cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The Role of Cortisol in the Central Control of Feeding in Zebrafish
Creators: name: Nipu, Niepukolie
Publisher: name: Graduate Studies
Year: 2022
Subjects: subject: Stress
subject: Cortisol
subject: Glucocorticoid receptor
subject: insulin
subject: Akt
subject: AMPK
subject: mTOR
subject: feeding
subject: Zebrafish.
subject: Biology--Animal Physiology

description: A generalized non-specific response to stress is the elevation of circulating corticosteroid levels in animals. In teleosts, cortisol is the primary corticosteroid, and the stressor-mediated elevation of this hormone leads to an increase in plasma glucose levels. Cortisol action is mediated by its binding to either the glucocorticoid receptor (GR) and/or the mineralocorticoid receptor (MR), both of which are ligand-bound transcription factors. Chronic cortisol exposure has been shown to reduce feed intake, but the mechanisms are far from clear. The objective ofthis thesis was to investigate the possible mechanisms leading to cortisol-mediated appetite suppression in fish. The hypothesis was that elevated plasma glucose levels in response to stressor-mediated cortisol elevation inhibits feeding by activating the brain glucose sensing mechanisms. Indeed, elevated blood glucose levels suppressed food intake by inhibiting AMP-activated protein kinase (AMPK) expression in the zebrafish (Danio rerio) brain. However, the suppression of feeding associated with cortisol was not due to elevated glucose levels, as the brain glucose uptake capacity and the expression of AMPK remained unchanged. Instead,cortisol stimulation reduced the expression of protein kinase B (Akt) and the mammalian targetof rapamycin (mTOR), while increasing the transcript abundance of regulated in development and DNA damage responses 1 (redd1), a marker of protein breakdown, in the zebrafish brain. Interestingly, the loss of GR did not rescue the cortisol-mediated suppression in feeding or the inhibition of brain Akt expression. However, lack of GR increased brain glucose uptake and rescued the brain mTOR expression, along with a reduction in redd1 transcript levels. The resultsindicate that GR activation by elevated cortisol levels restrict glucose uptake and increase thecapacity for protein breakdown in the zebrafish brain. The cortisol-mediated suppression of feeding was not rescued in the absence of GR, suggesting a possible role for MR in the feeding regulation. Overall, the results suggest that both GR and MR activation may contribute to the cortisol-mediated energy substrate repartitioning in the brain, leading to feed inhibition during stress in fish.
Synthesis and Biological Evaluation of Heterobifunctional Small Molecules for Proteasome-Mediated Protein Degradation of Myeloid Cell Leukemia 1 (MCL1)
Creators: name: Papatzimas, James W
Publisher: name: Graduate Studies
Year: 2020
Subjects: subject: Protein Degradation
subject: Ubiquitin Proteasome System
subject: MCL1
subject: Heterobifunctional Small Molecule Protein Degrader
subject: Chemistry--Organic
subject: Chemistry--Pharmaceutical
subject: Biology--Molecular
subject: Health Sciences--Oncology

