ecological studies, hydrological studies and the development of management plans for catchments around the Western Cape. SAEON now houses the archive of data collected by the Jonkershoek Forestry Research Center, which was originally held by the Council for Scientific and Industrial Research (CSIR).
A weekly structural VAR model of the US crude oil market
Creators: name: Valenti, Daniele
name: Bastianin, Andrea
name: Manera, Matteo
name: Valenti, Daniele
name: Bastianin, Andrea
name: Manera, Matteo
Publisher: name: Unknown
Year: 2022
Subjects: subject: Research Methods/ Statistical Methods
subject: Resource /Energy Economics and Policy
subject: COVID-19
subject: WTI price
subject: futures-spot price spread
subject: speculation
subject: structural VAR
subject: Bayesian VAR

description: We present a weekly structural Vector Autoregressive (VAR) model of the US crude oil market. Exploiting weekly data we can explain short-run crude oil price dynamics, including those related with the COVID-19 pandemic and with the Russia’s invasion of Ukraine. The model is set identified with a Bayesian approach that allows to impose restrictions directly on structural parameters of interest, such as supply and demand elasticises. Our model incorporates both the futures-spot price spread to capture shocks to the real price of crude oil driven by changes in expectations and US inventories to describe price fluctuations due to unexpected of variations of above-ground stocks. Including the futures-spot price spread is key for accounting for feedback effects from the financial to the physical market for crude oil and for identifying a new structural shock that we label expectational shock. This shock plays a crucial role when describing the series of events that have led to the spike in the price of crude oil recorded in the aftermath of Russia’s invasion of Ukraine.
OHEJP BIOPIGEE Information Material for Farming Schools
Creators: name: Tamino Dubbert
name: Sassu, Elena
name: Waller, Elizabeth
name: Smith, Richard
name: May, Hannah
name: Sjölund, Marie
Publisher: name: Zenodo
Year: 2022
Subjects: biosecurity
pig
salmonella
HEV
information

description: This is the BIOPIGEE information material for farming schools from the deliverable D-JRP21-WP6.22 Information for farming schools provided.
Entropy gives rise to topologically associating domains
Creators: name: Lawrimore, Josh
name: Bloom, Kerry
name: Forest, Mark G.
name: Vasquez, Paula A.
name: Adalsteinsson, David
name: Hult, Caitlin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: We investigate chromosome organization within the nucleus using polymer models whose formulation is closely guided by experiments in live yeast cells. We employ bead-spring chromosome models together with loop formation within the chains and the presence of nuclear bodies to quantify the extent to which these mechanisms shape the topological landscape in the interphase nucleus. By investigating the genome as a dynamical system, we show that domains of high chromosomal interactions can arise solely from the polymeric nature of the chromosome arms due to entropic interactions and nuclear confinement. In this view, the role of bio-chemical related processes is to modulate and extend the duration of the interacting domains.
Photo plot of Sonderend, Langeberg, site 3319DB/4
Creators: name: Jonkershoek Forestry Research Center
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: Jonkershoek Forestry Research Centre
photo plot
Langeberg
Sonderend

description: This is a scanned copy of a photo plot of Sonderend, Langeberg, site 3319DB/4. The Jonkershoek Forestry Research Center (part of the former South African Forestry Research Institute) was established in 1935 at Jonkershoek, near Stellenbosch, under the directorship of Dr C. L. Wicht. The initial aim was to determine how forestry activities in state plantations would affect climate, water conservation and erosion, and was later expanded to include studies of fynbos ecology, fire and alien species. Studies from the 1930s to the early 1990s saw the accumulation of a large amount of data dealing with fire experiments, detailed vegetation plot surveys, rare plant surveys and ecological studies, hydrological studies and the development of management plans for catchments around the Western Cape. SAEON now houses the archive of data collected by the Jonkershoek Forestry Research Center, which was originally held by the Council for Scientific and Industrial Research (CSIR).
Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila
Creators: name: Li, Yulong
name: Duronio, Robert J.
name: Armstrong, Robin L.
name: Macalpine, David M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The methylation state of lysine 20 on histone H4 (H4K20) has been linked to chromatin compaction, transcription, DNA repair and DNA replication. Monomethylation of H4K20 (H4K20me1) is mediated by the cell cycle-regulated histone methyltransferase PR-Set7. PR-Set7 depletion in mammalian cells results in defective S phase progression and the accumulation of DNA damage, which has been partially attributed to defects in origin selection and activation. However, these studies were limited to only a handful of mammalian origins, and it remains unclear how PR-Set7 and H4K20 methylation impact the replication program on a genomic scale. We employed genetic, cytological, and genomic approaches to better understand the role of PR-Set7 and H4K20 methylation in regulating DNA replication and genome stability in Drosophila cells. We find that deregulation of H4K20 methylation had no impact on origin activation throughout the genome. Instead, depletion of PR-Set7 and loss of H4K20me1 results in the accumulation of DNA damage and an ATR-dependent cell cycle arrest. Coincident with the ATR-dependent cell cycle arrest, we find increased DNA damage that is specifically limited to late replicating regions of the Drosophila genome, suggesting that PR-Set7-mediated monomethylation of H4K20 is critical for maintaining the genomic integrity of late replicating domains.
