cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Metal halide thermoelectrics: prediction of high-performance CsCu2I3
Creators: name: Park, Jong Woong
name: Jung, Young-Kwang
name: Walsh, Aron
Publisher: name: arXiv
Year: 2023
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: Thermoelectric devices can directly convert waste heat into electricity, which makes them an important clean energy technology. The underlying materials performance can be evaluated by the dimensionless figure of merit ZT. Metal halides are attractive candidates due to their chemical flexibility and ease of processing; however, the maximum ZT realized (ZT = 0.15) falls far below the level needed for commercialization (ZT > 1). Using a first-principles procedure we assess the thermoelectric potential of copper halide CsCu2I3, which features 1D Cu-I connectivity. The n-type crystal is predicted to exhibit a maximum ZT of 2.2 at 600 K along the b-axis. The strong phonon anharmonicity of this system is shown by locally stable non-centrosymmetric Amm2 structures that are averaged to form the observed centrosymmetric Cmcm space group. Our work provides insights into the structure-property relations in metal halide thermoelectrics and suggests a path forward to engineer higher-performance heat-to-electricity conversion.
description: 12 pages, 10 figures
Microwave-induced excess quasiparticles in superconducting resonators measured through correlated conductivity fluctuations
Creators: name: de Visser, P. J.
name: Baselmans, J. J. A.
name: Yates, S. J. C.
name: Diener, P.
name: Endo, A.
name: Klapwijk, T. M.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We have measured the number of quasiparticles and their lifetime in aluminium superconducting microwave resonators. The number of excess quasiparticles below 160 mK decreases from 72 to 17 $μ$m$^{-3}$ with a 6 dB decrease of the microwave power. The quasiparticle lifetime increases accordingly from 1.4 to 3.5 ms. These properties of the superconductor were measured through the spectrum of correlated fluctuations in the quasiparticle system and condensate of the superconductor, which show up in the resonator amplitude and phase respectively. Because uncorrelated noise sources vanish, fluctuations in the superconductor can be studied with a sensitivity close to the vacuum noise.
title: Evaluating Mass Spectrometry Approaches for Identifying Proteomic Changes in Maternal Urine in Pregnancy and Labour
Creators: name: , Sonali
Publisher: name: Graduate Studies
Year: 2025
Subjects: subject: Preterm birth
subject: Pregnancy
subject: Labour
subject: Data-dependent acquisition
subject: Data-independent acquisition
subject: Mass spectrometry
subject: Proteomics
subject: Biology--Molecular
subject: Education--Sciences
subject: Biochemistry

description: Preterm birth (PTB) is a critical global health issue, contributing to significant neonatal mortality and long-term complications. Almost half of the preterm births occur due to spontaneous preterm labour (PTL). Despite substantial research efforts, our knowledge of labour onset and progression leading to either preterm and term delivery is limited. With the intent of exploring more about the physiological processes of pregnancy and labour, we performed label-free shotgun proteomics on maternal urinary samples using two different modes of mass spectrometer – data- dependent acquisition (DDA) and data-independent acquisition (DIA). The goal was to assess what approach resulted in high quality and reproducible data by detecting and quantifying large number of proteins for a discovery study using urine samples. Comparative analysis of DDA and DIA demonstrated superior performance of DIA. DIA resulted in better data in terms of consistency of protein detection, retaining higher number of total proteins and uniquely detected proteins for downstream analysis and presence of fewer number of missing values. To investigate further, we expanded our discovery cohort and performed DIA proteomics. Proteomics data analysis revealed elevated levels of Defensin alpha 1 (DEFA1) and Kallikrein 1 (KLK1) in the Labour group while the Non Labour group showed elevated levels of Endosialin (CD248) and Leucine-rich alpha-2-glycoprotein (LRG1). To identify the proteomics changes with respect to gestational age, we compared Preterm Non Labour (PTNL) group with Term Non Labour (TNL) group. The PTNL group was found significantly enriched in Fatty acid binding protein 5 (FABP5) and Keratin type 1 cytoskeletal 16 (KRT16) while TNL group showed significant enrichment in Calmodulin (CALM1). Differential levels of aforementioned proteins seem to be associated with labour and changes with gestational age. Future studies are required to validate the observed trends in protein abundances in the study groups and to determine the potential of these proteins for prediction of preterm labour or preterm birth.
Structural basis of suppression of host translation termination by Moloney Murine Leukemia Virus
Creators: name: Tang, Xuhua
name: Zhu, Yiping
name: Baker, Stacey L.
name: Bowler, Matthew W.
name: Chen, Benjamin Jieming
name: Chen, Chen
name: Hogg, J. Robert
name: Goff, Stephen P.
name: Song, Haiwei
Publisher: name: Columbia University
Year: 2016
Subjects: Mouse leukemia viruses
Reverse transcriptase
Molecular biology
Virology
Biophysics
Genetic translation

