cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Next Generation Sequencing Facilitates Quantitative Analysis of miRNAs in hepatic fibrosis and normal tissues.
Creators: name: BGI
Publisher: name: CNGB
Year: 2014
Subjects: Transcriptome or Gene expression
Multiisolate

description: Aim: Hepatic fibrosis is a major worldwide medical problem and can develop into liver cirrhosis and hepatocellular carcinoma(HCC). Until now, there are no effective drugs for liver ﬁbrosis because the molecular mechanism of progression of liver fibrosis is not fully understood. MicroRNAs (miRNAs) are an important class of small non-coding functional RNAs that play a key role in many biological processes. The purpose of this study was to clarify how the aberrant expression of miRNAs participates in development of the liver fibrosis in rat liver fibrosis model. Methods: Fibrotic and paired normal liver tissues were collected and assesssed by deep sequencing technology. MiRNA proﬁling results were validated by quantitative real-time polymerase chain reaction (qRT-PCR) and bioinformatics was used to predict miRNA targets. Results: Nine deregulated miRNAs were induced in porcine serum (PS)-induced hepatic fibrosis versus normal liver. Further analysis revealed several signaling pathways (e.g., gap junction and neuroactive ligand-receptor interaction) may be associated with hepatic fibrogenesis. Conclusion: Several miRNAs are dysregulated in PS-induced hepatic fibrosis and seem to be closely associated with hepatic fibrogenesis. These results provide an experimental basis for understanding the mechanism of hepatic fibrosis.Overall design: We sequenced two samples, including case and control. Each sample has two replicates.
Begonia rhodoneura S. Julia
Creators: name: Sang, Julia
name: Kiew, Ruth
name: Yiing, Ling Chea
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Cucurbitales
Begoniaceae
Begonia
Begonia rhodoneura

description: 15. Begonia rhodoneura S.Julia
 Phytotaxa 99(1) (2013) 23; Kiew et al., Guide to Begonias of Borneo (2015) 228. Type: — MALAYSIA. Borneo. Sarawak. Marudi District: Gunung Mulu NP, Gunung Benarat, 15 April 2012, Julia et al. SFC 2801 (holotype SAR!).
 Distribution: — MALAYSIA. Borneo. Sarawak. Endemic in Gunung Mulu NP.
 Habitat: —In lowland limestone forest on limestone boulders or mossy rock faces, at 102–235 m elevation.
 Additional specimens examined: — MALAYSIA. Borneo. Sarawak. Marudi District: Gunung Mulu NP – Bukit Agung, Julia et al. SFC 2813 (SAR), SFC 2822 (SAR); Gunung Benarat, Baie et al. SFC 2833 (SAR), Abang Mohtar et al S 49472 (SAR); Lobang Cina, Abang Mohtar & Othman S 49413 (SAR), Anderson & Keng S 4452 (SAR). Gunung Buda NP – Gunung Buda, Julia et al. SFC 2824 (SAR), Burtt B 8342 (SAR).
 Notes: —Scrambling horizontally to 1.5 m tall or sometimes creeping on rock surfaces and tree trunks and rooting at the nodes; this species is rather bushy and much-branched. Its leaves are slightly velvety above, plain green, very oblique and asymmetric, broadly ovate, 6–14.5 × 6–13.5 cm with a cordate and overlapping leaf base and minutely toothed margin. The venation is palmate with 2 veins in the basal lobe, on the upper surface the dark red veins contrast with the predominantly dark green lamina. The racemose inflorescence is shorter than the petiole and the capsule is oblong, 19–30 × 10–17 mm.
description: Published as part of Sang, Julia, Kiew, Ruth & Yiing, Ling Chea, 2018, The Begonia flora of Gunung Mulu and Gunung Buda National Parks, Sarawak, Borneo, including five new species, pp. 58-79 in Phytotaxa 381 (1) on page 73, DOI: 10.11646/phytotaxa.381.1.9, http://zenodo.org/record/13726112
Evaluation of a blockchain-enabled resource management mechanism for NGNs
Creators: name: Xevgenis, Michael
name: Kogias, Dimitrios
name: Christidis, Ioannis
name: Patrikakis, Charalampos
name: Leligou, Helen C.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: A new era in ICT has begun with the evolution of Next Generation Networks (NGNs) and the development of human-centric applications. Ultra-low latency, high throughput, and high availability are a few of the main characteristics of modern networks. Network Providers (NPs) are responsible for the development and maintenance of network infrastructures ready to support the most demanding applications that should be available not only in urban areas but in every corner of the earth. The NPs must collaborate to offer high-quality services and keep their overall cost low. The collaboration among competitive entities can in principle be regulated by a trusted 3rd party or by a distributed approach/technology which can guarantee integrity, security, and trust. This paper examines the use of blockchain technology for resource management and negotiation among NPs and presents the results of experiments conducted in a dedicated real testbed. The implementation of the resource management mechanism is described in a Smart Contract (SC) and the testbeds use the Raft and the IBFT consensus mechanisms respectively. The goal of this paper is two-fold: to assess its performance in terms of transaction throughput and latency so that we can assess the granularity at which this solution can operate (e.g. support resource re-allocation among NPs on micro-service level or not) and define implementation-specific parameters like the consensus mechanism that is the most suitable for this use case based on performance metrics.
title: Performance Characterization Method of Broadband Terahertz Video Cameras
Creators: name: Jagtap, Vishal S.
name: Zatta, Robin
name: grzyb, janusz
name: Pfeiffer, Ullrich
Publisher: name: Bergische Universität Wuppertal
Year: 2021