Leucadendron salignum and Protea arborea seedling count in Jonkershoek, Jakkalsvlei fire break, site 3318DD
Creators: name: Jonkershoek Forestry Research Center
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: Jonkershoek Forestry Research Centre
Leucadendron salignum
Jonkershoek
seedling count
Protea arborea
Protea nitida

description: This is a scanned copy of document, including a map, noting the seedling count of Leucadendron salignum and Protea arborea in Jonkershoek, Jakkalsvlei fire break, site 3318DD. The Jonkershoek Forestry Research Center (part of the former South African Forestry Research Institute) was established in 1935 at Jonkershoek, near Stellenbosch, under the directorship of Dr C. L. Wicht. The initial aim was to determine how forestry activities in state plantations would affect climate, water conservation and erosion, and was later expanded to include studies of fynbos ecology, fire and alien species.  Studies from the 1930s to the early 1990s saw the accumulation of a large amount of data dealing with fire experiments, detailed vegetation plot surveys, rare plant surveys and ecological studies, hydrological studies and the development of management plans for catchments around the Western Cape. SAEON now houses the archive of data collected by the Jonkershoek Forestry Research Center, which was originally held by the Council for Scientific and Industrial Research (CSIR).
The bimodal and Gaussian Ising Spin Glasses in dimension two revisited
Creators: name: Lundow, P. H.
name: Campbell, I. A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: A new analysis is given of numerical simulation data on the archetype square lattice Ising Spin Glasses (ISG) with a bimodal ($\pm J$) and Gaussian interaction distributions. It is well established that the ordering temperature of both models is zero. The Gaussian has a non-degenerate ground state so exponent $η\equiv 0$ and it has a continuous distribution of energy levels. For the bimodal model, above a size dependent cross-over temperature $T^{*}(L)$ there is a regime of effectively continuous energy levels; below $T^{*}(L)$ there is a distinct regime dominated by the highly degenerate ground state plus an energy gap to the excited states. $T^{*}(L)$ tends to zero at very large $L$ leaving only the effectively continuous regime in the thermodynamic limit. We show that in this regime the critical exponent $η$ is not zero, so the effectively continuous regime $2$D bimodal ISG is not in the same universality class as the $2$D Gaussian ISG. The simulation data on both models are analyzed using a scaling variable $τ= T^2/(1+T^2)$ suitable for zero temperature transition ISGs, together with appropriate scaling expressions. Accurate simulation estimates can be obtained for the temperature dependence of the thermodynamic limit reduced susceptibility $χ(τ)$ and second moment correlation length $ξ(τ)$ over the entire range of temperature from zero to infinity. The Gaussian critical exponent from the simulations $ν= 3.5(1)$ is in full agreement with the well established value from the literature. The bimodal exponent from the thermodynamic limit regime analysis is $ν= 4.2(1)$, once again different from the Gaussian value.
description: 10 pages, 18 figures
Rad18 confers hematopoietic progenitor cell DNA damage tolerance independently of the Fanconi Anemia pathway in vivo
Creators: name: Yang, Yang
name: Vaziri, Cyrus
name: Li, Zhiguo
name: Magnuson, Terry
name: Tateishi, Satoshi
name: Poe, Jonathan C.
