cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The Chemical Signature of a Relic Star Cluster in the Sextans Dwarf Spheroidal Galaxy - Implications for Near-Field Cosmology
Creators: name: Karlsson, Torgny
name: Bland-Hawthorn, Joss
name: Freeman, Ken
name: Silk, Joe
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present tentative evidence for the existence of a dissolved star cluster at [Fe/H]=-2.7 in the Sextans dwarf spheroidal galaxy. We use the technique of chemical tagging to identify stars that are highly clustered in a multi-dimensional chemical abundance space (C-space). In a sample of six stars, three, possibly four stars are identified as potential cluster stars. The initial stellar mass of the parent cluster is estimated from two independent observations to M*,init=1.9^{+1.5}_{-0.9} (1.6^{+1.2}_{-0.8}) x 10^5 M_sol, assuming a Salpeter (Kroupa) initial mass function (IMF). If corroborated by follow-up spectroscopy, this star cluster is the most metal-poor system identified to date. Chemical signatures of remnant clusters in dwarf galaxies like Sextans provide us with a very powerful probe to the high-redshift Universe. From available observational data, we argue that the average star cluster mass in the majority of the newly discovered ultra-faint dwarf galaxies was notably lower than it is in the Galaxy today and possibly lower than in the more luminous, classical dwarf spheroidal galaxies. Furthermore, the mean cumulative metallicity function of the dwarf spheroidals falls below that of the ultra-faints, which increases with increasing metallicity as predicted from our stochastic chemical evolution model. These two findings, together with a possible difference in the ratio suggest that the ultra-faint dwarf galaxy population, or a significant fraction thereof, and the dwarf spheroidal population, were formed in different environments and would thus be distinct in origin.
description: 18 pages, 8 figures, new Fig. 5, some clarifications, references added, accepted for publication in the ApJ
Plicofollis layardi
Creators: name: Zainal Abidin, Danial Hariz
name: Lavoué, Sébastien
name: Mohd Abu Hassan Alshari, Norli Fauzani
name: Mohd. Nor, Siti Azizah
name: A. Rahim, Masazurah
name: Mohammed Akib, Noor Adelyna
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Siluriformes
Ariidae
Plicofollis
Plicofollis layardi

description: Plicofollis layardi (Günther, 1866) Material examined. MALAYSIA • 1, 280 mm TL; Kedah State, Kuala Kedah, Kuala Muda Whispering Market; 05.578°N, 100.341°E; 6 Dec. 2018; Danial H. Zainal Abidin, Norli F.M.A.H. Alshari leg.; USMFC (66) 00007.
description: Published as part of Zainal Abidin, Danial Hariz, Lavoué, Sébastien, Mohd Abu Hassan Alshari, Norli Fauzani, Mohd. Nor, Siti Azizah, A. Rahim, Masazurah & Mohammed Akib, Noor Adelyna, 2021, Ichthyofauna of Sungai Merbok Mangrove Forest Reserve, northwest Peninsular Malaysia, and its adjacent marine waters, pp. 601-631 in Check List 17 (2) on page 616, DOI: 10.15560/17.2.601
Tico Noyes 2023
Creators: name: Noyes, John Stuart
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Derbidae
Tico

description: Key to Costa Rican species of Tico
(Females)
 1. Hind tibia completely pale yellow; scape not longer than minimum width of frontovertex; funicle (Fig. 403) with F1-F3 transverse or quadrate, F4-F6 larger but quadrate, not more than 1.1X as long as broad........................... sinabelus sp.nov. (p. 161)
 - Hind tibia mostly dark brown; scape at least 1.2X as long as width of frontovertex; funicle (Fig. 410) with F1-F3 at least slightly longer than broad, F4-F6 larger and at least about 1.5X as long as broad................................. ryaspis sp.nov. (p. 162)
description: Published as part of Noyes, John Stuart, 2023, ENCYRTIDAE OF COSTA RICA (HYMENOPTERA: CHALCIDOIDEA), 4 Subfamily Encyrtinae: tribes Arrhenophagini, Habrolepidini, Cerapterocerini, Cheiloneurini, Trechnitini, Cercobelini, Polaszekiini, Protyndarichoidini, Gahaniellini and Syrphophagini (part), mainly primary parasitoids and hyperparasitoids of Coccoidea and Psylloidea (Hemiptera), pp. 1-921 in Taxonomic Monographs on Neotropical Hymenoptera (Oxford, England) (Oxford, England) 2 (11) on page 160, DOI: 10.5281/zenodo.8074943
Implicit essentialism : genetic concepts are implicitly associated with fate concepts
Creators: name: Gould, Wren
Publisher: name: University of British Columbia
Year: 2012