description: Integrated THz systems comprising index matched optical media introduce discontinuities in the propagation path leading to an etaloning effect. The etaloning hinders the absolute accuracy of a measuring instrument thereby limiting its applicability. A methodology using computational notch filtering is implemented here to extract the true performance of a measuring instrument. Specifically, the responsivity and NEP of the portable room temperature 1k-pixel terahertz CMOS camera have been investigated using a continuously tunable broadband spectrally pure terahertz photomixer source. Applying methodology revealed a peak responsivity of 20 MV/W at 822 GHz with a 6-dB bandwidth of 265 GHz and a minimum integrated NEP of 2.9 nW with 1024 frames averaging at 30fps.
description: This document is the accepted manuscript version that has been published in final form in: 2019 44th International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz). https://doi.org/10.1109/IRMMW-THz.2019.8874478
© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Taking the Universe's Temperature with Spectral Distortions of the Cosmic Microwave Background
Creators: name: Hill, J. Colin
name: Battaglia, Nick
name: Chluba, Jens
name: Ferraro, Simone
name: Schaan, Emmanuel
name: Spergel, David N.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The cosmic microwave background (CMB) energy spectrum is a near-perfect blackbody. The standard model of cosmology predicts small spectral distortions to this form, but no such distortion of the sky-averaged CMB spectrum has yet been measured. We calculate the largest expected distortion, which arises from the inverse Compton scattering of CMB photons off hot, free electrons, known as the thermal Sunyaev-Zel'dovich (tSZ) effect. We show that the predicted signal is roughly one order of magnitude below the current bound from the COBE-FIRAS experiment, but can be detected at enormous significance ($\gtrsim 1000σ$) by the proposed Primordial Inflation Explorer (PIXIE). Although cosmic variance reduces the effective signal-to-noise to $230σ$, this measurement will still yield a sub-percent constraint on the total thermal energy of electrons in the observable universe. Furthermore, we show that PIXIE can detect subtle relativistic effects in the sky-averaged tSZ signal at $30σ$, which directly probe moments of the optical depth-weighted intracluster medium electron temperature distribution. These effects break the degeneracy between the electron density and temperature in the mean tSZ signal, allowing a direct inference of the mean baryon density at low redshift. Future spectral distortion probes will thus determine the global thermodynamic properties of ionized gas in the universe with unprecedented precision. These measurements will impose a fundamental "integral constraint" on models of galaxy formation and the injection of feedback energy over cosmic time.
description: 4.5 pages + references, 2 figures, comments welcome; v2: references updated; v3: matches PRL accepted version
Effectiveness of Two-Talker Maskers That Differ in Talker Congruity and Perceptual Similarity to the Target Speech
Creators: name: Bowdrie, Kristina
name: Calandruccio, Lauren
name: Buss, Emily
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Previous work has shown that masked-sentence recognition is particularly poor when the masker is composed of two competing talkers, a finding that is attributed to informational masking. Informational masking tends to be largest when the target and masker talkers are perceptually similar. Reductions in masking have been observed for a wide range of target and masker differences, including language: Performance is better when the target and masker talkers speak in different languages, compared with the same language. The present study evaluated normal-hearing adults’ sentence recognition in a two-talker masker as a function of the perceptual similarity between the target and each of the two masker streams. The target was English, and the maskers were composed of English, time-reversed English, or Dutch. These three masker types are known to vary in the informational masking they exert. The two talkers within the two-talker maskers were either congruent (e.g., both English) or incongruent (e.g., one English, one Dutch). As predicted, mean performance was worse for the congruent English masker than the congruent time-reversed English or congruent Dutch maskers. Incongruent two-talker maskers, with just one English masker stream, were only modestly less effective than the congruent English masker. This result indicates that two-talker masker effectiveness was determined predominantly by the one masker stream that was most perceptually similar to the target. Speech recognition in a single-talker masker differed only marginally between the English, Dutch, and time-reversed English masker types, suggesting that perceptual similarity may be more critical in a two-talker than a one-talker masker.
title: Organic Nanoparticles for Photocatalytic Hydrogen Evolution
Creators: name: Yang, Haofan
Publisher: name: University of Liverpool Repository
Year: 2022

description: Solar energy is one of the most promising renewable energies. Photocatalytic solar hydrogen production provides a technologically simple and green way for hydrogen production, which is considered as the energy of the future. To be scalable, however, this approach requires more efficient photocatalysts. Photocatalysts at the nanoscale have extraordinary properties, resulting in orders of magnitude greater catalytic activities compared to bulk materials. The formation of heterojunction has also been demonstrated to be an effective strategy to enhance photocatalytic activities. This thesis will focus on the design and synthesis of efficient nano-photocatalysts for hydrogen production.
RNA-sequencing analysis of NGN3-GFP positive and negative cells purified from differentiating human embryonic stem cells
Creators: name: BGI
Publisher: name: CNGB
Year: 2014
Subjects: Transcriptome or Gene expression
Multiisolate