name: Gao, Yanzhe
name: Fedoriw, Yuri
name: Yang, Lisong
name: Desai, Siddhi
name: Araki, Kimi
name: Fedoriw, Andrew
name: Sarantopoulos, Stefanie
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: In cultured cancer cells the E3 ubiquitin ligase Rad18 activates Trans-Lesion Synthesis (TLS) and the Fanconi Anemia (FA) pathway. However, physiological roles of Rad18 in DNA damage tolerance and carcinogenesis are unknown and were investigated here. Primary hematopoietic stem and progenitor cells (HSPC) co-expressed RAD18 and FANCD2 proteins, potentially consistent with a role for Rad18 in FA pathway function during hematopoiesis. However, hematopoietic defects typically associated with fanc-deficiency (decreased HSPC numbers, reduced engraftment potential of HSPC, and Mitomycin C (MMC) -sensitive hematopoiesis), were absent in Rad18−/− mice. Moreover, primary Rad18−/− mouse embryonic fibroblasts (MEF) retained robust Fancd2 mono-ubiquitination following MMC treatment. Therefore, Rad18 is dispensable for FA pathway activation in untransformed cells and the Rad18 and FA pathways are separable in hematopoietic cells. In contrast with responses to crosslinking agents, Rad18−/− HSPC were sensitive to in vivo treatment with the myelosuppressive agent 7,12 Dimethylbenz[a]anthracene (DMBA). Rad18-deficient fibroblasts aberrantly accumulated DNA damage markers after DMBA treatment. Moreover, in vivo DMBA treatment led to increased incidence of B cell malignancy in Rad18−/− mice. These results identify novel hematopoietic functions for Rad18 and provide the first demonstration that Rad18 confers DNA damage tolerance and tumor-suppression in a physiological setting.
Simple permutation-based measure of quantum correlations and maximally-3-tangled states
Creators: name: Bhosale, Udaysinh T.
name: Lakshminarayan, Arul
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: Quantities invariant under local unitary transformations are of natural interest in the study of entanglement. This paper deduces and studies a particularly simple quantity that is constructed from a combination of two standard permutations of the density matrix, namely realignment and partial transpose. This bipartite quantity, denoted here as $R_{12}$, vanishes on large classes of separable states including classical-quantum correlated states, while being maximum for only maximally entangled states. It is shown to be naturally related to the 3-tangle in three qubit states via their two-qubit reduced density matrices. Upper and lower bounds on concurrence and negativity of two-qubit density matrices for all ranks are given in terms of $R_{12}$. Ansatz states satisfying these bounds are given and verified using various numerical methods. In rank-2 case it is shown that the states satisfying the lower bound on $R_{12}$ {\it vs} concurrence define a class of three qubit states that maximizes the tripartite entanglement (the 3-tangle) given an amount of entanglement between a pair of them. The measure $R_{12}$ is conjectured, via numerical sampling, to be always larger than the concurrence and negativity. In particular this is shown to be true for the physically interesting case of $X$ states.
description: Substantially improved version (now 16 pages, 11 figures) that is accepted for publication in Phys. Rev. A
Representations of Lie superalgebras with fusion flags
Creators: name: Kus, Deniz
Publisher: name: arXiv
Year: 2015
Subjects: subject: Representation Theory (math.RT)
subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics

description: We study the category of finite--dimensional representations for a basic classical Lie superalgebra $\Lg=\Lg_0\oplus \Lg_1$. For the ortho--symplectic Lie superalgebra $\Lg=\mathfrak{osp}(1,2n)$ we show that certain objects in that category admit a fusion flag, i.e. a sequence of graded $\Lg_0[t]$--modules such that the successive quotients are isomorphic to fusion products. Among these objects we find fusion products of finite--dimensional irreducible $\Lg$--modules, truncated Weyl modules and Demazure type modules. Moreover, we establish a presentation for these types of fusion products in terms of generators and relations of the enveloping algebra.
Solving strongly correlated electron models on a quantum computer
Creators: name: Wecker, Dave
name: Hastings, Matthew B.
name: Wiebe, Nathan
name: Clark, Bryan K.
name: Nayak, Chetan
name: Troyer, Matthias
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: One of the main applications of future quantum computers will be the simulation of quantum models. While the evolution of a quantum state under a Hamiltonian is straightforward (if sometimes expensive), using quantum computers to determine the ground state phase diagram of a quantum model and the properties of its phases is more involved. Using the Hubbard model as a prototypical example, we here show all the steps necessary to determine its phase diagram and ground state properties on a quantum computer. In particular, we discuss strategies for efficiently determining and preparing the ground state of the Hubbard model starting from various mean-field states with broken symmetry. We present an efficient procedure to prepare arbitrary Slater determinants as initial states and present the complete set of quantum circuits needed to evolve from these to the ground state of the Hubbard model. We show that, using efficient nesting of the various terms each time step in the evolution can be performed with just $\mathcal{O}(N)$ gates and $\mathcal{O}(\log N)$ circuit depth. We give explicit circuits to measure arbitrary local observables and static and dynamic correlation functions, both in the time and frequency domain. We further present efficient non-destructive approaches to measurement that avoid the need to re-prepare the ground state after each measurement and that quadratically reduce the measurement error.
description: 25 pages, 14 figures
Reversal of DNA damage induced Topoisomerase 2 DNA–protein crosslinks by Tdp2
Creators: name: Williams, Jason G.