description: Genetic essentialism is the tendency for people to think in more essentialist ways upon encountering genetic concepts. The current studies assessed whether genetic essentialist biases would also be evident at the automatic level. In two studies, using different versions of the Implicit Association Test (Greenwald, McGhee, & Schwartz, 1998), we found that participants were faster to categorize when genes and fate were linked, compared to when these two concepts were kept separate and opposing. In addition to the wealth of past findings of genetic essentialism with explicit and deliberative measures, these biases appear to be also evident with implicit measures.
Quantum Central Limit Theorems, Emergence of Classicality and Time-dependent Differential Entropy
Creators: name: Kieu, Tien D.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We derive some Quantum Central Limit Theorems for expectation values of macroscopically coarse-grained observables, which are functions of coarse-grained hermitean operators. Thanks to the hermicity constraints, we obtain positive-definite distribution for the expectation values of observables. These probability distributions open some pathway for an emergence of classical behaviours in the limit of infinitely large number of identical and non-interacting quantum constituents. This is in contradistinction to other mechanisms of classicality emergence due to environmental decoherence and consistent histories. The probability distributions so derived also enable us to evaluate the nontrivial time-dependence of certain differential entropies.
description: 23 pages
Candidate gene biodosimetry markers of exposure to external ionizing radiation in human blood: A systematic review
Creators: name: Lacombe, Jerome
name: Sima, Chao
name: Amundson, Sally A.
name: Zenhausern, Frederic
Publisher: name: Columbia University
Year: 2018
Subjects: Ionizing radiation--Physiological effect
Radiation dosimetry
Gene expression
Biochemical markers

description: Purpose
To compile a list of genes that have been reported to be affected by external ionizing radiation (IR) and to assess their performance as candidate biomarkers for individual human radiation dosimetry.

Methods
Eligible studies were identified through extensive searches of the online databases from 1978 to 2017. Original English-language publications of microarray studies assessing radiation-induced changes in gene expression levels in human blood after external IR were included. Genes identified in at least half of the selected studies were retained for bio-statistical analysis in order to evaluate their diagnostic ability.

Results
24 studies met the criteria and were included in this study. Radiation-induced expression of 10,170 unique genes was identified and the 31 genes that have been identified in at least 50% of studies (12/24 studies) were selected for diagnostic power analysis. Twenty-seven genes showed a significant Spearman’s correlation with radiation dose. Individually, TNFSF4, FDXR, MYC, ZMAT3 and GADD45A provided the best discrimination of radiation dose < 2 Gy and dose ≥ 2 Gy according to according to their maximized Youden’s index (0.67, 0.55, 0.55, 0.55 and 0.53 respectively). Moreover, 12 combinations of three genes display an area under the Receiver Operating Curve (ROC) curve (AUC) = 1 reinforcing the concept of biomarker combinations instead of looking for an ideal and unique biomarker.

Conclusion
Gene expression is a promising approach for radiation dosimetry assessment. A list of robust candidate biomarkers has been identified from analysis of the studies published to date, confirming for example the potential of well-known genes such as FDXR and TNFSF4 or highlighting other promising gene such as ZMAT3. However, heterogeneity in protocols and analysis methods will require additional studies to confirm these results.
Gradient boosting machines and careful pre-processing work best: ASHRAE Great Energy Predictor III lessons learned
Creators: name: Miller, Clayton
name: Hao, Liu
name: Fu, Chun
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: The ASHRAE Great Energy Predictor III (GEPIII) competition was held in late 2019 as one of the largest machine learning competitions ever held focused on building performance. It was hosted on the Kaggle platform and resulted in 39,402 prediction submissions, with the top five teams splitting $25,000 in prize money. This paper outlines lessons learned from participants, mainly from teams who scored in the top 5% of the competition. Various insights were gained from their experience through an online survey, analysis of publicly shared submissions and notebooks, and the documentation of the winning teams. The top-performing solutions mostly used ensembles of Gradient Boosting Machine (GBM) tree-based models, with the LightGBM package being the most popular. The survey participants indicated that the preprocessing and feature extraction phases were the most important aspects of creating the best modeling approach. All the survey respondents used Python as their primary modeling tool, and it was common to use Jupyter-style Notebooks as development environments. These conclusions are essential to help steer the research and practical implementation of building energy meter prediction in the future.
A continuum solvent model: the DISOLV program - algorithms, implementation, and validation
Creators: name: Kupervasser, Oleg
name: Zhabin, S. N.
name: Martynov, Ya. B.
name: Fedulov, K. M.
name: Oferkin, I. F.
name: Sulimov, A. V.
name: Sulimov, V. B.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the DISOLV program. The methods for solving the corresponding equations and for computing the analytic gradients are described. The analytic gradients are used for the fast local energy optimization of molecules in a solvent. An algorithm for the original smooth triangulated molecular surface construction is shortly discussed. The procedure for matching the model parameters and the results of the program application to proteins and ligands with the employment of the MMFF94 force field are described. The validation results show the capability of the program to reach a good accuracy (about several tenth of kcal/mol) in the case of the solvation energy calculation for reasonable time periods at arbitrary shifts of the triangulated grid in use for such large molecules as proteins. A good agreement between the calculated and experimentally measured solvation energies in water is obtained with a root-mean-square deviation about 0.8 kcal/mol for several hundreds of molecules.
description: 58 pages, English (35 pages) and Russian (23 pages) language versions
title: Evaluation of Glutamine Metabolism and Cellular Stress Responses in Fibroblasts from Patients with Mitochondrial Disease
Creators: name: Alhasan, Karm
Publisher: name: Graduate Studies
Year: 2025
Subjects: subject: Mitochondrial Disease
subject: Mitochondrial unfolded protein response
subject: Integrated stress response
subject: Glutamine metabolism
subject: Cellular Metabolism
subject: Health Sciences