description: NGN3-eGFP could be used to mark endocrine progenitor cells and their progeny in differentiating hESCs, suggesting that profiling analysis of NGN3-eGFP+ cells could lead to the discovery of novel gene participation. Six batches of NGN3-eGFP+ and NGN3-eGFP -cells purified by FACS from a reporter hES cell line cell cultures at stage 4 were pooled together, respectively. RNA-seq-based analysis of the two cell fractions identified a total of 3976 differentially expressed genes (P-value2), of which 72% are enriched in NGN3-GFP+ cells. As expected, all the genes expressed in pancreatic progenitor cells are enriched in NGN3-eGFP-cells; while all endocrine-associated genes are enriched in NGN3-eGFP+ cells. Among the 3976 genes, 195 have potential transcriptional factor activity and 453 are potential non-coding RNA genes, most of which have not been well investigated in pancreatic endocrine cells. The gene ontology term ‘integral to membrane’ GO: 0016021 identified 1003 differentially expressed genes that encoded ion channels, adhesion molecules and transporters.Overall design: NGN3-eGFP Postive and negtive cells were purified at stage 4 and subjected to RNA-sequncing
Begonia umbratica S. Julia
Creators: name: Sang, Julia
name: Kiew, Ruth
name: Yiing, Ling Chea
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Cucurbitales
Begoniaceae
Begonia
Begonia umbratica