name: Strom, Christina N.
name: Williams, R. Scott
name: Monian, Brinda
name: Perera, Lalith
name: Vilas, Caroline K.
name: Schellenberg, Matthew J.
name: Appel, C. Denise
name: Waters, Crystal A.
name: Ramsden, Dale A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Mammalian Tyrosyl-DNA phosphodiesterase 2 (Tdp2) reverses Topoisomerase 2 (Top2) DNA–protein crosslinks triggered by Top2 engagement of DNA damage or poisoning by anticancer drugs. Tdp2 deficiencies are linked to neurological disease and cellular sensitivity to Top2 poisons. Herein, we report X-ray crystal structures of ligand-free Tdp2 and Tdp2-DNA complexes with alkylated and abasic DNA that unveil a dynamic Tdp2 active site lid and deep substrate binding trench well-suited for engaging the diverse DNA damage triggers of abortive Top2 reactions. Modeling of a proposed Tdp2 reaction coordinate, combined with mutagenesis and biochemical studies support a single Mg2+-ion mechanism assisted by a phosphotyrosyl-arginine cation-π interface. We further identify a Tdp2 active site SNP that ablates Tdp2 Mg2+ binding and catalytic activity, impairs Tdp2 mediated NHEJ of tyrosine blocked termini, and renders cells sensitive to the anticancer agent etoposide. Collectively, our results provide a structural mechanism for Tdp2 engagement of heterogeneous DNA damage that causes Top2 poisoning, and indicate that evaluation of Tdp2 status may be an important personalized medicine biomarker informing on individual sensitivities to chemotherapeutic Top2 poisons.
Leucadendron pubescens, Cederberg site 3219AC
Creators: name: Jonkershoek Forestry Research Center
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: Jonkershoek Forestry Research Centre
Leucadendron pubescens
Cederberg

description: This is a scanned copy of a document on Leucadendron pubescens, Cederberg, site 3219AC. The Jonkershoek Forestry Research Center (part of the former South African Forestry Research Institute) was established in 1935 at Jonkershoek, near Stellenbosch, under the directorship of Dr C. L. Wicht. The initial aim was to determine how forestry activities in state plantations would affect climate, water conservation and erosion, and was later expanded to include studies of fynbos ecology, fire and alien species. Studies from the 1930s to the early 1990s saw the accumulation of a large amount of data dealing with fire experiments, detailed vegetation plot surveys, rare plant surveys and ecological studies, hydrological studies and the development of management plans for catchments around the Western Cape. SAEON now houses the archive of data collected by the Jonkershoek Forestry Research Center, which was originally held by the Council for Scientific and Industrial Research (CSIR).
Diversity Analysis of Culturable Epiphytic Microbial Consortia of Table Grape Berry Surface
Creators: name: Ranade, Yogita
name: Pathak, Pranav
name: Chandrashekar, Madhura
name: Saha, Sujoy
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: The health and yield of grapes are affected by the microorganisms associated with the grapevine. The diversity of microorganisms present on the wine grape varieties is well defined whereas, the information associated with the microorganisms of table grape varieties remains scarce. In the present study, culture-dependent method was used to isolate the microbes present on the surface of the commercial white seedless table grape cultivar, Thompson Seedless at different stages of berry development. The microbial load of the grape berry surface increased as the berry progressed toward the ripening stage resulting in the identification of core bacteria (29), filamentous fungi (19) and yeast (3). A diversity analysis study also revealed that Cladosporium cladosporioides, was found in the vineyard on grapes from the early berry development stages, as an emerging pre-harvest pathogen. The study would help in understanding and exploiting the microbiota of table grape berry in agronomic and biotechnological applications.
Robust detection of alternative splicing in a population of single cells
Creators: name: Prins, Jan F.
name: Welch, Joshua D.
name: Hu, Yin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but suffer from low coverage, 3′ bias and technical noise. These unique properties of single cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis of transcriptome variation to the gene level. To address these limitations, we developed SingleSplice, which uses a statistical model to detect genes whose isoform usage shows biological variation significantly exceeding technical noise in a population of single cells. Importantly, SingleSplice is tailored to the unique demands of single cell analysis, detecting isoform usage differences without attempting to infer expression levels for full-length transcripts. Using data from spike-in transcripts, we found that our approach detects variation in isoform usage among single cells with high sensitivity and specificity. We also applied SingleSplice to data from mouse embryonic stem cells and discovered a set of genes that show significant biological variation in isoform usage across the set of cells. A subset of these isoform differences are linked to cell cycle stage, suggesting a novel connection between alternative splicing and the cell cycle.
