cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Learning Robust Reward Machines from Noisy Labels
Creators: name: Parac, Roko
name: Nodari, Lorenzo
name: Ardon, Leo
name: Furelos-Blanco, Daniel
name: Cerutti, Federico
name: Russo, Alessandra
Publisher: name: arXiv
Year: 2024
Subjects: subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: This paper presents PROB-IRM, an approach that learns robust reward machines (RMs) for reinforcement learning (RL) agents from noisy execution traces. The key aspect of RM-driven RL is the exploitation of a finite-state machine that decomposes the agent's task into different subtasks. PROB-IRM uses a state-of-the-art inductive logic programming framework robust to noisy examples to learn RMs from noisy traces using the Bayesian posterior degree of beliefs, thus ensuring robustness against inconsistencies. Pivotal for the results is the interleaving between RM learning and policy learning: a new RM is learned whenever the RL agent generates a trace that is believed not to be accepted by the current RM. To speed up the training of the RL agent, PROB-IRM employs a probabilistic formulation of reward shaping that uses the posterior Bayesian beliefs derived from the traces. Our experimental analysis shows that PROB-IRM can learn (potentially imperfect) RMs from noisy traces and exploit them to train an RL agent to solve its tasks successfully. Despite the complexity of learning the RM from noisy traces, agents trained with PROB-IRM perform comparably to agents provided with handcrafted RMs.
description: Accepted at the 21st International Conference on Principles of Knowledge Representation and Reasoning (KR 2024)
Stochastic Geometry Based Modelling and Analysis of Uplink Cooperative Satellite-Aerial-Terrestrial Networks for Nomadic Communications with Weak Satellite Coverage
Creators: name: Dong, Wen-Yu
name: Yang, Shaoshi
name: Zhang, Ping
name: Chen, Sheng
Publisher: name: arXiv
Year: 2024
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: Signal Processing (eess.SP)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Cooperative satellite-aerial-terrestrial networks (CSATNs), where unmanned aerial vehicles (UAVs) are utilized as nomadic aerial relays (A), are highly valuable for many important applications, such as post-disaster urban reconstruction. In this scenario, direct communication between terrestrial terminals (T) and satellites (S) is often unavailable due to poor propagation conditions for satellite signals, and users tend to congregate in regions of finite size. There is a current dearth in the open literature regarding the uplink performance analysis of CSATN operating under the above constraints, and the few contributions on the uplink model terrestrial terminals by a Poisson point process (PPP) relying on the unrealistic assumption of an infinite area. This paper aims to fill the above research gap. First, we propose a stochastic geometry based innovative model to characterize the impact of the finite-size distribution region of terrestrial terminals in the CSATN by jointly using a binomial point process (BPP) and a type-II Mat{é}rn hard-core point process (MHCPP). Then, we analyze the relationship between the spatial distribution of the coverage areas of aerial nodes and the finite-size distribution region of terrestrial terminals, thereby deriving the distance distribution of the T-A links. Furthermore, we consider the stochastic nature of the spatial distributions of terrestrial terminals and UAVs, and conduct a thorough analysis of the coverage probability and average ergodic rate of the T-A links under Nakagami fading and the A-S links under shadowed-Rician fading. Finally, the accuracy of our theoretical derivations are confirmed by Monte Carlo simulations. Our research offers fundamental insights into the system-level performance optimization for the realistic CSATNs involving nomadic aerial relays and terrestrial terminals confined in a finite-size region.
description: 17 pages, 16 pages, 2 tables, accepted to appear on IEEE Journal on Selected Areas in Communications, Aug. 2024
EXAMINING SIMULTANEOUS ALCOHOL AND ∆9-TETRAHYDROCANNABINOL SELF-ADMINISTRATION ON BEHAVIORAL FLEXIBILITY AND DORSAL STRIATAL CB1 EXPRESSION IN CHAP MICE
Creators: name: Millie, Lauren
Publisher: name: Purdue University Graduate School
Year: 2020
Subjects: Psychopharmacology
Psychophysiology

