cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA‐dependent RNA polymerase (RdRp) inhibition: an in-silico analysis
Creators: name: Singh, Satyam
name: Sk, Md Fulbabu
name: Sonawane, Avinash
name: Kar, Parimal
name: Sadhukhan, Sushabhan
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: 60506 Virology

description: The sudden outburst of Coronavirus disease (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) poses a massive threat to global public health. Currently, no therapeutic drug or vaccine exists to treat COVID-19. Due to the time taking process of new drug development, drug repurposing might be the only viable solution to tackle COVID-19. RNA‐dependent RNA polymerase (RdRp) catalyzes SARS-CoV-2 RNA replication and hence, is an obvious target for antiviral drug design. Interestingly, several plant-derived polyphenols effectively inhibit the RdRp of other RNA viruses. More importantly, polyphenols have been used as dietary supplementations for a long time and played beneficial roles in immune homeostasis. We were curious to study the binding of polyphenols with SARS-CoV-2 RdRp and assess their potential to treat COVID-19. Herein, we made a library of polyphenols that have shown substantial therapeutic effects against various diseases. They were successfully docked in the catalytic pocket of RdRp. The investigation reveals that EGCG, theaflavin (TF1), theaflavin-3’-O-gallate (TF2a), theaflavin-3’-gallate (TF2b), theaflavin 3,3'-digallate (TF3), hesperidin, quercetagetin, and myricetin strongly bind to the active site of RdRp. Further, a 150-ns molecular dynamic simulation revealed that EGCG, TF2a, TF2b, TF3 result in highly stable bound conformations with RdRp. The binding free energy components calculated by the MM-PBSA also confirm the stability of the complexes. We also performed a detailed analysis of ADME prediction, toxicity prediction, and target analysis for their druggability. Overall, our results suggest that EGCG, TF2a, TF2b, TF3 can inhibit RdRp and represent an effective therapy for COVID-19. Communicated by Ramaswamy H. Sarma
31840: Help yourself
Creators: name: Project, Lockdown2020 and Beyond
Publisher: name: University of Oxford
Year: 2023
Subjects: classificationCode: 479999
subject: Other language, communication and culture not elsewhere classified

description: Now I'm not commuting anymore, I can walk the dog around our neighbourhood in the daylight. One of the things I've noticed, aside from beautiful flowers in front gardens, are boxes of items left out for people to take. Everyone seems to be having a clear out and, with no charity shops or council refuse sites open and less rubbish and recycling collections, they're finding other ways to dispose of items no longer required. Rather than being vilified, this version of skip diving is actively encouraged. The boxes mostly contain children's toys, books and DVDs, but I've seen tomato seedlings and even a wine rack (useful as most people are drinking more, or trying not to). My favourite find so far is a Haynes ownership manual for senior citizens, a timely reminder of how we are trying to protect our older family members, friends and neighbours.
Quantum Gravity Bounds on N=1 Effective Theories in Four Dimensions
Creators: name: Martucci, Luca
name: Risso, Nicolo
name: Weigand, Timo
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We propose quantum gravitational constraints on effective four-dimensional theories with N=1 supersymmetry. These Swampland constraints arise by demanding consistency of the worldsheet theory of a class of axionic, or EFT, strings whose existence follows from the Completeness Conjecture of quantum gravity. Modulo certain assumptions, we derive positivity bounds and quantization conditions for the axionic couplings to the gauge and gravitational sector at the two- and four-derivative level, respectively. We furthermore obtain general bounds on the rank of the gauge sector in terms of the gravitational couplings to the axions. We exemplify how these bounds rule out otherwise consistent effective supergravity theories as theories of quantum gravity. Our derivations of the quantum gravity bounds are tested and further motivated in concrete string theoretic settings. In particular, this leads to a sharper version of the bound on the gauge group rank in F-theory on elliptic four-folds with a smooth base, which improves the known geometrical Kodaira bounds. We furthermore provide a detailed derivation of the EFT string constraints in heterotic string compactifications including higher derivative corrections to the effective action and apply the bounds to M-theory compactifications on $G_2$ manifolds.
description: 84 pages, 2 figures; v2: typos corrected, references added
Discretization of hyperbolic type Darboux integrable equations preserving integrability
Creators: name: Habibullin, Ismagil
name: Zheltukhina, Natalya
name: Sakieva, Alfia
Publisher: name: arXiv
Year: 2011
Subjects: subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences

description: A method of integrable discretization of the Liouville type nonlinear partial differential equations is suggested based on integrals. New examples of discrete Liouville type models are presented.
description: 16 pages
Quantifying stripe rust reactions in wheat using a handheld NDVI remote sensor
Creators: name: A. Arora
name: R.K. Sharma
name: M.S. Saharan
name: K. Venkatesh
name: N. Dilbaghi
name: I. Sharma
name: R. Tiwari
Publisher: name: Gates Open Research
Year: 2019