description: Retroviral reverse transcriptase (RT) of Moloney murine leukemia virus (MoMLV) is expressed in the form of a large Gag–Pol precursor protein by suppression of translational termination in which the maximal efficiency of stop codon read-through depends on the interaction between MoMLV RT and peptidyl release factor 1 (eRF1). Here, we report the crystal structure of MoMLV RT in complex with eRF1. The MoMLV RT interacts with the C-terminal domain of eRF1 via its RNase H domain to sterically occlude the binding of peptidyl release factor 3 (eRF3) to eRF1. Promotion of read-through by MoMLV RNase H prevents nonsense-mediated mRNA decay (NMD) of mRNAs. Comparison of our structure with that of HIV RT explains why HIV RT cannot interact with eRF1. Our results provide a mechanistic view of how MoMLV manipulates the host translation termination machinery for the synthesis of its own proteins.
Derivation of the Ghost Gutzwiller Approximation from Quantum Embedding principles: the Ghost Density Matrix Embedding Theory
Creators: name: Lanatà, Nicola
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Establishing the underlying links between the diverse landscape of theoretical frameworks for simulating strongly correlated matter is crucial for advancing our understanding of these systems. In this work, we focus on the Ghost Gutzwiller Approximation (gGA), an extension of the Gutzwiller Approximation (GA) based on the variational principle. We derive a framework called "Ghost Density Matrix Embedding Theory" (gDMET) from quantum embedding (QE) principles similar to those in Density Matrix Embedding Theory (DMET), which reproduces the gGA equations for multi-orbital Hubbard models with a simpler implementation. This derivation highlights the crucial role of the ghost degrees of freedom, not only as an extension to the GA, but also as the key element in establishing a consistent conceptual connection between DMET and the gGA. This connection further elucidates how gGA overcomes the systematic accuracy limitations of standard GA and achieves results comparable to Dynamical Mean Field Theory (DMFT). Furthermore, it offers an alternative interpretation of the gGA equations, fostering new ideas and generalizations.
description: 24 pages, 3 figures
title: Parallels and Divergences in Multisystem Proteinopathy Genes: Stress Granules, Autophagy, and Myogenic Deficits
Creators: name: Pontifex, Carly Sabine
Publisher: name: Graduate Studies
Year: 2025
Subjects: subject: Multisystem Proteinopathy
subject: T-cell Intracellular Antigen1
subject: Sequestosome1
subject: Valosin-Containing Protein
subject: lysosome
subject: autophagosome
subject: autophagic flux
subject: single nucleus RNAseq
subject: myogenesis
subject: NF-ΚB
subject: autophagy
subject: digenic modifier
subject: Neuroscience

description: Multisystem Proteinopathy (MSP) is a disease that causes some combination of inclusion body myopathy with rimmed vacuoles, Paget’s disease of bone, and ALS/FTD. Several different genes give rise to the unique phenotypic expression of MSP. Given the variety of genes that cause MSP and the specificity of the phenotype and tissue involvement, we asked; what are the unifying pathogenic features of MSP? To address this, we examined three areas of interest: stress granules, autophagy, and myogenesis. The currently identified roster of MSP genes have several structural and functional commonalities which fall into two categories: LC3B-intracting domain containing autophagy adaptors (SQSTM1, VCP, OPTN) and prion-like domain containing stress granule proteins (HNRNPA2B1, HNRNPA1, MATR3, TIA1). Previous studies identified that a non-pathogenic variant of the non-classical MSP protein, TIA1 N357S , can act as a phenotype modifier with SQSTM1P392L leading to distal muscle weakness rather than proximal muscle weakness seen with monogenic SQSTM1 mutations. Here we show that the same TIA1 variant is able to act as a modifier with VCP R159H to produce the same distal weakness. We established three major findings: 1) The non-classical MSP gene TIA1 N357S can modify the myopathy phenotype of both VCP and SQSTM1 to produce distal rather than proximal muscle weakness at the onset of disease, and that TIA1b expression drives the increase of TIA1 expression in diseased muscle and also fails to colocalize with SQSTM1—implying that upregulation of TIA1b is important for muscle stress response and also that TIA1b stress granules have reduced clearance by autophagy. 2) VCP and SQSTM1 both exhibit lysosome accumulation, which may be an emergent feature of inclusion body myopathies. 3) Impaired myogenesis via resistance to the master regulator of myogenesis MyoD, is a feature of MSP.
U-TILISE: A Sequence-to-sequence Model for Cloud Removal in Optical Satellite Time Series
Creators: name: Stucker, Corinne
name: Garnot, Vivien Sainte Fare
name: Schindler, Konrad
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Image and Video Processing (eess.IV)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Satellite image time series in the optical and infrared spectrum suffer from frequent data gaps due to cloud cover, cloud shadows, and temporary sensor outages. It has been a long-standing problem of remote sensing research how to best reconstruct the missing pixel values and obtain complete, cloud-free image sequences. We approach that problem from the perspective of representation learning and develop U-TILISE, an efficient neural model that is able to implicitly capture spatio-temporal patterns of the spectral intensities, and that can therefore be trained to map a cloud-masked input sequence to a cloud-free output sequence. The model consists of a convolutional spatial encoder that maps each individual frame of the input sequence to a latent encoding; an attention-based temporal encoder that captures dependencies between those per-frame encodings and lets them exchange information along the time dimension; and a convolutional spatial decoder that decodes the latent embeddings back into multi-spectral images. We experimentally evaluate the proposed model on EarthNet2021, a dataset of Sentinel-2 time series acquired all over Europe, and demonstrate its superior ability to reconstruct the missing pixels. Compared to a standard interpolation baseline, it increases the PSNR by 1.8 dB at previously seen locations and by 1.3 dB at unseen locations.
description: Published in the IEEE Transactions on Geoscience and Remote Sensing
Sphyraena jello Cuvier 1829
Creators: name: Zainal Abidin, Danial Hariz
name: Lavoué, Sébastien
name: Mohd Abu Hassan Alshari, Norli Fauzani
name: Mohd. Nor, Siti Azizah
name: A. Rahim, Masazurah
name: Mohammed Akib, Noor Adelyna
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Perciformes
Sphyraenidae
Sphyraena
Sphyraena jello