description: Although marijuana and alcohol are two of the most commonly used drugs in the United States, relatively little is understood about how these drugs interact to effect drug use, cognitive behaviors, and neurophysiological changes. Specific drug use patterns such as simultaneous use may produce differential effects for consumption and other behaviors in addition to unique neurobiological changes compared to singular drug use. In order to better understand the effects of simultaneous alcohol and marijuana (SAM) use, we used the selectively bred crossed High Alcohol Preferring mice to examine consummatory, cognitive, and neurobiological changes following chronic alcohol and THC self-administration. We hypothesized that SAM mice would consume more drug than animals exposed to either substance alone. We used an operant behavioral flexibility paradigm to assess cognitive impairments believing that drug-exposed animals would show deficits relative to Control animals, with SAM mice being the most impaired of all drug conditions. Finally, we assessed CB1 receptor changes in the dorsal striatum, as this region is critical for behavioral flexibility (Bissonette & Powell, 2012; Ragozzino, 2007), CB1 receptors are the primary target of THC and these receptors are involved in numerous alcohol related behaviors (Maldonado et al., 2006; Pava & Woodward, 2012). Contrary to our hypothesis, SAM animals did not consume higher levels of drug compared to mice exposed to only THC or alcohol. Interestingly, female THC consumption was robust when THC was consumed alone but was reduced when simultaneous access to alcohol was available. Surprisingly, although we speculated that drug- exposed mice would be impaired compared to Control animals, and that SAM animals would likely be more compromised than THC and alcohol for Reversal Learning and Attentional Set-Shifting respectively, behavioral flexibility deficits were absent in our paradigm. Finally, alterations to dorsal striatal CB1 receptor expression were observed following a Short Abstinence period. Despite an absence of cognitive behavioral effects, this research contributes to furthering our understanding of co-drug use for consummatory and neurobiological changes, both of which are critically necessary given the evolving landscape surrounding simultaneous alcohol and recreational marijuana use.
sj-pdf-1-avc-10.1177_20402066211030380 - Supplemental material for V3-Loop genotypes do not predict maraviroc susceptibility of CCR5-tropic virus or clinical response through week 48 in HIV-1–infected, treatment-experienced persons receiving optimized background regimens
Creators: name: Lewis, ME
name: Simpson, P
name: Mori, J
name: Jubb, B
name: Sullivan, J
name: McFadyen, L
name: van der Ryst, E
name: Craig, C
name: Robertson, DL
name: Westby, M
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 111599 Pharmacology and Pharmaceutical Sciences not elsewhere classified
subject: FOS: Clinical medicine
subject: Cell Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Supplemental material, sj-pdf-1-avc-10.1177_20402066211030380 for V3-Loop genotypes do not predict maraviroc susceptibility of CCR5-tropic virus or clinical response through week 48 in HIV-1–infected, treatment-experienced persons receiving optimized background regimens by ME Lewis, P Simpson, J Mori, B Jubb, J Sullivan, L McFadyen, E van der Ryst, C Craig, DL Robertson and M Westby in Antiviral Chemistry and Chemotherapy
ACCUMULATION AND EFFECTS OF MICRO- AND NANOPLASTIC PARTICLES IN TERRESTRIAL ECOSYSTEMS
Creators: name: Adhikari, Kaushik
Publisher: name: Washington State University
Year: 2024
Subjects: Biosolids
Contaminants
Earthworms
Microplastics
Nanoplastics
Plants uptake

description: Micro- and nanopplastic particles, because of their widespread utilization, are ubiquitous in the environment, and consequently can have significant impacts on ecosystems. The accumulation of microplastics in agricultural soil can potentially negatively impact soil health and plant growth. The overall goal of this dissertation is to assess the accumulation of micro- and nanoplastics in an agricultural soil, and the interaction of these micro- and nanoplas- tics with soil organisms such as earthworms and plants. In a study involving interactions of microplastics with earthworms (Lumbricus terrestris), we found that that the plastics particles were ingested by earthworms and incorporated into the cast. Both, biodegradable polybutylene adipate co-terephthalate (PBAT) and conventional polyethylene particles were ingested by earthworms, but only PBAT underwent degradation during the passage through the earthworms’ intestines. The microplastics did not cause significant changes of the mi- crobial populations in the earthworms’ guts, casts, and soil. Findings from the research withbiosolids-amended soil demonstrated that long-term application of biosolids to agricultural soil led to microplastic accumulation in the soil, but also showed that atmospheric deposi- tion of microplastics is a substantial input to microplastics accumulation. The study with nanoplastics uptake in plants revealed the accumulation of nanoplastics around root cap cells, but showing little evidence of uptake inside plant roots beyond the Casparian strip. As biosolids application and atmospheric deposition lead to micro- and nanoplastics accu- mulation in soil, the persistence of micro- and nanoplastics could lead to impacts on soil organisms and plant growth. Measuring and quantifying micro- and nanoplastics in soils of- fers insights into plastic accumulation, but only understanding the interactions of the plastic particles with soil organisms and plants provides additional information about their potential impacts. Overall, the results of this dissertation highlight that micro- and nanoplastics can accumulate in agricultural soil, and that these particles can potentially impact soil health and plant growth.
Additional file 2 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Creators: name: Gao, Guangliang
name: Liu, Rui
name: Hu, Silu
name: He, Mengnan
name: Zhang, Jiaman
name: Gao, Dengfeng
name: Li, Jing
name: Hu, Jiwei
name: Wang, Jiwen
name: Wang, Qigui
name: Li, Mingzhou
name: Jin, Long
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Fig. S2. Gene expression in goose liver induced by high-fat diet (HFD). A Correlation matrix for goose liver mRNA profiles based on Pearson's correlation coefficient; B The transcriptome of goose HFD and normal liver with the typical NAFLD markers; C The gene enrichment analysis for the up-regulated DEGs in goose HFD liver tissues; D The gene enrichment analysis for the down-regulated DEGs in goose HFD liver tissues.
Sample of hydrogen-rich superluminous supernovae from the Zwicky Transient Facility
Creators: name: Pessi, P. J.
name: Lunnan, R.
name: Sollerman, J.
name: Schulze, S.
name: Gkini, A.
name: Gangopadhyay, A.
name: Yan, L.
name: Gal-Yam, A.
name: Perley, D. A.
name: Chen, T. -W.
name: Hinds, K. R.
name: Brennan, S. J.
name: Hu, Y.
name: Singh, A.
name: Andreoni, I.
name: Cook, D. O.
name: Fremling, C.
name: Ho, A. Y. Q.
name: Sharma, Y.
name: van Velzen, S.
name: Kangas, T.
name: Wold, A.
name: Bellm, E. C.
name: Bloom, J. S.
name: Graham, M. J.
name: Kasliwal, M. M.
name: Kulkarni, S. R.
name: Riddle, R.
name: Rusholme, B.
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Hydrogen-rich superluminous supernovae (SLSNe II) are rare. The exact mechanism producing their extreme light curve peaks is not understood. Analysis of single events and small samples suggest that CSM interaction is the main responsible for their features. However, other mechanisms can not be discarded. Large sample analysis can provide clarification. We aim to characterize the light curves of a sample of 107 SLSNe II to provide valuable information that can be used to validate theoretical models. We analyze the gri light curves of SLSNe II obtained through ZTF. We study peak absolute magnitudes and characteristic timescales. When possible we compute g-r colors, pseudo-bolometric light curves, and estimate lower limits for their total radiated energy. We also study the luminosity distribution of our sample and estimate the percentage of them that would be observable by the LSST. Finally, we compare our sample to other H-rich SNe and to H-poor SLSNe I. SLSNe II are heterogeneous. Their median peak absolute magnitude is -20.3 mag in optical bands. Their rise can take from two weeks to over three months, and their decline from twenty days to over a year. We found no significant correlations between peak magnitude and timescales. SLSNe II tend to show fainter peaks, longer declines and redder colors than SLSNe I. We present the largest sample of SLSNe II light curves to date, comprising of 107 events. Their diversity could be explained by considering different CSM morphologies. Although, theoretical analysis is needed to explore alternative scenarios. Other luminous transients, such as Active Galactic Nuclei, Tidal Disruption Events or SNe Ia-CSM, can easily become contaminants. Thus, good multi-wavelength light curve coverage becomes paramount. LSST could miss 30 percent of the ZTF events in the its footprint in gri bands. Redder bands become important to construct complete samples.
description: 36 pages. 28 figures. 9 tables
Supplemental Material, sj-docx-1-jpx-10.1177_23743735211033750 - Ophthalmology Provider Ratings and Patient, Disease, and Appointment Factors
Creators: name: Han, Michael M.
name: Hsueh, Jessica
name: Chen, Andrew X.
name: Greenlee, Tyler E.
name: Conti, Thais F.
name: Rose, Susannah L.
name: Singh, Rishi P.
name: Rachitskaya, Aleksandra V.
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 111708 Health and Community Services
subject: FOS: Health sciences
subject: Medicine