description: Protein–protein interactions (PPIs) have emerged as significant targets for therapeutic development, owing to their critical nature in diverse biological processes. However, these kinds of protein interactions are difficult to perturb using traditional medicinal chemistry strategies. This has given rise to the development of a new method of addressing disease related proteins known as targeted protein degradation (TPD). TPD employs heterobifunctional small molecules which are capable of recruiting the cell’s natural recycling machinery, the ubiquitin proteasome system (UPS), and inducing proximity between this natural degradation machinery and a protein of interest (POI) to promote proteasomal degradation of the protein into its amino acid subunits. An ideal PPI-based target is the anti-apoptotic protein myeloid cell leukemia 1 (MCL1), a critical prosurvival factor in cancers such as multiple myeloma (MM) where MCL1 levels directly correlate to disease progression. Current strategies for halting the antiapoptotic properties of MCL1 revolve around inhibiting its sequestration of proapoptotic factors. Existing inhibitors disrupt endogenous regulatory proteins; however, this strategy leads to an increase of MCL1 protein expression, a detrimental effect for several diseases. MCL1 has also been a challenging biological target to inhibit due to the prolific on-target cardiotoxicity associated with global MCL1 inhibition or knockdown.This work showcases the development of the first in class heterobifunctional small molecules capable of selectively targeting MCL1 through TPD methodology, leading to successful degradation. A synthesis program was embarked upon where chemical probes and cellular assay-guided structure activity relationship (SAR) studies motivated the optimization of these degrader compounds. We have confirmed the involvement of the E3 ubiquitin ligase CUL4A–DDB1 cereblon (CRBN) ubiquitination pathway through rigorous UPS checkpoint validation, making these MCL1 degraders a first step toward a new class of antiapoptotic B-cell lymphoma 2 (BCL2) family protein degraders.
A Disc-Corona Model for a Rotating Black Hole
Creators: name: Gong, Xiaolong
name: Li, Lixin
name: Ma, Renyi
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We propose a disc-corona model in which a geometrically thin, optically thick disc surrounds a Kerr black hole, and magnetic fields exert a time-steady torque on the inner edge of the accretion disc. The analytical expression of the total gravitational power is derived from the thin-disc dynamics equations by using this new boundary condition. It is shown that the magnetic torque can considerably enhance the amount of energy released in the disc-corona system. Furthermore, the global solutions of this disc-corona system are obtained numerically. We find that the fraction of the power dissipated into the corona in the total for such disc-corona system increases with the increasing dimensionless black hole spin parameter $a_\ast $, but is insensitive on the $Δ\varepsilon $ which is the additional radiative efficiency parameter relevant to magnetic torque, for $Δ\varepsilon > 1$. In addition, the emerged spectra from this disc-corona system are simulated by using Monte-Carlo method, and the effect of the different parameters on the output spectra is discussed.
Boundary-locality and perturbative structure of entanglement spectra in gapped systems
Creators: name: Alba, Vincenzo
name: Haque, Masudul
name: Laeuchli, Andreas M.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The entanglement between two parts of a many-body system can be characterized in detail by the entanglement spectrum. Focusing on gapped phases of one-dimensional systems, we show how this spectrum is dominated by contributions from the boundary between the parts. This contradicts the view of an "entanglement Hamiltonian" as a bulk entity. The boundary-local nature of the entanglement spectrum is clarified through its hierarchical level structure, through the combination of two single-boundary spectra to form a two-boundary spectrum, and finally through consideration of dominant eigenfunctions of the entanglement Hamiltonian. We use the boundary-locality to formulate a perturbative scheme for calculating entanglement spectra.
description: 4 pages, 3 figures; supplementary material added (6 pages, 2 figures); minor revisions to match the published version in Physical Review Letters
Advancing the methods and accessibility of cost-effectiveness and value of information analyses in health care
Creators: name: Sadatsafavi, Mohsen
Publisher: name: University of British Columbia
Year: 2012

description: This thesis comprises three methodological advancements that address important issues related to cost-effectiveness analysis (CEA) and expected value of information (EVI) analysis in health technology assessment. Aims: 1) To develop a practical sampling scheme for the incorporation of external evidence in CEAs conducted alongside randomized controlled trials (RCT); 2) To develop non-parametric methods for the calculation of the expected value of sample information (EVSI) for RCT-based CEAs; 3) To develop a computationally efficient algorithm for the calculation of single-parameter expected value of partial perfect information (EVPPI) for RCT-based and model-based CEAs. The theories and methods laid out in this work are accompanied by real-world CEA and EVI analyses of the Canadian Optimal Therapy of Chronic Obstructive Pulmonary Diseases (OPTIMAL) trial, a RCT on combination pharmaceutical therapies in chronic obstructive pulmonary diseases (COPD). Results: 1) The ‘vetted bootstrap’ is a semi-parametric algorithm based on rejection sampling and bootstrapping that allows the incorporation of external evidence into RCT-based CEAs. Implementing this method to incorporate external information on the effect size of treatment in the OPTIMAL trial required only minor modifications to the original CEA algorithm. 2) A Bayesian interpretation of the bootstrap allows non-parametric calculation of EVSI through two-level resampling. In the case study, incorporation of missing value imputation and adjustment for covariate imbalance in EVI calculations generated EVSI and the expected value of perfect information (EVPI) values that were significantly different than those calculated conventionally, demonstrating the flexibility of this method and the potential impact of modeling such aspects of the analysis on EVI calculations. 3) The new method enabled the calculation of EVPPI for the effect size of treatment for the exemplary RCT data, and showed a significant (up to 25 times in terms of root-mean-squared error) improvement in efficiency compared to the conventional EVPPI calculation methods in a series of simulations. Summary: This thesis provides several original advancements in the methodology of the CEA and EVI analysis of RCTs and enables several analytical approaches that have hitherto been available only through parametric modeling of RCT data.
Split-Flow Integrated Small-Scale LNG Production Process with Cryogenic Carbon Dioxide Capture
Creators: name: Ostovar, Arash -
Publisher: name: Graduate Studies
Year: 2020
Subjects: subject: Small-Scale LNG
subject: Carbon Dioxide Capture
subject: Cryogenic Process
subject: NGL Recovery
subject: Engineering--Chemical

