cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Characterization of Thermobifida fusca cellulase activity on unnatural cellulose allomorphs
Creators: name: Liu, Yuxin
Publisher: name: No Publisher Supplied
Year: 2018

description: Cellulases have traditionally been studied in the context of cellulose degradation to fermentable sugars, like glucose, for ethanol production. Cellulose recalcitrance to enzymatic degradation has long been considered as a critical technological barrier for commercialization of cellulosic biofuels. Recent research has led to the development of a cost-effective ammonia-based pretreatment method that allows modification of the crystalline allomorphic structure of cellulose from native cellulose-I to cellulose-III.* Chundawat and co-workers have already demonstrated that cellulose-III is up to five folds more digestible than native cellulose I by Trichoderma reesei derived fungal cellulase enzymes. † This improvement in fungal cellulase cocktail activity was shown to be largely arising due to enhanced endolytic-exolytic cellulase enzyme synergy on pretreated cellulose-III. Here, we explore the activity of cellulases secreted by a highly cellulolytic actinomycete called Thermobifida fusca. To the best of our knowledge, the work here signifies the first reported attempt to characterize the activity of T. fusca expressed cellulase cocktails and purified bacterial cellulases on pretreated cellulose-III. The four specific objectives that were completed to accomplish this goal were; (i) develop and optimize a cell culturing method for T. fusca growth to maximize recovered cellulase activity, (ii) characterize the activity of isolated crude T. fusca cellulase cocktails on native and ammonia-pretreated cellulose allomorphs, (iii) develop a protein purification protocol to isolate and purify T. fusca exocellulase (Cel6B) to electrophoretic homogeneity, and (iv) run enzyme synergism ‘re-start’ hydrolysis assays on isolated exocellulase Cel6B in concert with another bacterial endocellulase (CelE) to confirm if bacterial cellulases also show improved endo- exosynergistic activity on cellulose-III. Our results led further credence to our initial hypothesis that free cellulolytic enzyme cocktails, derived from either fungal or bacterial sources, show enhanced endo-exo synergy on pretreated cellulose-III. We also discuss future research directions and the relevance of the research to our understanding about how cellulases deconstruct various crystalline cellulose allomorphs in general.
Neutrino mass and lepton-asymmetry in Scotogenic model
Creators: name: Satapathy, Sumit
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: In this literature we show how the scotogenic frame work can be a common origin for explaining neutrino mass, lepton asymmetry and give a dark matter candidate. We start out with the extension of the Standard Model with fermions, which are odd under a discrete symmetry, with the SM-like fermions we also have a doublet scalar field like Higgs but odd under discrete symmetry. This model has potential similar to the inert doublet model, which implies we can have a Dark Matter candidate similar to IDM, the Dark matter aspect and calculation of DM parameters are not discussed extensively. In this model, we can calculate the mass of neutrinos from loop corrections that were massless at the tree level, and define a physical mass matrix which requires the inclusion of the Weinberg operator. Then we look at lepton number violation through decays of heavy Majorana neutrinos, these generate a lepton asymmetry, then with the help of sphalerons they convert the excess of lepton number to baryon number, this conversion is quantified by conversion factor. To calculate the number densities we use the Boltzmann equation, and CP asymmetry parameter which gives us the net lepton number produced, at last, the present baryon-to-photon ratio is estimated.
description: 15 pages
Could Nucleobases form in the ISM? A Theoretical Study in the Hoursehead nebula
Creators: name: Coelho, Luciene da Silva
name: Mendoza, Edgar
name: Friaça, Amancio Cesar dos Santos
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences
subject: 85-02

description: This work presents the results of a theoretical study that analyzed the possibility of nucleobases to form in the interstellar medium, in the Horsehead nebula, which is a region considered an archetype of molecular cloud. Performing the Meudon PDR code, the reactions of the nitrogen bases formation from formamide, which is a precursor compound identified in several interstellar environment, where simulated. The model showed that at least cytosine and uracil presented significant abundances. Finally, from thermochemical and quantum calculations, a investigation was carried out on the formation reactions considered for the nucleobases and no insurmountable energy barrier which would prevent the reactions was found.
description: 9 pages, 5 figures
Digital Repository of Mathematical Formulae
Creators: name: Cohl, Howard S.
name: McClain, Marjorie A.
name: Saunders, Bonita V.
name: Schubotz, Moritz
name: Williams, Janelle C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Digital Libraries (cs.DL)
subject: FOS: Computer and information sciences