description: 16. Begonia umbratica S.Julia
 Phytotaxa 99(1) (2013) 24; Kiew et al., Guide to Begonias of Borneo (2015)270. Type: — MALAYSIA. Borneo. Sarawak. Marudi District: Gunung Mulu NP, Bukit Agung, 16 April 2012, Julia et al. SFC 2814 (holotype SAR!).
 Distribution: — MALAYSIA. Borneo. Sarawak. Endemic in Gunung Mulu NP.
 Habitat: —In lowland limestone forest, it grows on limestone-derived soil at the base of vertical cliffs or on steep scree slopes with a guano layer or in wet and shaded conditions at 102–220 m elevation.
 Additional specimens examined: — MALAYSIA. Borneo. Sarawak. Marudi District: Gunung Mulu NP – Boardwalk to Deer Cave, Julia et al. S 99203 (SAR), Julia et al. S 99205 (SAR), Julia et al. S 99202 (SAR), Julia et al. S 99220 (SAR); Bukit Berar, Julia et al. S 99213 (SAR), Julia et al. S 99214 (SAR). Gunung Buda NP – Gunung Buda, Chai S 39468 (SAR).
 Notes: —A rather shrubby cane-like herb to 1 m tall, often bushy and branched. It has a ridged and robust stem, to 5–7 mm diameter when dried. The stems, leaves and petioles are velvety with dense unbranched, short multicellular hairs. Its leaves are held horizontally, oblique, broadly ovate, 13–20 × 11.5–21 cm, broad side 7–11 cm, asymmetric with an acumen to 1 cm long. The stipules have a distinct midrib, are lanceolate, ca. 30 × 8 mm. Its venation is palmate, the veins laxly arranged. The racemose inflorescence, 3–4 cm long, is shorter than the petiole and is supported by a rather large bract, 30–35 × 10–14 mm.
description: Published as part of Sang, Julia, Kiew, Ruth & Yiing, Ling Chea, 2018, The Begonia flora of Gunung Mulu and Gunung Buda National Parks, Sarawak, Borneo, including five new species, pp. 58-79 in Phytotaxa 381 (1) on page 73, DOI: 10.11646/phytotaxa.381.1.9, http://zenodo.org/record/13726112
Loud Music Exposure and Cochlear Synaptopathy in Young Adults: Isolated Auditory Brainstem Response Effects but No Perceptual Consequences
Creators: name: Buss, Emily
name: Grose, John H.
name: Hall, Joseph W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: The purpose of this study was to test the hypothesis that listeners with frequent exposure to loud music exhibit deficits in suprathreshold auditory performance consistent with cochlear synaptopathy. Young adults with normal audiograms were recruited who either did (n = 31) or did not (n = 30) have a history of frequent attendance at loud music venues where the typical sound levels could be expected to result in temporary threshold shifts. A test battery was administered that comprised three sets of procedures: (a) electrophysiological tests including distortion product otoacoustic emissions, auditory brainstem responses, envelope following responses, and the acoustic change complex evoked by an interaural phase inversion; (b) psychoacoustic tests including temporal modulation detection, spectral modulation detection, and sensitivity to interaural phase; and (c) speech tests including filtered phoneme recognition and speech-in-noise recognition. The results demonstrated that a history of loud music exposure can lead to a profile of peripheral auditory function that is consistent with an interpretation of cochlear synaptopathy in humans, namely, modestly abnormal auditory brainstem response Wave I/Wave V ratios in the presence of normal distortion product otoacoustic emissions and normal audiometric thresholds. However, there were no other electrophysiological, psychophysical, or speech perception effects. The absence of any behavioral effects in suprathreshold sound processing indicated that, even if cochlear synaptopathy is a valid pathophysiological condition in humans, its perceptual sequelae are either too diffuse or too inconsequential to permit a simple differential diagnosis of hidden hearing loss.
Milliwatt terahertz harmonic generation from topological insulator metamaterials
Creators: name: Tielrooij, Klaas-Jan
name: Principi, Alessandro
name: Reig, David Saleta
name: Block, Alexander
name: Varghese, Sebin
name: Schreyeck, Steffen
name: Brunner, Karl
name: Karczewski, Grzegorz
name: Ilyakov, Igor
name: Ponomaryov, Oleksiy
name: de Oliveira, Thales V. A. G.
name: Chen, Min
name: Deinert, Jan-Christoph
name: Carbonell, Carmen Gomez
name: Valenzuela, Sergio O.
name: Molenkamp, Laurens W.
name: Kiessling, Tobias
name: Astakhov, Georgy V.
name: Kovalev, Sergey
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optics (physics.optics)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Achieving efficient, high-power harmonic generation in the terahertz spectral domain has technological applications, for example in sixth generation (6G) communication networks. Massless Dirac fermions possess extremely large terahertz nonlinear susceptibilities and harmonic conversion efficiencies. However, the observed maximum generated harmonic power is limited, because of saturation effects at increasing incident powers, as shown recently for graphene. Here, we demonstrate room-temperature terahertz harmonic generation in a Bi$_2$Se$_3$ topological insulator and topological-insulator-grating metamaterial structures with surface-selective terahertz field enhancement. We obtain a third-harmonic power approaching the milliwatt range for an incident power of 75 mW - an improvement by two orders of magnitude compared to a benchmarked graphene sample. We establish a framework in which this exceptional performance is the result of thermodynamic harmonic generation by the massless topological surface states, benefiting from ultrafast dissipation of electronic heat via surface-bulk Coulomb interactions. These results are an important step towards on-chip terahertz (opto)electronic applications.
Emerging Technologies for Gut Microbiome Research
Creators: name: Azcarate-Peril, M. Andrea
name: Roach, Jeffrey
name: Arnold, Jason W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches will improve the efficiency and quality of microbiome research. Here, we will discuss emerging technologies and their potential impact on gut microbiome studies.
Calculated electron paramagnetic resonance $g$-tensor and hyperfine parameters for zinc vacancy and N related defects in ZnO
Creators: name: Dabsamut, Klichchupong
name: Boonchun, Adisak
name: Lambrecht, Walter R. L.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Various defects in ZnO, focused on substitutional N$_O$ and N$_2$ in various sites, O-site, interstitial and Zn-site are studied using first-principles calculations with the goal of understanding the electron paramagnetic resonance (EPR) center reported for N$_2$ in ZnO and substitutional N on the O-site. The $g$ tensors are calculated using the gauge including projector augmented wave (GIPAW) method and compared with experiments. The $g$-tensor of the free N$_2^+$ and N$_2^-$ radicals and their various contributions within the GIPAW theory are analyzed first to provide a baseline reference for the accuracy of the method and for understanding the N$_2$ behavior in ZnO. Previous controversies on the site location of N$_2$ in ZnO for this EPR center and on the shallow or deep nature and donor or acceptor nature of this center are resolved. We find that the N$_2$ on the Zn site is mostly zinc-vacancy like in its spin density and $g$-tensor, while for the O-site, a model with the N$_2$ axis lying in-the basal plane and the singly occupied $π_g$-orbital along the {\bf c} axis provides good agreement with experiment. For the interstitial location, if the N$_2$ is not strongly interacting with the surroundings, no levels in the gap are found and hence also no possible EPR center. The calculated $g$-tensors for N$_O$ and $V_ Zn$ are also found to be in good agreement with experiment. The effects of different functionals affecting the localization of the spin density are shown to affect the $g$-tensor values.
Begonia vulgare S. Julia & Kiew
Creators: name: Sang, Julia
name: Kiew, Ruth
name: Yiing, Ling Chea
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Cucurbitales
Begoniaceae
Begonia
Begonia vulgare