description: This thesis addressed three challenges facing the processing of natural gas. First, energy is usually required to produce energy, but it takes more energy to produce liquified natural gas (LNG) than other fossil fuels. In other words, LNG production is a very energy-intensive process, which makes it less competitive. Second, many cryogenic NGL-recovery facilities have been working under full capacity due to low natural gas prices and limited accessible new markets. The last challenge concerns the classic aqueous alkanolamine-based sweetening process, which involves saturating gas with water and restricting the LNG production temperature to be begin from ambient temperature and needs a finishing process to handle the produced acid gas.With a view to address these challenges, first, a novel integrated small-scale LNG process concept was developed that can not only maximize the economic value of NGL recovery facilities but also produce LNG via a more efficient and greener process. This was achieved through comprehensive process simulations, optimizations, and heat integration studies. These studies were performed using the Aspen HYSYS simulation package to find an efficient integrated LNG production process that can use available sources of heating/cooling in a cryogenic NGL-recovery facility without sacrificing the NGL production yield. In the development process, it was determined that an adsorption process (nonsolvent) can remove CO2 at cryogenic temperatures and treat natural gas with the aim of meeting the LNG specification (CO2=50 ppm). This led me to the development of the “split-flow integrated small-scale LNG production process (SFI-LNG)”, which has two main pillars—the cryogenic CO2 removal process and the semi-C3-MR liquefaction process.Second, to validate the cryogenic removal of CO2, zeolite-based adsorbents were synthesized and characterized before they were successfully tested under cryogenic conditions.Third, a bench-scale experimental setup was designed and constructed to prove the concept of cryogenic CO2 removal. Finally, the concept was proven at the bench scale.The principle of cryogenic CO2 removal is based on the selective adsorption of CO2 by a Faujasite (FAU)-based adsorbent under cryogenic conditions, which exhibits a high adsorption rate with great recyclability. In addition, there is no need for a finishing process to deal with acid gas, as highly pure CO2 can be produced as a byproduct.
Second-Generation African Youth in Calgary: Transnational Practices and Perspectives
Creators: name: Obeng-Akrofi, Animwaa
Publisher: name: Graduate Studies
Year: 2020
Subjects: subject: Second generation
subject: transnationalism
subject: transnational connections
subject: multiculturalism
subject: phenomenological approach
subject: intellectual transnationalism
subject: Social Sciences

description: The African population in Canada is growing as a result of Canadian immigration policies from over the last decade. Research has shown that, like many other immigrants, African immigrants in Canada engage in transnationalism (Owusu, 2003), which means they maintain multiple relationships across borders. However, very few studies have focused on second-generation immigrants (Kalu, 2017; Goitom, 2018), also known as “the second generation,” and the studies that have been done on this population have mostly revolved around the issue of their identity formation and integration. There is also a gap in the literature with regards to the relationship between birth order of the second-generation African youth and their transnational ties. This study addresses these gaps in the literature by studying the transnational connections of second-generation Africans in Calgary. The theories of multiculturalism and transnationalism inform the conceptual framework that I have used for this study. Drawing on a qualitative research methodology with a phenomenological approach, I conducted a content analysis on 30 in-depth interviews with second-generation youth (24 females and 6 males) who had sub-Saharan Africa roots and were living in Calgary. The findings indicate that the second-generation African youth engage in six types of transnationalism—sociocultural, economic, political, social-psychological, psychological, and religious—as well as a new type that I have called “intellectual transnationalism.” Also, my research demonstrates that there is a relationship between the birth order of those within the second generation and their transnational connections.
Implementación PIDs en América Latina. Experiencia de la Universidad de Chile
Creators: name: Donoso Vegas, Rodrigo
Publisher: name: Zenodo
Year: 2023
Subjects: PIDsLATAM23
Identificadores persistentes
Persistent identifiers
Ciencia Abierta
Open Science
PIDs

description: “Identificadores persistentes (PIDs) y ciencia abierta en Latinoamérica” (#PIDsLATAM23) organizado por DataCite, ORCID y ROR es un evento enteramente dedicado a los identificadores persistentes y la ciencia abierta en la región. Dirigido a directores y gestores de investigación, bibliotecarios y personal técnico, en este encuentro hablamos sobre los beneficios de los identificadores persistentes y cómo su adopción contribuye a la ciencia abierta y a un ecosistema de investigación más abierto y robusto. Este evento se realiza en colaboración con la csv,conf,v7. Esta presentación de Rodrigo Donoso Vegas ofrece una visión de la implementación de PIDs de la Universidad de Chile.
Modeling of Low Salinity Waterflooding in Petroleum Reservoirs
Creators: name: Nikpoor, Mohammad Hossain
Publisher: name: Graduate Studies
Year: 2020
Subjects: subject: Geochemistry
subject: FOS: Earth and related environmental sciences
subject: Geology