description: The purpose of the NIST Digital Repository of Mathematical Formulae (DRMF) is to create a digital compendium of mathematical formulae for orthogonal polynomials and special functions (OPSF) and of associated mathematical data. The DRMF addresses needs of working mathematicians, physicists and engineers: providing a platform for publication and interaction with OPSF formulae on the web. Using MediaWiki extensions and other existing technology (such as software and macro collections developed for the NIST Digital Library of Mathematical Functions), the DRMF acts as an interactive web domain for OPSF formulae. Whereas Wikipedia and other web authoring tools manifest notions or descriptions as first class objects, the DRMF does that with mathematical formulae. See http://gw32.iu.xsede.org/index.php/Main_Page.
title: Obesity-Induced Diabetes and Lower Urinary Tract Fibrosis Promote Urinary Voiding Dysfunction in a Mouse Model
Creators: name: Gharaee−Kermani, Mehrnaz
name: Rodriguez-Nieves, Jose A.
name: Macoska, Jill A.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Background: Progressive aging- and inflammation-associated fibrosis effectively remodels the extracellular matrix to increase prostate tissue stiffness and reduce urethral flexibility, resulting in urinary flow obstruction and Lower Urinary Tract Symptoms (LUTS). In the current study we sought to test whether senescence-accelerated mouse prone (SAMP)6 mice, which were reported to develop prostatic fibrosis, would also develop LUTS, and whether these symptoms would be exacerbated by diet-induced obesity and concurrent Type 2 Diabetes Mellitus (T2DM).

Methods: To accomplish this, SAMP6 and AKR/J background strain mice were fed regular mouse chow, low fat diet chow, or high fat diet chow for 8 months, then subjected to glucose tolerance tests, assessed for plasma insulin levels, evaluated for urinary voiding function, and assessed for lower urinary tract fibrosis.

Results: The results of these studies show that SAMP6 mice and AKR/J background strain mice develop diet-induced obesity and T2DM concurrent with urinary voiding dysfunction. Moreover, urinary voiding dysfunction was more severe in SAMP6 than AKR/J mice and was associated with pronounced prostatic and urethral tissue fibrosis. Conclusions: Taken together, these studies suggest that obesity, T2DM, lower urinary tract fibrosis, and urinary voiding dysfunction are inextricably and biologically linked.
title: Cxcl-Type Chemokines−Induced Fibrosis In The Lower Urinary Tract
Creators: name: Gharaee−Kermani, Mehrnaz
name: Macoska, Jill A.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Introduction: Recent studies from our group suggest that extracellular matrix (ECM) deposition and fibrosis characterize the peri−urethral prostate tissues of some men suffering from Lower Urinary Tract Symptoms (LUTS). Fibrosis can generally be regarded as an errant wound−healing process in response to chronic inflammation, and studies have shown that the aging prostate tissue microenvironment is rich with inflammatory cells and proteins. However, it is unclear whether these same inflammatory proteins, particularly CXC−type chemokines, can mediate myofibroblast phenoconversion and the ECM deposition necessary for the development of prostatic tissue fibrosis.

Methods: Peri−urethral prostate tissues were disaggregated and subjected to FACS for expression of CD45 and collagen I. Primary stromal fibroblasts were cultured from explanted human peri−urethral prostatic tissues. N1 immortalized or primary prostate stromal fibroblasts were treated in serum−free defined media with TGF−β, CXCL5, CXCL8, or CXCL12 and evaluated using immunofluorescence or qRT−PCR for αSMA, collagen I, collagen III, vimentin, calponin, and tenascin protein and transcript expression, and by gel contraction assays for functional myofibroblast phenoconversion. The specificity of these responses to treatment with CXCL12 was assessed using a small molecule inhibitor, AMD3100, of the CXCL12 receptor, CXCR4.

Results: The results of these studies showed that peri−urethral prostate tissues comprised both myofibroblastic and fibroblastic cell types, but that CD45+/collagen I+ fibrocytic cells were identified exclusively in peri−urethral tissues from men suffering from LUTS. Both N1 immortalized and primary prostate stromal fibroblasts exhibited complete and functional myofibroblast phenoconversion and were induced to express collagen I, collagen III and αSMA gene transcripts and proteins in response to treatment with CXC−type chemokines, even in the absence of exogenous TGF−β1.

