cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Poly(oxymethylene) Ethers: Alternative Diesel Fuels with Low Sooting Tendencies
Creators: name: Zhu, Junqing
name: Arellano-Treviño, Martha
A.
name: Bartholet, Danielle
name: Chan, Fan Liang
name: Foust, Thomas D.
name: Lucas, Stephen
name: Pfefferle, Lisa D.
name: Reardon, Kenneth F.
name: Ruddy, Daniel A.
name: Windom, Bret C.
name: McEnally, Charles S.
Publisher: name: figshare
Year: 2022
Subjects: subject: 90201 Automotive Combustion and Fuel Engineering (incl. Alternative/Renewable Fuels)
subject: FOS: Environmental engineering

description: Presentation given at the 2022 ACS Fall Meeting in Chicago IL on August 25 2022. Soot has been identified as the second-largest source of climate change after CO2 and it contributes to ambient fine particulates that cause millions of deaths worldwide each year. Diesel engines contribute significantly to total soot emissions because diesel fuels have high sooting tendencies. Poly(oxymethylene) ethers (POMEs) are alternative diesel fuels that can be produced from waste CO2 with low soot emissions. The structures of the POMEs in these earlier studies are alternating oxygen and carbon atoms terminated with methyl groups on both ends. Unfortunately, these methyl-POMEs suffer from high water solubility and low energy density. Replacing the methyl groups with larger alkyl groups can overcome these disadvantages, but at the cost of higher sooting tendencies. To optimize this trade-off, the sooting tendencies of methyl-POMEs and alkyl-POMEs need to be quantified.
 In this work, a series of methyl-POMEs and alkyl-POMEs were synthesized and their sooting tendencies were quantified. The test compounds contained a wide range of terminating groups (methyl, ethyl, propyl, iso-propyl, butyl, iso-butyl, sec-butyl, iso-pentyl, and tetrahydrofurfuryl), cases where the terminating groups were identical at the two ends and where they differed, and from one to five oxymethylene units. The sooting tendencies were characterized by the Yield Sooting Index (YSI), which is based on the maximum soot concentration measured in coflow diffusion flames whose fuel is CH4 doped with 1000 ppm or 3000 ppm of each test compound. The YSIs of the POMEs vary significantly with fuel structure, but in all cases are at least one order of magnitude lower than a certification diesel fuel. We proposed some decomposition pathways that justified the difference among the YSIs. The lower heating value (LHV) was also measured to evaluate the energy penalty of the oxygen atoms. The calculated YSI/LHV of the POMEs are lower than conventional diesel fuels and their components.
Der Glaube derer, die Verfolgung erleiden, möge nicht durch Lügen und falsche Versprechungen erschüttert werden
Publisher: name: Herder Korrespondenz
Year: 1970

description: Herder Korrespondenz, Bd. 11 Nr. 2 (1956): Herder Korrespondenz, Band 11, Heft 2
HIV test uptake among MSM in China: Implications for enhanced HIV test promotion campaigns among key populations
Creators: name: Emch, Michael E.
name: Meng, Gang
name: Wei, Chongyi
name: Muessig, Kathryn E.
name: Han, Larry
name: Bien, Cedric H.
name: Tucker, Joseph D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Despite global efforts to increase HIV test uptake among men who have sex with men (MSM), social stigma and negative attitudes toward homosexuality hinder the effectiveness of traditional test promotion campaigns. Increasing HIV test uptake requires greater understanding of the conditions that facilitate decisions to get tested. We conducted an online survey hosted by two of the most highly frequented MSM web portals in China. A generalised ordered logistic regression analysis was conducted to determine factors associated with HIV testing behaviour. Compared to men who had never tested for HIV, men who had tested in the past year were more likely to have never engaged in sex with women, have multiple male sex partners in the past 3 months and have disclosed their sexual orientation to others. MSM found testing at local Chinese Centers for Disease Control and Prevention (80.7%), gay men’s community-based organisations (80.2%) and public hospitals (70.9%) to be acceptable, while saunas (50.5%) and gay bars (41.8%) were found to be unacceptable testing venues. Our study shows that MSM in China prefer to test at venues that guarantee confidentiality, quality and quick results. Our study also suggests that self-testing may be a feasible approach to increase test uptake.
How does a national poverty programme influence sexual debut among Kenyan adolescents?
Creators: name: Pettifor, Audrey
name: Handa, Sudhanshu
name: Thirumurthy, Harsha
name: Halpern, Carolyn Tucker
name: Rosenberg, Molly
name: Palermo, Tia
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Cash transfer programmes have recently emerged as promising interventions for HIV prevention among adolescents in Africa. However, the pathways through which risk reduction occurs are not well understood. We examine data on 1429 adolescents and youth from the Kenya Cash Transfer for Orphans and Vulnerable Children, which has been shown to result in delayed sexual debut among adolescents. We explored three potential mediating pathways: schooling, socioeconomic status and psychosocial status. None of these hypothesised mediators greatly altered the main effect. However, school attendance had a larger protective effect on sexual debut among females but was only increased by the programme among males. This gendered pattern of effects may explain why we did not see a mediating effect of the cash transfer through schooling, despite schooling’s protective effects against early sexual debut. Results also suggest that cash transfer programmes in Africa can contribute to the reduction of HIV related risk behaviours.
Supplementary files to Vision Transformers for Retinal Image Analysis: A Systematic Review.docx
Creators: name: Ye, En Zhou
name: Ye, En Hui
name: Ye, Joseph
name: Ye, Run Zhou
Publisher: name: figshare
Year: 2023
Subjects: Epidemiological methods