description: Oil production from reservoirs is traditionally categorized into three phases: primary, secondary, and tertiary (also known as Enhanced Oil Recovery, EOR). Per the US Department of Energy, utilizing primary and secondary methods of production can leave up to 75% of the oil in place. The way to further increase oil production is through EOR. Although more expensive to employ in a field, EOR can increase production from a well up to 75% recovery.Low Salinity Waterflooding (LSW) is a promising technique for improving oil recovery in petroleum reservoirs because of its relatively simple implementation, lower cost, and fewer environmental problems associated with this process compared to other EOR methods. Worldwide companies (including BP, Shell, Statoil, and Saudi Aramco) are involved in the research and development of this technique.Most studies on the subject have focused on the experimental and some on the theoretical aspects, with varying, sometimes contradictory conclusions. However, the optimum conditions that improve oil recovery by LSW flooding are still uncertain due to the lack of understanding of the underlying fluid-rock interaction mechanisms. There has been much modeling research on the modeling of the process in sandstone reservoirs in an attempt to understand these mechanisms and identify the main ones that maximize the recovery in order to design successful field applications. Most of these studies have concluded that the macroscopic mechanism for improved recovery in LSW is wettability alteration due to different microscopic rock-fluid and fluid-fluid interactions when low salinity water is introduced to the system. A few investigations have focused on the possibility of fine migration and its potential effect during LSW.In this thesis, I will review and model the mechanisms in oil reservoirs and focus on fine migration and its similarity to the polymer flooding and asphaltene flow and precipitation whose models exist in commercial reservoir simulators. Parts of this research will be integrated into a reservoir simulator to test and validate the ideas. At the end, I will extend my work into hybrid LSW processes and their optimization.
Analyzing Semantic Faithfulness of Language Models via Input Intervention on Question Answering
Creators: name: Chaturvedi, Akshay
name: Bhar, Swarnadeep
name: Saha, Soumadeep
name: Garain, Utpal
name: Asher, Nicholas
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computation and Language (cs.CL)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Transformer-based language models have been shown to be highly effective for several NLP tasks. In this paper, we consider three transformer models, BERT, RoBERTa, and XLNet, in both small and large versions, and investigate how faithful their representations are with respect to the semantic content of texts. We formalize a notion of semantic faithfulness, in which the semantic content of a text should causally figure in a model's inferences in question answering. We then test this notion by observing a model's behavior on answering questions about a story after performing two novel semantic interventions: deletion intervention and negation intervention. While transformer models achieve high performance on standard question answering tasks, we show that they fail to be semantically faithful once we perform these interventions for a significant number of cases (~50% for deletion intervention, and ~20% drop in accuracy for negation intervention). We then propose an intervention-based training regime that can mitigate the undesirable effects for deletion intervention by a significant margin (from ~ 50% to ~6%). We analyze the inner-workings of the models to better understand the effectiveness of intervention-based training for deletion intervention. But we show that this training does not attenuate other aspects of semantic unfaithfulness such as the models' inability to deal with negation intervention or to capture the predicate-argument structure of texts. We also test InstructGPT, via prompting, for its ability to handle the two interventions and to capture predicate-argument structure. While InstructGPT models do achieve very high performance on predicate-argument structure task, they fail to respond adequately to our deletion and negation interventions.
PONE-D-21-18801
Creators: name: Vazquez del mercado, Mónica
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 60804 Animal Immunology
subject: FOS: Biological sciences

description: S1 File. Immunoprecipitation gel imagesS2 Figure. Histology of kidneys from control and prophylactic DNA vaccination in a murine lupus model. ARRIVE
Combining High-scale Inflation with Low-energy SUSY
Creators: name: Antusch, Stefan
name: Dutta, Koushik
name: Halter, Sebastian
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We propose a general scenario for moduli stabilization where low-energy supersymmetry can be accommodated with a high scale of inflation. The key ingredient is that the stabilization of the modulus field during and after inflation is not associated with a single, common scale, but relies on two different mechanisms. We illustrate this general scenario in a simple example, where during inflation the modulus is stabilized with a large mass by a Kahler potential coupling to the field which provides the inflationary vacuum energy via its F-term. After inflation, the modulus is stabilized, for instance, by a KKLT superpotential.
description: 24 pages, 2 figues. v2: Minor corrections. References added
Electric field calculation and ionization signal simulation in liquid xenon detectors for PET
Creators: name: Huang, Zhu
Publisher: name: University of British Columbia
Year: 2012

description: Electric field calculations and ionization signal simulations in a liquid xenon detector for Positron Emission Tomography have been performed. The electric field was calculated using Opera 3D, a Finite Element Method application software. The uniformity of the electric field inside of the detector was evaluated by calculating the deviation of drifting electrons under the applied electric field. The ionization signals of the detector have been simulated. The comparison between simulation results and measurement signals was made.
Functional John and Löwner conditions for pairs of log-concave functions
Creators: name: Ivanov, Grigory
name: Naszódi, Márton
Publisher: name: arXiv
Year: 2022
Subjects: subject: Metric Geometry (math.MG)
subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: 52A23