Line intercept in Hottentots Holland, Lebanon State Forest, site 3419AA/7
Creators: name: Jonkershoek Forestry Research Center
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: Jonkershoek Forestry Research Centre
Hottentots Holland
Lebanon State Forest

description: This is a scanned copy of a line intercept in Hottentots Holland, Lebanon State Forest, site 3419AA/7. The Jonkershoek Forestry Research Center (part of the former South African Forestry Research Institute) was established in 1935 at Jonkershoek, near Stellenbosch, under the directorship of Dr C. L. Wicht. The initial aim was to determine how forestry activities in state plantations would affect climate, water conservation and erosion, and was later expanded to include studies of fynbos ecology, fire and alien species. Studies from the 1930s to the early 1990s saw the accumulation of a large amount of data dealing with fire experiments, detailed vegetation plot surveys, rare plant surveys and ecological studies, hydrological studies and the development of management plans for catchments around the Western Cape. SAEON now houses the archive of data collected by the Jonkershoek Forestry Research Center, which was originally held by the Council for Scientific and Industrial Research (CSIR).
Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme
Creators: name: Al-Hashimi, Hashim M.
name: Mustoe, Anthony M.
name: Brooks, Charles L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use coarse-grained molecular dynamics simulations to explore how secondary structure shapes the tertiary free-energy landscape of the Azoarcus ribozyme. We show that steric and connectivity constraints posed by secondary structure strongly limit the accessible conformational space of the ribozyme, and that these so-called topological constraints in turn pose strong free-energy penalties on forming different tertiary contacts. Notably, native A-minor and base-triple interactions form with low conformational free energy, while non-native tetraloop/tetraloop–receptor interactions are penalized by high conformational free energies. Topological constraints also give rise to strong cooperativity between distal tertiary interactions, quantitatively matching prior experimental measurements. The specificity of the folding landscape is further enhanced as tertiary contacts place additional constraints on the conformational space, progressively funneling the molecule to the native state. These results indicate that secondary structure assists the ribozyme in navigating the otherwise rugged tertiary folding landscape, and further emphasize topological constraints as a key force in RNA folding.
Modeling Access Differences to Reduce Disparity in Resource Allocation
Creators: name: Andrews, Kenya
name: Ohannessian, Mesrob
name: Berger-Wolf, Tanya
Publisher: name: arXiv
Year: 2024
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Motivated by COVID-19 vaccine allocation, where vulnerable subpopulations are simultaneously more impacted in terms of health and more disadvantaged in terms of access to the vaccine, we formalize and study the problem of resource allocation when there are inherent access differences that correlate with advantage and disadvantage. We identify reducing resource disparity as a key goal in this context and show its role as a proxy to more nuanced downstream impacts. We develop a concrete access model that helps quantify how a given allocation translates to resource flow for the advantaged vs. the disadvantaged, based on the access gap between them. We then provide a methodology for access-aware allocation. Intuitively, the resulting allocation leverages more vaccines in locations with higher vulnerable populations to mitigate the access gap and reduce overall disparity. Surprisingly, knowledge of the access gap is often not needed to perform access-aware allocation. To support this formalism, we provide empirical evidence for our access model and show that access-aware allocation can significantly reduce resource disparity and thus improve downstream outcomes. We demonstrate this at various scales, including at county, state, national, and global levels.
description: Association for Computing Machinery (2022)
The aperiodic X-ray variability of the accreting millisecond pulsar SAX J1808.4-3658
Creators: name: Bult, Peter
name: van der Klis, Michiel
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We have studied the aperiodic variability of the 401 Hz accreting millisecond X-ray pulsar SAX J1808.4-3658 using the complete data set collected with the Rossi X-ray Timing Explorer over 14 years of observation. The source shows a number of exceptional aperiodic timing phenomena that are observed against a backdrop of timing properties that show consistent trends in all five observed outbursts and closely resemble those of other atoll sources. We performed a detailed study of the enigmatic ~410 Hz QPO, which has only been observed in SAX J1808.4-3658. We find that it appears only when the upper kHz QPO frequency is less than the 401 Hz spin frequency. The difference between the ~410 Hz QPO frequency and the spin frequency follows a similar frequency correlation as the low frequency power spectral components, suggesting that the ~410 Hz QPO is a retrograde beat against the spin frequency of a rotational phenomenon in the 9 Hz range. Comparing this 9 Hz beat feature with the Low-Frequency QPO in SAX J1808.4-3658 and other neutron star sources, we conclude that these two might be part of the same basic phenomenon. We suggest that they might be caused by retrograde precession due to a combination of relativistic, classical and magnetic torques. Additionally we present two new measurements of the lower kHz QPO, allowing us, for the first time, to measure the frequency evolution of the twin kHz QPOs in this source. The twin kHz QPOs are seen to move together over 150 Hz, maintaining a centroid frequency separation of $(0.446 \pm 0.009) ν_{spin}$.