description: Background: Mitochondrial diseases (MDs) are a group of genetic disorders with diverse patient phenotypes resulting from mitochondrial dysfunction. Pathologies are often poorly understood, and therapies are limited. Previously, we identified abnormalities in glutamine metabolism as well as an upregulation of the integrated stress response (ISR) and mitochondrial unfolded protein response (UPRmt) in dermal fibroblasts of patients with the dilated cardiomyopathy with ataxia syndrome (DCMA), a systemic mitochondrial disease (MD) caused by deficiency of DNAJC19. However, it is unclear whether these changes are unique to DCMA or shared across other MDs. Aims: To investigate changes in glutamine metabolism and stress responses in dermal fibroblasts from patients with Barth Syndrome (BTHS), complex I deficiency (C1D), and Kearns-Sayre syndrome (KSS) and healthy fibroblasts treated with mitochondrial disruptors. We hypothesized that, regardless of cause, mitochondrial dysfunction will lead to abnormal glutamine metabolism and activation of the ISR and UPRmt. Methods: Fibroblasts from healthy individuals (N=6) and patients with a diagnosis of BTHS (N=2), C1D (N=3) and KSS (N=3) were cultured in media containing heavy isotope-labelled glutamine [5-13C 2-15N]. After 48 hours, extracellular media was extracted and metabolites were quantified using liquid-chromatography-mass spectrometry (LC-MS). To validate findings, we also treated healthy fibroblasts (N=2) with dinitrophenol (DNP) and rotenone. The expression of ISR- and UPRmt-associated genes was quantified via qPCR. Results: Levels of the dual-heavy isotope-labelled glutamine (5-13C 2-15N) and glutamine-derived isotopomers were not significantly different in C1D, KSS and BTHS, compared to controls. In healthy fibroblasts, DNP (1 mM) reduced 5-13C 2-15N glutamine uptake, whereas rotenone (100 nM) had no effect. The ISR and UPRmt were not upregulated in BTHS, C1D, or KSS although data were limited by small numbers. Exposure to 500 nM rotenone and 1 mM DNP significantly upregulated ISR/UPRmt-associated genes ATF4 and ATF5 in healthy fibroblasts. Conclusions: These preliminary findings suggest that glutamine metabolism and the activation of cellular stress responses in MD fibroblasts differs depending on extent and/or etiology of mitochondrial dysfunction. Our results support the observation that DCMA fibroblasts have a unique dysregulation of glutamine metabolism and stress responses which may have implications for pathophysiology and treatment.
The MSSM Higgs Sector with a Dynamical Goldstino Supermultiplet
Creators: name: Petersson, Christoffer
name: Romagnoni, Alberto
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We consider a supersymmetric realization of the MSSM Higgs sector, where the soft terms are promoted to supersymmetric operators and a minimal weakly coupled hidden sector is included. The model exhibits long-lived meta-stable vacua in which supersymmetry and electroweak symmetry are spontaneously broken. The spectrum contains, in addition to the usual MSSM particles and the goldstino fermion, a CP-even and a CP-odd scalar in the neutral Higgs sector corresponding to the complex sgoldstino scalar. By treating all the components of the goldstino supermultiplet dynamically and taking into account their interactions with the Higgs fields, additional couplings beyond those of the MSSM are induced. When the supersymmetry breaking scale is low, these couplings can raise the masses of all the Higgs particles above the LEP bound, already at tree level and for any value of tan(beta). The model includes a scenario where, for any choice of the supersymmetry breaking scale, the set of parameters is reduced to the standard set (mu, Bmu, tan(beta)) of the MSSM Higgs sector but where novel decays of doublet-like states into sgoldstino-like states are kinematically allowed.
description: 24 pages; v2: references added
The Neo-Fisher Effect: Econometric Evidence from  Empirical and Optimizing  Models
Creators: name: Uribe, Martin
Publisher: name: Columbia University
Year: 2018
Subjects: subject: Economics
subject: Econometrics
subject: FOS: Economics and business
subject: Monetary policy
subject: Inflation (Finance)--Econometric models
subject: Bayesian statistical decision theory--Mathematical models

description: This paper investigates whether permanent monetary tightenings increase  inflation in the short run. It  estimates, using U.S. data,  an empirical and a New-Keynesian model driven by transitory and permanent monetary and real shocks. Temporary increases in the nominal interest-rate lead, in accordance with conventional wisdom, to a decrease in  inflation and output and an increase in real rates. The main result  of the paper is that permanent increases in the nominal interest rate lead to an immediate  increase in inflation and output  and a decline in  real rates. Permanent monetary shocks explain more than 40 percent of inflation changes.
The Fundamental Surface of Quad Lenses
Creators: name: Woldesenbet, Addishiwot G.
name: Williams, Liliya L. R.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: In a quadruply imaged lens system the angular distribution of images around the lens center is completely described by three relative angles. We show empirically that in the 3D space of these angles, spanning 180 x 180 x 90 degrees, quads from simple two-fold symmetric lenses of arbitrary radial density profile and arbitrary radially dependent ellipticity or external shear define a nearly invariant 2D surface. We give a fitting formula for the surface using SIS+elliptical lensing potential. Various circularly symmetric mass distributions with shear up to 0.4 deviate from it by typically, rms~0.1 deg, while elliptical mass distributions with ellipticity of up 0.4 deviate from it by rms~1.5 deg. The existence of a near invariant surface gives a new insight into the lensing theory and provides a framework for studying quads. It also allows one to gain information about the lens mass distribution from the image positions alone, without any recourse to mass modeling. As an illustration, we show that about 3/4 of observed galaxy-lens quads do not belong to this surface within observational error, and so require additional external shear or substructure to be modeled adequately.
description: 24 pages, 9 figures, accepted to MNRAS
Plicofollis polystaphylodon
Creators: name: Zainal Abidin, Danial Hariz
name: Lavoué, Sébastien
name: Mohd Abu Hassan Alshari, Norli Fauzani
name: Mohd. Nor, Siti Azizah
name: A. Rahim, Masazurah
name: Mohammed Akib, Noor Adelyna
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Siluriformes
Ariidae
Plicofollis
Plicofollis polystaphylodon