Conclusions: These findings suggest that CXC−type chemokines, particularly CXCL12, can efficiently and completely mediate myofibroblast phenoconversion and may thereby promote fibrotic changes in prostate tissue architecture associated with the development and progression of male lower urinary tract dysfunction.
title: Pathogenesis of Atherosclerosis: Focusing on the Role of Exercise and Flavonoids
Creators: name: Garelnabi, Mahdi
name: Mahini, Halleh
Publisher: name: eScholarship@UMMS
Year: 2013

description: Atherosclerotic coronary artery disease accounts for the majority of death in the world. A number of determinants most of them associated with lifestyle starting from early childhood onwards are responsible for Cardiovascular Diseases (CVD). Some risk factors facilitate the development of atherosclerosis, while others participate in the plaques formation, resulting in the manifestation of the disease.

Objectives: In the current study we investigated the role of exercise and antioxidants intakes; specifically quercetin in mouse model. We looked into the sex responses to the quercetin intake and physical activity. We also looked into the effect of quercetin treatment on HepG2 cell line.

Study design: Animals (males and females), normal and LDL-/- C57BL6 were used in these studies. Animals were fed atherogenic diet and quercetin and subjected to exercise or sedentary life. HpG2 cells were treated at different dosages for several hours. Animal tissues (liver and aorta) and cell harvest analyzed for the level of inflammation, oxidative stress and lipoprotein metabolism gene expression. Adipose tissues were also harvested from these animals; leptin and adiponectin and other related genes were assessed. We also investigated selected miRs namely miR 21, 125b and 451 in atherosclerosis development and progression. These miRs expression were measured in liver and aorta.

Results and conclusion: Interestingly; although we observed significant reduction in atherosclerotic plaque size in exercising and quercetin taking animals; these treatments have shown differential effects on lipoprotein plasma levels and associated gene expression, similar findings were also observed in HepG2 cell culture and in inflammation associated gene expression.
Variations of $α$ and $G$ from nonlinear multidimensional gravity
Creators: name: Bronnikov, K. A.
name: Skvortsova, M. V.
Publisher: name: arXiv
Year: 2013
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: To explain the recently reported large-scale spatial variations of the fine structure constant $α$, we apply some models of curvature-nonlinear multidimensional gravity. Under the reasonable assumption of slow changes of all quantities as compared with the Planck scale, the original theory reduces to a multi-scalar field theory in four dimensions. On this basis, we consider different variants of isotropic cosmological models in both Einstein and Jordan conformal frames. One of the models turns out to be equally viable in both frames, but in the Jordan frame the model predicts simultaneous variations of $α$ and the gravitational constant $G$, equal in magnitude. Large-scale small inhomogeneous perturbations of these models allow for explaining the observed spatial distribution of $α$ values.
description: 11 pages, 2 figures. arXiv admin note: substantial text overlap with arXiv:1301.3098
title: Nationwide Trends in Cardiovascular Disease Spending among the Elderly, 2000-2009
Creators: name: Fouayzi, Hassan
name: Rosen, Allison B.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Background/Aims: One in every six health care dollars is spent on individuals with cardiovascular disease (CVD), and this spending will likely increase as the U.S. population ages. In order to understand the value of our substantial investment in CVD care, it is important to understand trends in CVD spending and, because value varies by patient risk, whether these trends vary across subpopulations with different CVD risk. The aim of this study was to assess national trends in CVD spending among different CVD risk subgroups.

Methods: We examined trends during 2000-2009 in CVD-related and inflation-adjusted average spending using Medicare Current Beneficiary Survey data. We studied a total sample of 35,378 non-institutionalized, fee-for-Service Medicare beneficiaries 65 years or older. Analyses were conducted overall and stratified according to presence of CVD and, in those without CVD, level of CVD risk (high versus low).