description: Sphyraena jello Cuvier, 1829 Material examined. MALAYSIA • 1, 211 mm TL; Kedah State, Merbok, Pompang Sungai Merbok; 05.664°N, 100.381°E; 6 Dec. 2018; Danial H. Zainal Abidin, Norli F.M.A.H. Alshari leg.; USMFC (62) 00004. • 1, 143 mm TL; Kedah State, Kampung Batu Lintang, Pompang Batu Lintang; 05.625°N, 100.394°E; 17 Jul. 2019; Sébastien Lavoué leg.; USMFC (62) 00007.
description: Published as part of Zainal Abidin, Danial Hariz, Lavoué, Sébastien, Mohd Abu Hassan Alshari, Norli Fauzani, Mohd. Nor, Siti Azizah, A. Rahim, Masazurah & Mohammed Akib, Noor Adelyna, 2021, Ichthyofauna of Sungai Merbok Mangrove Forest Reserve, northwest Peninsular Malaysia, and its adjacent marine waters, pp. 601-631 in Check List 17 (2) on page 625, DOI: 10.15560/17.2.601
The CUL4-DDB1 ubiquitin ligase complex controls adult and embryonic stem cell differentiation and homeostasis
Creators: name: Gao, Jie
name: Buckley, Shannon M.
name: Cimmino, Luisa
name: Guillamot, Maria
name: Strikoudis, Alexandros
name: Cang, Yong
name: Goff, Stephen P.
name: Aifantis, Iannis
Publisher: name: Columbia University
Year: 2015
Subjects: Ubiquitin
Molecular biology
Stem cells
Cell differentiation
Hematopoiesis
Regenerative medicine

description: Little is known on post-transcriptional regulation of adult and embryonic stem cell maintenance and differentiation. Here we characterize the role of Ddb1, a component of the CUL4-DDB1 ubiquitin ligase complex. Ddb1 is highly expressed in multipotent hematopoietic progenitors and its deletion leads to abrogation of both adult and fetal hematopoiesis, targeting specifically transiently amplifying progenitor subsets. However, Ddb1 deletion in non-dividing lymphocytes has no discernible phenotypes. Ddb1 silencing activates Trp53 pathway and leads to significant effects on cell cycle progression and rapid apoptosis. The abrogation of hematopoietic progenitor cells can be partially rescued by simultaneous deletion of Trp53. Conversely, depletion of DDB1 in embryonic stem cell (ESC) leads to differentiation albeit negative effects on cell cycle and apoptosis. Mass spectrometry reveals differing protein interactions between DDB1 and distinct DCAFs, the substrate recognizing components of the E3 complex, between cell types. Our studies identify CUL4-DDB1 complex as a novel post-translational regulator of stem and progenitor maintenance and differentiation.
FROM CLICKS TO CHOICES: THE INFLUENCE OF SOCIAL MEDIA ON MIGRATION DECISIONS
Creators: name: Wame, Mensah Agyemang
name: Nana, Yaa Asantewaa Ampofo
Publisher: name: AMERICAN SERIAL
Year: 2024
Subjects: migration
social media
rural-urban migration
integration
information dissemination

description: The advent of social media has profoundly shaped contemporary migration patterns, particularly in facilitating rural-to-urban migration dynamics. Drawing on insights from Awumbila et al. (2017), Dekker et al. (2018), Alencar (2018), and Hidayati (2019), this study investigates the transformative role of social media in driving migration trends on a global scale. By providing migrants with access to abundant information and networking opportunities, social media platforms have emerged as pivotal tools influencing migration decision-making processes. The integration of social media into migration dynamics has not only facilitated the dissemination of information about destination conditions but also fostered connections and integration efforts among migrants. As highlighted by Dekker et al. (2018), social media minimizes migration costs and risks while enhancing migrants' access to relevant information, thus serving as a catalyst for migration flows. Moreover, Hidayati (2019) underscores the significance of social media networks in facilitating integration and connection opportunities for migrants, thereby fostering a sense of community and support both pre- and post-migration. By synthesizing insights from multiple studies, this research sheds light on the multifaceted impact of social media on migration dynamics, highlighting its potential to reshape spatial mobility patterns and influence settlement decisions.
Products of sequentially pseudocompact spaces
Creators: name: Lipparini, Paolo
Publisher: name: arXiv
Year: 2012
Subjects: subject: General Topology (math.GN)
subject: FOS: Mathematics
subject: 54D20, 54B10