description: Quantifying stripe rust reactions in wheat using a handheld NDVI remote sensor
Hadronic light-by-light scattering contribution to the muon $g-2$ from lattice QCD: semi-analytical calculation of the QED kernel
Creators: name: Asmussen, Nils
name: Chao, En-Hung
name: Gérardin, Antoine
name: Green, Jeremy R.
name: Hudspith, Renwick J.
name: Meyer, Harvey B.
name: Nyffeler, Andreas
Publisher: name: arXiv
Year: 2022
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: Hadronic light-by-light scattering is one of the virtual processes that causes the gyromagnetic factor $g$ of the muon to deviate from the value of two predicted by Dirac's theory. This process makes one of the largest contributions to the uncertainty of the Standard Model prediction for the muon $(g-2)$. Lattice QCD allows for a first-principles approach to computing this non-perturbative effect. In order to avoid power-law finite-size artifacts generated by virtual photons in lattice simulations, we follow a coordinate-space approach involving a weighted integral over the vertices of the QCD four-point function of the electromagnetic current carried by the quarks. Here we present in detail the semi-analytical calculation of the QED part of the amplitude, employing position-space perturbation theory in continuous, infinite four-dimensional Euclidean space. We also provide some useful information about a computer code for the numerical implementation of our approach that has been made public at https://github.com/RJHudspith/KQED.
description: 84 pages, 13 figures; text matches the published version
31844: Covid Cohort
Creators: name: Project, Lockdown2020 and Beyond
Publisher: name: University of Oxford
Year: 2023
Subjects: classificationCode: 479999
subject: Other language, communication and culture not elsewhere classified

description: I'm part of the "Covid Cohort", one of hundreds of thousands of Masters students who suddenly found their course cut short one day in March, just like my godson who didn't get to finish his BTEC, my niece her undergraduate degree or my friend's daughter, her GCSEs or even go to her prom. I'm lucky in that I'm a part-time student, so at least I (should) get to go back in September, but everyone else on my course was full-time, so I may never see them again. Over a half were international, some already too late to get home to Iran or China, and so became stuck on campus, with no part-time jobs or facilities. Those who got back to Canada or Poland in time had to self-isolate away from their families for two weeks after they landed. Meanwhile we all try to finish assignments, revising, listen to pre-recorded lectures and write dissertations, whilst worrying about what Covid-19 means to our families and our futures.
Quasar Clustering in Cosmological Hydrodynamic Simulations: Evidence for mergers
Creators: name: DeGraf, Colin
name: Di Matteo, Tiziana
name: Springel, Volker
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We examine the clustering properties of a population of quasars drawn from fully hydrodynamic cosmological simulations that directly follow black hole growth. We find that the black hole correlation function is best described by two distinct components: contributions from BH pairs occupying the same dark matter halo ('1-halo term') which dominate at scales below 300 kpc/h, and contributions from BHs occupying separate halos ('2-halo term') which dominate at larger scales. From the 2-halo BH term we find a typical host halo mass for faint-end quasars (those probed in our simulation volumes) ranging from 10^11 to a few 10^12 solar masses from z=5 to z=1 respectively (consistent with the mean halo host mass). The BH correlation function shows a luminosity dependence as a function of redshift, though weak enough to be consistent with observational constraints. At small scales, the high resolution of our simulations allows us to probe the 1-halo clustering in detail, finding that the 1-halo term follows an approximate power law, lacking the characteristic decrease in slope at small scales found in 1-halo terms for galaxies and dark matter. We show that this difference is a direct result of a boost in the small-scale quasar bias caused by galaxies hosting multiple quasars (1-subhalo term) following a merger event, typically between a large central subgroup and a smaller, satellite subgroup hosting a relatively small black hole. We show that our predicted small-scale excess caused by such mergers is in good agreement with both the slope and amplitude indicated by recent small-scale measurements. Finally, we note the excess to be a strong function of halo mass, such that the observed excess is well matched by the multiple black holes of intermediate mass (10^7-10^8 solar masses) found in hosts of 4-8*10^11 solar masses, a range well probed by our simulations.
description: 12 pages, 10 figures. Submitted to MNRAS
31846: Exercise
Creators: name: Project, Lockdown2020 and Beyond
Publisher: name: University of Oxford
Year: 2023
Subjects: classificationCode: 479999
subject: Other language, communication and culture not elsewhere classified