description: Contains the supplementary material file for the manuscript entitled "Vision Transformers for Retinal Image Analysis: A Systematic Review"
Many needles in the haystack -- on the contribution of VLBI to cracking the FRB puzzle
Creators: name: Kirsten, Franz
Publisher: name: Zenodo
Year: 2023

description: It has been a little over fifteen years since the discovery of Fast Radio Bursts (FRBs) and we are still unsure about what type of object generates these enigmatic millisecond-duration bursts. The phenomenon is extremely common -- we expect several thousands of bursts per sky per day -- and we find roughly a dozen of new bursts each week. The bursts' properties tell us that they originate from cosmologic distances and that the emission must be coherent in nature. Broadly speaking, there are two types of FRBs: the repeating ones and those that apparently do not repeat. It is an open question whether the two populations share a common origin; some statistical studies indicate that this might not be the case. Amongst aspects such a the burst structure, bandwidth, duration and polarisation properties, a key ingredient required to solve the FRB puzzle is the local environment FRBs reside in. In combination with high-resolution optical data, VLBI-localisations of FRBs allow us to draw robust conclusions about the physical properties in the immediate surroundings of these sources and thus obtain clues about the possible progenitors. In this talk I will review our current understanding of FRBs with a particular focus on the contribution of VLBI in this endeavour.
Supplementary files to Vision Transformers for Retinal Image Analysis: A Systematic Review.docx
Creators: name: Ye, En Zhou
name: Ye, En Hui
name: Ye, Joseph
Publisher: name: figshare
Year: 2023
Subjects: Epidemiological methods

description: Contains the supplementary material file for the manuscript entitled "Vision Transformers for Retinal Image Analysis: A Systematic Review"
Alarms about structural alerts
Creators: name: Braga, Rodolpho C.
name: Capuzzi, Stephen J.
name: Muratov, Eugene N.
name: Sedykh, Alexander
name: Mokshyna, Elena
name: Farag, Sherif
name: Fourches, Denis
name: Tropsha, Alexander
name: Low, Yen
name: Zakharov, Alexey V.
name: Politi, Regina
name: Andrade, Carolina H.
name: Alves, Vinicius M.
name: Kuz'Min, Victor E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Integrative approach for safety assessment of new chemicals by combining structural alerts and QSAR models.
He-Accreting WDs: AM CVn stars with WD Donors
Creators: name: Piersanti, Luciano
name: Yungelson, Lev R.
name: Tornambe', Amedeo
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We study the physical and evolutionary properties of the "WD family" of AM CVn stars by computing realistic models of IDD systems. We evaluate self-consistently both the mass transfer rate from the donor, as determined by GW emission and interaction with the binary companion, and the thermal response of the accretor to mass deposition. We find that, after the onset of mass transfer, all the considered systems undergo a strong non-dynamical He-flash. However, due to the compactness of these systems, the expanding accretors fill their Roche lobe very soon, thus preventing the efficient heating of the external layers of the accreted CO WDs. Moreover, due to the loss of matter from the systems, the orbital separations enlarge and mass transfer comes to a halt. The further evolution depends on the value of $\dot{M}$, after the donors fill again their lobe. On one hand, if the accretion rate, as determined by the actual value of (M$_{don}$,M$_{acc}$), is high enough, the accretors experience several He-flashes of decreasing strength and then quiescent He-burning sets in. Later on, since the mass transfer rate in IDD is a permanently decreasing function of time, accretors experience several recurrent strong flashes. On the other hand, for intermediate and low values of $\dot{M}$, the accretors enter the strong flashes accretion regime. As expected, in all the considered systems the last He-flash is the strongest one, even if a dynamical event never occurs. When the mass accretion rate decreases below (2-3)$\times 10^{-8} M_\odot yr^{-1}$, the compressional heating of the He-shell becomes less efficient than the neutrino cooling, so that all the accretors in the considered systems evolve into massive degenerate objects. Our results suggest that SNe .Ia or type Ia Supernovae due to Edge-Lit Detonation in the WD family of AM CVn stars should be much more rare than previously expected.
description: 14 pages, 13 figures, 3 tables. Accepted for the publication on MNRAS. Corrected typos in the Abstract
title: Iowa Byington Reed diary 32, January 1, 1931-December 31, 1932
Creators: name: Reed, Iowa Byington
Publisher: name: University of Iowa. Libraries
Year: 2012
Subjects: subject: FOS: History and archaeology
valueUri: http://www.oecd.org/science/inno/38235147.pdf
subject: FOS: History and archaeology
subject: Domestic life
valueUri: http://id.loc.gov/vocabulary/graphicMaterials/tgm003216