description: We show that the product of any number of sequentially pseudocompact topological spaces is still sequentially pseudocompact. The definition of sequential pseudocompactness can be given in (at least) two ways: we show their equivalence. Some of the results of the present note already appeared in A. Dow, J. R. Porter, R. M. Stephenson, R. G. Woods, Spaces whose pseudocompact subspaces are closed subsets, Appl. Gen. Topol. 5 (2004), 243-264.
description: 8 pages v.2 added a reference; v.3 corrected a misprint
title: Proceedings of the 8th International Conference of STEM in Education (STEM 2024)
title: Proceedings of STEM 2024
titleType: AlternativeTitle
Creators: name: Pratim Sengupta
name: Clark, Douglas
name: Lock, Jennifer
Publisher: name: University of Calgary
Year: 2024
Subjects: subject: STEM Education
subject: Learning Sciences
subject: Arts and STEM Education
subject: Transdisciplinarity

description: NA
description: Proceedings of the 8th International Conference of STEM in Education (STEM 2024)
A new method with an explant culture of the utricle for assessing the influence of exposure to low-frequency noise on the vestibule
Creators: name: Ohgami, Nobutaka
name: He, Tingchao
name: Oshino-Negishi, Reina
name: Gu, Yishuo
name: Li, Xiang
name: Kato, Masashi
Publisher: name: Taylor & Francis
Year: 2020
Subjects: Biophysics
Cell Biology
Molecular Biology
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Developmental Biology

description: Health risks attributed to low-frequency noise (LFN) exposure are a serious global issue. Therefore, the development of a method for a prevention based upon risk assessments for LFN is important. Previously in vivo exposure of mice to LFN at 100 Hz, 95 dB for 1 hr produced imbalance with breakage of the otoconial membrane, which covers hair cells as well as impaired activity of hair cells in the vestibule. However, methods for inhibition of LFN-mediated imbalance have not been developed. At present, there are no apparent techniques available with in vitro or ex vivo assessments to evaluate LFN-mediated imbalance by direct administration of preventive chemicals into the vestibule. Our findings demonstrated the usefulness of an explant culture of the utricle with a fluorescent styryl dye, FM1-43FX. In addition, examination of the morphology of the otoconial membrane with explant cultures of utricles was conducted to determine the risk of LFN. Ex vivo exposure of the utricle to LFN at 100 Hz, 95 dB for 1 hr induced breaks in the otoconial membrane as well as decreased uptake of FM1-43FX in hair cells. Taken together, the results of this study provide a novel technique for assessing the risk of LFN exposure using an ex vivo experiment.
Observation of anomalous diffusion and fractional self-similarity in one dimension
Creators: name: Sagi, Yoav
name: Brook, Miri
name: Almog, Ido
name: Davidson, Nir
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We experimentally study anomalous diffusion of ultra-cold atoms in a one dimensional polarization optical lattice. The atomic spatial distribution is recorded at different times and its dynamics and shape are analyzed. We find that the width of the cloud exhibits a power-law time dependence with an exponent that depends on the lattice depth. Moreover, the distribution exhibits fractional self-similarity with the same characteristic exponent. The self-similar shape of the distribution is found to be well-fitted by a Lévy distribution, but with a characteristic exponent that differs from the temporal one. Numerical simulations suggest that this may be due to correlations between the atoms' velocity and flight duration.
description: 4 pages, 5 figures
Sphyraena qenie Klunzinger 1870
Creators: name: Zainal Abidin, Danial Hariz
name: Lavoué, Sébastien
name: Mohd Abu Hassan Alshari, Norli Fauzani
name: Mohd. Nor, Siti Azizah
name: A. Rahim, Masazurah
name: Mohammed Akib, Noor Adelyna
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Perciformes
Sphyraenidae
Sphyraena
Sphyraena qenie

description: Sphyraena qenie Klunzinger, 1870 Figure 4M Material examined. MALAYSIA • 3, 337– 359 mm TL; Kedah State, Kuala Kedah, Kuala Muda Whispering Market; 05.578°N, 100.341°E; 4 Mar. 2019; Danial H. Zainal Abidin, Norli F.M.A.H. Alshari leg.; USMFC (62) 00005.
description: Published as part of Zainal Abidin, Danial Hariz, Lavoué, Sébastien, Mohd Abu Hassan Alshari, Norli Fauzani, Mohd. Nor, Siti Azizah, A. Rahim, Masazurah & Mohammed Akib, Noor Adelyna, 2021, Ichthyofauna of Sungai Merbok Mangrove Forest Reserve, northwest Peninsular Malaysia, and its adjacent marine waters, pp. 601-631 in Check List 17 (2) on page 625, DOI: 10.15560/17.2.601
Measurement of the cross-sections of the electroweak and total production of a $Z γ$ pair in association with two jets in $pp$ collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector
Creators: name: ATLAS Collaboration
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: This Letter presents the measurement of the fiducial and differential cross-sections of the electroweak production of a $Z γ$ pair in association with two jets. The analysis uses 140 fb$^{-1}$ of LHC proton-proton collision data taken at $\sqrt{s}$=13 TeV recorded by the ATLAS detector during the years 2015-2018. Events with a $Z$ boson candidate decaying into either an $e^+e^-$ or $μ^+ μ^-$ pair, a photon and two jets are selected. The electroweak component is extracted by requiring a large dijet invariant mass and a large rapidity gap between the two jets and is measured with an observed and expected significance well above five standard deviations. The fiducial $pp \rightarrow Z γjj$ cross-section for the electroweak production is measured to be 3.6 $\pm$ 0.5 fb. The total fiducial cross-section that also includes contributions where the jets arise from strong interactions is measured to be $16.8^{+2.0}_{-1.8}$ fb. The results are consistent with the Standard Model predictions. Differential cross-sections are also measured using the same events and are compared with parton-shower Monte Carlo simulations. Good agreement is observed between data and predictions.
description: 44 pages in total, author list starting page 27, 6 figures, 3 tables, submitted to PLB. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2018-36/
Trichosomus trachinoides
Creators: name: Zainal Abidin, Danial Hariz
name: Lavoué, Sébastien
name: Mohd Abu Hassan Alshari, Norli Fauzani
name: Mohd. Nor, Siti Azizah
name: A. Rahim, Masazurah
name: Mohammed Akib, Noor Adelyna
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Brachyceridae
Trichosomus
Trichosomus trachinoides