description: Plicofollis polystaphylodon (Bleeker, 1846) Material examined. MALAYSIA • 1, 400 mm TL; Kedah State, Kuala Kedah, Kuala Muda Whispering Market; 05.578°N, 100.341°E; 19 Mar. 2019; Danial H. Zainal Abidin, Norli F.M.A.H. Alshari leg.; USMFC (66) 00010.
description: Published as part of Zainal Abidin, Danial Hariz, Lavoué, Sébastien, Mohd Abu Hassan Alshari, Norli Fauzani, Mohd. Nor, Siti Azizah, A. Rahim, Masazurah & Mohammed Akib, Noor Adelyna, 2021, Ichthyofauna of Sungai Merbok Mangrove Forest Reserve, northwest Peninsular Malaysia, and its adjacent marine waters, pp. 601-631 in Check List 17 (2) on page 616, DOI: 10.15560/17.2.601
Locally mediated entanglement in linearised quantum gravity
Creators: name: Christodoulou, Marios
name: Di Biagio, Andrea
name: Aspelmeyer, Markus
name: Brukner, Časlav
name: Rovelli, Carlo
name: Howl, Richard
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The current interest in laboratory detection of entanglement mediated by gravity was sparked by an information--theoretic argument: entanglement mediated by a local field certifies that the field is not classical. Previous derivations of the effect modelled gravity as instantaneous; here we derive it from linearised quantum general relativity while keeping Lorentz invariance explicit, using the path integral formalism. In this framework, entanglement is clearly mediated by a quantum feature of the field. We also point out the possibility of observing retarded entanglement, which cannot be explained by an instantaneous interaction. This is a difficult experiment for gravity, but is plausible for the analogous electromagnetic case.
description: 6 pages + 4 pages of supplementary, 1 figure. document updated to be the closest to the PRL version published in March 2023
Supplement Table S2
Creators: name: Lyu, Houchen
name: Zhao, Sizheng
name: Li, Jiatian
name: Li, Xiaoxiao
name: Wang, Yilun
name: Xie, Dongxing
name: Zeng, Chao
name: Lei, Guanghua
name: Wei, Jie
name: Li, Hui
Publisher: name: figshare
Year: 2022
Subjects: classificationCode: 320208
subject: Endocrinology

description: Supplement Table S2
The Fleming-Viot limit of an interacting spatial population with fast density regulation
Creators: name: Gupta, Ankit
Publisher: name: arXiv
Year: 2012
Subjects: subject: Probability (math.PR)
subject: Populations and Evolution (q-bio.PE)
subject: FOS: Mathematics
subject: FOS: Biological sciences
subject: 60J68, 60J85, 60G57, 60F99

description: We consider population models in which the individuals reproduce, die and also migrate in space. The population size scales according to some parameter $N$, which can have different interpretations depending on the context. Each individual is assigned a mass of 1/N and the total mass in the system is called \emph{population density}. The dynamics has an intrinsic density regulation mechanism that drives the population density towards an equilibrium. We show that under a timescale separation between the \emph{slow} migration mechanism and the \emph{fast} density regulation mechanism, the population dynamics converges to a Fleming-Viot process as the scaling parameter $N$ approaches $\infty$. We first prove this result for a basic model in which the birth and death rates can only depend on the population density. In this case we obtain a \emph{neutral} Fleming-Viot process. We then extend this model by including position-dependence in the birth and death rates, as well as, offspring dispersal and immigration mechanisms. We show how these extensions add \emph{mutation} and \emph{selection} to the limiting Fleming-Viot process. All the results are proved in a multi-type setting, where there are $q$ types of individuals interacting with each other. We illustrate the usefulness of our convergence result by discussing applications in population genetics and cell biology.
title: Correlating Obstructive Symptoms with Stricture Severity in Ileal Crohn’s Disease
Creators: name: Saunders, Bethany
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Crohns Disease
subject: Medicine
subject: Strictures
subject: Bowel Obstruction
subject: Surgery
subject: Symptoms
subject: Obstructive Symptoms
subject: Medicine and Surgery