description: Supplemental Material, sj-docx-1-jpx-10.1177_23743735211033750 for Ophthalmology Provider Ratings and Patient, Disease, and Appointment Factors by Michael M. Han, Jessica Hsueh, Andrew X. Chen, Tyler E. Greenlee, Thais F. Conti, Susannah L. Rose, Rishi P. Singh and Aleksandra V. Rachitskaya in Journal of Patient Experience
Evaluating near-surface wind speeds simulated by the CRCM6-GEM5 model using AmeriFlux data over North America
Creators: name: Whittaker, Tim
name: Di Luca, Alejandro
name: Roberge, Francois
name: Winger, Katja
Publisher: name: arXiv
Year: 2024
Subjects: subject: Atmospheric and Oceanic Physics (physics.ao-ph)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: We evaluate the performance of various configurations of the Canadian Regional Climate Model (CRCM6-GEM5) in simulating 10-meter wind speeds using data from 27 AmeriFlux stations across North America. The assessment employs a hierarchy of error metrics, ranging from simple mean bias to advanced metrics that account for the dependence of wind speeds on variables such as friction velocity and stability. The results reveal that (i) the value of roughness length (z0) has a large effect on the simulation of wind speeds, (ii) using a lower limit for the Obhukov length instead of a lower limit for the lowest level wind speed seems to deteriorate the simulation of wind speeds under very stable conditions, (iii) the choice of stability function has a small but noticeable impact on the wind speeds, (iv) the turbulent orographic form drag scheme shows improvement over effective roughness length approach.
Fine-Grained Anomaly Detection For In Depth Data Protection
Creators: name: Mehnaz, Shagufta
Publisher: name: Purdue University Graduate School
Year: 2020
Subjects: System and network security

description: Data represent a key resource for all organizations we may think of. Thus, it is not surprising that data are the main target of a large variety of attacks. Security vulnerabilities and phishing attacks make it possible for malicious software to steal business or privacy sensitive data and to undermine data availability such as in recent ransomware attacks.Apart from external malicious parties, insider attacks also pose serious threats to organizations with sensitive information, e.g., hospitals with patients’ sensitive information. Access control mechanisms are not always able to prevent insiders from misusing or stealing data as they often have data access permissions. Therefore, comprehensive solutions for data protection require combining access control mechanisms and other security techniques,such as encryption, with techniques for detecting anomalies in data accesses. In this the-sis, we develop fine-grained anomaly detection techniques for ensuring in depth protection of data from malicious software, specifically, ransomware, and from malicious insiders.While anomaly detection techniques are very useful, in many cases the data that is used for anomaly detection are very sensitive, e.g., health data being shared with untrusted service providers for anomaly detection. The owners of such data would not share their sensitive data in plain text with an untrusted service provider and this predicament undoubtedly hinders the desire of these individuals/organizations to become more data-driven. In this thesis, we have also built a privacy-preserving framework for real-time anomaly detection.
The Effects of Fiber Orientation State of Extrusion Deposition Additive Manufactured Fiber-Filled Thermoplastic Polymers
Creators: name: Pibulchinda, Pasita
Publisher: name: Purdue University Graduate School
Year: 2020
Subjects: Composite and hybrid materials
Additive manufacturing
Modelling and simulation