description: Trichosomus trachinoides (Cuvier, 1829) Material examined. MALAYSIA • 1, 39 mm TL; Kedah State, Kampung Batu Lintang, Pompang Batu Lintang; 05.625°N, 100.394°E; 17 Jul. 2019; Sébastien Lavoué leg.; USMFC (115) 00001. • 1, 40 mm TL; Kedah State, Kampung Batu Lintang, Pompang Batu Lintang; 05.625°N, 100.394°E; 17 Jul. 2019; Sébastien Lavoué leg.; USMFC (115) 00002.
description: Published as part of Zainal Abidin, Danial Hariz, Lavoué, Sébastien, Mohd Abu Hassan Alshari, Norli Fauzani, Mohd. Nor, Siti Azizah, A. Rahim, Masazurah & Mohammed Akib, Noor Adelyna, 2021, Ichthyofauna of Sungai Merbok Mangrove Forest Reserve, northwest Peninsular Malaysia, and its adjacent marine waters, pp. 601-631 in Check List 17 (2) on page 626, DOI: 10.15560/17.2.601
Potent and reversible lentiviral vector restriction in murine induced pluripotent stem cells
Creators: name: Geis, Franziska K.
name: Galla, Melanie
name: Hofmann, Dirk
name: Kuehle, Johannes
name: Zychlinski, Daniela
name: Maetzig, Tobias
name: Schott, Juliane W.
name: Schwarzer, Adrian
name: Gofnet, Christine
name: Goff, Stephen P.
name: Schambach, Axel
Publisher: name: Columbia University
Year: 2017
Subjects: Lentiviruses
Stem cells
Peptidylprolyl isomerase
Retroviruses

description: Background
Retroviral vectors are derived from wild-type retroviruses, can be used to study retrovirus-host interactions and are effective tools in gene and cell therapy. However, numerous cell types are resistant or less permissive to retrovirus infection due to the presence of active defense mechanisms, or the absence of important cellular host co-factors. In contrast to multipotent stem cells, pluripotent stem cells (PSC) have potential to differentiate into all three germ layers. Much remains to be elucidated in the field of anti-viral immunity in stem cells, especially in PSC.

Results
In this study, we report that transduction with HIV-1-based, lentiviral vectors (LV) is impaired in murine PSC. Analyses of early retroviral events in induced pluripotent stem cells (iPSC) revealed that the restriction is independent of envelope choice and does not affect reverse transcription, but perturbs nuclear entry and proviral integration. Proteasomal inhibition by MG132 could not circumvent the restriction. However, prevention of cyclophilin A (CypA) binding to the HIV-1 capsid via use of either a CypA inhibitor (cyclosporine A) or CypA-independent capsid mutants improved transduction. In addition, application of higher vector doses also increased transduction. Our data revealed a CypA mediated restriction in iPSC, which was acquired during reprogramming, associated with pluripotency and relieved upon subsequent differentiation.

Conclusions
We showed that murine PSC and iPSC are less susceptible to LV. The block observed in iPSC was CypA-dependent and resulted in reduced nuclear entry of viral DNA and proviral integration. Our study helps to improve transduction of murine pluripotent cells with HIV-1-based vectors and contributes to our understanding of retrovirus-host interactions in PSC.
title: The RAD51C-XRCC3 Homologous Recombination Repair Complex: Structural Basis for its Interactions and Cancer Associated Mutations
Creators: name: Pepper, Jordan Tan
Publisher: name: Cumming School of Medicine
Year: 2025
Subjects: subject: RAD51 Paralog
subject: Homologous Recombination
subject: DNA Repair
subject: Protein
subject: DNA
subject: SAXS
subject: XL-MS
subject: Structural Biology
subject: Biology--Cell
subject: Biochemistry