Results: From 2000 to 2009, among patients with CVD, overall annual spending increased by 29% (95%CI: 20-39), from $11,726 to $15,109. Medicare and out-of-pocket (OOP) spending increased by 39% (95%CI: 26-51), from $7,017 to $9,741 and by 14% (95%CI: 1-26), from $1,800 to $2,047 respectively. In individuals with high CVD risk, overall spending, Medicare, and out-of-pocket spending increased by 44% (95% CI: 12-76), from $7,204 to $10,404; by 75% (95% CI: 22-129), from $3,789 to $6,657; and by 12% (95% CI: -14-37), from $1,328 to $1,484 respectively. For those at low CVD risk, changes in spending were not statistically significant. Per capita averages in 2009 were: overall: $7,938 (SE=608), Medicare: $4,444 (SE=512), and OOP: $1,567 (SE=107).

Conclusions: We observed significant increases in spending, especially among patients with pre-existing CVD and those at high CVD risk. More research is needed to investigate whether these increases in spending impacted health-related outcomes and whether different CVD subpopulations benefited differently from this spending growth.
Discovery of a Strong Lensing Galaxy Embedded in a Cluster at z = 1.62
Creators: name: Wong, Kenneth C.
name: Tran, Kim-Vy H.
name: Suyu, Sherry H.
name: Momcheva, Ivelina G.
name: Brammer, Gabriel B.
name: Brodwin, Mark
name: Gonzalez, Anthony H.
name: Halkola, Aleksi
name: Kacprzak, Glenn G.
name: Koekemoer, Anton M.
name: Papovich, Casey J.
name: Rudnick, Gregory H.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We identify a strong lensing galaxy in the cluster IRC 0218 (also known as XMM-LSS J02182$-$05102) that is spectroscopically confirmed to be at $z=1.62$, making it the highest-redshift strong lens galaxy known. The lens is one of the two brightest cluster galaxies and lenses a background source galaxy into an arc and a counterimage. With Hubble Space Telescope (HST) grism and Keck/LRIS spectroscopy, we measure the source redshift to be $z_{\rm S}=2.26$. Using HST imaging in ACS/F475W, ACS/F814W, WFC3/F125W, and WFC3/F160W, we model the lens mass distribution with an elliptical power-law profile and account for the effects of the cluster halo and nearby galaxies. The Einstein radius is $θ_{\rm E}=0.38^{+0.02}_{-0.01}$" ($3.2_{-0.1}^{+0.2}$ kpc) and the total enclosed mass is M$_{\rm tot} (< θ_{\rm E})=1.8^{+0.2}_{-0.1}\times10^{11}~{\rm M}_{\odot}$. We estimate that the cluster environment contributes $\sim10$% of this total mass. Assuming a Chabrier IMF, the dark matter fraction within $θ_{\rm E}$ is $f_{\rm DM}^{\rm Chab} = 0.3_{-0.3}^{+0.1}$, while a Salpeter IMF is marginally inconsistent with the enclosed mass ($f_{\rm DM}^{\rm Salp} = -0.3_{-0.5}^{+0.2}$). The total magnification of the source is $μ_{\rm tot}=2.1_{-0.3}^{+0.4}$. The source has at least one bright compact region offset from the source center. Emission from Ly$α$ and [O III] are likely to probe different regions in the source.
description: Accepted for publication in ApJL; emulateapj format; 6 pages, 3 figures, 1 table
A New Class of Complex Ejecta Resulting from the Interaction of two CMEs and its Expected Geoeffectiveness
Creators: name: Lugaz, N.
name: Farrugia, C. J.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: A significant portion of transients measured by spacecraft at 1 AU does not show the well-defined properties of magnetic clouds (MCs). Here, we propose a new class of complex, non-MC ejecta resulting from the interaction of two CMEs with different orientation, which differ from the previously studied multiple-MC event. At 1 AU, they are associated with a smooth rotation of the magnetic field vector over an extended duration and do not show clear signs of interaction. We determine the characteristics of such events based on a numerical simulation and identify and analyze a potential case in the long-duration CME measured in situ in 2001 March 19-22. Such events may result in intense, long-duration geo-magnetic storms, with sawtooth events, and may sometimes be misidentified as isolated CMEs.
description: Accepted to GRL; 5 pages, slightly different figures in print version
Force-Directed Graph Layouts Revisited: A New Force Based on the T-Distribution
Creators: name: Zhong, Fahai
name: Xue, Mingliang
name: Zhang, Jian
name: Zhang, Fan
name: Ban, Rui
name: Deussen, Oliver
name: Wang, Yunhai
Publisher: name: arXiv
Year: 2023
Subjects: subject: Graphics (cs.GR)
subject: Data Structures and Algorithms (cs.DS)
subject: Human-Computer Interaction (cs.HC)
subject: Social and Information Networks (cs.SI)
subject: FOS: Computer and information sciences