description: Extrusion Deposition Additive Manufacturing (EDAM) is a process in which fiber-filled thermoplastic polymers are mixed and melted in an extruder and deposited onto a build plate in a layer-by-layer basis. Anisotropy caused by flow-induced orientation of discontinuous fibers along with the non-isothermal cooling process gives rise to internal stresses in printed parts which results in part deformation. The deformation and residual stresses can be abated by modifying the fiber orientation in the extrudate to best suit the print geometry. To that end, the focus of this research is on understanding the effect of fiber orientation state and fiber properties on effective properties of the printed bead and the final deformation of a part. The properties of three different orientation tensors of glass fiber-filled polyamide and carbon fiber-filled polyamide were experimentally and virtually characterized via micromechanics. A thermo-mechanical simulation framework developed in ABAQUS© was used to understand the effects of the varying fiber orientation tensor and fiber properties on the final deformation of printed parts. In particular, a medium-size geometry that is prone to high deformation was simulated and compared among the three orientation tensors and two material systems. This serves to be a good preliminary study to understand microscopic properties induced deformations in EDAM.
sj-docx-1-psp-10.1177_01461672211037138 – Supplemental material for Psychology and the Threat of Contagion: Feeling Vulnerable to a Disease Moderates the Link Between Xenophobic Thoughts and Support for Ingroup-Protective Actions
Creators: name: Kim, Heejung S.
name: Eom, Kimin
name: Chuang, Roxie
name: Sherman, David K.
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 170199 Psychology not elsewhere classified
subject: FOS: Psychology

description: Supplemental material, sj-docx-1-psp-10.1177_01461672211037138 for Psychology and the Threat of Contagion: Feeling Vulnerable to a Disease Moderates the Link Between Xenophobic Thoughts and Support for Ingroup-Protective Actions by Heejung S. Kim, Kimin Eom, Roxie Chuang and David K. Sherman in Personality and Social Psychology Bulletin
Single-photon super-resolved spectroscopy from spatial-mode demultiplexing
Creators: name: Amato, Luigi Santamaria
name: Sgobba, Fabrizio
name: Pallotti, Deborah
name: Lupo, Cosmo
Publisher: name: arXiv
Year: 2024
Subjects: subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We demonstrate spectroscopy of incoherent light with sub-diffraction resolution. In a proof-of-principle experiment we analyze the spectrum of a pair of incoherent point-like sources whose separation is below the diffraction limit. The two sources mimic a planetary system, with a brighter source for the star and a dimmer one for the planet. Acquiring spectral information about the secondary source is hard because the two images have a substantial overlap. This limitation is solved by leveraging a structured measurement based on spatial-mode demultiplexing, where light is first sorted in its Hermite-Gaussian components in the transverse field, then measured by photon detection. This allows us to effectively decouple the photons coming from the two sources. An application is suggested to enhance exoplanets' atmosphere spectroscopy. A number of experiments of super-resolution imaging based on spatial demultiplexing have been conducted in the past few years, with promising results. Here, for the first time to the best of our knowledge, we extend this concept to the domain of spectroscopy.
description: 11 pages, 6 figures, comments welcome
Effective Injectivity of Specialization Maps for Elliptic Surfaces
Creators: name: Billingsley, Tyler R
Publisher: name: Purdue University Graduate School
Year: 2020
Subjects: Algebra and number theory

description: This dissertation concerns two questions involving the injectivity of specialization homomorphisms for elliptic surfaces. We primarily focus on elliptic surfaces over the projective line defined over the rational numbers. The specialization theorem of Silverman proven in 1983 says that, for a fixed surface, all but finitely many specialization homomorphisms are injective. Given a subgroup of the group of rational sections with explicit generators, we thus ask the following.Given some rational number, how can we effectively determine whether or not the associated specialization map is injective?What is the set of rational numbers such that the corresponding specialization maps are injective?The classical specialization theorem of Neron proves that there is a set S which differs from a Hilbert subset of the rational numbers by finitely many elements such that for each number in S the associated specialization map is injective. We expand this into an effective procedure that determines if some rational number is in S, yielding a partial answer to question 1. Computing the Hilbert set provides a partial answer to question 2, and we carry this out for some examples. We additionally expand an effective criterion of Gusic and Tadic to include elliptic surfaces with a rational 2-torsion curve.
sj-pdf-1-ajs-10.1177_03635465211032979 – Supplemental material for Prevalence and Burden of Self-Reported Health Problems in Junior Male Elite Ice Hockey Players: A 44-Week Prospective Cohort Study
Creators: name: Nordstrøm, Anine
name: Bahr, Roald
name: Clarsen, Ben
name: Talsnes, Ove
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 110314 Orthopaedics
subject: FOS: Clinical medicine
subject: 110604 Sports Medicine
subject: FOS: Health sciences
subject: 110323 Surgery