description: 17. Begonia vulgare S.Julia & Kiew
 Phytotaxa 99(1) (2013) 26; Kiew et al., Guide to Begonias of Borneo (2015) 278. Type: — MALAYSIA. Borneo. Sarawak. Marudi District: Gunung Mulu NP, Deer Cave, 2 Oct 2007, Julia et al. S 99208 (holotype SAR!).
 Distribution: — MALAYSIA. Borneo. Sarawak. Endemic in Gunung Mulu NP where it is very common and widespread.
 Habitat: —In both limestone and non-limestone lowland forests to 460 m elevation in deeply to lightly shaded areas.
 Additional specimens examined: — MALAYSIA. Borneo. Sarawak. Marudi District: Gunung Mulu NP – Near boardwalk to Deer Cave, Julia et al. S 99209 (SAR), S 99210 (SAR), SFC 6677 (SAR); Trail to Kuala Litut, Julia et al. S 99211 (SAR), SFC 6692 (SAR); Melinau Gorge, Sub-camp 5, Lewis 315 (K, SAR); Bukit Agung, Julia et al. SFC 2815 (SAR); Lobang Cina, Julia et al. SFC 3012 (SAR), Julia et al. SFC 2806 (SAR); Camp 4, Ling et al. SFC 6913 (SAR); Camp 1, Ling et al. SFC 6933 (SAR); trail to Clearwater Cave, Julia et al. SFC 6669 (SAR); Camp 5, below Melinau Gorge, Julia et al. SFC 6683 (SAR); trail from Kuala Terikan to Camp 5, Julia et al. SFC 6686 (SAR); Sungai Lansat, Julia et al. SFC 6805 (SAR); Subcamp 2, downstream of Sungai Paku, Lewis 292 (K, KEP); path from subcamp 5, Lewis 304 (K).
 Notes: —Bushy cane-like begonia to 2 m tall with a dense paniculate inflorescence that is longer than the petiole, male flowers with 2 tepals, and large glabrous fruits, 35–45 mm long, 17–27 mm wide with rounded wing tips. The leaves are slightly oblique, narrowly ovate, 13.5–18 × 6.5–12.5 cm, broad side 4–6.5 cm, asymmetric with a small basal lobe 1–1.5 cm long, and range in colour from dull green or yellowish green or sometimes bronzy above, are covered on both surfaces by very sparse stiff short hairs, and have pinnate venation.
description: Published as part of Sang, Julia, Kiew, Ruth & Yiing, Ling Chea, 2018, The Begonia flora of Gunung Mulu and Gunung Buda National Parks, Sarawak, Borneo, including five new species, pp. 58-79 in Phytotaxa 381 (1) on pages 73-74, DOI: 10.11646/phytotaxa.381.1.9, http://zenodo.org/record/13726112
Improving Viral Protease Inhibitors to Counter Drug Resistance
Creators: name: Schiffer, Celia A.
name: Kurt Yilmaz, Nese
name: Swanstrom, Ronald
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Drug resistance is a major problem in health care, undermining therapy outcomes and necessitating novel approaches to drug design. Extensive studies on resistance to viral protease inhibitors, particularly those of HIV-1 and hepatitis C virus (HCV) protease, revealed a plethora of information on the structural and molecular mechanisms underlying resistance. These insights led to several strategies to improve viral protease inhibitors to counter resistance, such as exploiting the essential biological function and leveraging evolutionary constraints. Incorporation of these strategies into structure-based drug design can minimize vulnerability to resistance, not only for viral proteases but for other quickly evolving drug targets as well, toward designing inhibitors one step ahead of evolution to counter resistance with more intelligent and rational design.
Maximal Non-Classicality in Multi-Setting Bell Inequalities
Creators: name: Tavakoli, Armin
name: Zohren, Stefan
name: Pawlowski, Marcin
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The discrepancy between maximally entangled states and maximally non-classical quantum correlations is well-known but still not well understood. We aim to investigate the relation between quantum correlations and entanglement in a family Bell inequalities with $N$-settings and $d$ outcomes. Using analytical as well as numerical techniques, we derive both maximal quantum violations and violations obtained from maximally entangled states. Furthermore, we study the most non-classical quantum states in terms of their entanglement entropy for large values of $d$ and many measurement settings. Interestingly, we find that the entanglement entropy behaves very differently depending on whether $N=2$ or $N> 2$: when $N=2$ the entanglement entropy is a monotone function of $d$ and the most non-classical state is far from maximally entangled, whereas when $N> 2$ the entanglement entropy is a non-monotone function of $d$ and converges to that of the maximally entangled state in the limit of large $d$.
description: Updated version
Scylla paramamosain Transcriptome or Gene expression
Creators: name: BGI
Publisher: name: CNGB
Year: 2014
Subjects: transcriptome
Monoisolate

description: The transcriptome and the expression profiling under the infection provides an invaluable new data for a functional genomics resource and biological research in S.paramamosain. The signaling cascades are regulated by V.parahaemolyticus infection in mud crab. These results will facilitate our comprehensive understanding of the mechanisms involved in the immune response to bacterial infection and diseases prevention in crab aquaculture.
Transcriptome sequencing of Ovis aries
Creators: name: BGI
Publisher: name: CNGB
Year: 2014
Subjects: Transcriptome or Gene expression
Multiisolate

description: We have completed the high quality reference genome for domestic sheep (Oar v3.1) and performed a detailed survey of gene expression across different tissues. RNA-seq data of 7 tissue types from the reference female Texel and skin tissue from a Gansu alpine fine wool sheep were sequenced.Overall design: Here is the part of the RNA-seq data sequenced in BGI, including 7 tissue types from the reference female Texel and skin type from a Gansu alpine fine wool sheep.
Can maker-taker fees prevent algorithmic cooperation in market making?
Creators: name: Han, Bingyan
Publisher: name: arXiv
Year: 2022
Subjects: subject: Trading and Market Microstructure (q-fin.TR)
subject: Multiagent Systems (cs.MA)
subject: FOS: Economics and business
subject: FOS: Computer and information sciences

description: In a semi-realistic market simulator, independent reinforcement learning algorithms may facilitate market makers to maintain wide spreads even without communication. This unexpected outcome challenges the current antitrust law framework. We study the effectiveness of maker-taker fee models in preventing cooperation via algorithms. After modeling market making as a repeated general-sum game, we experimentally show that the relation between net transaction costs and maker rebates is not necessarily monotone. Besides an upper bound on taker fees, we may also need a lower bound on maker rebates to destabilize the cooperation. We also consider the taker-maker model and the effects of mid-price volatility, inventory risk, and the number of agents.
The geodesic flow on nilmanifolds
Creators: name: Kocsard, Alejandro
name: Ovando, Gabriela P.
name: Reggiani, Silvio
Publisher: name: arXiv
Year: 2015
Subjects: subject: Differential Geometry (math.DG)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics
subject: 53C30, 53C25, 22E25, 57S20