description: With exercise limited to an hour near to home, once a day, and two dogs to walk separately, we've been looking for other ways to keep our fitness levels up. We haven't yet succumbed to the 9am Joe Wicks workout that the nation's schoolchildren have taken to en masse. instead I roll out my yoga mat every day at 5pm and do my practice listening to the Government's briefing. i'd like to think it keeps me positive through the bad news, whilst also ironing out those knots in my shoulders from hunching over my laptop all day. I've dug out my hula-hoop, but am yet to manage 30 seconds, but still better at this than skipping. Meanwhile my other half, a keen cyclist, has a turbo trainer set-up in the garage, where he can be found at 6.30am (in full gear) Zwifting around virtual Yorkshire or following the GCN live workouts. I tried running around our garden, but gave up for fear of an injury, so now tack a short run on after a dog walk (and worry whether this is breaking the rules). On Sundays we allow ourselves the luxury of being able to exercise together and head out for a cycle. The roads are empty of cars, but full of cyclists, alone, in pairs and in families. Club members who can't meet in person set one another challenges; I complete a virtual duathlon (over three days), a notparkrun and attempt to draw rainbows on Strava.
General Electric Quarterly Survey 65-02, Version I & II
Creators: name: Electric, General
Publisher: name: Roper Center for Public Opinion Research
Year: 2022

description: Most important problem (1); topics of interest (3); favorite institution (1); importance of various topics (10); groups associated with various topics (10); company-consumer relations (1); spending additional money (1); opinions of various items (10); fair attendance (2); appliance repairs (5); changes in lifestyle (4); reading habits (1); knowledge about General Electric (2).
Quantification of acidic sites of nanoscopic hydroxylated magnesium fluorides by FTIR and (15)N MAS NMR spectroscopy
Creators: name: Hemman, Felix
name: Agirrezabal-Telleria, Iker
name: Jaeger, Christian
name: Kemnitz, Erhard
Publisher: name: Humboldt-Universität zu Berlin
Year: 2015
Subjects: subject: 540 Chemie und zugeordnete Wissenschaften

description: Lewis and Brønsted sites were quantified in a series of weak acidic hydroxylated magnesium fluorides by Fourier transform infrared spectroscopy (FTIR) and solid state nuclear magnetic resonance spectroscopy (NMR) with pyridine as probe molecule. Molar extinction coefficients, which are necessary for quantitative FTIR measurements, were calculated by an easy approach. It utilizes the fact that both signals, used for the quantification by FTIR, are caused by the same deformation vibration mode of pyridine. Comparison of quantitative FTIR experiments and quantification by NMR shows that concentrations of acidic sites determined by FTIR spectroscopy have to be interpreted with caution. Furthermore, it is shown that the transfer of molar extinction coefficients from one catalyst to another may lead to wrong results. Molar extinction coefficients and concentrations of acidic sites determined by FTIR spectroscopy are affected by grinding and probably the particle size of the sample. High temperature during FTIR experiments has further impact on the quantification results.
Position-controlled Telecom Single Photon Emitters Operating at Elevated Temperatures
Creators: name: Laferrière, Patrick
name: Haffouz, Sofiane
name: Northeast, David B.
name: Poole, Philip J.
name: Williams, Robin L.
name: Dalacu, Dan
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Single photon emitters are a key component for enabling the practical use of quantum key distribution protocols for secure communications. For long-haul optical networks it is imperative to use photons at wavelengths that are compatible with standard single mode fibers: 1.31 μm and 1.55 μm. We demonstrate high purity single photon emission at 1.31 μm using deterministically positioned InP photonic waveguide nanowires containing single InAsP quantum dot-in-a-rod structures. At 4 K the detected count rate in fiber was 1.9 Mcps under above-band pulsed laser excitation at 80 MHz corresponding to a single photon collection efficiency at the first lens of 25%. At this count rate, the probability of multiphoton emission is g(2)(0) = 0.021. We have also evaluated the performance of the source as a function of temperature. Multiphoton emission probability increases with temperature with values of 0.11, 0.34 and 0.57 at 77 K, 220 K and 300 K, respectively, which is attributed to an overlap of temperature-broadened excitonic emission lines. These results are a promising step towards scalably fabricating telecom single photon emitters that operate under relaxed cooling requirements.
Economic evaluation of the Community-Level Interventions for Pre-eclampsia (CLIP) in Sindh, Pakistan
Creators: name: Khowaja, Asif Raza
Publisher: name: University of British Columbia
Year: 2018