description: Supplemental material, sj-pdf-1-ajs-10.1177_03635465211032979 for Prevalence and Burden of Self-Reported Health Problems in Junior Male Elite Ice Hockey Players: A 44-Week Prospective Cohort Study by Anine Nordstrøm, Roald Bahr, Ben Clarsen and Ove Talsnes in The American Journal of Sports Medicine
Extreme softening of QCD phase transition under weak acceleration: first principle Monte Carlo results for gluon plasma
Creators: name: Chernodub, M. N.
name: Goy, V. A.
name: Molochkov, A. V.
name: Stepanov, D. V.
name: Pochinok, A. S.
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study the properties of gluon plasma subjected to a weak acceleration using first-principle numerical Monte Carlo simulations. We use the Luttinger (Tolman-Ehrenfest) correspondence between temperature gradient and gravitational field to impose acceleration in imaginary time formalism. Under acceleration, the system resides in global thermal equilibrium. Our results indicate that even the weakest acceleration up to $a \simeq 16$ MeV drastically softens the deconfinement phase transition, converting the first-order phase transition of a static system to a soft crossover for accelerating gluons. The accelerating environment can be relevant to the first moments of the early Universe and the initial glasma regime of relativistic heavy ion collisions. In particular, our results imply that the acceleration, if present, may also inhibit the detection of the thermodynamic phase transition from quark-gluon plasma to the hadronic phase.
description: 10 pages, 4+4(SM) figures, v2. Acknowledgments added, v3. Extended published version
Additional file 3 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Creators: name: Gao, Guangliang
name: Liu, Rui
name: Hu, Silu
name: He, Mengnan
name: Zhang, Jiaman
name: Gao, Dengfeng
name: Li, Jing
name: Hu, Jiwei
name: Wang, Jiwen
name: Wang, Qigui
name: Li, Mingzhou
name: Jin, Long
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3: Fig. S3. Data summary for the mouse Hi-C data. The summary of total contacts (A), composition of alignable reads (B) , unique reads (C) and valid contacts (D).
Biochemical Investigation of the de novo DNA Methyltransferases DNMT3A and DNMT3B
Creators: name: Norvil, Allison B
Publisher: name: Purdue University Graduate School
Year: 2020
Subjects: Enzymes
Epigenetics (incl. genome methylation and epigenomics)
Plant cell and molecular biology
Animal cell and molecular biology
Structural biology (incl. macromolecular modelling)
Biochemistry and cell biology not elsewhere classified

description: DNA methylation is an epigenetic modification that is nearly ubiquitous. Eukaryotic DNA methylation contributes to the regulation of gene expression and maintaining genome integrity. In mammals, DNA methylation occurs primarily on the C5 carbon of cytosine in a CpG dinucleotide context and is catalyzed by the DNA methyltransferases, DNMT1, DNMT3A and DNMT3B. While dnmt3a and dnmt3b genes are highly homologous, the enzymes have distinct functions. Some previous reports suggested differences in the enzymatic behavior of DNMT3A and 3B, which could affect their biological roles. The goal of my thesis work was to characterize kinetics mechanisms of DNMT3A and 3B, and to identify the similarities and differences in their catalytic properties that contribute to their distinct biological functions. Given the sequence similarity between the enzymes, we asked whether DNMT3B was kinetically similar to DNMT3A. In a series of experiments designed to distinguish between various kinetics mechanisms, we reported that unlike DNMT3A, DNMT3B methylated tandem CpG on DNA in a processive manner. We also reported that the disruption of the R-D interface, critical for the cooperativity of DNMT3A, had no effect on DNMT3B activity, supporting the non-cooperative mechanism of this enzyme. DNMT3A is frequently mutated in numerous cancers. Acute Myeloid Leukemia (AML) is a malignancy of hematopoietic stem cells in which numerous patients exhibit a high frequency of the heterozygous somatic mutation Arg882His in DNMT3A. Through thorough consensus motif building, we discovered a strong similarity in CpG flanking sequence preference between DNMT3A Arg882His variant and DNMT3B enzyme. Moreover, we found that the variant enzyme has the same kinetics mechanism as DNMT3B, indicating a gain-of-function effect caused by the mutation. This change is significant because the variant enzyme can aberrantly methylate DNMT3B targets in AML cells and effect global gene expression. In particular, given that DNMT3B has been shown to have oncogenic properties, this suggests that the Arg882His variant can acquire similar oncogenic properties and drive AML development. Taken together, my thesis work provides novel insights into the relationship between the biochemical properties and the biological functions of DNMT3A and 3B.
Additional file 4 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Creators: name: Gao, Guangliang
name: Liu, Rui
name: Hu, Silu
name: He, Mengnan
name: Zhang, Jiaman
name: Gao, Dengfeng
name: Li, Jing
name: Hu, Jiwei
name: Wang, Jiwen
name: Wang, Qigui
name: Li, Mingzhou
name: Jin, Long
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4: Fig. S4. The Hi-C data access resolution for the HFD (A) and normal liver (B) groups in mouse.
Precursor to Quantum Criticality in Ce-Au-Al Quasicrystal Approximants
Creators: name: Khansili, A.
name: Huang, Y. -C.
name: Häussermann, U.
name: Gomez, C. Pay
name: Rydh, A.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Rare-earth element containing aperiodic quasicrystals and their related periodic approximant crystals can exhibit non-trivial physical properties at low temperatures. Here, we investigate the 1/1 and 2/1 approximant crystal phases of the Ce-Au-Al system by studying the ac-susceptibility and specific heat at low temperatures and in magnetic fields up to 12 T. We find that these systems display signs of quantum criticality similar to the observations in other claimed quantum critical systems, including the related Yb-Au-Al quasicrystal. In particular, the ac-susceptibility at low temperatures shows a diverging behavior $χ\propto 1/T$ as the temperature decreases as well as cutoff-behavior in magnetic field. Notably, the field dependence of $χ$ closely resembles that of quantum critical systems. However, the ac-susceptibility both in zero and nonzero magnetic fields can be understood from the splitting of a ground state Kramers doublet of Ce$^{3+}$. The high-temperature Curie-Weiss fit yields an effective magnetic moment of approximately 2.54$μ_{\mathrm{B}}$ per Ce for both approximant systems, which is reduced to $\sim$2.0$μ_{\mathrm{B}}$ at temperatures below 10 K. The low-temperature specific heat is dominated by the Schottky anomaly originating from the splitting of the Ce$^{3+}$ Kramers doublet, resulting in an entropy of $R\ln 2$ at around 10 K.
description: 11 pages, 4 figures, 5 supplementary figures
sj-docx-1-sms-10.1177_20563051211035350 – Supplemental material for The Role of Subjective Construals on Reporting and Reasoning about Social Media Use
Creators: name: Lee, Angela Y.
name: Katz, Roberta
name: Hancock, Jeffrey
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 200199 Communication and Media Studies not elsewhere classified
subject: FOS: Media and communications