description: 18 pages, 9 figures, 7 tables. Accepted for publication in ApJ
Selective single cell isolation for genomics using microraft arrays
Creators: name: Jones, Corbin D.
name: Yeh, Jen Jen
name: Prins, Jan F.
name: Allbritton, Nancy L.
name: DiSalvo, Matthew
name: Williams, Lindsay A.
name: Welch, Joshua D.
name: Marayati, Raoud
name: Sims, Christopher E.
name: Brandt, Alicia T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Genomic methods are used increasingly to interrogate the individual cells that compose specific tissues. However, current methods for single cell isolation struggle to phenotypically differentiate specific cells in a heterogeneous population and rely primarily on the use of fluorescent markers. Many cellular phenotypes of interest are too complex to be measured by this approach, making it difficult to connect genotype and phenotype at the level of individual cells. Here we demonstrate that microraft arrays, which are arrays containing thousands of individual cell culture sites, can be used to select single cells based on a variety of phenotypes, such as cell surface markers, cell proliferation and drug response. We then show that a common genomic procedure, RNA-seq, can be readily adapted to the single cells isolated from these rafts. We show that data generated using microrafts and our modified RNA-seq protocol compared favorably with the Fluidigm C1. We then used microraft arrays to select pancreatic cancer cells that proliferate in spite of cytotoxic drug treatment. Our single cell RNA-seq data identified several expected and novel gene expression changes associated with early drug resistance.
Supplementary documentation for SAEON's field instrument data collected at the Cathedral Peak 4A station
Creators: name: South African Environmental Observation Network (SAEON) Grasslands-Forests-Wetlands Node
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: SAEON field instruments
Standard Operating Procedures
Calibration
Cathedral Peak
Meteorological
Tipping bucket
Precipitation
Air temperature

description: This package contains supporting information for the meteorological data collected at Cathedral Peak's 4A station, as part of the South African Environmental Observation Network's monitoring projects.
Supplementary documentation for SAEON's field instrument data collected at the Jonkershoek 25B station
Creators: name: South African Environmental Observation Network (SAEON) Fynbos Node
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: SAEON field instruments
Standard Operating Procedures
Calibration
Jonkershoek
Meteorological
Tipping bucket rain gauge
Rainfall
air temperature

description: This package contains supporting information for the meteorological data collected at Jonkershoek's 25B station, as part of the South African Environmental Observation Network's monitoring projects.
Amauropelta boliviana A. R. Sm. 2017, sp. nov.
Creators: name: Smith, Alan R.
name: Kessler, Michael
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Polypodiales
Thelypteridaceae
Amauropelta
Amauropelta boliviana

description: Amauropelta boliviana A.R.Sm., sp. nov. (Fig. 1)
Distinguished from related species by the tall, narrow, erect caudices only 1 cm wide; abruptly reduced proximal pinnae, the lowest ca. 1 mm long; small, barely visible indusia; nearly glabrous costae and lamina abaxially (hairs, if present, confined to the proximal regions of the costae); and numerous adpressed hairs on the laminar tissue between veins adaxially.
 Type:— BOLIVIA. Cochabamba: Prov. Carrasco, campamento Sehuencas, segundo sitio de “camping”, pasando el puente del Río Fuerte, 17º29’81”S, 65º16’38”W, 2250 m, I. Jimenez 213 (holotype UC!; isotype LPB).
Plants terrestrial; stems erect, caudices very narrow, to 10 × 1 cm; petioles stramineous, darkened at only at the very base, to ca. 20 cm × 2 mm, proximally with a few scales, these brown, ovate-lanceolate, to ca. 4 × 1.5 mm, glabrous, glabrescent, or sparsely hairy, scales lacking distally on stipes; leaves to ca. 85 cm long; blades chartaceous, pinnate-pinnatifid, proximal ca. 5 pinna pairs abruptly reduced, the shortest ca. 1 mm long, blade apex confluent, pinnatifid, gradually tapering; rachises stramineous to tan, glabrous or glabrescent abaxially; pinnae sessile or petiolulate <1 mm, opposite or subopposite proximally, becoming alternate distally, widest just beyond the base, to 9 × 2 cm, deeply pinnatifid or nearly pinnatisect to within 1 mm of costae, segments 3–4 mm wide; aerophores lacking at pinna bases; lamina buds lacking; veins 8–10 pairs per segment, lowermost pair from adjacent segments meeting margins well above sinuses; costal scales lacking; costae, veins, and margins glabrous abaxially, or with sparse, straight hairs, also with tiny stipitate glands 0.05 mm long on costae and laminar surfaces between veins, sessile resinous glands lacking; indument adaxially along, costae, costules, veins, and laminar tissue between veins, costal hairs on ridges, 0.2–0.4 mm long, ascending, hairs on laminar tissue ca. 0.2 mm long, adpressed; sori medial, round, discrete; indusia present, small and difficult to see in mature fronds, glabrous or slightly ciliate and stipitate-glandular on margins, round-reniform, to ca. 0.5 mm diam. and seemingly fragmentary at times.