description: Iowa Byington Reed's diaries contain daily entries covering her life from age twenty to just a few weeks before her death at age eighty-four (1872-1936).
Saddle point inflation in string-inspired theory
Creators: name: Hamada, Yuta
name: Kawai, Hikaru
name: Kawana, Kiyoharu
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The observed value of the Higgs mass indicates the possibility that there is no supersymmetry below the Planck scale and that the Higgs can play the role of the inflaton. We examine the general structure of the saddle point inflation in string-inspired theory without supersymmetry. We point out that the string scale is fixed to be around the GUT scale $\sim10^{16}$GeV in order to realize successful inflation. We find that the inflaton can be naturally identified with the Higgs field.
description: 12 pages, 2 figures(v1); Version to appear on PTEP(v2)
QSAR models of human data can enrich or replace LLNA testing for human skin sensitization
Creators: name: Alves, Vinicius M.
name: Kleinstreuer, Nicole
name: Muratov, Eugene N.
name: Fourches, Denis
name: Tropsha, Alexander
name: Strickland, Judy
name: Thornton, Thomas E.
name: Andrade, Carolina H.
name: Braga, Rodolpho C.
name: Capuzzi, Stephen J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: An example of structural transformation of human skin sensitizers into various non-sensitizers based on interpretation of QSAR models.
Entangling the whole by beam splitting a part
Creators: name: Croal, Callum
name: Peuntinger, Christian
name: Chille, Vanessa
name: Marquardt, Christoph
name: Leuchs, Gerd
name: Korolkova, Natalia
name: Mišta, Ladislav
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A beam splitter is a basic linear optical element appearing in many optics experiments and is frequently used as a continuous-variable entangler transforming a pair of input modes from a separable Gaussian state into an entangled state. However, a beam splitter is a passive operation that can create entanglement from Gaussian states only under certain conditions. One such condition is that the input light is squeezed. We demonstrate experimentally that a beam splitter can create entanglement even from modes which do not possess such a squeezing provided that they are correlated to but not entangled with a third mode. Specifically, we show that a beam splitter can create three-mode entanglement by acting on two modes of a three-mode fully separable Gaussian state without entangling the two modes themselves. This beam splitter property is a key mechanism behind the performance of the protocol for entanglement distribution by separable states. Moreover, the property also finds application in collaborative quantum dense coding in which decoding of transmitted information is assisted by interference with a mode of the collaborating party.
description: 5 pages, 3 figures
Post-newtonian analysis of precessing convention for spinning compact binaries
Creators: name: Gupta, Anuradha
name: Gopakumar, Achamveedu
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: A precessing source frame, constructed using the Newtonian orbital angular momentum ${\bf L_{\rm N}}$, can be invoked to model inspiral gravitational waves from generic spinning compact binaries. An attractive feature of such a precessing convention is its ability to remove all spin precession induced modulations from the orbital phase evolution. However, this convention usually employs a post-Newtonian (PN) accurate precessional equation, appropriate for the PN accurate orbital angular momentum ${\bf L}$, to evolve the ${\bf L_{\rm N}}$-based precessing source frame. This influenced us to develop inspiral waveforms for spinning compact binaries in a precessing convention that explicitly employ ${\bf L}$ to describe the binary orbits. Our approach introduces certain additional 3PN order terms in the evolution equations for the orbital phase and frequency with respect to the usual ${\bf L_{\rm N}}$-based implementation of the precessing convention. We examine the practical implications of these additional terms by computing the match between inspiral waveforms that employ ${\bf L}$ and ${\bf L_{\rm N}}$-based precessing conventions. The match estimates are found to be smaller than the optimal value, namely $0.97$, for a non-negligible fraction of unequal mass spinning compact binaries.
description: 20 pages, 4 figures, matches published version
DESIGN_AND_DEVELOPMENT_OF_A_BASIC_THERMOACOUSTIC_COOLING_DEVICE.pdf
Creators: name: Islam, Sazid Ul
Publisher: name: figshare
Year: 2023
Subjects: Acoustics and noise control (excl. architectural acoustics)
Energy generation, conversion and storage (excl. chemical and electrical)

description: Thermoacoustic cooling uses acoustic power to transport heat from a low temperature zone to a high temperature zone in a resonator tube through a stack. This can be an alternative cooling technology for its eco-friendly working fluid and less moving parts. This report represents the design of a small thermoacoustic refrigerator producing a temperature difference of maximum 2.6°C. It explains the design choices with reasons for using specific parameters. Temperature differences were tested with air and helium as refrigerants. Sine and Square wave sound were delivered, and the test was continued for around 30 minutes to 1 hour. Sound frequency ranging from 50 Hz to 22,000 Hz at an irregular interval was supplied. A Photo Film reel was used to construct the stack. Amplifier circuit along with its components were constructed for the experiment.
Kinase analysis in alcoholic hepatitis identifies p90RSK as a potential mediator of liver fibrogenesis
Creators: name: Moreno, Montserrat
name: Templin, Markus F.
name: Ginès, Pere
name: Coll, Mar
name: Blaya, Delia
name: Affò, Silvia
name: Morales-Ibanez, Oriol
name: Arroyo, Vicente
name: Knorpp, Thomas
name: Mique, Rosa
name: Millán, Cristina
name: Rodrigo-Torres, Daniel
name: Perea, Luis
name: Odena, Gemma
name: Caballería, Juan
name: Sancho-Bru, Pau
name: Bataller, Ramon
name: Altamirano, José
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Alcoholic hepatitis (AH) is often associated with advanced fibrosis, which negatively impacts survival. We aimed at identifying kinases deregulated in livers from patients with AH and advanced fibrosis in order to discover novel molecular targets.
The Kullback-Leibler Divergence as an Estimator of the Statistical Properties of CMB Maps
Creators: name: Ben-David, Assaf
name: Liu, Hao
name: Jackson, Andrew D.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The identification of unsubtracted foreground residuals in the cosmic microwave background maps on large scales is of crucial importance for the analysis of polarization signals. These residuals add a non-Gaussian contribution to the data. We propose the Kullback-Leibler (KL) divergence as an effective, non-parametric test on the one-point probability distribution function of the data. With motivation in information theory, the KL divergence takes into account the entire range of the distribution and is highly non-local. We demonstrate its use by analyzing the large scales of the Planck 2013 SMICA temperature fluctuation map and find it consistent with the expected distribution at a level of 6%. Comparing the results to those obtained using the more popular Kolmogorov-Smirnov test, we find the two methods to be in general agreement.
description: 12 pages, 5 figures, minor change, as published in JCAP
Apostolischer Brief Papst Pius' XII. an die Bischöfe und Gläubigen Osteuropas
Creators: name: Pius XII., Papst
Publisher: name: Herder Korrespondenz
Year: 1970