description: The RAD51 paralogs are crucial proteins involved in the repair of double-stranded DNA breaks (DSBs) via homologous recombination repair (HRR). There are six human RAD51 paralogs, RAD51B, RAD51C, RAD51D, XRCC2, XRCC3, and SWSAP1, and mutations in these genes are associated with cancer and other diseases. The RAD51 paralogs operate as discrete multi-protein complexes whose functional roles and structures are not fully understood. A key RAD51 paralog complex is the RAD51C-XRCC3 heterodimer (CX3), which is the focus of this thesis. I used biochemical, structural, and computational approaches to 1) profile disease and cancer-linked missense mutations found in RAD51C in the context of CX3, 2) determine the structural details of human CX3, and 3) identify and characterize potential CX3 protein interaction partners. I used the Alvinella pompejana ortholog of CX3 to investigate the impact of 5 different cancer associated missense mutations of human RAD51C on protein stability and biochemistry using heterologous expression and purification, mass photometry, fluorescence polarization assays, molecular dynamics simulations, and in silico mutation stability calculators. To investigate human CX3, I used a combination of small-angle X-ray scattering, cross-linking mass-spectrometry, structural prediction models and analysis to uncover features of how RAD51 family members interact with one another. Finally, I used affinity-purification and mass-spectrometry proteomics to detect possible CX3 protein-protein interaction partners, which I then attempted to verify using fluorescence-detection size-exclusion chromatography, with post-hoc analysis of candidate interaction partners using AlphaFold 3 and in silico calculation of interprotein energetics and affinity. From this work, I uncover insights in the structure of the CX3 complex, its possible roles in HRR, and a pathway towards characterizing it in association with interaction partners.
A Quasar Catalog with Simultaneous UV, Optical and X-ray Observations by Swift
Creators: name: Wu, Jian
name: Berk, Daniel Vanden
name: Grupe, Dirk
name: Koch, Scott
name: Gelbord, Jonathan
name: Schneider, Donald P.
name: Gronwall, Caryl
name: Wesolowski, Sarah
name: Porterfield, Blair L.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We have compiled a catalog of optically-selected quasars with simultaneous observations in UV/optical and X-ray bands by the Swift Gamma Ray Burst Explorer. Objects in this catalog are identified by matching the Swift pointings with the Sloan Digital Sky Survey Data Release 5 quasar catalog. The final catalog contains 843 objects, among which 637 have both UVOT and XRT observations and 354 of which are detected by both instruments. The overall X-ray detection rate is ~60% which rises to ~85% among sources with at least 10 ks of XRT exposure time. We construct the time-averaged spectral energy distribution for each of the 354 quasars using UVOT photometric measurements and XRT spectra. From model fits to these SEDs, we find that the big blue bump contributes about 0.3 dex to the quasar luminosity. We re-visit the alpha_ox-L_uv relation by selecting a clean sample with only type 1 radio-quiet quasars; the dispersion of this relation is reduced by at least 15% compared to studies that use non-simultaneous UV/optical and X-ray data. We only found a weak correlation between L/L_Edd and alpha_uv. We do not find significant correlations between alpha_x and alpha_ox, alpha_ox and alpha_uv, and alpha_x and Log L(0.3-10 keV). The correlations between alpha_uv and alpha_x, alpha_ox and alpha_x, alpha_ox and alpha_uv, L/L_Edd and alpha_x, and L/L_Edd and alpha_ox are stronger amongst low-redshift quasars, indicating that these correlations are likely driven by the changes of SED shape with accretion state.
description: 63 pages, 22 figures, accepted by ApJS
Restriction of HIV-1-based lentiviral vectors in adult primary marrow-derived and peripheral mobilized human CD34+ hematopoietic stem and progenitor cells occurs prior to viral DNA integration
Creators: name: Griffin, Daniel
name: Goff, Stephen P.
Publisher: name: Columbia University
Year: 2016
Subjects: Gene therapy
Lentiviruses
Stem cells
HIV infections
Molecular biology

description: Background
Gene therapy is currently being attempted using a number of delivery vehicles including lentiviral-based vectors. The delivery and insertion of a gene using lentiviral-based vectors involves multiple discrete steps, including reverse transcription of viral RNA into DNA, nuclear entry, integration of viral DNA into the host genome and expression of integrated genes. Transduction of murine stem cells by the murine leukemia viruses is inefficient because the expression of the integrated DNA is profoundly blocked. Transduction of human stem cells by lentivirus vectors is also inefficient, but the cause and specific part of the retroviral lifecycle where this block occurs is unknown.

Results
Here we demonstrate that the dominant point of restriction of an HIV-1-based lentiviral vector in adult human hematopoietic stem and progenitor cells (HSPCs) from bone marrow and also those obtained following peripheral mobilization is prior to viral DNA integration. We specifically show that restriction of HSPCs to an HIV-1-based lentiviral vector is prior to formation of nuclear DNA forms.

Conclusions
Murine restriction of MLV and human cellular restriction of HIV-1 are fundamentally different. While murine restriction of MLV occurs post integration, human restriction of HIV-1 occurs before integration.
“Her knowledge of flora and fauna came mostly from fiction" : the adolescent as green subject in three Canadian young adult novels
Creators: name: Taylor, Karen Ann
Publisher: name: University of British Columbia
Year: 2012