description: Crohn’s Disease (CD) can manifest as inflammatory (non-stricturing), fibrostenotic (stricturing) and fistulizing or penetrating phenotypes. Stricturing CD, the main focus of this thesis, involves luminal narrowing and, which is often progressive leading to obstruction of the affected bowel segment. Obstructive symptoms (OS) in CD strictures can be assessed using the Stricture Definition and Treatment (STRIDENT) trial-used OS scoring system and CREOLE OS score. Clinically, OS are typically linked to advanced strictures, strictures can often result in dietary restrictions and surgery. No studies have been published to date, evaluating the severity of CD strictures and OS. Understanding the correlation between symptoms and strictures is crucial as regulatory bodies assess drug efficacy based on symptom response in CD trials. Intestinal ultrasound (IUS) accurately evaluates strictures morphology, with stricture severity and length, using established criteria: bowel wall thickness > 3mm, luminal narrowing (<1cm), with any pre-stenotic dilation (PSD) size (cm). The aim of this thesis based stsudy aims to determine if the OS of pain, bloating, nausea and/ or vomiting when comparing among CD phenotypes, and if specific OS correlate with any of the definitive stricture parameters.
Topological Surface States and Dirac point tuning in ternary Bi2Te2Se class of topological insulators
Creators: name: Neupane, M.
name: Xu, S. -Y.
name: Wray, L. A.
name: Petersen, A.
name: Shankar, R.
name: Alidoust, N.
name: Liu, Chang
name: Fedorov, A.
name: Ji, H.
name: Allred, J. M.
name: Hor, Y. S.
name: Chang, T. -R.
name: Jeng, H. -T.
name: Lin, H.
name: Bansil, A.
name: Cava, R. J.
name: Hasan, M. Z.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Using angle-resolved photoemission spectroscopy, we report electronic structure for representative members of ternary topological insulators. We show that several members of this family, such as Bi2Se2Te, Bi2Te2Se, and GeBi2Te4, exhibit a singly degenerate Dirac-like surface state, while Bi2Se2S is a fully gapped insulator with no measurable surface state. One of these compounds, Bi2Se2Te, shows tunable surface state dispersion upon its electronic alloying with Sb (SbxBi2-xSe2Te series). Other members of the ternary family such as GeBi2Te4 and BiTe1.5S1.5 show an in-gap surface Dirac point, the former of which has been predicted to show nonzero weak topological invariants such as (1;111); thus belonging to a different topological class than BiTe1.5S1.5. The measured band structure presented here will be a valuable guide for interpreting transport, thermoelectric, and thermopower measurements on these compounds. The unique surface band topology observed in these compounds contributes towards identifying designer materials with desired flexibility needed for thermoelectric and spintronic device fabrication.
description: 9 pages, 6 figures; Related results at http://online.kitp.ucsb.edu/online/topomat11/hasan/
Additional file 11 of Physiological, metabolomic, and transcriptomic reveal metabolic pathway alterations in Gymnocypris przewalskii due to cold exposure
Creators: name: Liu, Sijia
name: Tian, Fei
name: Qi, Delin
name: Qi, Hongfang
name: Wang, Yang
name: Xu, Shixiao
name: Zhao, Kai
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 11.
title: Evaluating the Phenotypic Consequences of DNA-PKcs Deficiency
Creators: name: Kenny, Jacey
Publisher: name: Graduate Studies
Year: 2025
Subjects: subject: Biology--Molecular
subject: Biochemistry

description: DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a serine/threonine protein kinase with a well-established role in the repair of DNA double strand breaks. Similarly, Ataxia-Telangiectasia Mutated (ATM) is a protein kinase that plays a central role in downstream signalling response to DNA damage. DNA-PKcs and ATM are members of the phosphatidylinositol 3-kinase-like protein kinase (PIKK) family, which serve critical roles in the cellular response to DNA damage. To better understand the non-canonical roles of DNA-PKcs and ATM, our lab generated human cell lines with CRISPR/Cas9-mediated disruption of these proteins, marking the starting point of my project. My work demonstrates that loss of DNA-PKcs and/or ATM expression results in slower proliferation compared to parental cells, while inhibition of DNA-PKcs or ATM kinase activity had a comparatively minor effect on cell proliferation. My data suggests that this phenotype is not due to increased apoptosis, endogenous DNA damage or cell cycle defects. Comparison of the metabolite profiles of the matched control and CRISPR cell lines suggested enrichment of amino acids in the HeLa CRISPR DNA-PKcs cells which led me to hypothesize that the CRISPR cell lines have a reduced rate of protein translation. I present evidence that cells deficient in DNA-PKcs and ATM exhibit impaired global, new protein translation, revealing a potentially novel mechanism for the slow growth phenotype. This work adds to a growing body of evidence encouraging further exploration of DNA-PKcs and ATM as therapeutic targets in cancer and other diseases.
title: Stream Starting Soon: Exploring Theatrical Design Principles to Evoke Feelings of Safety for Livestreamers
Creators: name: Colins, Mathilda
Publisher: name: Graduate Studies
Year: 2025
Subjects: subject: Livestreaming
subject: Theatre Design
subject: Safe Spaces
subject: Minority Communities
subject: Inclusion
subject: Procedural Content Generation (PCG)
subject: Generative Art
subject: Computer Science
subject: Theater