description: Supplemental material, sj-docx-1-sms-10.1177_20563051211035350 for The Role of Subjective Construals on Reporting and Reasoning about Social Media Use by Angela Y. Lee, Roberta Katz and Jeffrey Hancock in Social Media + Society
Induced Gravitational Waves probing Primordial Black Hole Dark Matter with Memory Burden
Creators: name: Kohri, Kazunori
name: Terada, Takahiro
name: Yanagida, Tsutomu T.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Quantum evaporation of a black hole is conventionally studied semiclassically by assuming self-similarity of the black hole throughout the evaporation process. However, its validity was recently questioned, and the lifetime of a black hole is conjectured to be much extended by the memory burden effect. It gives rise to the possibility that the primordial black holes (PBHs) lighter than $10^{10}$ grams are the dark matter in the Universe. To probe such PBH dark matter, we study gravitational waves (GWs) induced by primordial curvature perturbations that produced the PBHs. We find $Ω_\text{GW}(f_\text{peak})h^2 = 7 \times 10^{-9}$ with the peak frequency $f_\text{peak} = 1\times 10^{3} \, (M_\text{PBH}/(10^{10}\,\mathrm{g}))^{-1/2}\, \mathrm{Hz}$, and the induced GWs associated with the PBH dark matter whose initial mass is greater than about $10^7$ grams can be tested by future observations such as Cosmic Explorer. Furthermore, the scenario can be in principle confirmed by detecting another GW signal from the mergers of PBHs, which leads to high-frequency GWs with $f_\text{peak} = 2 \times 10^{27}\, (M_\text{PBH, ini}/(10^{10}\, \mathrm{g}))^{-1} \, \mathrm{Hz} $. On the other hand, the induced GW signals stronger than expected would contradict the dark matter abundance and exclude the memory burden effect.
description: 23 pages, 5 figures; published version
Placeholders, Lessons, and Emasculators: The Literary Function of Women in Early Christian Texts
Creators: name: Cwikla, Anna
Publisher: name: unknown
Year: 2024

description: Scholarship on women in ancient Christian texts has primarily aimed to argue either that these texts were patriarchal and hostile to women or to show that on the contrary, women's capabilities and roles were held in higher esteem than we might assume. This dissertation highlights the literary function of female characters—the roles they play for the aims of the texts where they appear—to offer a way to study them beyond the framework of critique or apologetics. While the study of women in early Christianity has generally categorized women by their biographical details, such as their marital status, I propose three new categories—placeholders, lessons, and emasculators—as a means of accounting for and organizing the data we have about these women. These categories are based on the literary function of the women within their respective texts. The discussion of each category features a main exemplum and text. The category of placeholders focuses on Mary in the Gospel of Thomas, lessons through women discusses Bilhah in the Testament of Reuben, and emasculators discusses Judith in the book of Judith. The character of Thecla from the Acts of Paul and Thecla is used throughout the dissertation as a recurring point of comparison for each category and woman. Overall, this study argues that understanding the literary function of these women is effective for identifying similarities among female characters from various corpora and traditions.
Objection Overruled! Lay People can Distinguish Large Language Models from Lawyers, but still Favour Advice from an LLM
Creators: name: Schneiders, Eike
name: Seabrooke, Tina
name: Krook, Joshua
name: Hyde, Richard
name: Leesakul, Natalie
name: Clos, Jeremie
name: Fischer, Joel
Publisher: name: arXiv
Year: 2024
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: Computers and Society (cs.CY)
subject: FOS: Computer and information sciences