description: In this paper we study the geodesic flow on nilmanifolds equipped with a left-invariant metric. We write the underlying definitions and find general formulas for the Poisson involution. As an example we develop the Heisenberg Lie group equipped with its canonical metric. We prove that a family of first integrals giving the complete integrability can be read off at the Lie algebra of the isometry group. We also explain the complete integrability on compact quotients and for any invariant metric.
description: 24 pages
Towards Multidisciplinary HIV-Cure Research: Integrating Social Science with Biomedical Research
Creators: name: Ross, Anna Laura
name: Tucker, Joseph D.
name: Dubé, Karine
name: Grossman, Cynthia I.
name: Noseda, Veronica
name: Rausch, Dianne M.
name: Auerbach, Judith D.
name: Possas, Cristina
name: Ananworanich, Jintanat
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The quest for a cure for HIV remains a timely and key challenge for the HIV research community. Despite significant scientific advances, current HIV therapy regimens do not completely eliminate the negative impact of HIV on the immune system; and the economic impact of treating all people infected with HIV globally, for the duration of their lifetimes, presents significant challenges. This article discusses, from a multi-disciplinary approach, critical social, behavioral, ethical, and economic issues permeating the HIV cure research agenda. As part of a search for an HIV cure, both the perspective of patients/participants and clinical researchers should be taken into account. In addition, continued efforts should be made to involve and educate the broader community.
MPEC 2024-R152 : 2024 RB5
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2024
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469
subject: 2024 RB5

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
MeDIP sequencing of Ovis aries
Creators: name: BGI
Publisher: name: CNGB
Year: 2014
Subjects: Epigenomics
Monoisolate

description: We have completed the high quality reference genome for domestic sheep (Oar v3.1).Overall design: Early-stage Illumina GA sequence platform sequenced less reads in high GC content regions than in other regions. To read through higher GC content regions, we generated 2 Gb MeDIP-seq data for filling gaps in sheep reference genome assembly.
Algebraical Entropy and Arrow of Time
Creators: name: Gogberashvili, Merab
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Physics (physics.gen-ph)
subject: FOS: Physical sciences

description: Usually, it is supposed that irreversibility of time appears only in macrophysics. Here, we attempt to introduce the microphysical arrow of time assuming that at a fundamental level nature could be non-associative. Obtaining numerical results of a measurement, which requires at least three ingredients: object, device and observer, in the non-associative case depends on ordering of operations and is ambiguous. We show that use of octonions as a fundamental algebra, in any measurement, leads to generation of unavoidable 18.6~bit relative entropy of the probability density functions of the active and passive transformations, which correspond to the groups G2 and SO(7), respectively. This algebraical entropy can be used to determine the arrow of time, analogically as thermodynamic entropy does.
description: 8 pages, no figures
Improved tagmentation-based whole genome bisulfite sequencing for input DNA from less than 100 cells
Creators: name: BGI
Publisher: name: CNGB
Year: 2014
Subjects: Epigenomics
Multiisolate

description: We improved the tagmentation-based whole genome bisulfite sequencing technology, enabling stable library construction with complexity from minimally 0.5ng of initial genomic DNA, which equals less than 100 cells. This new approach is highly attractive for the complete methylome analysis of very limited cell numbers, e.g., pre-implantation embryos, or tiny biopsy specimens.Overall design: Applying this newly modified T-WGBS, we sequenced the methylome of a rice strain using libraries constructed from 10 ng, 1 ng and 0.5 ng of input genomic DNA. Two libraries were independently constructed and sequenced for each aliquot of input genomic DNA
Viral Carcinogenesis Beyond Malignant Transformation: EBV in the Progression of Human Cancers
Creators: name: Pagano, Joseph S.
name: Müller-Coan, Bárbara G.
name: Elgui de Oliveira, Deilson
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Cancer progression begins when malignant cells colonize adjacent sites, and it is characterized by increasing tumor heterogeneity, invasion and dissemination of cancer cells. Clinically, progression is the most relevant stage in the natural history of cancers. A given virus is usually regarded as oncogenic because of its ability to induce malignant transformation of cells. Nonetheless, oncogenic viruses may also be important for the progression of infection-associated cancers. Recently this hypothesis has been addressed because of studies on the contribution of the Epstein–Barr virus (EBV) to the aggressiveness of nasopharyngeal carcinoma (NPC). Several EBV products modulate cancer progression phenomena, such as the epithelial–mesenchymal transition, cell motility, invasiveness, angiogenesis, and metastasis. In this regard, there are compelling data about the effects of EBV latent membrane proteins (LMPs) and EBV nuclear antigens (EBNAs), as well as nontranslated viral RNAs, such as the EBV-encoded small nonpolyadenylated RNAs (EBERs) and viral microRNAs, notably EBV miR-BARTs. The available data on the mechanisms and players involved in the contribution of EBV infection to the aggressiveness of NPC are discussed in this review. Overall, this conceptual framework may be valuable for the understanding of the contribution of some infectious agents in the progression of cancers.
Brain transcriptome of Larimichthys crocea (Large yellow croaker) under hypoxia
Creators: name: BGI
Publisher: name: CNGB
Year: 2014
Subjects: Transcriptome or Gene expression
Multiisolate