description: Toxic behaviour is prevalent in livestreaming communities, particularly for minority groups such as LGBTQ+, POC, and women. To combat this, current solutions employ automatic or human content moderation. While necessary, moderation is a content-based intervention that is largely reactive, removing harmful content after it has already been posted. Drawing inspiration from physical theatre, I explore an alternative approach that seeks to create digital safe spaces by proactively fostering positive emotions for the livestreamer so that they engage in behaviours that encourage feelings of safety for others in their community. I leverage the field of theatre and the elements and principles of design to offer a Framework of Controllable Qualities, where “Controllable Qualities” refers to customizable audiovisual sensory cues used to create a particular mood or atmosphere in a space (such as the volume of a Sound, the colour of a Light, or the texture of a Costume). I illustrate the application of my framework with four manually-created design probes (background images informed by the framework) deployed by participating livestreamers in a small, exploratory qualitative study. The design probes aimed to foster a spectrum of feelings of safety from extremely safe, to extremely unsafe. Through a qualitative study, I examine the values and practices that livestreamers and moderators held surrounding the creation of digital safe spaces, and if the presence of the design probes influenced feelings of safety for the livestreamer. Drawing on their feedback, I created a computational program built in Processing to automatically generate design probes. I make four contributions: 1) a richer understanding of how to translate physical theatrical design elements to a digital livestream context through the creation of a Framework of Controllable Qualities, 2) the application of a subset of the Framework of Controllable Qualities to inform the design of manual and automatically generated design probes to foster feelings of safety, 3) a deeper understanding of livestreamer and moderator practices to foster safety and inclusivity within a livestream community, and 4) an understanding of livestreamer and moderator experiences with the manually-created design probes and its influence (if any) on feelings of safety for the livestreamer.
Butis butis butis (Hamilton 1822
Creators: name: Zainal Abidin, Danial Hariz
name: Lavoué, Sébastien
name: Mohd Abu Hassan Alshari, Norli Fauzani
name: Mohd. Nor, Siti Azizah
name: A. Rahim, Masazurah
name: Mohammed Akib, Noor Adelyna
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Perciformes
Eleotridae
Butis
Butis butis

description: Butis butis (Hamilton, 1822) Figure 3J Material examined. MALAYSIA • 2, 21– 25 mm TL; Kedah State, Kampung Batu Lintang, Pompang Batu Lintang; 05.625°N, 100.394°E; 17 Jul. 2019; Sébastien Lavoué leg.; USMFC (33) 00012. • 3, 113– 125 mm TL; Kedah State, Kampung Batu Lintang, Pompang Batu Lintang; 05.624°N, 100.395°E; 19 Apr. 2019; Danial H. Zainal Abidin, Norli F.M.A.H. Alshari leg.; USMFC (33) 00003. • 2, 95– 106 mm TL; Kedah State, Kampung Batu Lintang, Pompang Batu Lintang; 05.625°N, 100.394°E; 17 Jul. 2019; Sébastien Lavoué leg.; USMFC (33) 00014.
description: Published as part of Zainal Abidin, Danial Hariz, Lavoué, Sébastien, Mohd Abu Hassan Alshari, Norli Fauzani, Mohd. Nor, Siti Azizah, A. Rahim, Masazurah & Mohammed Akib, Noor Adelyna, 2021, Ichthyofauna of Sungai Merbok Mangrove Forest Reserve, northwest Peninsular Malaysia, and its adjacent marine waters, pp. 601-631 in Check List 17 (2) on page 617, DOI: 10.15560/17.2.601
title: An Attention-Based Deep Learning Approach for Forecasting Electricity Prices in Real-Time Electricity Markets
Creators: name: Do Carmo Junior, Jose Eustaquio
Publisher: name: Schulich School of Engineering
Year: 2025
Subjects: subject: Real-time electricity markets
subject: Electricity price forecasting
subject: Price volatility
subject: Deep learning
subject: Engineering--Electronics and Electrical

description: Real-time electricity markets are characterized by irregular and sudden price swings, leading to high price volatility and significant uncertainties for market participants. Accurate and informative electricity price forecasts are essential to reduce these uncertainties and enable more effective decision-making in energy generation, consumption, strategy planning, and risk management. This thesis presents a new forecasting framework for electricity prices in real-time markets, leveraging the capabilities of deep learning and advanced feature engineering. The proposed methodology integrates the Temporal Fusion Transformer (TFT), a deep learning model applied to time series forecasting, with dynamic clustering techniques to enhance forecasting accuracy. This is done by combining Hierarchical Density-Based Spatial Clustering of Applications with Noise and Dynamic Time Warping to cluster generators based on attributes such as geographical location, fuel type, installed capacity, and generation patterns. These clusters provide new covariates for forecasting models, enabling the method to adapt to the unique characteristics of any electricity market. The effectiveness of the proposed framework is demonstrated through a case study of the Ontario electricity market, where the methodology outperforms the forecasts of the system operator in terms of average error, accuracy, precision, and recall across a six-hour forecast horizon. This study underlines the framework's versatility and offers valuable insights into electricity price behavior, aiding market participants in mitigating risks and optimizing energy strategies.
Wishart Processes and Wishart Distributions: An Affine Processes Point of View
Creators: name: Mayerhofer, Eberhard
Publisher: name: arXiv
Year: 2012
Subjects: subject: Probability (math.PR)
subject: Statistics Theory (math.ST)
subject: FOS: Mathematics