description: John's fundamental theorem characterizing the largest volume ellipsoid contained in a convex body $K$ in $\mathbb{R}^d$ has seen several generalizations and extensions. One direction, initiated by V. Milman is to replace ellipsoids by positions (affine images) of another body $L$. Another, more recent direction is to consider logarithmically concave functions on $\mathbb{R}^d$ instead of convex bodies: we designate some special, radially symmetric log-concave function $g$ as the analogue of the Euclidean ball, and want to find its largest integral position under the constraint that it is pointwise below some given log-concave function $f$. We follow both directions simultaneously: we consider the functional question, and allow essentially any meaningful function to play the role of $g$ above. Our general theorems jointly extend known results in both directions. The dual problem in the setting of convex bodies asks for the smallest volume ellipsoid, called \emph{L{ö}wner's ellipsoid}, containing $K$. We consider the analogous problem for functions: we characterize the solutions of the optimization problem of finding a smallest integral position of some log-concave function $g$ under the constraint that it is pointwise above $f$. It turns out that in the functional setting, the relationship between the John and the L{ö}wner problems is more intricate than it is in the setting of convex bodies.
description: 34 pages
Additional file 11: of Downregulation of miR-133a-3p promotes prostate cancer bone metastasis via activating PI3K/AKT signaling
Creators: name: Tang, Yubo
name: Pan, Jincheng
name: Huang, Shuai
name: Peng, Xinsheng
name: Zou, Xuenong
name: Luo, Yongxiang
name: Ren, Dong
name: Zhang, Xin
name: Li, Ronggang
name: He, Peiheng
name: Wa, Qingde
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Plant Biology

description: Figure S3. Real-time PCR analysis of miR-133a-3p expression in the indicated PC-3, C4-2B and VCaP cells. Transcript levels were normalized by U6 expression. Error bars represent the mean ± s.d. of three independent experiments. *P < 0.05. (PDF 173 kb)
Limits on the deterministic creation of pure single-photon states using parametric down-conversion
Creators: name: Christ, Andreas
name: Silberhorn, Christine
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Parametric down-conversion (PDC) is one of the most widely used methods to create pure single-photon states for quantum information applications. However little attention has been paid to higher-order photon components in the PDC process, yet these ultimately limit the prospects of generating single-photons of high quality. In this paper we investigate the impacts of higher-order photon components and multiple frequency modes on the heralding rates and single-photon fidelities. This enables us to determine the limits of PDC sources for single-photon generation. Our results show that a perfectly single-mode PDC source in conjunction with a photon-number resolving detector is ultimately capable of creating single-photon Fock states with unit fidelity and a maximal state creation probability of 25%. Hence an array of 17 switched sources is required to build a deterministic (>99% emission probability) pure single-photon source.
description: 7 pages, 6 figures
Using machine learning algorithms to determine the post-COVID state of a person by his rhythmogram
Creators: name: Stasenko, Sergey
name: Kovalchuk, Andrey
name: Evgeny, Eremin
name: Zarechnova, Natalya
name: Tsirkova, Maria
name: Permyakov, Sergey
name: Parin, Sergey
name: Polevaya, Sofia
Publisher: name: arXiv
Year: 2022
Subjects: subject: Signal Processing (eess.SP)
subject: Human-Computer Interaction (cs.HC)
subject: Machine Learning (cs.LG)
subject: Tissues and Organs (q-bio.TO)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: In this study we applyed machine-learning algorithms to determine the post-COVID state of a person. During the study, a marker of the post-COVID state of a person was found in the electrocardiogram data. We have shown that this marker in the patient's ECG signal can be used to diagnose a post-COVID state.
Charged-particle bound states in periodic boxes
Creators: name: Yu, Hang
name: König, Sebastian
name: Lee, Dean
Publisher: name: arXiv
Year: 2022
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We consider the binding energy of a two-body system with a repulsive Coulomb interaction in a finite periodic volume. We define the finite-volume Coulomb potential as the usual Coulomb potential, except that the distance is defined as the shortest separation between the two bodies in the periodic volume. We investigate this problem in one and three-dimensional periodic boxes and derive the asymptotic behavior of the volume dependence for bound states with zero angular momentum in terms of Whittaker functions. We benchmark our results against numerical calculations and show how the method can be used to extract asymptotic normalization coefficients for charged-particle bound states. The results we derive here have immediate applications for calculations of atomic nuclei in finite periodic volumes for the case where the leading finite-volume correction is associated with two charged clusters.
description: 26 pages, 6 figures (2 in main text). Matches published version and includes Supplemental Material
Limits of Fault-Tolerance on Resource-Constrained Quantum Circuits for Classical Problems
Creators: name: G, Uthirakalyani.
name: Nayak, Anuj K.
name: Chatterjee, Avhishek
name: Varshney, Lav R.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Existing lower bounds on redundancy in fault-tolerant quantum circuits are applicable when both the input and the intended output are quantum states. These bounds may not necessarily hold, however, when the input and the intended output are classical bits, as in the Deutsch-Jozsa, Grover, or Shor algorithms. Here we show that indeed, noise thresholds obtained from existing bounds do not apply to a simple fault-tolerant implementation of the Deutsch-Jozsa algorithm. Then we obtain the first lower bound on the minimum required redundancy for fault-tolerant quantum circuits with classical inputs and outputs. Recent results show that due to physical resource constraints in quantum circuits, increasing redundancy can increase noise, which in turn may render many fault-tolerance schemes useless. So it is of both practical and theoretical interest to characterize the effect of resource constraints on the fundamental limits of fault-tolerant quantum circuits. Thus as an application of our lower bound, we characterize the fundamental limit of fault-tolerant quantum circuits with classical inputs and outputs under resource constraint-induced noise models.
Improving Correlation Function Fitting with Ridge Regression: Application to Cross-Correlation Reconstruction
Creators: name: Matthews, Daniel J.
name: Newman, Jeffrey A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: FOS: Physical sciences