description: Background: Hypertensive disorders of pregnancy, particularly pre-eclampsia and eclampsia (PE/E), can lead to life-threatening complications or even the death of a mother or a newborn. Because there are few clinical trials of community-based interventions for PE/E, there is little evidence about the cost-effectiveness of these interventions. The aim of this dissertation is to conduct an economic evaluation of the Community-Level Interventions for Pre-eclampsia (CLIP) combined with routine pregnancy care, compared to routine pregnancy care alone, in Sindh, Pakistan. Methods: A mixed-methods (i.e., qualitative and quantitative) approach to economic evaluation was undertaken alongside the CLIP Trial. A literature review of published epidemiological and economic studies was carried out to document evidence on PE/E interventions and guide the design of the economic model. Data were collected through focus groups, a structured questionnaire embedded into CLIP Trial surveillance, a cross-sectional survey of health facilities, and program budgetary reviews. The cost-effectiveness analysis was performed using a societal perspective. Probabilistic analysis was applied to estimate incremental cost-effectiveness ratios (ICERs), and sensitivity analysis was done to characterize uncertainties. Results: The literature review found economic studies mainly in developed countries and focused only on costs to the health system. Focus groups revealed a large burden of out-of-pocket spending and productivity losses to pregnant women and families. Health care providers and decision makers identified upfront technology costs as a key challenge for the health system. Maternal and newborn care costs varied significantly between and within public and private sectors. In the probabilistic analysis of the base case, the incremental cost of the intervention as compared to control was $20,438, while the years of life lost was -37 (i.e., negative health gains), indicating a wide range of statistical uncertainty around ICERs. Overall, the probability that ICERs fell below the country-specific threshold was less than 30%. Conclusion: This dissertation highlights knowledge gaps for costs and cost-effectiveness of PE/E interventions in low- and-middle-income countries (LMICs). The economic analysis indicates that CLIP is not a cost-effective strategy, compared to routine pregnancy care. More research is needed to conduct the process evaluation to inform policy decisions on resource allocation in Sindh, Pakistan.
31848: Grey Market
Creators: name: Project, Lockdown2020 and Beyond
Publisher: name: University of Oxford
Year: 2023
Subjects: classificationCode: 479999
subject: Other language, communication and culture not elsewhere classified