description: These lecture notes provide an introduction to the theory of Wishart distributions and Wishart processes, particularly what concerns their existence and their realizations as solutions of Wishart SDEs. The material is based on recent developments in the theory of affine processes and related fields.
description: This is the final version of Part II of the CIMPA lecture notes on Wishart processes, to be published jointly with Piotr Graczyk (part I) in a corresponding volume in September 2012. They are based on presentations at the CIMPA workshop in Hammamet, Tunesia (Sept. 2011)
Hidden Numerical Sequences in the Periodic Table: The Strange Case of Correlation between the Atomic Numbers of Technetium and Protactinium
Creators: name: Ray, Arghya
Publisher: name: Zenodo
Year: 2019
Subjects: cosmology
nuclear chemistry
periodic table
mathematical series

description: Atomic numbers of Hydrogen, Helium, Boron, Neon, Calcium, Technetium, and Protactinium are members of a cryptic numerical progression series. Contextually, this research paper involves postulation and hypothesis formulation around some elements from the periodic table. The atomic numbers of these selected elements form a numerical series. Let’s call it an arithmetico-exponential series. The main assumption to decipher the existence of such a series is instigated by the occurrence of certain elements that behave very exceptionally.

Copyright registration number: cg5QcXsO0hQScErG
description: However, there are certain questions for future research. Why are atomic numbers expressed in terms of integers? Are negative or fractional atomic numbers possible? In the case negative atomic number be possible, we are most likely going to have an 'electron rest negative-mass' value too (which will possibly be expressed in terms of atomic mass unit). And in the case this happens in reality (that is just theoretical chemistry though), will it affect the observed atomic weight of Hydrogen? Should it be given a neutronic number equal to zero, and should the  periodic table be rearranged according to neutronic numbers? If this happens, then the periodic table itself would start to ooze off at the post Polonium nucleic configurations
Finite-sided deformation spaces of complete affine 3-manifolds
Creators: name: Charette, Virginie
name: Drumm, Todd A.
name: Goldman, William M.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 57M05, 20H10, 30F60

description: A Margulis spacetime is a complete affine 3-manifold M with nonsolvable fundamental group. Associated to every Margulis spacetime is a noncompact complete hyperbolic surface S. We show that every Margulis spacetime is orientable, even though S may be nonorientable. We classify Margulis spacetimes when S is homeomorphic to a two-holed cross-surface, that is, the complement of two disjoint discs in the real projective plane. We show that every such manifold is homeomorphic to a solid handlebody of genus two, and admits a fundamental polyhedron bounded by crooked planes. Furthermore, the deformation space is a bundle of convex quadrilateral cones over the space of marked hyperbolic structures. The sides of each quadrilateral cone are defined by invariants of the two boundary components and the two orientation-reversing simple curves. The two-holed cross-surface, together with the three-holed sphere, are the only topologies for which the deformation space of complete affine structures is finite-sided.
description: 29 pages, 8 figures. Accepted for publication in the Journal of Topology
Hydrogen Atom in Electric and Magnetic Fields: Dynamical Symmetries, Superintegrable and Integrable Systems, Exact Solutions
Creators: name: Liberman, Mikhail A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: The Hamiltonian of a pure hydrogen atom possesses the SO(4) symmetry group generated by the integrals of motion: the angular momentum and the Runge-Lenz vector. The pure hydrogen atom is a supersymmetric and superintegrable system, since the Hamilton-Jacobi and the Schrödinger equations are separable in several different coordinate systems and has an exact analytical solution. The Schrödinger equation for a hydrogen atom in a uniform electric field (Stark effect) is separable in parabolic coordinates. The system has two conserved quantities: z-projections of the generalized Runge-Lenz vector and of the angular momentum. The problem is integrable and has the symmetry group SO(2)xSO(2). The ion of the hydrogen molecule (problem of two Coulomb centers) has similar symmetry group SO(2)xSO(2) generated by two conserved z-projections of the generalized Runge-Lenz and of the angular momentum on the internuclear axis. The corresponding Schrödinger equation is separable in the elliptical coordinates. For the hydrogen atom in a uniform magnetic field, the respective Schrödinger equation is not separable. The problem is non-separable and non-integrable and is considered as a representative example of quantum chaos that cannot be solved by any analytical method. Nevertheless, an exact analytical solution describing the quantum states of a hydrogen atom in a uniform magnetic field can be obtained as a convergent power series in two variables, the radius and the sine of the polar angle. The energy levels and wave functions for the ground and excited states can be calculated exactly, with any desired accuracy, for an arbitrary strength of the magnetic field. Therefore, the problem can be considered superintegrable, although it does not possess supersymmetry and additional integrals of motion.
description: 29 pages, 3 figures
Auditory dysfunction in type 2 Stickler Syndrome
Creators: name: Alexander, Philip
name: Gomersall, Philip
name: Stancel-Lewis, Jack
name: Fincham, Gregory Scott
name: Poulson, Arabella
name: Richards, Allan
name: McNinch, Annie
name: Baguley, David M.
name: Snead, Martin
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Otology
Stickler Syndrome
Type 2
Conductive
Sensorineural
Hearing loss
Retinal detachment
COL11A1
COL2A1