description: In this paper, we propose the t-FDP model, a force-directed placement method based on a novel bounded short-range force (t-force) defined by Student's t-distribution. Our formulation is flexible, exerts limited repulsive forces for nearby nodes and can be adapted separately in its short- and long-range effects. Using such forces in force-directed graph layouts yields better neighborhood preservation than current methods, while maintaining low stress errors. Our efficient implementation using a Fast Fourier Transform is one order of magnitude faster than state-of-the-art methods and two orders faster on the GPU, enabling us to perform parameter tuning by globally and locally adjusting the t-force in real-time for complex graphs. We demonstrate the quality of our approach by numerical evaluation against state-of-the-art approaches and extensions for interactive exploration.
description: To appear in IEEE Transactions on Visualization and Computer Graphics
Responsible Conduct of Research Scenario: Conflict of Interest
Publisher: name: Online Ethics Center
Year: 2008
Subjects: Conflict of Interest
Research and Practice

description: This video of a hypothetical scenario was created as part of a series of videos on Responsible Conduct of Research (RCR) by the Office of Research, University of Nebraska-Lincoln and the Collaborative Institutional Training Initiative (CITI). The videos were created by Dan Vasgird, Chet Kincaid, and Virginia Smith.
title: Level of Pain and Disability at Time of TKR across the Past 10 Years: Results from Two National Cohorts
Creators: name: Franklin, Patricia D.
name: Harrold, Leslie R.
name: Snyder, Benjamin
name: Lewis, Courtland
name: Noble, Philip C.
name: Ayers, David C.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Introduction: A recent analysis reported a growing numbers of younger US adults with knee pain consistent with osteoarthritis (OA), although parallel analyses of knee x-rays found no increase in the classic radiographic signs of OA. The accompanying editorial evoked the need to understand if surgeons are performing surgery at an earlier stage in the condition.1 We compared pre-operative demographic and symptom profiles of a national US cohort of OA patients undergoing primary total knee replacement (TKR) in 2011-2012 with a national US cohort of patients from 2000-2004 to evaluate change, if any, in the timing of surgery as measured by patient pain and function.

Methods: Following informed consent, the 2011-2012 national research study collected comprehensive data including demographic, comorbidity, and patient-reported pain and physical function, from a national sample of TKR patients. Comparable data from a national sample collected by one implant manufacturer between 2000-2004 were analyzed. Descriptive statistics compared the demographic and symptom profiles of the two cohorts.

Results: There were fewer females in the 2011-2012 cohort (n=2363) compared to the 2000-2004 cohort (n=7144) (61.62%, vs. 66.72%). The 2011-2012 cohort was younger than the 2000-2004 cohort (66.7 years, vs. 68.12 years) and had a lower mean BMI (31.5 vs 32.3). Pre-operative physical function scores (SF36/PCS) were 3 points higher in 2011-2012 than 2000-2004 (33.2 vs. 30.41). When compared to the national PCS norm of 50 (SD=10), TKR patients from both time periods reported pre-operative function levels almost 2 standard deviations below the national norm. There was no significant difference in terms of emotional health (SF36/MCS scores: 51.85 for the 2011-2012 cohort vs. 51.83 for the 2000-2004 cohort).

Conclusion: Despite the significant growth in the use of primary TKR in the last decade, especially among younger patients, TKR patients continue to report significant disability at the time of surgery.
Responsible Conduct of Research Scenario: Data
Publisher: name: Online Ethics Center
Year: 2008
Subjects: Confidentiality
Data Management
Research and Practice