description: I seem to have unknowingly joined the local grey market. Our street's Covid-19 WhatsApp has evolved into a source of how to get hold of things in short-supply. I've been given free eggs destined for a school that had to close suddenly (bring your own box) and flour from an unknown distributor that someone "uses at work". A shout goes up when difficult to find items, such as toilet rolls, potatoes, bread or pasta are in stock somewhere. Meanwhile those who are able to go to the shops offer to pick up items for others, or add them to their delivery if they get a coveted slot. Money is exchanged in sanitised plastic bags and goods are left on doorsteps. We all think twice about what we should ask for in case it's not considered essential; people sheepishly say that Ovaltine is for their mum's night-time drink and marmite for their kid's lunches "if that's ok?" I'm reminded of the man who was ostracised by his village for asking for apple sauce for his roast pork. My neighbour is collecting donations for the local church food bank, and it becomes a handy way to pass on anything that was mis-delivered. Other things are available too, my appeal for a USB keyboard receives two offers in under a minute, and bags of buttons for mask mates are left on my doorstep. Dog crates are loaned for puppy training, emergency plumbers sourced and we've all learning to star-gaze, thanks to our local amateur astronomer.
Quantifying the performance of machine learning models in materials discovery
Creators: name: Borg, Christopher K. H.
name: Muckley, Eric S.
name: Nyby, Clara
name: Saal, James E.
name: Ward, Logan
name: Mehta, Apurva
name: Meredig, Bryce
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The predictive capabilities of machine learning (ML) models used in materials discovery are typically measured using simple statistics such as the root-mean-square error (RMSE) or the coefficient of determination ($r^2$) between ML-predicted materials property values and their known values. A tempting assumption is that models with low error should be effective at guiding materials discovery, and conversely, models with high error should give poor discovery performance. However, we observe that no clear connection exists between a "static" quantity averaged across an entire training set, such as RMSE, and an ML property model's ability to dynamically guide the iterative (and often extrapolative) discovery of novel materials with targeted properties. In this work, we simulate a sequential learning (SL)-guided materials discovery process and demonstrate a decoupling between traditional model error metrics and model performance in guiding materials discoveries. We show that model performance in materials discovery depends strongly on (1) the target range within the property distribution (e.g., whether a 1st or 10th decile material is desired); (2) the incorporation of uncertainty estimates in the SL acquisition function; (3) whether the scientist is interested in one discovery or many targets; and (4) how many SL iterations are allowed. To overcome the limitations of static metrics and robustly capture SL performance, we recommend metrics such as Discovery Yield ($DY$), a measure of how many high-performing materials were discovered during SL, and Discovery Probability ($DP$), a measure of likelihood of discovering high-performing materials at any point in the SL process.
Thermodynamics of rotating Bose gases in a trap
Creators: name: Fan, Jinghan
name: Gu, Qiang
name: Guo, Wei
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Novel ground state properties of rotating Bose gases have been intensively studied in the context of neutral cold atoms. We investigate the rotating Bose gas in a trap from a thermodynamic perspective, taking the charged ideal Bose gas in magnetic field (which is equivalent to a neutral gas in a synthetic magnetic field) as an example. It is indicated that the Bose-Einstein condensation temperature is irrelevant to the magnetic field, conflicting with established intuition that the critical temperature decreases with the field increasing. The specific heat and Landau diamagnetization also exhibit intriguing behaviors. In contrast, we demonstrate that the condensation temperature for neutral Bose gases in a rotating frame drops to zero in the fast rotation limit, signaling a non-condensed quantum phase in the ground state.
description: 4 pages, 1 figure
Electric field-induced interfacial instability in a ferroelectric nematic liquid crystal
Creators: name: Máthé, Marcell Tibor
name: Farkas, Bendegúz
name: Péter, László
name: Buka, Ágnes
name: Jákli, Antal
name: Salamon, Péter
Publisher: name: arXiv
Year: 2022
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Studies of sessile droplets and fluid bridges of a ferroelectric nematic liquid crystal in externally applied electric fields are presented. It is found that above a threshold, the interface of the fluid with air undergoes a fingering instability or ramification, resembling to Rayleigh-type instability observed in charged droplets in electric fields or circular drop-type instabilities observed in ferromagnetic liquids in magnetic field. The frequency dependence of the threshold voltage was determined in various geometries. The nematic director and ferroelectric polarization direction was found to point along the tip of the fingers that appear to repel each other, indicating that the ferroelectric polarization is essentially parallel to the director. The results are interpreted in connection to the Rayleigh and circular drop-type instabilities.
Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19
Creators: name: Sehailia, Moussa
name: Chemat, Smain
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Medicinal herbs have proved along history to be a source of multiple cures. In this paper, we demonstrate how hydroxychloroquine can act as a good inhibitor of SARS-CoV-2 Spike protein receptor-binding-domain using molecular docking studies. We also unveil how hydroxychloroquine can interfere in the prevention of Lys353 in hACE2 from interacting with the corresponding binding hotspot present on the Spike protein. Further screening of artemisinin & derived compounds produced better Vina docking score than hydroxychloroquine (-7.1 kcal mol−1 for artelinic acid vs. −5.5 kcal mol−1 for hydroxychloroquine). Artesunate, artemisinin and artenimol, showed two mode of interactions with Lys353 and Lys31 binding hotspots of the Spike protein. Molecular dynamics analysis confirmed that the formed complexes are able to interact and remain stable in the active site of their respective targets. Given that these molecules are effective antivirals with excellent safety track records in humans against various ailment, we recommend their potential repurposing for the treatment of SARS-CoV-2 patients after successful clinical studies. In addition, an extraction protocol for artemisinin from Artemisia annua L. is proposed in order to cope with the potential urgent global demand. Communicated by Ramaswamy H. Sarma HighlightsHydroxychloroquine role to prevent hACE2 from interacting with SARS-CoV-2 Spike protein is unveiledArtemisinin & derivatives entangle Lys353 & Lys31 binding hotspots of virus Spike protein and prevent infectionArtemisinin, artesunate and artenimol stand as strong repurposing cadidates for COVID-19 clinical trials Hydroxychloroquine role to prevent hACE2 from interacting with SARS-CoV-2 Spike protein is unveiled Artemisinin & derivatives entangle Lys353 & Lys31 binding hotspots of virus Spike protein and prevent infection Artemisinin, artesunate and artenimol stand as strong repurposing cadidates for COVID-19 clinical trials
Polysaccharides like pentagalloylglucose, parishin a and stevioside inhibits the viral entry by binding the Zika virus envelope protein
Creators: name: Sharma, Nitin
name: Kumar, Prateek
name: Giri, Rajanish
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: ZIKV belongs to a flavivirus family in which class II fusion proteins involve a low pH-dependent membrane fusion leading to infection of host cells. Envelope (E) protein is primarily responsible for the viral host membrane fusion and is the major target for inhibiting viral entry. Our findings reveal that compounds like PGG, Parishin A, and Stevioside have shown a high affinity for E protein and found to be active against various other viral infections. The binding of these molecules to E protein was found to decrease the RMSD and RMSF values of the ligand protein complex and restricted the Radius of Gyration in molecular dynamics simulation analysis. Further, the binding free energy calculations suggested the stability of complexes throughout simulations trajectory that could reduce the flexibility of the linker so as to block the folding back event of membrane fusion. A recent study has shown that PGG inhibits the early stages of viral entry in HCV and ZIKV. Therefore, we propose that PGG inhibits the entry of virion via binding the E protein and restricting the conformational rearrangement during membrane fusion. Communicated by Ramaswamy H. Sarma
Privately Fine-Tuning Large Language Models with Differential Privacy
Creators: name: Behnia, Rouzbeh
name: Ebrahimi, Mohamamdreza
name: Pacheco, Jason
name: Padmanabhan, Balaji
Publisher: name: arXiv
Year: 2022
Subjects: subject: Cryptography and Security (cs.CR)
subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: Pre-trained Large Language Models (LLMs) are an integral part of modern AI that have led to breakthrough performances in complex AI tasks. Major AI companies with expensive infrastructures are able to develop and train these large models with billions and millions of parameters from scratch. Third parties, researchers, and practitioners are increasingly adopting these pre-trained models and fine-tuning them on their private data to accomplish their downstream AI tasks. However, it has been shown that an adversary can extract/reconstruct the exact training samples from these LLMs, which can lead to revealing personally identifiable information. The issue has raised deep concerns about the privacy of LLMs. Differential privacy (DP) provides a rigorous framework that allows adding noise in the process of training or fine-tuning LLMs such that extracting the training data becomes infeasible (i.e., with a cryptographically small success probability). While the theoretical privacy guarantees offered in most extant studies assume learning models from scratch through many training iterations in an asymptotic setting, this assumption does not hold in fine-tuning scenarios in which the number of training iterations is significantly smaller. To address the gap, we present \ewtune, a DP framework for fine-tuning LLMs based on Edgeworth accountant with finite-sample privacy guarantees. Our results across four well-established natural language understanding (NLU) tasks show that while \ewtune~adds privacy guarantees to LLM fine-tuning process, it directly contributes to decreasing the induced noise to up to 5.6\% and improves the state-of-the-art LLMs performance by up to 1.1\% across all NLU tasks. We have open-sourced our implementations for wide adoption and public testing purposes.
description: Publised at IEEE ICDM Workshop on Machine Learning for Cybersecurity (MLC) 2022
Variational quantum simulation of critical Ising model with symmetry averaging
Creators: name: Sewell, Troy J.
name: Bao, Ning
name: Jordan, Stephen P.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Here, we investigate the use of deep multi-scale entanglement renormalization (DMERA) circuits as a variational ansatz for ground states of gapless systems. We use the exactly-solvable one-dimensional critical transverse-field Ising model as a testbed. Numerically exact simulation of the ansatz can in this case be carried out to hundreds of qubits by exploiting efficient classical algorithms for simulating matchgate circuits. We find that, for this system, DMERA strongly outperforms a standard QAOA-style ansatz, and that a major source of systematic error in correlation functions approximated using DMERA is the breaking of the translational and Kramers-Wannier symmetries of the transverse-field Ising model. We are able to reduce this error by up to four orders of magnitude by symmetry averaging, without incurring additional cost in qubits or circuit depth. We propose that this technique for mitigating systematic error could be applied to NISQ simulations of physical systems with other symmetries.
description: 10 pages, 6 figures. Updated version with some text additions and figure reformatting after publication in PRA
title: Theorising Christian Anarchism A Political Commentary on the Gospel
Creators: name: Christoyannopoulos, Alexandre J.M.E.
Publisher: name: University of Kent
Year: 2022