description: Using the lens of ecocriticism, this thesis focuses on the literary portrayal of nature in three contemporary realistic Canadian young adult novels: Mistik Lake by Martha Brooks, The Lightkeeper’s Daughter by Iain Lawrence, and The Uninvited by Tim Wynne-Jones. Ecocriticism—the critical and political inquiry into the discourses influencing our ideas of nature—questions our understanding of and relationship to the environment and to ecological concerns as portrayed in literary texts. As such, this research takes a green cultural-studies approach and draws upon sources from environmentalist criticism and literary studies to investigate the ways in which the three novels characterize the natural world, the quality of the relationship between the adolescent and nature, and how this relationship might influence readers’ attitudes toward the environment. The resultant explication describes the ways the narratives construct the natural world and produce the adolescent as green subject and provides insight into the young adult’s indeterminate and ambiguous relationship to the natural world.
title: A Framework for Semantic Enterprise Transformations
Creators: name: Reimer, Timothy James
Publisher: name: Graduate Studies
Year: 2025
Subjects: subject: semantic transformation
subject: microservice orchestration
subject: natural language queries
subject: choreographed microservices
subject: orchestrated microservices
subject: graph databases
subject: traversal patterns
subject: natural language processing
subject: Computer Science

description: Semantic transformation within message exchange between heterogenous systems provides a challenge for any enterprise. The primary reason for this challenge is that the required transformations are based on arbitrary codes that do not adhere to any grammatical or linguistic structure or rules. These codes are assigned to describe an entity or attribute such as order type or equipment ID. In any message exchange, the meaning of the data must be preserved. This is done today by applying translation lookups to simple cross-reference tables or files scattered across the computing landscape for each application use case. Such tables are maintained manually and can cause processing delays due to failed transactions that rely on semantic transformation values. The research presented in this dissertation introduces generic transformation patterns and applies these patterns to an underlying graph structure. By generalizing semantic transformations through patterns and graphs (Chapter 5), it is possible not only to determine a traversal path to find a corresponding code value, but to predict missing nodes through the use of graph embeddings (Chapter 7). The presented architecture is based on microservices. This allows for horizontal and vertical scalability and provides an abstraction to the transformation query such that various forms of queries can be submitted and semantically transformed without changes to the underlying traversal algorithms. The thesis demonstrates two scenarios. The first is a natural language scenario (Chapter 6), and the second is an event stream scenario. In the natural language scenario, a natural language query is provided, and the system returns the expected code-based results. This use case demonstrates the benefits of integrating NLP capabilities for users to search and find transformation codes via a web front-end. The second scenario demonstrates an IoT case where components of sensor data need to be enriched so that downstream data analytics applications can deliver the correct KPIs and dashboards. The value of this research is demonstrated by a cost analysis for failed transactions (Chapter 8) and by the benefits the presented semantic transformation architecture would provide to corporations. This research therefore underlines the importance of incorporating semantic transformations into organizations’ overall data architecture and strategy.
Right-handed Sneutrino Inflation in SUSY B-L with Inverse Seesaw
Creators: name: Khalil, Shaaban
name: Sil, Arunansu
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We propose a scenario for realizing inflation in the framework of supersymmetric B-L extension of the Standard Model. We find that one of the associated right-handed sneutrinos (the superpartner of the Standard Model singlet fermion) can provide a new non-trivial inflationary trajectory at tree level (therefore breaking B-L during inflation). As soon as the inflation ends, the right-handed sneutrino falls into the supersymmetric vacuum, with a vanishing vacuum expectation value, so that B-L symmetry is restored. In this class of models, the B-L gauge symmetry will be radiatively broken at a TeV scale and light neutrino masses are generated through the inverse seesaw mechanism.
description: 5 pages, 2 figures; version to be published in Phys. Rev. D
Nuclear matrix protein Matrin 3 is a regulator of ZAP-mediated retroviral restriction
Creators: name: Erazo, Angela
name: Goff, Stephen P.
Publisher: name: Columbia University
Year: 2015
Subjects: Gene expression
Nuclear matrix
Retroviruses
Antiretroviral agents
Molecular biology
Biochemistry

description: Background
Matrin 3 is a nuclear matrix protein involved in multiple nuclear processes. In HIV-1 infection, Matrin 3 serves as a Rev cofactor important for the cytoplasmic accumulation of HIV-1 transcripts. ZAP is a potent host restriction factor of multiple viruses including retroviruses HIV-1 and MoMuLV. In this study we sought to further characterize Matrin 3 functions in the regulation of HIV gene expression.

Results
Here we describe a function for Matrin 3 as a negative regulator of the ZAP-mediated restriction of retroviruses. Mass spectrometry analysis of Matrin 3-associated proteins uncovered interactions with proteins of the ZAP degradation complex, DDX17 and EXOSC3. Coimmunoprecipitation studies confirmed Matrin 3 associations with DDX17, EXOSC3 and ZAP, in a largely RNA-dependent manner, indicating that RNA is mediating the Matrin 3 interactions with these components of the ZAP degradation complex. Silencing Matrin 3 expression caused a remarkably enhanced ZAP-driven inhibition of HIV-1 and MoMuLV luciferase reporter viruses. This effect was shared with additional nuclear matrix proteins. ZAP targets multiply-spliced HIV-1 transcripts, but in the context of Matrin 3 suppression, this ZAP restriction was broadened to unspliced and multiply-spliced RNAs.