description: Large Language Models (LLMs) are seemingly infiltrating every domain, and the legal context is no exception. In this paper, we present the results of three experiments (total N = 288) that investigated lay people's willingness to act upon, and their ability to discriminate between, LLM- and lawyer-generated legal advice. In Experiment 1, participants judged their willingness to act on legal advice when the source of the advice was either known or unknown. When the advice source was unknown, participants indicated that they were significantly more willing to act on the LLM-generated advice. The result of the source unknown condition was replicated in Experiment 2. Intriguingly, despite participants indicating higher willingness to act on LLM-generated advice in Experiments 1 and 2, participants discriminated between the LLM- and lawyer-generated texts significantly above chance-level in Experiment 3. Lastly, we discuss potential explanations and risks of our findings, limitations and future work.
description: ACMConference on Human Factors in Computing Systems (CHI'25)
Additional file 5 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Creators: name: Gao, Guangliang
name: Liu, Rui
name: Hu, Silu
name: He, Mengnan
name: Zhang, Jiaman
name: Gao, Dengfeng
name: Li, Jing
name: Hu, Jiwei
name: Wang, Jiwen
name: Wang, Qigui
name: Li, Mingzhou
name: Jin, Long
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 5: Fig. S5. The heatmaps display the correlation coefficients of HiCRep analysis for the mouse samples.
RUSSIAN IMMIGRANTS: TRANSNATIONALISM IN THE CONTEXT OF U.S.-RUSSIA RELATIONS SINCE 2014
Creators: name: Yaryyeva, Annagul
Publisher: name: Purdue University Graduate School
Year: 2020
Subjects: Migration
International relations

description: This dissertation examines the transnational realities of Russian immigrants in the United States. Drawing insights from personal accounts, I discuss immigrants’ motives to immigrate to the United States and to stay connected to their homeland. I illustrate that political and economic factors, as well as the goals to enhance professional and personal lives, have shaped immigrants’ decisions to come to the United States. At the same time, I show that determined to fulfill their social and civic responsibilities, Russian immigrants maintain ties to their families and friends back in Russia and also remain civically engaged in Russian society. This dissertation also illustrates that a more intricate understanding of Russian immigrants today cannot be achieved in isolation from the political relations between Russia and the United States that have been rapidly deteriorating since 2014. There are different ways that Russian immigrants respond to the geopolitical divide between the two nation-states. Some Russian immigrants, for example, condemn Russia’s foreign policy and global political behavior. Their criticism is often met with hostilities from Russians who have not emigrated. Other Russian immigrants, on the other hand, disapprove U.S. actions toward Russia and Russian society and consequently encounter antagonisms in the United States. These immigrants recount their experiences of exclusion from the U.S. social fabric. There are also those Russian immigrants who question international acts of the political leaders of both countries. Coping with antagonistic attitudes from Russian and U.S. societies toward their political views and/or ethnic background, these individuals emphasize a growing detachment from both nations. Based on individual accounts, I argue that the contemporary tensions that have emerged between the two nations-states create a barrier to the development of a transnational identity among Russian immigrants. Specifically, living in a hostile political environment, Russian immigrants do not share a simultaneous sense of belonging in relation to Russia and the United States. By focusing on Russian immigrants’ experiences with U.S.-Russia relations, this dissertation also brings to light individual efforts to contest confrontations that shape the political landscape between Russia and the United States. As transnational subjects with cross-border ties and lives, Russian immigrants utilize their transnational positions and cultural competencies to impact international views of Russian and U.S. nationals. They frequently resort to transnational dialogues and socio-cultural acts to raise social awareness and sympathies between their home and host nations. By developing and investing their efforts into improving U.S.-Russia ties, the ultimate goal that Russian immigrants seek to achieve is to discourage members of Russian and U.S. societies from seeing each other as enemy nations.
sj-pdf-1-cjk-10.1177_20543581211037429 – Supplemental material for Impact of Perioperative Complications on Living Kidney Donor Health-Related Quality of Life and Mental Health: Results From a Prospective Cohort Study
Creators: name: Garcia-Ochoa, Carlos
name: Feldman, Liane S.
name: Nguan, Chris
name: Monroy-Caudros, Mauricio
name: Arnold, Jennifer B.
name: Barnieh, Lianne
name: Boudville, Neil
name: Cuerden, Meaghan S.
name: Dipchand, Christine
name: Gill, John S.
name: Karpinski, Martin
name: Klarenbach, Scott
name: Knoll, Greg
name: Lok, Charmaine E.
name: Miller, Matthew
name: Prasad, G. V. Ramesh
name: Sontrop, Jessica M.
name: Storsley, Leroy
name: Garg, Amit X.
Publisher: name: SAGE Journals
Year: 2021
Subjects: Medicine