description: This thesis argues that there is a tradition in political theology and in political theory that deserves to be called "Christian anarchism." The various thinkers that contribute to this tradition have never before been considered to be part of a theoretical movement or tradition, and the originality of this thesis is to weave these thinkers together and present a generic theory of Christian anarchism. . Taken together, thinkers like Tolstoy, Ellul, Elliott and Andrews put forward a comprehensive exegesis of Jesus' teaching and example as implying a critique of the state and a vision of a stateless society. Based on this understanding of the Gospel, they accuse both the state and the church of contradicting, betraying and corrupting the essence of Christianity. Some Christian anarchists - Eller in particular - even see Romans 13 and the "render unto Caesar" passage as not discrediting but indeed confirming their interpretation, and although more activist Christian anarchists sometimes disagree on the potential role of civil disobedience, they do all stress that what matters above all is obedience to God Moreover, they all call for the "true" church to lead the Christian anarchist revolution by example, despite the very demanding sacrifices which this involves. They point to numerous examples of similar witness ever since the early church, and themselves strive to emulate such examples in their own lives - the Catholic Worker movement being perhaps the most notable example in this regard Thus, Christian anarchist thinkers' critique of the current order and appeal to follow God's radical commandments echoes the voices of the prophets of old, calling society to return to God's covenant. By weaving their scattered voices together - by theorising Christian anarchism - this thesis provides a political commentary on the Gospel which contributes as much to political theory as it does to political theology.
Asymmetric Dark Matter from a GeV Hidden Sector
Creators: name: Cohen, Timothy
name: Phalen, Daniel J.
name: Pierce, Aaron
name: Zurek, Kathryn M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Asymmetric Dark Matter (ADM) models relate the dark matter density to the baryon asymmetry, so that a natural mass scale for ADM is around a few GeV. In existing models of ADM, this mass scale is unexplained; here we generate this GeV scale for dark matter (DM) from the weak scale via gauge kinetic mixing with a new Abelian dark force. In addition, this dark sector provides an efficient mechanism for suppressing the symmetric abundance of DM through annihilations to the dark photon. We augment this sector with a higher dimensional operator responsible for communicating the baryon asymmetry to the dark sector. Our framework also provides DM candidate for gauge mediation models. It results in a direct detection cross section of interest for current experiments: sigma less than or similar to 10^{-42} cm^2 for DM masses in the range 1 - 15 GeV.
description: 21 pages, 4 figures
Charge-spin duality in non-equilibrium transport of helical liquids
Creators: name: Liu, Chao-Xing
name: Budich, Jan Carl
name: Recher, Patrik
name: Trauzettel, Bjoern
Publisher: name: arXiv
Year: 2010
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Non-equilibrium transport properties of charge and spin sector of two edges of a quantum spin Hall insulator are investigated theoretically in a four-terminal configuration. A simple duality relation between charge and spin sector is found for two helical Tomonaga Luttinger liquids (hTTLs) connected to non-interacting electron reservoirs. If the hTLLs on opposite edges are coupled locally or non-locally, the mixing between them yields interesting physics where spin information can be easily detected by a charge measurement and vice versa. Particularly, we show how a pure spin density in the absence of charge current can be generated in a setup that contains two hTLL and one spinful Tomonaga Luttinger liquid in between.
description: 12 pages and 3 figures
Generalized Miller Formulae
Creators: name: Ettoumi, W.
name: Petit, Y.
name: Kasparian, J.
name: Wolf, J. -P.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We derive the spectral dependence of the non-linear susceptibility of any order, generalizing the common form of Sellmeier equations. This dependence is fully defined by the knowledge of the linear dispersion of the medium. This finding generalizes the Miller formula to any order of non-linearity. In the frequency-degenerate case, it yields the spectral dependence of non-linear refractive indices of arbitrary order.
description: 12 pages, 1 figure (4 panels)
Uncommon grounds : LGBTIQ farmers, agriculture, and ecologies of social difference
Creators: name: Edward, Joshua Brett
Publisher: name: University of British Columbia
Year: 2018