description: Herder Korrespondenz, Bd. 11 Nr. 1 (1956): Herder Korrespondenz, Band 11, Heft 1
Associated production of a top pair and a Higgs boson beyond NLO
Creators: name: Broggio, Alessandro
name: Ferroglia, Andrea
name: Pecjak, Ben D.
name: Signer, Adrian
name: Yang, Li Lin
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We consider soft gluon emission corrections to the production of a top-antitop pair in association with a Higgs boson at hadron colliders. In particular, we present a soft-gluon resummation formula for this production process and gather all elements needed to evaluate it at next-to-next-to-leading logarithmic order. We employ these results to obtain approximate next-to-next-to-leading order (NNLO) formulas, and implement them in a bespoke parton-level Monte Carlo program which can be used to calculate the total cross section along with arbitrary differential distributions. We use this tool to study the phenomenological impact of the approximate NNLO corrections, finding that they increase the total cross section and the differential distributions which we evaluated in this work.
description: 35 pages, 5 tables and 12 figures. Version published in JHEP 1603 (2016) 124
Effectiveness and safety of sofosbuvir plus ribavirin for the treatment of HCV genotype 2 infection: results of the real-world, clinical practice HCV-TARGET study
Creators: name: Fried, Michael W.
name: Sulkowski, Mark S.
name: Di Bisceglie, Adrian
name: Nelson, David R.
name: Galati, Joseph S.
name: Pockros, Paul
name: Welzel, Tania M.
name: Frazier, Lynn M.
name: Darling, Jama
name: Zeuzem, Stefan
name: Lim, Joseph K.
name: Kuo, Alexander
name: Reddy, Rajender K.
name: Vainorius, Monika
name: Alqahtani, Saleh
name: Akushevich, Lucy
name: Morelli, Giuseppe
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Due to a high efficacy in clinical trials, sofosbuvir (SOF) and ribavirin (RBV) for 12 or 16 weeks is recommended for treatment of patients with HCV genotype (GT) 2 infection. We investigated safety and effectiveness of these regimens for GT2 in HCV-TARGET participants.
Photochemical and Chemical Cocatalysts for Cu-Catalyzed ATRP: From Cocatalyst Properties to Polymerization Mechanisms
Creators: name: Sun, Mingkang
Publisher: name: Carnegie Mellon University
Year: 2023
Subjects: subject: 30305 Polymerisation Mechanisms
subject: FOS: Chemical sciences

description: In this thesis, development photochemical or chemical cocatalysts for Cu-catalyzed ATRP is discussed. Chapter 1 introduces the mechanism of ATRP and other important reversibledeactivation radical polymerization (RDRP) methods, which provides fundamental knowledge and the state-of-the-art of research on the development of cocatalysts for ATRP. Chapters 2-8 are research projects that I have worked on during my Ph.D. study, which are divided into three themes: (I) Photochemical Cocatalysts for Cu-Catalyzed ATRP (Chapters 2-5); (II) Chemical Cocatalysts for Cu-Catalyzed ATRP (Chapters 6-7); (III) Applications of Polymerbased Materials (Chapter 8). Both experimental and computational methods were used to study the structure and properties of cocatalysts and related materials. Chapters 2-5 (Theme I) focus on the application of photochemical cocatalysts for Cucatalyzed ATRP and the development of photoactive crosslinked polymer networks. Chapter 2 discusses the synthesis and properties of a photoluminescent polymer prepared via the hydrothermal reaction of polyacrylonitrile (PAN), ht-PLPPAN. Chapter 3 introduces the application of ht-PLPPAN as a photo-cocatalyst in light-mediated Cu-catalyzed ATRP. Different mechanisms under different light irradiations are discussed. Chapter 4 extends the work on PAN to structurally tailored and engineered macromolecular (STEM) networks and discusses the unusual photoluminescence properties of STEM networks containing PAN. Chapter 5 introduces another type of photoluminescent network by immobilizing photoactive iridium (III) complexes onto a commercially available poly(ethylene glycol) (PEG)-based resin, ChemMatrix. Chapters 6-7 (Theme II) focuses on the application of chemical cocatalysts for Cucatalyzed ATRP. In Chapter 6, Cu-catalyzed ATRP using liquid metal micro/nanodroplets as the supplemental activator and reducing agent (SARA) is studied. Chapter 7 extends the application of SARA ATRP to N,N-dimethylacrylamide (DMAA) and less polar organic solvents, as well as the synthesis of block copolymers (BCPs) containing polyethylene and polyacrylamides. Chapter 8 (Theme III) demonstrates the application of BCP-derived nanocarbon materials as fuel cell cathode catalysts. The influence of the composition of the polyacrylonitrile-b-poly(n-butyl acrylate) (PAN-b-PBA) precursor on the nanocarbon properties is discussed. Finally, Chapter 9 provides a summary and future perspectives on the development of cocatalysts for Cu-catalyzed ATRP. Appendices summarized the academic papers published or already submitted during my Ph.D. study, as well as other group activities and related achievements.
title: Iowa Byington Reed diary 33, January 1, 1933-December 31, 1934
Creators: name: Reed, Iowa Byington
Publisher: name: University of Iowa. Libraries
Year: 2012
Subjects: subject: FOS: History and archaeology
valueUri: http://www.oecd.org/science/inno/38235147.pdf
subject: FOS: History and archaeology
subject: Domestic life
valueUri: http://id.loc.gov/vocabulary/graphicMaterials/tgm003216