description: This video of a hypothetical scenariowas created as part of a series of videos on Responsible Conduct of Research (RCR) by the Office of Research at theUniversity of Nebraska-Lincoln and the Collaborative Institutional Training Initiative (CITI). The videos were created by Dan Vasgird, Chet Kincaid, and Virginia Smith.
Ab-Initio Theory of Moiré Superlattice Bands in Layered Two-Dimensional Materials
Creators: name: Jung, Jeil
name: Raoux, Arnaud
name: Qiao, Zhenhua
name: MacDonald, Allan H.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: When atomically thin two-dimensional (2D) materials are layered they often form incommensurate non-crystalline structures that exhibit long-period moir{\' e} patterns when examined by scanning probes. In this paper we present an approach which uses information obtained from {\it ab initio} calculations performed on short-period crystalline structures to derive effective Hamiltonians that are able to efficiently describe the influence of the moir{\' e} pattern superlattices on electronic properties. We apply our approach to the cases of graphene on graphene (G/G) and graphene on hexagonal boron nitride (G/BN), deriving explicit effective Hamiltonians that have the periodicity of the moir{\' e} pattern and can be used to calculate electronic properties of interest for arbitrary twist angles and lattice constants.
description: 20 pages, 24 figures
Responsible Conduct of Research Scenario: Research Misconduct
Publisher: name: Online Ethics Center
Year: 2008
Subjects: Fabrication
Falsification
Handling Misconduct Allegations
Research and Practice
Research Misconduct

description: This video of a hypothetical scenario was created as part of a series of videos on Responsible Conduct of Research (RCR) by the Office of Research, University of Nebraska-Lincoln and the Collaborative Institutional Training Initiative (CITI). The videos were created by Dan Vasgird, Chet Kincaid, and Virginia Smith.
title: Who Opens Alerts to Physicians? (And Who Doesn’t?)
Creators: name: Field, Terry S.
name: Fouayzi, Hassan
name: Cutrona, Sarah L.
name: Gagne, Shawn J.
name: Ogarek, Jessica
name: Sundaresan, Devi
name: Garber, Lawrence D.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Background: Electronic medical records (EMR) provide opportunities to implement systems of information flow, such as alerts to providers.

Methods: Within a group practice with an EMR, we conducted a trial of automated alerts to the in-baskets of primary care physicians and staff when patients were discharged from hospital to home. We generated alerts for new medications or monitoring needs. Staff received alerts to schedule office visits. Using EMR “digital crumbs”, we tracked when alerts were viewed. We analyzed the impact of physician age, gender, department, and employment status (full-time, part-time) as well as patient conditions (age, gender, comorbidity, and number of office visits in the previous year) on timely opening.

Results: Of 763 alerts to physicians, 616 (81%) were opened within one day. Characteristics associated with timely opening were age < 50 (OR 1.7, 95% CI 1.1, 2.6) and full-time employment (OR 2.9, 95% CI 1.6, 5.2). Of 1928 alerts to staff, 1173 (61%) were opened within one day. Staff of male physicians were more likely to open the alerts within one day (OR 1.8, 95% CI 1.4, 2.4) as were working for the Family Medicine department (OR 1.9, 95% CI 1.3, 2.6) or a sub-specialty department (OR 16.6, 95% CI 2.3, 122.3). Staff of full-time physicians were less likely to open alerts (OR 0.64, 95% CI 0.47, 0.87). Adjusting for patient characteristics had no impact on results.

Conclusion: Special efforts may be required to reach physicians working part-time and older physicians. Characteristics related to staff opening of alerts are specific to this group practice, but the high level of variability across physician types and departments is likely to be an issue in many settings. Design of a system directed at reaching staff quickly may require in-depth assessment of work flow and communication patterns in clinical departments.
Probing dipole-forbidden autoionizing states by isolated attosecond pulses
Creators: name: Chu, Wei-Chun
name: Morishita, Toru
name: Lin, C. D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We propose a general technique to retrieve the information of dipole-forbidden resonances in the autoionizing region. In the simulation, a helium atom is pumped by an isolated attosecond pulse in the extreme ultraviolet (EUV) combined with a few-femtosecond laser pulse. The excited wave packet consists of the $^1S$, $^1P$, and $^1D$ states, including the background continua, near the $2s2p(^1P)$ doubly excited state. The resultant electron spectra with various laser intensities and time delays between the EUV and laser pulses are obtained by a multilevel model and an ab initio time-dependent Schrödinger equation calculation. By taking the ab initio calculation as a "virtual measurement", the dipole-forbidden resonances are characterized by the multilevel model. We found that in contrast to the common assumption, the nonresonant coupling between the continua plays a significant role in the time-delayed electron spectra, which shows the correlation effect between photoelectrons before they leave the core. This technique takes the advantages of ultrashort pulses uniquely and would be a timely test for the current attosecond technology.
description: 10 pages, 6 figures
title: Intervention to Reduce Adverse Outcomes among Older Adults Discharged from Skilled Nursing Facilities to Home
Creators: name: Field, Terry S.
name: Ogarek, Jessica
name: Kanaan, Abir O.
name: Donovan, Jennifer L.
name: Preusse, Peggy
name: Sundaresan, Devi
name: Gagne, Shawn J.
name: Garber, Lawrence D.
name: Tjia, Jennifer
name: Cutrona, Sarah L.
name: Gurwitz, Jerry H.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Background: Older adults may be at risk for adverse outcomes after discharge from skilled nursing facilities (SNF), but little research has focused on this transition.