description: Brain transcriptome at 0h, 1h, 3h, 6h, 12h, 24h, 48h after hypoxia stressOverall design: Large yellow croakers (body weight at 90-100 g) were purchased from the mariculture farm in Ningde, Fuzhou, China. The fish were maintained at 25 °C in aerated water tanks (dissolved oxygen concentration: 7.8±0.5 mg per liter) with a flow through seawater supply. After 7 days of acclimation, these fish were used for the following experiments. Hypoxic time-course experiments were conducted at 25 °C using published method 30, by bubbling nitrogen gas into an aquarium. The desired pO2 was controlled by using dissolved oxygen meter (, Canada). At the onset of the time course, the oxygen content of the tank was lowered from an aerated pO2 of 100% (7.8 mg per liter) down to 20% (1.6±0.2 mg per liter) over a 30-min period. At the 1-, 3-, 6-, 12-, 24-, and 48-h time points, fish were sampled and sequenced.
Il compito impossibile? La valutazione nei Centri per bambini e famiglie come strumento di crescita professionale
Creators: name: Sità, Chiara
name: Mortari, Luigina
Publisher: name: Rivista Italiana di Educazione Familiare
Year: 2016

description: The parent and toddler centers design a complex area of practice, mainly focused on prevention-oriented strategies and family empowerment. The paper presents the results of a research founded by the Italian Ministry of Education, called “Evaluation for the improvement of educational contexts. A research involving University and local communities in the participatory development of innovative assessment models”. The research has been completed in 2013 and focuses on evaluation in parent toddler centers, here considered as highly complex socio-educational settings. The survey involved 17 Centers in the Verona region, and examined the different and sometimes conflicting evaluation models involved in practices and the professionals’ perspectives on evaluation. The educators of 4centers have attended a process of shared construction through group reflection facilitated by researchers, aiming to build context-sensitive evaluation guidelines for the centers. This reflective process has enabled us to explore the relationship between assessment practices and the identity of the service, and to re-conceptualize the evaluation as a tool for improving practice and empowering professionals.
description: Rivista Italiana di Educazione Familiare, n° 2 luglio-dicembre 2015
Congenital scolisis may be associated with both of rare mutation and allele-specific methylation
Creators: name: BGI
Publisher: name: CNGB
Year: 2014
Subjects: Epigenomics
Multiisolate

description: Congenital scoliosis (CS) is a congenital disease that results in anomalous vertebral development. Research indicates that both genetic and environmental factors during pregnancy contribute to the risk of CS development, however, the exact mechanisms underlying CS pathogenesis remain unclear. To address this issue, we have generated both genetic (by exon capture sequencing) and epigenetic (by MeDIP) maps from a CS disease-discordant monozygotic twin pair. We compared the differences in the presence of common and rare SNPs between the twins as well as investigated differences in methylation patterns. Our data indicated that rare mutations are more likely to underlie CS development than common mutations, and that these are also more likely to play a role than do genomic methylation patterns. We did, however, identify a difference in the allele-specific-methylation between the twins in the SVIL gene which has functions in categories relevant to this disease, which raises the possibility of a novel mechanism promoting CS pathogenesis.Overall design: DNA was extracted from peripheral blood of a monozygotic twin pair that was discordant for CS, with T-P affected with CS and T-H non-affected. Followed by MeDIP-seq and exome-seq.
Begonia xiphophylloides Kiew
Creators: name: Sang, Julia
name: Kiew, Ruth
name: Yiing, Ling Chea
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Cucurbitales
Begoniaceae
Begonia
Begonia xiphophylloides

description: 19. Begonia xiphophylloides Kiew (Figure 10)
 Phytotaxa 99(1) (2013) 31. Type: — MALAYSIA. Borneo. Sarawak. Marudi District: Gunung Mulu NP, Sungai Melinau, 16 April 1978, Kiew RK 267 (holotype KEP!; isotype K!).
 Distribution: — MALAYSIA. Borneo. Sarawak. Endemic in Gunung Mulu NP.
 Habitat: —Common in riparian forest at ca. 70 m elevation, on sandy banks or on limestone rocks.
 Additional specimens examined: — MALAYSIA.Borneo. Sarawak. Marudi District: Gunung Mulu NP – Melinau Gorge, Abang Mohtar S 49655 (SAR); Sungai Melinau below Melinau Gorge, Kiew 299 (KEP), 321 (KEP), Julia et al. SFC 6681 (SAR), Julia et al. SFC 6682 (SAR); sub-camp 5, Melinau Gorge, Lewis 308 (SAR), Lewis 329 (SAR); Bukit Pantu, Julaihi et al. S 74882 (SAR), Abang Mohtar & Othman S 49749 (SAR); trail from Camp 5 to Kuala Litut, Julia et al. SFC 6696 (SAR).
 Notes: —A bushy much-branched, erect plant to 30 cm tall. It is distinctive in its slightly asymmetric but nonoblique, narrow leaves about four or more times longer than wide, its sessile inflorescence with one or two female flowers from the leaf axis and a raceme of very small male flowers above.
description: Published as part of Sang, Julia, Kiew, Ruth & Yiing, Ling Chea, 2018, The Begonia flora of Gunung Mulu and Gunung Buda National Parks, Sarawak, Borneo, including five new species, pp. 58-79 in Phytotaxa 381 (1) on pages 76-77, DOI: 10.11646/phytotaxa.381.1.9, http://zenodo.org/record/13726112
Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming (RNA-seq)
Creators: name: BGI
Publisher: name: CNGB
Year: 2014
Subjects: Transcriptome or Gene expression
Multiisolate