 Range:— Bolivia (CO).
 Ecology:— Rare, known only from the type; terrestrial in montane, evergreen cloud forests; 2250 m.
 Notes: —Nearest affinities are uncertain, but possibly with A. ptarmiciformis. That species has much more numerous, longer, stouter hairs on the costae abaxially and smaller, more delicate fronds.
description: Published as part of Smith, Alan R. & Kessler, Michael, 2017, Prodromus of a fern flora for Bolivia. XXX. Thelypteridaceae, pp. 1-34 in Phytotaxa 331 (1) on page 7, DOI: 10.11646/phytotaxa.331.1.1, http://zenodo.org/record/13722062
The sharpness of gamma-ray burst prompt emission spectra
Creators: name: Yu, Hoi-Fung
name: van Eerten, Hendrik J.
name: Greiner, Jochen
name: Sari, Re'em
name: Bhat, P. Narayana
name: von Kienlin, Andreas
name: Paciesas, William S.
name: Preece, Robert D.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We aim to obtain a measure of the curvature of time-resolved spectra that can be compared directly to theory. This tests the ability of models such as synchrotron emission to explain the peaks or breaks of GBM prompt emission spectra. We take the burst sample from the official Fermi GBM GRB time-resolved spectral catalog. We re-fit all spectra with a measured peak or break energy in the catalog best-fit models in various energy ranges, which cover the curvature around the spectral peak or break, resulting in a total of 1,113 spectra being analysed. We compute the sharpness angles under the peak or break of the triangle constructed under the model fit curves and compare to the values obtained from various representative emission models: blackbody, single-electron synchrotron, synchrotron emission from a Maxwellian or power-law electron distribution. We find that 35% of the time-resolved spectra are inconsistent with the single-electron synchrotron function, and 91% are inconsistent with the Maxwellian synchrotron function. The single temperature, single emission time and location blackbody function is found to be sharper than all the spectra. No general evolutionary trend of the sharpness angle is observed, neither per burst nor for the whole population. It is found that the limiting case, a single temperature Maxwellian synchrotron function, can only contribute up to $58^{+23}_{-18}$% of the peak flux. Our results show that even the sharpest but non-realistic case, the single-electron synchrotron function, cannot explain a large fraction of the observed GRB prompt spectra. Because of the fact that any combination of physically possible synchrotron spectra added together will always further broaden the spectrum, emission mechanisms other than optically thin synchrotron radiation are likely required in a full explanation of the spectral peaks or breaks of the GRB prompt emission phase.
description: 16 pages, 13 figures, 2 tables, accepted for publication in A&A
Population dynamics of Protea repens in Langeberg, Grootvadersbosch, site 3321CD/4
Creators: name: Jonkershoek Forestry Research Center
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: Jonkershoek Forestry Research Centre
population dynamics
Langeberg
Grootvadersbosch
Protea repens

description: This is a scanned copy of a document noting the population dynamics of Protea repens in Grootvadersbosch, Langeberg, site 3321CD/4. The Jonkershoek Forestry Research Center (part of the former South African Forestry Research Institute) was established in 1935 at Jonkershoek, near Stellenbosch, under the directorship of Dr C. L. Wicht. The initial aim was to determine how forestry activities in state plantations would affect climate, water conservation and erosion, and was later expanded to include studies of fynbos ecology, fire and alien species. Studies from the 1930s to the early 1990s saw the accumulation of a large amount of data dealing with fire experiments, detailed vegetation plot surveys, rare plant surveys and ecological studies, hydrological studies and the development of management plans for catchments around the Western Cape. SAEON now houses the archive of data collected by the Jonkershoek Forestry Research Center, which was originally held by the Council for Scientific and Industrial Research (CSIR).