description: Iowa Byington Reed's diaries contain daily entries covering her life from age twenty to just a few weeks before her death at age eighty-four (1872-1936).
Heterotic M2-branes
Creators: name: Lambert, Neil
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We construct the action for N M2-branes on $S^1/{Z}_2$. The resulting theory has a gauge anomaly but this can be cancelled if the two fixed point planes each support 8 chiral Fermions in the fundamental of U(N). Taking the low energy limit leads to the worldsheet theory of N free heterotic strings whose quantization induces an $E_8$ spacetime gauge symmetry on each fixed point plane. Thus this paper presents a non-abelian worldvolume analogue of the classic Horava-Witten analysis.
description: reference added
Novel Methods for the Design and Analysis of Molecular Dynamics Simulations of Protein Systems
Creators: name: Kottke, Christopher
Publisher: name: Carnegie Mellon University
Year: 2023
Subjects: subject: 30406 Proteins and Peptides
subject: FOS: Chemical sciences
subject: 30403 Characterisation of Biological Macromolecules
subject: 170203 Knowledge Representation and Machine Learning
subject: FOS: Psychology

description: The application of atomistic molecular dynamics simulation to biological processes is a field of study with ever widening potential as computational power grows. However, the continual growth in the computational resources available to researchers provides a difficult challenge. As simulations become more complex and run for longer spans of time, our ability to analyze their behavior and understand the processes at work diminishes. The work detailed here seeks to address this problem by developing new computational tools, modifying existing tools, and applying machine learning methods to analyze and learn from molecular dynamics simulations. These methods include feature selection (Chapter 1), unsupervised clustering (Chapter 2), black-box optimization for simulation design (Chapter 3), proposing novel reaction coordinates for umbrella sampling (Chapter 4), and developing an A* search heuristic for allosteric pathway analysis (Chapter 5).
Onsager coefficients in periodically driven systems
Creators: name: Proesmans, Karel
name: Broeck, Christian Van den
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We evaluate the Onsager matrix for a system under time-periodic driving by considering all its Fourier components. By application of the second law, we prove that all the fluxes converge to zero in the limit of zero dissipation. Reversible efficiency can never be reached at finite power. The implication for an Onsager matrix, describing reduced fluxes, is that its determinant has to vanish. In the particular case of only two fluxes, the corresponding Onsager matrix becomes symmetric.
Germline variation in inflammation-related pathways and risk of Barrett's oesophagus and oesophageal adenocarcinoma
Creators: name: Gammon, Marilie D.
name: Vaughan, Thomas L.
name: MacGregor, Stuart
name: Shaheen, Nicholas J.
name: Whiteman, David C.
name: Liu, Geoffrey
name: Bernstein, Leslie
name: Buas, Matthew F.
name: Corley, Douglas A.
name: Jankowski, Janusz
name: Thrift, Aaron P.
name: Levine, David M.
name: Lagergren, Jesper
name: Harrison, Rebecca
name: Chegwidden, Laura
name: Moayyedi, Paul
name: Wu, Anna H.
name: Prenen, Hans
name: Caldas, Carlos
name: Risch, Harvey A.
name: Barr, Hugh
name: Iyer, Prassad
name: Attwood, Stephen
name: Madeleine, Margaret M.
name: Chow, Wong-Ho
name: Watson, Peter
name: Pharoah, Paul D.
name: MacDonald, David
name: Hardie, Laura J.
name: He, Qianchuan
name: Fitzgerald, Rebecca C.
name: Gharahkhani, Puya
name: Johnson, Lisa G.
name: Decaestecker, John
name: Bird, Nigel C.
name: Onstad, Lynn
name: Ye, Weimin
name: Tomlinson, Ian
name: Love, Sharon
name: Palles, Claire
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Esophageal adenocarcinoma (EA) incidence has risen sharply in Western countries over recent decades. Local and systemic inflammation, operating downstream of disease-associated exposures, is considered an important contributor to EA pathogenesis. Several risk factors have been identified for EA and its precursor, Barrett’s esophagus (BE), including symptomatic reflux, obesity, and smoking. The role of inherited genetic susceptibility remains an area of active investigation. To explore whether germline variation related to inflammatory processes influences susceptibility to BE/EA, we used data from a genome-wide association study (GWAS) of 2,515 EA cases, 3,295 BE cases, and 3,207 controls. Our analysis included 7,863 single nucleotide polymorphisms (SNPs) in 449 genes assigned to five pathways: cyclooxygenase (COX), cytokine signaling, oxidative stress, human leukocyte antigen, and NFκB. A principal components-based analytic framework was employed to evaluate pathway-level and gene-level associations with disease risk. We identified a significant signal for the COX pathway in relation to BE risk (P=0.0059, FDR q=0.03), and in gene-level analyses found an association with MGST1 (microsomal glutathione-S-transferase 1; P=0.0005, q=0.005). Assessment of 36 MGST1 SNPs identified 14 variants associated with elevated BE risk (q<0.05). Of these, four were subsequently confirmed (P<5.5 × 10−5) in a meta-analysis encompassing an independent set of 1,851 BE cases and 3,496 controls. Three of these SNPs (rs3852575, rs73112090, rs4149204) were associated with similar elevations in EA risk. This study provides the most comprehensive evaluation of inflammation-related germline variation in relation to risk of BE/EA, and suggests that variants in MGST1 influence disease susceptibility.
Poljoprivrednikov kalendar
Creators: name: Milovac, Željko
name: Vasiljević, Marjana
Publisher: name: Zenodo
Year: 2022