description: Funder: University of Nottingham
description: Abstract: Purpose: To present the extent and site of lesion of auditory dysfunction in a large cohort of individuals with type 2 Stickler Syndrome. Type 2 Stickler Syndrome results from a mutation in the gene coding for α-1 type XI pro-collagen, which has been identified in the human vitreous, cartilage and the cochlea of the mouse. The condition is characterised by classic ocular abnormalities, auditory dysfunction, osteoarthropathy and oro-facial dysplasia. Methods: This is a population study which used a combination of audiometric, tympanometric, and self-report measures on a series of 65 individuals (mean age 29.2 years, range 3–70, female 63.1%) with genetically confirmed type 2 Stickler Syndrome. Results: Hearing impairment was identified in at least one ear for 69% of individuals. Analysis against age-matched normative data showed that reduced hearing sensitivity was present across all test frequencies. Sensorineural hearing loss was most common (77% of ears), with conductive (3%), mixed (7%) and no hearing loss (13%), respectively. The proportion of hypermobile tympanic membranes (24%) was less than previously documented in type 1 Stickler Syndrome. When present, this appears to arise as a direct result of collagen abnormalities in the middle ear. Self-report measures of speech and spatial hearing in sound were comparable to a non-syndromic cohort with similar audiometric thresholds. Conclusions: Auditory impairment in type 2 Stickler Syndrome is predominantly associated with cochlear hearing loss of varying severities across affected individuals. The impact on hearing thresholds can be seen across the frequency range, suggesting a contribution of defective collagen throughout the cochlea. Self-report questionnaires showed that difficulties understanding speech, and spatial information in sound (such as that used for localisation), were worse than a young, normal-hearing population but comparable to a non-syndromic cohort with similar audiometric thresholds. Therefore, it is likely that hearing loss in type 2 Stickler Syndrome arises in the auditory periphery, without significant central processing deficits.
Additional file 12 of Physiological, metabolomic, and transcriptomic reveal metabolic pathway alterations in Gymnocypris przewalskii due to cold exposure
Creators: name: Liu, Sijia
name: Tian, Fei
name: Qi, Delin
name: Qi, Hongfang
name: Wang, Yang
name: Xu, Shixiao
name: Zhao, Kai
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 12.
Reconciling species diversity in a tropical plant clade (Canarium, Burseraceae)
Creators: name: Federman, Sarah
name: Donoghue, Michael J.
name: Daly, Douglas C.
name: Eaton, Deren A. R.
Publisher: name: Columbia University
Year: 2018
Subjects: Canarium
Plants--Phylogeny
Plant species diversity
Biogeography
Plant morphology

description: The challenges associated with sampling rare species or populations can limit our ability to make accurate and informed estimates of biodiversity for clades or ecosystems. This may be particularly true for tropical trees, which tend to be poorly sampled, and are thought to harbor extensive cryptic diversity. Here, we integrate genomics, morphology, and geography to estimate the number of species in a clade of dioecious tropical trees (Canarium L.; Burseraceae) endemic to Madagascar, for which previous taxonomic treatments have recognized between one and 33 species. By sampling genomic data from even a limited number of individuals per taxon, we were able to clearly reject both previous hypotheses, and support instead an intermediate number of taxa. We recognize at least six distinct clades based on genetic structure and species delimitation analyses that correspond clearly with geographic and discrete morphological differences. Two widespread clades co-occur broadly throughout eastern wet forests, one clade is endemic to western dry forests, and several slightly admixed clades are more narrowly distributed in mountainous regions in the north. Multiple previously described taxa were recovered as paraphyletic in our analyses, some of which were associated with admixed individuals, suggesting that hybridization contributes to taxonomic difficulties in Canarium. An improved understanding of Canarium species diversity has important implications for conservation efforts and understanding the origins of diversity in Madagascar. Our study shows that even limited genomic sampling, when combined with geography and morphology, can greatly improve estimates of species diversity for difficult tropical clades.
Probing Cosmology with Baryon Acoustic Oscillations using Gravitational Waves
Creators: name: Kumar, Sumit
Publisher: name: arXiv
Year: 2022
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The third-generation (3G) gravitational wave (GW) detectors such as the Einstein telescope (ET) or Cosmic Explorer (CE) are expected to play an important role in cosmology. With the help of 3G detectors, we will be able to probe large-scale structure (LSS) features such as baryon acoustic oscillations (BAO), galaxy bias, etc. We explore the possibility to do precision cosmology, with the 3G GW detectors by measuring the angular BAO scale using localization volumes of compact binary merger events. Through simulations, we show that with a 3G detector network, by probing the angular BAO scale using purely GW observations, we can constrain the Hubble constant for the standard model of cosmology ($Λ$CDM) with $90\%$ credible regions as $H_0 = 59.4^{+ 33.9}_{-17.7} ~\mathrm{km}~\mathrm{s}^{-1}~\mathrm{Mpc}^{-1}$. When combined with BAO measurements from galaxy surveys, we show that it can be used to constrain various models of cosmology such as parametrized models for dark energy equations of state. We also show how cosmological constraints using BAO measurements from GW observations in the 3G era will complement the same from spectroscopic surveys.
description: 12 pages, 6 figures, 3 tables -- Accepted for publication in The Astrophysical Journal. Version matching the accepted paper