Development of Agriculture's Human Resources: A Report on Problems of Low-Income Farmers
Creators: name: United States Department Of Agriculture
name: United States Department Of Agriculture
Publisher: name: Unknown
Year: 1955
Subjects: Agricultural and Food Policy
Agricultural Finance
Community/Rural/Urban Development
Labor and Human Capital
Teaching/Communication/Extension/Profession

description: Excerpts from the Preface: This study has been focused on farm people—their needs, their goals and the obstacles they encounter. The principal cause of concentrations of farm people with low earnings has been found to be the inadequate agricultural resources in certain areas rather than any lack in the people themselves. Proposed solutions of the problem of low income might be based on ideas about the merits of rural as contrasted with urban life. Solutions might be strongly influenced by an opinion as to the size of farm deemed desirable from the standpoint of the national interest. Instead, the hopes of the people themselves have been taken as a guide. Proposed solutions are those which the people most concerned have chosen, as shown by their economic and social behavior. Recommendations are of such a nature as to speed the adjustments which have proved sound over a long period of years. This study, therefore, sets up no goals other than those voluntarily chosen by the people. The basic philosophy is that people will make wise decisions if they are informed regarding their various opportunities and if their capabilities are enhanced so as to increase the number of choices available to them. Insofar as individuals make wise decisions the national welfare will be advanced. Special attention has been focused on the young people in the belief that they stand to gain most from a program which will increase the number of opportunities, the awareness of them, and capacities to take advantage of them. The study emphasizes that the foundation for programs to increase opportunities available to low- income people is the interest and enterprise of local people and communities. But cooperative effort by local communities, private enterprises and the State and Federal Governments can make possible much more rapid improvements in levels of living of low-income families.
description: This report was prepared for the Secretary of Agriculture under his broad authorization, by representatives of various agencies of the United States Department of Agriculture. Numerous task forces were used to develop various sections of the study. These had the active help and cooperation of other departments of the Government. Suggestions were invited from interested groups and organizations from all across the Nation.
A new strain energy function for modelling ligaments and tendons whose fascicles have a helical arrangement of fibrils
Creators: name: Shearer, Tom
Publisher: name: arXiv
Year: 2015
Subjects: subject: Tissues and Organs (q-bio.TO)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: A new strain energy function for the hyperelastic modelling of ligaments and tendons whose fascicles have a helical arrangement of fibrils is derived. The stress-strain response of a single fascicle whose fibrils exhibit varying levels of crimp throughout its radius is calculated and used to determine the form of the strain energy function. The new constitutive law is used to model uniaxial extension test data for human patellar tendon and is shown to provide an excellent fit, with the average relative error being 9.8%. It is then used to model shear and predicts that the stresses required to shear a tendon are much smaller than those required to uniaxially stretch it to the same strain level. Finally, the strain energy function is used to model ligaments and tendons whose fascicles are helical, and the relative effects of the fibril helix angle, the fascicle helix angle and the fibril crimp variable are compared. It is shown that they all have a significant effect; the fibril crimp variable governs the non-linearity of the stress-strain curve, whereas the helix angles primarily affect its stiffness. Smaller values of the helix angles lead to stiffer tendons; therefore, the model predicts that one would expect to see fewer helical sub-structures in stiff positional tendons, and more in those that are required to be more flexible.
The delivery of therapeutic oligonucleotides
Creators: name: Juliano, Rudolph L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The oligonucleotide therapeutics field has seen remarkable progress over the last few years with the approval of the first antisense drug and with promising developments in late stage clinical trials using siRNA or splice switching oligonucleotides. However, effective delivery of oligonucleotides to their intracellular sites of action remains a major issue. This review will describe the biological basis of oligonucleotide delivery including the nature of various tissue barriers and the mechanisms of cellular uptake and intracellular trafficking of oligonucleotides. It will then examine a variety of current approaches for enhancing the delivery of oligonucleotides. This includes molecular scale targeted ligand-oligonucleotide conjugates, lipid- and polymer-based nanoparticles, antibody conjugates and small molecules that improve oligonucleotide delivery. The merits and liabilities of these approaches will be discussed in the context of the underlying basic biology.
Supplementary documentation for SAEON's field instrument data collected at the Cathedral Peak MET 3 Texas station
Creators: name: South African Environmental Observation Network (SAEON) Grasslands-Forests-Wetlands Node
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: SAEON field instruments
Standard Operating Procedures
Calibration
Cathedral Peak
Meteorological
Tipping bucket
Precipitation

description: This package contains supporting information for the meteorological data collected at Cathedral Peak's MET 3 Texas station, as part of the South African Environmental Observation Network's monitoring projects.