Conclusions
Here we reveal an unprecedented role for a nuclear matrix protein, Matrin 3, in the regulation of ZAP’s antiretroviral activity. Suppressing Matrin 3 powers a heightened and broader ZAP restriction of HIV-1 gene expression. This study suggests that this ZAP regulatory mechanism is shared with additional nuclear matrix proteins.
title: Course Calendar
Creators: name: Bow Valley College
Publisher: name: Bow Valley College
Year: 2025

description: Welcome to Bow Valley College! You've made a very important decision to further your education, and our team of dedicated instructors and staff will help you get there - faster. We offer a variety of ways to learn that will accommodate your learning style - whether it's in class, at home, online, or a combination of independent learning with in-class support. We're a fast, focused, and flexible institution that's here to support you in achieving your goals! This calendar was created especially for Bow Valley College students. Inside, you'll find information on a variety of topics, including: Your program of study, its courses and future career options • Financial assistance • Important dates • Services for students and the community, such as the day care and job search • College administration • College policies, procedures and regulations At Bow Valley College, we're dedicated to helping you succeed.
Microwave-to-optical conversion in a room-temperature $^{87}$Rb vapor with frequency-division multiplexing control
Creators: name: Smith, Benjamin D.
name: Babaei, Bahar
name: Narayanan, Andal
name: LeBlanc, Lindsay J.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Coherent microwave-to-optical conversion is crucial for transferring quantum information generated in the microwave domain to optical frequencies, where propagation losses can be minimised. Among the various physical platforms that have realized coherent microwave-to-optical transduction, those that use atoms as transducers have shown rapid progress in recent years. In this paper we report an experimental demonstration of coherent microwave-to-optical conversion that maps a microwave signal to a large, tunable 550(30) MHz range of optical frequencies using room-temperature $^{87}$Rb atoms. The inhomogeneous Doppler broadening of the atomic vapor advantageously supports the tunability of an input microwave channel to any optical frequency channel within the Doppler width, along with simultaneous conversion of a multi-channel input microwave field to corresponding optical channels. In addition, we demonstrate phase-correlated amplitude control of select channels, resulting in complete extinction of one of the channels, providing an analog to a frequency domain beam splitter across five orders of magnitude in frequency. With frequency-division multiplexing capability, multi-channel conversion, and amplitude control of frequency channels, neutral atomic systems may be effective quantum processors for quantum information encoded in frequency-bin qubits.
D4.1 Synthesis of findings on the impact of institutional frameworks from the set of 15 case studies
Creators: name: Kamperman Sanders, Anselm
name: CAZZINI, FRANCESCO
name: Nunes Chaib, André
Publisher: name: Zenodo
Year: 2023

description: This report looks at the impact of institutional frameworks in the 15 case studies (CS) and aims at synthesizing the related learnings therefrom.
The CS reports show variety in terms of completeness and detail of analysis on legal and institutional matters, also a reflection of the planned ongoing CS work and the differences in CS focus with respect to analysis methods and empirical settings. To a variable degree, CS reports focus on international trade, domestic law, supply chain organization, competition, food production, investment and social as well as environmental sustainability questions. In other words, the CS reports vary in terms of in-depth consideration of legal, governance and institutional aspects.
Furthermore, several areas of law such as international environmental law and human rights law have received limited coverage in the CS. Also, other areas of law related to Intellectual Property (IP) are receiving little attention, in particular with respect to patents, trademarks, copyrights, and geographical indications. This is remarkable since such areas of law are related to competition and innovation issues and may be especially relevant in the agricultural trade and sustainability nexus in the future, considering also the forthcoming transition pathways analysis (WP5).
The report provides an initial synthesis of general findings and then a dedicated focus for every CS, based on information that is currently available.
title: Modelling, Migration, and Inversion for Angle Domain Common Image Gathers
Creators: name: Su, Ziguang
Publisher: name: Graduate Studies
Year: 2025
Subjects: subject: ADCIG
subject: Inversion
subject: Migration
subject: Modeling
subject: Seismic
subject: Geophysics
subject: FOS: Earth and related environmental sciences

description: Angle Domain Common-Image Gathers (ADCIGs) are crucial for seismic amplitude-versus-angle analysis, facilitating the prediction of lithology, fluid properties. ADCIGs, which represent angle-dependent reflectivities, are challenging to compute accurately due to the high accuracy requirements of migration and inversion algorithms. This thesis focuses on developing an new algorithm to integrate the modeling, migration, and inversion of ADCIGs. The modeling of ADCIGs is based on acoustic and elastic wave equations, and the results are compared with the exact Zoeppritz equations to validate the accuracy of the modeling process. The migration of ADCIGs is based on reflection angle extraction methods in Reverse Time Migration (RTM) fullfilling the requirement of the true amplitude migration. The inversion of ADCIGs predicts both velocity and angle-dependent reflectivity based on Full Waveform Inversion (FWI). Advances in high-performance computing and FWI algorithms have significantly improved the generation of accurate velocity models and other parameters across diverse geological settings. However, the FWI sensitivity kernel in acoustic variable-density media differs by parameterization method, and the time-domain gradient equation in velocity-density media has multiple arguments. I tested several velocity-density gradient equations in time-domain full waveform inversion (FWI) for acoustic variable-density media. Additionally, I derived a new FWI sensitivity kernel based on scattering theory, and proposed an iterative non-linear inversion method to predict both velocity and amplitude-preserved reflectivity. This method combines angle domain RTM migration with FWI. The iterative inversion method is based on time-domain FWI using the nonlinear conjugate-gradient method. The results demonstrate that the new FWI sensitivity kernel has higher resolution in certain high-dip structures compared to previously published methods, and the angle domain FWI can predict ADCIGs in shallow zones with high accuracy.