description: Cross-correlation techniques provide a promising avenue for calibrating photometric redshifts and determining redshift distributions using spectroscopy which is systematically incomplete (e.g., current deep spectroscopic surveys fail to obtain secure redshifts for 30-50% or more of the galaxies targeted). In this paper we improve on the redshift distribution reconstruction methods presented in Matthews & Newman (2010) by incorporating full covariance information into our correlation function fits. Correlation function measurements are strongly covariant between angular or spatial bins, and accounting for this in fitting can yield substantial reduction in errors. However, frequently the covariance matrices used in these calculations are determined from a relatively small set (dozens rather than hundreds) of subsamples or mock catalogs, resulting in noisy covariance matrices whose inversion is ill-conditioned and numerically unstable. We present here a method of conditioning the covariance matrix known as ridge regression which results in a more well behaved inversion than other techniques common in large-scale structure studies. We demonstrate that ridge regression significantly improves the determination of correlation function parameters. We then apply these improved techniques to the problem of reconstructing redshift distributions. By incorporating full covariance information, applying ridge regression, and changing the weighting of fields in obtaining average correlation functions, we obtain reductions in the mean redshift distribution reconstruction error of as much as ~40% compared to previous methods. In an appendix, we provide a description of POWERFIT, an IDL code for performing power-law fits to correlation functions with ridge regression conditioning that we are making publicly available.
description: 10 pages, 6 figures
Design, Synthesis and Evaluation of Novel Pannexin 1 Channel Modulators
Creators: name: Navis, Kathleen E.
Publisher: name: Graduate Studies
Year: 2020
Subjects: subject: Chemistry--Organic

description: Pannexin 1 (Panx1) channels are transmembrane proteins that release ATP and play an important role in intercellular communication. They are widely expressed in somatic and nervous system tissues, and their activity has been associated with many pathologies including stroke, epilepsy, addiction, inflammation and chronic pain. While there are a variety of known Panx1 inhibitors, there is a dearth of sufficiently potent and selective drugs targeting Panx1, and relatively little is known about the mechanism of channel inhibition. Structure-activity relationship (SAR) studies can provide information about the critical functional groups controlling substrate activity and lead to the development of more potent inhibitors. This thesis outlines the importance of Panx1 channels as a potential therapeutic target and describes the synthesis, SAR and evaluation of novel inhibitors based on biological assays. In silico modeling was also used to identify compounds from the ZINC database with similar pharmacophore characteristics to known Panx1 inhibitors. The compounds developed over the course of study may have potential as novel drugs for the relief of multiple important pathologies. Provisional patent protection for this work is currently being pursued.
Medium-induced emissions of hard gluons
Creators: name: Apolinário, Liliana
name: Armesto, Néstor
name: Salgado, Carlos A.
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We present a derivation of the medium-induced gluon radiation spectrum beyond the current limitation of soft gluon emission. Making use of the path integral approach to describe the propagation of high-energy particles inside a medium, we study the limiting case of a hard gluon emission. Analytical and numerical results are presented and discussed within the multiple soft scattering approximation. An ansatz interpolating between soft and hard gluon emissions is provided. The Landau-Pomeranchuk-Migdal effect is observed in the expected kinematic region.
description: 17 pages, 6 figures. Minor corrections, references updated. Accepted by Phys. Lett. B
Role of cyclin-dependent kinase 5 (Cdk5) in mitochondrial permeability transition pore (mPTP) opening and intracellular Ca2+ dynamics
Creators: name: Navaneetha Krishnan, Saranya
Publisher: name: Graduate Studies
Year: 2020
Subjects: subject: Breast cancer
subject: Cyclin-dependent kinase 5
subject: Mitochondria
subject: Calcium,Reactive oxygen species
subject: Apoptosis
subject: Health Sciences--Oncology
subject: Biology--Cell
subject: Biology--Molecular