description: This work is an ethnography of queer farmers throughout British Columbia and acknowledges that by working within such a diverse population, there exists no singular representation of “queer individuals,” “farmers,” and / or “queer farmers.” The research design integrates a qualitative, post-structuralist ethnographic and auto-ethnographic methodology based upon individual narratives and a review of both local (British Columbia) and non-local (national and international) print and web sources (academic and non-academic) related to gender, and especially sexuality, in agricultural production and practice. This study recognizes the existence of ecologies of social difference. I define ecologies of social difference as the role of ecological indicators, settings, and contexts as mediators and moderators in the intersections of social difference (i.e., the role of ecology in shaping both positively and negatively greater inequalities, inequities, injustices). This study draws from several intellectual lineages, from queer theory to feminist political ecology, to illustrate how agriculture might be transformed within a queer ecological context. Rooted in my belief that understandings of agriculture and ecology are shaped and impacted by gender and sexuality even as understandings of gender and sexuality are shaped and impacted by practices within and perceptions of agriculture and ecology, this work seeks to challenge heteronormative assumptions of both gender and sexuality and agriculture and ecology. It presupposes that queer sexualities can provide lenses through which farmers are not only creating new agricultural practices, but also new queer identities. These new, heretofore unstudied, lenses may then lead to the identification of new perspectives, practices, innovations and understandings of agricultural and ecological sustainability.
Magnetism in superconducting EuFe$_2$As$_{1.4}$P$_{0.6}$ single crystals studied by local probes
Creators: name: Munevar, J.
name: Micklitz, H.
name: Alzamora, M.
name: Arguello, C.
name: Goko, T.
name: Ning, F. L.
name: Aczel, A. A.
name: Munsie, T.
name: Williams, T. J.
name: Chen, G. F.
name: Yu, W.
name: Luke, G. M.
name: Uemura, Y. J.
name: Baggio-Saitovitch, E.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We have studied the magnetism in superconducting single crystals of EuFe2 As1.4 P0.6 by using the local probe techniques of zero-field muon spin rotation/relaxation and 151 Eu/57 Fe Mössbauer spec- troscopy. All of these measurements reveal magnetic hyperfine fields below the magnetic ordering temperature TM = 18 K of the Eu2+ moments. The analysis of the data shows that there is a coexistence of ferromagnetism, resulting from Eu2+ moments ordered along the crystallographic c-axis, and superconductivity below TSC \approx 15 K. We find indications for a change in the dynamics of the small Fe magnetic moments (\sim 0.07 μB) at the onset of superconductivity: below TSC the Fe magnetic moments seem to be "frozen" within the ab-plane.
2D actin images
Creators: name: Leterrier, Christophe
Publisher: name: Zenodo
Year: 2021
Subjects: shareloc.xyz
shareloc.xyz:dataset
2d
storm
phalloidin-647
cos7
actin
smlm

description: Open in Shareloc.XYZ

description: CCOS cells labeled for actin images by 2D STORM (Uploaded via https://shareloc.xyz)
Anatomy of an RNA virus : dissecting the host-virus interactions that govern dicistrovirus gene expression and transmission
Creators: name: Kerr, Craig Howard
Publisher: name: University of British Columbia
Year: 2018