description: Institute of Field and Vegetable Crops is one of the 18 partner organizations in the "Legumes Translated" project. The project supports innovations in legume cultivation systems through access to knowledge, exchange of experiences and cultivation technology. The working group led by the Institute "Soybean Growing in Southeast Europe" generates knowledge about the technology of growing this plant species. There is an unbreakable link between scientific research and the experience of agricultural producers in defining and disseminating best production practices. The team of the Institute consists of scientists and researchers who have identified challenges in soybean production; one of them is the occurrence of pests in soybean production, what is seen through already published practice notes in English language https://www.legumestranslated.eu/ .
title: Iowa Byington Reed diary 34, January 1, 1935-January 31, 1936
Creators: name: Reed, Iowa Byington
Publisher: name: University of Iowa. Libraries
Year: 2012
Subjects: subject: FOS: History and archaeology
valueUri: http://www.oecd.org/science/inno/38235147.pdf
subject: FOS: History and archaeology
subject: Domestic life
valueUri: http://id.loc.gov/vocabulary/graphicMaterials/tgm003216

description: Iowa Byington Reed's diaries contain daily entries covering her life from age twenty to just a few weeks before her death at age eighty-four (1872-1936).
The global prevalence of IBS in adults remains elusive due to the heterogeneity of studies: a Rome Foundation working team literature review
Creators: name: Hungin, A Pali S.
name: Schmulson, Max
name: Whitehead, William
name: Friger, Michael
name: Freud, Tamar
name: Fukudo, Shin
name: Gwee, Kok Ann
name: Kang, Jin-Yong
name: Dumitrascu, Dan
name: Sperber, Ami D.
name: Gerson, Charles
name: Ghoshal, Uday C.
name: Bolotin, Arkady
name: Minhu, Chen
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: OBJECTIVES: The global prevalence of IBS is difficult to ascertain, particularly in light of the heterogeneity of published epidemiological studies. The aim was to conduct a literature review, by experts from around the world, of community-based studies on IBS prevalence.

DESIGN: Searches were conducted using predetermined search terms and eligibility criteria, including papers in all languages. Pooled prevalence rates were calculated by combining separate population survey prevalence estimates to generate an overall combined meta-prevalence estimate. The heterogeneity of studies was assessed.

RESULTS: 1451 papers were returned and 83, including 288 103 participants in 41 countries, met inclusion criteria. The mean prevalence among individual countries ranged from 1.1% in France and Iran to 35.5% in Mexico. There was significant variance in pooled regional prevalence rates ranging from 17.5% (95% CI 16.9% to 18.2%) in Latin America, 9.6% (9.5% to 9.8%) in Asia, 7.1% (8.0% to 8.3%) in North America/Europe/Australia/New Zealand, to 5.8% (5.6% to 6.0%) in the Middle East and Africa. There was a significant degree of heterogeneity with the percentage of residual variation due to heterogeneity at 99.9%.