description: Cyclin-dependent kinase 5 (Cdk5), which plays a role in the development and progression of many human cancers, localizes in the mitochondria, a key determinant of apoptotic cell death. Cdk5 is upregulated in breast cancer cells and Cdk5 loss increases cancer cell sensitivity to chemotherapeutic drugs. However, the molecular mechanism by which Cdk5 loss promotes cell death remains unclear. I hypothesized that Cdk5 loss activates the intrinsic apoptotic pathway in breast cancer cells. I demonstrated that Cdk5-deficient breast cancer cells exhibit increased mitochondrial depolarization, mitochondrial reactive oxygen species (mtROS) levels, and mitochondrial fragmentation that is associated with an increase in both intracellular Ca2+ level and calcineurin activity, and dynamin related protein 1 (DRP1) Ser637 dephosphorylation. To define mitochondria-mediated apoptotic pathway, I utilized various inhibitors of mitochondrial function. Apoptosis is completely prevented by mitochondrial permeability transition pore (mPTP) inhibition, almost fully inhibited by blocking ROS and unaffected by inhibition of mitochondrial fission, suggesting that apoptosis in breast cancer cells due to Cdk5 loss occurs via a novel mPTP-dependent mechanism that acts primarily through ROS increase. Since calcium is the major regulator of mPTP opening, I hypothesized that Cdk5 regulates intracellular calcium homeostasis. Using primary mouse embryonic fibroblasts (MEFs) isolated from Cdk5?/? mouse embryos, I showed that loss of Cdk5 increases inositol 1,4,5-trisphosphate receptor (IP3R)-mediated Ca2+ release from internal stores. Cdk5 associates with and phosphorylates the IP3R1 Ca2+ channel at Ser421 and such phosphorylation controls IP3R1-mediated Ca2+ release as loss of Cdk5, and thus loss of IP3R1 Ser421 phosphorylation, triggers an increase in IP3R1-mediated Ca2+ release in Cdk5?/? MEFs. Analysis of subcellular fractions of MEFs demonstrates that Cdk5 localizes in the mitochondria-associated endoplasmic reticulum membrane (MAM) and Cdk5 loss causes increased ER-mitochondria tethering, a process required for Ca2+ transfer from the ER to the mitochondria. Inhibition of ER Ca2+ release or mitochondrial Ca2+ uptake in Cdk5?/? MEFs prevents mPTP opening, indicating that mPTP opening in Cdk5?/? MEFs is due to increased Ca2+ transfer from the ER to the mitochondria. Altogether, our findings suggest that Cdk5 regulates IP3R1-mediated calcium release and mitochondrial Ca2+ homeostasis that are disturbed upon Cdk5 loss, which lead to mPTP opening.
Monte Carlo Simulation of Long Hard-Sphere Polymer Chains in Two to Five Dimensions
Creators: name: Schnabel, Stefan
name: Janke, Wolfhard
Publisher: name: arXiv
Year: 2023
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We perform simulations for long hard-sphere polymer chains using a recently developed binary-tree based Monte Carlo method. Systems in two to five dimensions with free and periodic boundary conditions and up to $10^7$ repeat units are considered. We focus on the scaling properties of the end-to-end distance and on the entropy and their dependence on the sphere diameter. To this end new methods for measuring entropy and its derivatives are introduced. By determining the Flory exponent $ν$ and the weakly universal amplitude ratio of end-to-end distance to radius of gyration we find that the system generally reproduces the behavior of self-avoiding lattice walks in strong support of universality.
description: 14 pages, 15 figures
Accurately summarizing an outbreak using epidemiological models takes time
Creators: name: Case, B. K. M.
name: Young, Jean-Gabriel
name: Hébert-Dufresne, Laurent
Publisher: name: arXiv
Year: 2023
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Dynamical Systems (math.DS)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: Physics and Society (physics.soc-ph)
subject: Methodology (stat.ME)
subject: FOS: Biological sciences
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Recent outbreaks of monkeypox and Ebola, and worrying waves of COVID-19, influenza and respiratory syncytial virus, have all led to a sharp increase in the use of epidemiological models to estimate key epidemiological parameters. The feasibility of this estimation task is known as the practical identifiability (PI) problem. Here, we investigate the PI of eight commonly reported statistics of the classic Susceptible-Infectious-Recovered model using a new measure that shows how much a researcher can expect to learn in a model-based Bayesian analysis of prevalence data. Our findings show that the basic reproductive number and final outbreak size are often poorly identified, with learning exceeding that of individual model parameters only in the early stages of an outbreak. The peak intensity, peak timing, and initial growth rate are better identified, being in expectation over 20 times more probable having seen the data by the time the underlying outbreak peaks. We then test PI for a variety of true parameter combinations, and find that PI is especially problematic in slow-growing or less-severe outbreaks. These results add to the growing body of literature questioning the reliability of inferences from epidemiological models when limited data are available.
description: 7 pages, 4 figures
Escape Dynamics in the Discrete Repulsive ϕ^4-Model
Creators: name: Achilleos, V.
name: Álvarez, A.
name: Cuevas, J.
name: Frantzeskakis, D. J.
name: Karachalios, N. I.
name: Kevrekidis, P. G.
name: Sánchez-Rey, B.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: We study deterministic escape dynamics in the framework of the discrete Klein-Gordon modelwith a repulsive quartic on-site potential. Using a combination of analytical techniques, based on differential and algebraic inequalities and selected numerical illustrations, we first derive conditions for collapse of an initially excited single-site unit, for both the Hamiltonian and the linearly damped versions of the system and showcase different potential fates of the single-site excitation, such as the possibility to be "pulled back" from outside the well or to "drive over" the barrier some of its neighbors. Next, we study the evolution of a uniform (small) segment of the chain and, in turn, consider the conditions that support its escape and collapse of the chain. Finally, our path from one to the few and finally to the many excited sites is completed by a modulational stability analysis and the exploration of its connection to the escape process for plane wave initial data. This reveals the existence of three distinct regimes, namely modulational stability, modulational instability without escape and, finally, modulational instability accompanied by escape. These are corroborated by direct numerical simulations. In each of the above cases, the variations of the relevant model parameters enable a consideration of the interplay of discreteness and nonlinearity within the observed phenomenology.
description: To be published in Physica D
Identifying quantum many-body integrability and chaos using eigenstates trace distances
Creators: name: Khasseh, Reyhaneh
name: Zhang, Jiaju
name: Heyl, Markus
name: Rajabpour, M. A.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: While the concepts of quantum many-body integrability and chaos are of fundamental importance for the understanding of quantum matter, their precise definition has so far remained an open question. In this work, we introduce an alternative indicator for quantum many-body integrability and chaos, which is based on the statistics of eigenstates by means of nearest-neighbor subsystem trace distances. We show that this provides us with a faithful classification through extensive numerical simulations for a large variety of paradigmatic model systems including random matrix theories, free fermions, Bethe-ansatz solvable systems, and models of many-body localization. While existing indicators, such as those obtained from level-spacing statistics, have already been utilized with great success, they also face limitations. This concerns for instance the quantum many-body kicked top, which is exactly solvable but classified as chaotic in certain regimes based on the level-spacing statistics, while our introduced indicator signals the expected quantum many-body integrability. We discuss the universal behaviors we observe for the nearest-neighbor trace distances and point out that our indicator might be useful also in other contexts such as for the many-body localization transition.
description: 7+6 pages, 3+6 Figures
Numerical simulations of black-hole binaries and gravitational wave emission
Creators: name: Sperhake, Ulrich
name: Berti, Emanuele
name: Cardoso, Vitor
Publisher: name: arXiv
Year: 2011
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: FOS: Physical sciences