description: Supplemental material, sj-pdf-1-cjk-10.1177_20543581211037429 for Impact of Perioperative Complications on Living Kidney Donor Health-Related Quality of Life and Mental Health: Results From a Prospective Cohort Study by Carlos Garcia-Ochoa, Liane S. Feldman, Chris Nguan, Mauricio Monroy-Caudros, Jennifer B. Arnold, Lianne Barnieh, Neil Boudville, Meaghan S. Cuerden, Christine Dipchand, John S. Gill, Martin Karpinski, Scott Klarenbach, Greg Knoll, Charmaine E. Lok, Matthew Miller, G. V. Ramesh Prasad, Jessica M. Sontrop, Leroy Storsley and Amit X. Garg in Canadian Journal of Kidney Health and Disease
Analysis of Droplet Impact on a Liquid Pool
Creators: name: Bhopatkar, Radhika Arvind
Publisher: name: Purdue University Graduate School
Year: 2020
Subjects: Mechanical engineering not elsewhere classified

description: Secondary atomization is very important in applications like IC engine and aircraft engine performance, agricultural sprays, and inkjet printing to name a few. In case of IC engines and aircraft engines, a good understanding of the modes of secondary atomization and the resultant drop size can contribute to improving the fuel injection and hence the efficiency of the engine. Similarly, with the help of appropriate secondary atomization desired agro-spray quality, ink usage and print quality can be achieved which would optimize the usage of chemicals and ink respectively and avoid any harmful effects on the environment. One of the reasons for secondary atomization that occurs very often in most of the spray applications is the drop impact on a solid or liquid surface. Especially it is cardinal to understand the impact of a drop on a liquid film since even in case of impact of liquid drops on a solid surface ultimately the drops that are injected at a later time are going have a target surface as a thin liquid film on the solid base due to the accumulation of the previously injected drops. Analysis of drop impact on a liquid film with non-dimensional thickness ranging from 0.1 to 1 has been done thoroughly before (Cossali et al., 2004, Vander Waal et al., 2006, Moreira et al., 2010), however, analysis of drop impact on a liquid film with non-dimensional thickness greater than 1 is still in a rudimentary stage. This work focuses on determining the probability density functions for the secondary drop sizes for drops produced in case of drop impact on a liquid film while varying the h/d ratio beyond 1. The experimental set-up used to study drop impact includes a droplet generator and DIH system as mentioned in, Yao et al. (2017). The DIH set-up includes a CW laser, spatial filter, beam expander and a collimator as adapted from Guildenbecher et al. (2016). The height of drop impact is varied to vary the impact We, by adjusting the syringe height. Three fluids- DI-Water, ethanol and glycerol are tested for examining the effect of viscosity on the resultant drop sizes. Results are plotted with respect to viscosity, impact We and the non-dimensional film thickness, as the fragmentation of drops is directly associated to these parameters. Results indicate that majority of the secondary droplets lie in the size range of 25 µm to 50 µm. It is also observed that the tendency of secondary atomization from crown splashing increases with the increase in We and decreases with increase in Oh.
$E_A$-cordial labeling of graphs and its implications for $A$-antimagic labeling of trees
Creators: name: Cichacz, Sylwia
Publisher: name: arXiv
Year: 2024
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics

description: If $A$ is a finite Abelian group, then a labeling $f \colon E (G) \rightarrow A$ of the edges of some graph $G$ induces a vertex labeling on $G$; the vertex $u$ receives the label $\sum_{v\in N(u)}f (v)$, where $N(u)$ is an open neighborhood of the vertex $u$. A graph $G$ is $E_A$-cordial if there is an edge-labeling such that (1) the edge label classes differ in size by at most one and (2) the induced vertex label classes differ in size by at most one. Such a labeling is called $E_A$-cordial. In the literature, so far only $E_A$-cordial labeling in cyclic groups has been studied.
 The corresponding problem was studied by Kaplan, Lev and Roditty. Namely, they introduced $A^*$-antimagic labeling as a generalization of antimagic labeling \cite{ref_KapLevRod}. Simply saying, for a tree of order $|A|$ the $A^*$-antimagic labeling is such $E_A$-cordial labeling that the label $0$ is prohibited on the edges.
 In this paper, we give necessary and sufficient conditions for paths to be $E_A$-cordial for any cyclic $A$. We also show that the conjecture for $A^*$-antimagic labeling of trees posted in \cite{ref_KapLevRod} is not true.
sj-pdf-2-sci-10.1177_00368504211035597 – Supplemental material for Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus)
Creators: name: Tian, Hai-feng
name: Hu, Qiao-mu
name: Li, Zhong
Publisher: name: SAGE Journals
Year: 2021
Subjects: Biological Sciences not elsewhere classified

description: Supplemental material, sj-pdf-2-sci-10.1177_00368504211035597 for Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus) by Hai-feng Tian, Qiao-mu Hu and Zhong Li in Science Progress
Supplemental Material, sj-docx-1-psg-10.1177_22925503211024753 - Single Digit Index Finger Amputation—To Replant or Not?
Creators: name: Thibedeau, Marshall
name: Ramji, Maleka
name: McKenzie, Madeleine
name: Yeung, Justin
name: Nickerson, Duncan Alexander
Publisher: name: SAGE Journals
Year: 2021
Subjects: subject: 110323 Surgery
subject: FOS: Clinical medicine

description: Supplemental Material, sj-docx-1-psg-10.1177_22925503211024753 for Single Digit Index Finger Amputation—To Replant or Not? by Marshall Thibedeau, Maleka Ramji, Madeleine McKenzie, Justin Yeung and Duncan Alexander Nickerson in Plastic Surgery