CONCLUSIONS: The main finding is the extent of methodological variance in the studies reviewed and the degree of heterogeneity among them. Based on this, we concluded that publication of a single pooled global prevalence rate, which is easily calculated, would not be appropriate or contributory. Furthermore, we believe that future studies should focus on regional and cross-cultural differences that are more likely to shed light on pathophysiology.
The Proton Radius from Electron Scattering Data
Creators: name: Higinbotham, Douglas W.
name: Kabir, Al Amin
name: Lin, Vincent
name: Meekins, David
name: Norum, Blaine
name: Sawatzky, Brad
Publisher: name: arXiv
Year: 2015
Subjects: subject: Nuclear Experiment (nucl-ex)
subject: Mathematical Physics (math-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: [Background] The proton charge radius extracted from recent muonic hydrogen Lamb shift measurements is significantly smaller than that extracted from atomic hydrogen and electron scattering measurements. [Purpose] In an attempt to understand the discrepancy, we review high-precision electron scattering results from Mainz, Jefferson Lab, Saskatoon and Stanford. [Method] We make use of stepwise regression techniques using the $F$-test as well as the Akaike information criterion to systematically determine the predictive variables to use for a given set and range of electron scattering data as well as to provide multivariate error estimates. [Results] Starting with the precision, low four-momentum transfer ($Q^2$) data from Mainz (1980) and Saskatoon (1974), we find that a stepwise regression of the Maclaurin series using the $F$-test as well as the Akaike information criterion justify using a linear extrapolation which yields a value for the proton radius that is consistent with the result obtained from muonic hydrogen measurements. Applying the same Maclaurin series and statistical criteria to the 2014 Rosenbluth results on $G_E$ from Mainz, we again find that the stepwise regression tends to favor a radius consistent with the muonic hydrogen radius but produces results that are extremely sensitive to the range of data included in the fit. Making use of the high-$Q^2$ data on $G_E$ to select functions which extrapolate to high $Q^2$, we find that a Padé ($N=M=1$) statistical model works remarkably well, as does a dipole function with a 0.84 fm radius, $G_E(Q^2) = ( 1 + Q^2/0.66\,\mathrm{GeV}^2)^{-2}$. [Conclusions] From this statistical analysis, we conclude that the electron scattering result and the muonic hydrogen result are consistent. It is the atomic hydrogen results that are the outliers.
description: 10 pages, 7 figures, 7 tables
Generation of 9450 G-code combinations with variable radius, loop number, layer height and feed rate for 3D bioprintable cellularized vascular bioconstructs
Creators: name: Nistor, Alexandru
name: Arjoca, Stelian
Publisher: name: figshare
Year: 2022
Subjects: subject: 110323 Surgery
subject: FOS: Clinical medicine
subject: Additive Manufacturing

description: G-code files of helical tubes of different sizes G-code files were generated using in-house developed Python scripts. The archive contains 9450 G-code files that can be used to 3D-(bio)print helical tubes of different sizes. Files are stored in a hierarchical structure of subfolders.
 Loading files into printer Appropriate file can be loaded into 3D printer or bioprinter. This was developed specifically for Cellink BIO X bioprinter with 3 printheads.
 Filename convention helical-tube_r=Amm_h=Bmm_Cloops_f=Dmmps.gcode where A = helix radius = 0.1  3.0 mm (0.1 mm step) B = height between consecutive layers (loops) = 0.1  0.5 mm (0.05 mm step) C = number of loops of the helix = 10, 20, 30, 40 or 50 loops D = printing feedrate = 1, 2, 3, 4, 5, 6 or 7 mm/s
 Example: helical-tube_r=0.1mm_h=0.1mm_10loops_f=3mmps.gcode
Accessing Data using the Distributed Oceanographic Data System: Integrating Scientific Data Access APIs with the World Wide Web
Creators: name: Gallagher, James
Publisher: name: Zenodo
Year: 1995

description: This presentation provides a general discussion of the DODS data delivery design at the SIGNIDR (Special Interest Group on Networked Information, Discovery, and Retrieval) conference in 1995. 

Summary of the presentation

The slide deck presents the Distributed Oceanographic Data System (DODS) and its architecture for providing scientists with online access to research data using familiar analysis tools. The focus includes the characteristics of research data, the changing landscape of data availability on the Internet, and the challenges associated with network transfer protocols. The author emphasizes the need for a standardized transport mechanism for scientific data access, introducing the Data Access Protocol (DAP) as a solution. The DAP includes three messages: Dataset Descriptor Structure, Dataset Attribute Structure, and a data message. The text also provides insights into the server and client architecture of DODS. The summary concludes with an overview of the current status of DODS, including the development of servers, client-stubs, and ongoing efforts to enhance the protocol and documentation.
The Role of Law in the Treatment Decisions of Doctors
Creators: name: Dent, Chris
Publisher: name: Monash University
Year: 2022
Subjects: Other law and legal studies not elsewhere classified

description: The health system is complex. Regulating those who operate within it, however, is key to the effective promotion of the goals of the system. Regulating individuals can, in turn, be understood in terms of the regulation of their decisions. Julia Black’s ‘decentred regulation’, with her notion of the ‘ungovernable’ individual, is a step in the right path towards understanding the regulation of decisions, but it does not go far enough. With a discussion of the intersection of law and ideas from behavioural economics and psychology, this article explores the regulation of the health system in terms of the embedded decision-making of medical practitioners. The analysis will be rounded out with an assessment of four categories of decisions — conscientious objection, defensive medicine, decisions (properly seen as errors) that lead to patient harm and the prescription of ‘active placebos’.
The Role of Law in the Treatment Decisions of Doctors
Creators: name: Dent, Chris
Publisher: name: Monash University
Year: 2022
Subjects: Other law and legal studies not elsewhere classified