description: We review recent progress in numerical relativity simulations of black-hole (BH) spacetimes. Following a brief summary of the methods employed in the modeling, we summarize the key results in three major areas of BH physics: (i) BHs as sources of gravitational waves (GWs), (ii) astrophysical systems involving BHs, and (iii) BHs in high-energy physics. We conclude with a list of the most urgent tasks for numerical relativity in these three areas.
description: Updated version, references added; 47 pages, 3 figures
Non-Hermiticity induces localization: good and bad resonances in power-law random banded matrices
Creators: name: De Tomasi, Giuseppe
name: Khaymovich, Ivan M.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The power-law random banded matrix (PLRBM) is a paradigmatic ensemble to study the Anderson localization transition (AT). In $d$-dimension the PLRBM are random matrices with algebraic decaying off-diagonal elements $H_{\vec{n}\vec{m}}\sim 1/|\vec{n}-\vec{m}|^α$, having AT at $α=d$. In this work, we investigate the fate of the PLRBM to non-Hermiticity. We consider the case where the random on-site diagonal potential takes complex values, mimicking an open system, subject to random gain-loss terms. We provide an analytical understanding of the model by generalizing the Anderson-Levitov resonance counting technique to the non-Hermitian case. This generalization identifies two competing mechanisms due to non-Hermiticity: one favoring localization and the other delocalization. The competition between the two gives rise to AT at $d/2\le α\le d$. The value of the critical $α$ depends on the strength of the on-site potential, reminiscent of Hermitian disordered short-range models in $d>2$. Within the localized phase, the wave functions are algebraically localized with an exponent $α$ even for $α
description: 4.5 pages, 4 figures, 57 references + 5 pages, 4 figures in Appendices