description: Viruses exist as obligate intracellular parasites, with one of the largest classifications of viruses being the positive single stranded RNA viruses ((+)ssRNA). Viral families in this group are incredibly diverse in their replication schemes and host tropisms. Despite this, there exist fundamental principles between them. Unravelling these common mechanisms can give rise to a greater understanding of virus biology and lead to the development of novel antiviral therapies and biotechnology. Members of the Dicistroviridae contain monopartite, (+)ssRNA genomes, between 8 to 10 kilobases in size. Infectious to agriculturally and economically important arthropods, these viruses have served as model systems to study fundamental cellular processes such as translation and innate immunity. Dicistroviruses contain two open reading frames (ORFs), which are translated by two distinct internal ribosome entry sites (IRESs). The 5’ untranslated region IRES drives translation of the viral non-structural proteins encoded in ORF1, whereas the intergenic region (IGR) IRES directs translation of the viral structural proteins of ORF2. The scheme by which these viruses replicate is poorly described. Here, we develop the first infectious clones of the dicistrovirus type species, Cricket paralysis virus (CrPV), termed CrPV-2 and -3. We demonstrate that this clone is fully infectious in Drosophila S2 cells and causes mortality when injected into adult flies. Utilizing this clone, we examined how specific mutations in the IGR IRES affect viral gene expression in vivo. Moreover, we demonstrate that the CrPV IGR IRES uses an unusual mechanism for +1-frame translation of a hidden overlapping ORF, which is important for viral pathogenesis. Finally, using a combination of biochemical and mass spectrometry based approaches we show that CrPV may usurp cellular pathways to obtain an envelope. This thesis offers insights into the complex replication scheme of dicistroviruses and provides a foundation for future studies into the life cycle of these viruses.
Spectroscopic Bogoliubov features near the unitary limit
Creators: name: Domanski, T.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We analyze the single particle excitation spectrum of the ultracold fermion atom system close to the unitary limit where there has been found experimental evidence for the Bogoliubov quasiparticles below as well as above the transition temperature Tc. We consider the short-range correlations originating from the preformed pairs and try to reproduce the experimental data adapting phenomenological selfenergy previously used for description of the anti-nodal spectra of the underdoped cuprate superconductors. We show that it fairly fits the lineshapes obtained by the momentum resolved RF spectroscopy for {40}^K atoms.
description: 4 pages + epsilon
Comment on: Bell tests explained by classical optics without quantum entanglement
Creators: name: Gill, Richard D.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In a paper published in the journal Physics Essays in 2021, the author D.L. Mamas writes "A polarized photon interacts with a polarizer through the component of the photon's electric field which is aligned with the polarizer. This component varies as the cosine of the angle through which the polarizer is rotated, explaining the cosine observed in Bell test data. Quantum mechanics is unnecessary and plays no role". Mamas is right that according to this physical model, one will observe a negative cosine. However, the amplitude of the cosine curve is 50%, not 100%, and it consequently does not violate any Bell-CHSH inequality. Mamas' physical model is a classic local hidden variables model. The result is illustrated with a Monte Carlo simulation.
description: Version 5. Accepted by Physics Essays. 5pp
Intermittence of the Map of Kinetic Sunyaev-Zel'dovich Effect and Turbulence of IGM
Creators: name: Zhu, Weishan
name: Feng, Long-Long
name: Fang, Li-Zhi
Publisher: name: arXiv
Year: 2011
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We investigate the possibility of detecting the turbulent state of the IGM with the kinetic Sunyaev-Zel'dovich (kSZ) effect. Being sensitive to the divergence-free component of the momentum field of the IGM, the kSZ effect might be used to probe the vorticity of the turbulent IGM. With cosmological hydrodynamical simulation in the concordance $Λ$CDM universe, we find that the structure functions of 2D kSZ maps show strong intermittence, and the intermittent exponents follow a law similar to the She-Leveque scaling formula of fully developed turbulence. We also find that the intermittence is weak in the maps of thermal Sunyaev-Zel'dovich (tSZ) effect. Nevertheless, the superposition of the kSZ and tSZ effects still contain significant intermittence. We conclude that the turbulent behavior of the IGM may be revealed by the observation of SZ effect on angular scales equal to or less than 0.5 arcminute, corresponding to the multipole parameter $l\geq 2 \times10^4$.
description: 10 pages, 4 figures, accepted for publication in ApJL
Coherent spin ratchets: A spin-orbit based quantum ratchet mechanism for spin-polarized currents in ballistic conductors
Creators: name: Scheid, Matthias
name: Pfund, Andreas
name: Bercioux, Dario
name: Richter, Klaus
Publisher: name: Universität Regensburg
Year: 2007
Subjects: subject: 530 Physik
subject: 73.23.-b
subject: 05.60.Gg
subject: 72.25.-b

description: We demonstrate that the combined effect of a spatially periodic potential, lateral confinement, and spin-orbit interaction gives rise to a quantum ratchet mechanism for spin-polarized currents in two-dimensional coherent conductors. Upon adiabatic ac driving, in the absence of a net static bias, the system generates a directed spin current while the total charge current is zero. We analyze the underlying mechanism by employing symmetry properties of the scattering matrix and numerically verify the effect for different setups of ballistic conductors. The spin current direction can be changed upon tuning the Fermi energy or the strength of the Rashba spin-orbit coupling.