description: Reactivation of the pluripotency network during somatic cell reprogramming by exogenous transcription factors involves chromatin remodeling and the recruitment of RNA polymerase II (Pol II) to target loci. Here, we report that Pol II is engaged at pluripotency promoters in reprogramming but remains paused and inefficiently released. We also show that bromodomain-containing protein 4 (BRD4) stimulates productive transcriptional elongation of pluripotency genes by dissociating the pause release factor P-TEFb from an inactive complex containing HEXIM1. Consequently, BRD4 overexpression enhances reprogramming efficiency and HEXIM1 suppresses it, whereas Brd4 and Hexim1 knockdown do the opposite. We further demonstrate that the reprogramming factor KLF4 helps recruit P-TEFb to pluripotency promoters. Our work thus provides a mechanism for explaining the reactivation of pluripotency genes in reprogramming and unveils an unanticipated role for KLF4 in transcriptional pause release.Overall design: Examination of differential gene expression after overexpression of Cdk9-DN at 4 time points of somatic cell reprogramming
On solving dynamical equations in general homogeneous isotropic cosmologies with scalaron
Creators: name: Filippov, Alexandre T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We study general dynamical equations describing homogeneous isotropic cosmologies coupled to a scalaron $ψ$. For flat cosmologies ($k=0$), we analyze in detail the gauge-independent equation describing the differential, $χ(α)\equivψ^\prime(α)$, of the map of the metric $α$ to the scalaron field $ψ$, which is the main mathematical characteristic locally defining a `portrait' of a cosmology in `$α$-version'. In the `$ψ$-version', a similar equation for the differential of the inverse map, $\barχ(ψ)\equiv χ^{-1}(α)$, can be solved asymptotically or for some `integrable' scalaron potentials $v(ψ)$. In the flat case, $\barχ(ψ)$ and $χ(α)$ satisfy the first-order differential equations depending only on the logarithmic derivative of the potential. Once we know a general analytic solution for one of these $χ$-functions, we can explicitly derive all characteristics of the cosmological model. In the $α$-version, the whole dynamical system is integrable for $k\neq 0$ and with any `$α$-potential', $\bar{v}(α)\equiv v[ψ(α)]$, replacing $v(ψ)$. There is no a priori relation between the two potentials before deriving $χ$ or $\barχ$, which implicitly depend on the potential itself, but relations between the two pictures can be found by asymptotic expansions or by inflationary perturbation theory. Explicit applications of the results to a more rigorous treatment of the chaotic inflation models and to their comparison with the ekpyrotic-bouncing ones are outlined in the frame of our `$α$-formulation' of isotropic scalaron cosmologies. In particular, we establish an inflationary perturbation expansion for $χ$. When all the conditions for inflation are satisfied and $χ$ obeys a certain boundary (initial) condition, we get the standard inflationary parameters, with higher-order corrections.
description: New version: 33 pages instead 32; revised and extended Abstract, Sections 4.3, 5; edited Section 1, changed a few titles; corrected misprints
I nidi domiciliari nelle Marche: una nuova realtà educativa
Creators: name: Sirignano, Chiara
Publisher: name: Rivista Italiana di Educazione Familiare
Year: 2016

description: The article aims at defining one of the integrated services for early childhood education, that is, the homeschooling. Such educational reality, in fact, is spreading also in Italy thanks to the promotion and the investment of several regions. Specifically the reference laws of the Region Marche were examined, along with the professional profile and training of the educator in homeschooling. Finally, a questionnaire was submitted to both homeschooling educators and parents of children taking advantage of this service. It was, thus, possible to define the profile of educators working in this field, their motivations and the difficulties experienced during their activities, while parents were investigated about the reasons behind such a choice letting them express their full satisfaction.
description: Rivista Italiana di Educazione Familiare, n° 1 gennaio-giugno 2016
Reproducible Metabolome Annotation Workflow (MAW) - Automated Structure Identification with Spectral and Compound Databases
Creators: name: Mahnoor Zulfiqar
Publisher: name: Zenodo
Year: 2022

description: Analytical techniques combined with computational metabolomics enable annotation of natural products. Here we introduce Metabolome Annotation Workflow (MAW) for molecular annotation from Tandem Mass Spectrometry data. MAW links spectral features from the .mzML input files to final tentative compound from different open source compound and spectral databases. We are currently working on applying best practices for supporting reproducibility and the FAIR principles in MAW. This workflow comes with tools to predict the chemical class and sub-structure of the unknown compounds.