description: The health system is complex. Regulating those who operate within it, however, is key to the effective promotion of the goals of the system. Regulating individuals can, in turn, be understood in terms of the regulation of their decisions. Julia Black’s ‘decentred regulation’, with her notion of the ‘ungovernable’ individual, is a step in the right path towards understanding the regulation of decisions, but it does not go far enough. With a discussion of the intersection of law and ideas from behavioural economics and psychology, this article explores the regulation of the health system in terms of the embedded decision-making of medical practitioners. The analysis will be rounded out with an assessment of four categories of decisions — conscientious objection, defensive medicine, decisions (properly seen as errors) that lead to patient harm and the prescription of ‘active placebos’.
E.M. Jellinek: The Hungarian Connection
Creators: name: Ward, Judit Hajnal
Publisher: name: No Publisher Supplied
Year: 2014

description: This is the second in a series of papers depicting the mostly undocumented life of E.M. Jellinek. This paper establishes the connection between Jellinek Morton, a well-known figure in Hungary in the early part of the 20th Century, and E.M. Jellinek, one of the founders of alcohol studies. Newly found documents in Hungary and at the Rutgers Center of Alcohol Studies Library and Archives provide compelling evidence of this connection and shed some light on the mysterious circumstances of his 1920 disappearance from Hungary. The information in these papers was first presented at the 36th Annual Substance Abuse Librarians and Information Specialists (SALIS) Conference on May 1st, 2014, by seven presenters in a panel entitled “Mystery and speculations: Piecing together E.M. Jellinek’s redemption.”
Bioengineering of Implantable Autologous-based 3D Vascular Bioconstructs using Rapid Prototyping TechniquesG-code files of helical tubes of different sizes
Creators: name: Nistor, Alexandru
name: Arjoca, Stelian
Publisher: name: figshare
Year: 2022
Subjects: subject: 110323 Surgery
subject: FOS: Clinical medicine
subject: Additive Manufacturing

description: G-code files of helical tubes of different sizes G-code files were generated using in-house developed Python scripts. The archive contains 9450 G-code files that can be used to 3D-(bio)print helical tubes of different sizes. Files are stored in a hierarchical structure of subfolders.
 Loading files into printer Appropriate file can be loaded into 3D printer or bioprinter. This was developed specifically for Cellink BIO X bioprinter with 3 printheads.
 Filename convention helical-tube_r=Amm_h=Bmm_Cloops_f=Dmmps.gcode where A = helix radius = 0.1  3.0 mm (0.1 mm step) B = height between consecutive layers (loops) = 0.1  0.5 mm (0.05 mm step) C = number of loops of the helix = 10, 20, 30, 40 or 50 loops D = printing feedrate = 1, 2, 3, 4, 5, 6 or 7 mm/s
 Example: helical-tube_r=0.1mm_h=0.1mm_10loops_f=3mmps.gcode
The role of GPR65 and GALC in Multiple Sclerosis: Establishing the functional consequences of an MS associated variant on chromosome 14q31.3
Creators: name: Liao, Wenjia
Publisher: name: Apollo - University of Cambridge Repository
Year: 2018
Subjects: Multiple Sclerosis
GPR65
GALC

description: Genome-wide association studies have identified an extensive catalogue of unequivocally associated genetic variants, each of which provides a clue to the aetiology of multiple sclerosis (MS). Unfortunately, for the vast majority of these quite how the genetic change contributes to the development of the disease is unknown. However, preliminary work undertaken by one of my predecessors suggested that the functionally relevant variant underlying the association identified on chromosome 14q31.3 might exert its effect by influencing T cell activation in a pH dependent manner. From a genetics perspective the ImmunoChip study showed that the lead most strongly associated single nucleotide polymorphism (SNP) tagging this association was rs74796499, which lies in a region of genome containing two protein coding genes; the lysosomal enzyme galactosylceramidase (GALC) and acid sensing surface receptor G-protein coupled receptor 65 (GPR65). In my thesis I attempted to validate and replicate this finding, and also to explore the possibility of other pH dependent effects of this SNP. In order to undertake this work, I first developed a system capable of maintain cultured cells at a stable pH for prolonged periods. Using this system I was able to show that the activation of human lymphocytes to stimulation with anti-CD3/CD28 antibodies is maximal at neutral pH and reduced in both acidic and alkaline conditions. Unfortunately, I was unable to replicate the provisional finding that carrying the protective allele at rs74796499 resulted in greater inhibition of CD25 expression in acidic conditions. However, I did observe nominally significant evidence that the expression of the early activation marker CD69 was induced by culturing cells in unstimulated but acidic conditions, and that this expression was highest in individuals carrying the protective allele at rs74796499. In my first attempt to validate and replicate this new finding I not only found further evidence to support this effect on CD69 in unstimulated cells but also found nominally significant evidence that the expression of lactosylceramide (LacCer, CD17) was lower in ex-vivo cells from individuals carrying the protective allele at rs74796499. Unfortunately, in my final confirmatory experiments I was unable to replicate either of these effects. In summary despite carefully studying over 160 healthy subjects, I was unable to find any statistically significant evidence that rs74796499 genotype exerts any effects the expression of either CD25, CD69 or LacCer in ex-vivo cells or stimulated and unstimulated cells cultured under a range of pH conditions.