Objective: To assess the impact of an alert system on the rates of adverse outcomes among older adults discharged from SNFs to home.

Methods: Within a multispecialty group practice, we tracked 30-day re-hospitalizations after SNF discharges during an intervention that provided discharge alerts to primary care physicians. We compared them to discharges from the pre-intervention period matched on age, gender and SNF. For the first 100 intervention discharges and their matches, we performed chart reviews to identify adverse drug events (ADEs). Multivariate analyses controlled for age, gender and intervention status.

Results: We matched 313 intervention SNF discharges to 313 previous discharges. There was a slight reduction in the rate of 30-day re-hospitalization (30% vs. 31%) adjusted. Within the ADE study, 30% of the discharges during the intervention period and 30% of matched discharges had ADEs within 45 days. Among the 83 ADEs identified, 28% were deemed preventable; 69% resulted in symptom duration more than one day; 69% occurred within the first 14 days after discharge. This was a highly vulnerable population: mean age 82.5 (standard deviation (SD) 6.7); mean number of prescribed medications 11.9 (SD 8); 17% had Charlson Comorbidity Scores of ≥4. Common clinical conditions included myocardial infarction (24%), heart failure (22%), COPD (23%), and major depression (28%). Patients with scores of ≥4 were more likely to experience an ADE than those with lower scores (adjusted OR 2.5 (CI 1.2, 5.5), RD 0.21).

Conclusion: Simply providing alerts when these vulnerable patients are discharged from SNFs is not sufficient to lower rates of adverse outcomes. Further research is required to track trajectories and identify additional points for interventions.
title: Statin Discontinuation among Nursing Home Residents with Advanced Dementia
Creators: name: Tjia, Jennifer
name: Cutrona, Sarah L.
name: Peterson, Daniel J.
name: Briesacher, Becky A.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Background: Statin use in elderly individuals with life-limiting illness such as advanced dementia is controversial.

Objective: To describe factors associated with statin discontinuation and estimate impact of discontinuation on 28-day hospitalizations in nursing home (NH) residents with advanced dementia.

Methods: Retrospective cohort study of NH residents ≥ 65 years with recent progression to advanced dementia from 5 large U.S. states drawn from the 2007-2008 Minimum Data Set 2.0. We identified residents using statins. Clinical characteristics and 28-day hospitalization risk were compared for residents discontinuing and continuing statins. Multivariable Cox proportional hazard models identified factors associated with time to statin discontinuation and time to hospitalization. Sensitivity analysis using self-controlled case series examined the role of confounding-by-indication on risk estimation from the cohort approach.

Results: Of 10,212 residents with decline to advanced dementia, 16.6% were prescribed statins (n=1,699). Statin users had mean age of 83.1 yrs, 68.9% were female, and mean medication burden was 10.3 (SD 4.8, range 1-31). Over one-third (n=632) discontinued in follow-up. Median time to discontinuation was 36 days after decline to advanced dementia (IQR [25%, 75%]: 12 days, 110 days). After adjustment, factors independently associated with increased hazard of discontinuation included residence in a NH in Florida relative to California, hospitalization in the 30 days prior to decline to advanced dementia, greater medication burden, and having cancer. The 28-day hospitalization risk was higher for residents discontinuing statins compared to continuing (adjusted hazard ratio = 1.78, CI 1.61,2.58). The SCCS estimate for 28-day hospitalization risk following statin discontinuation compared to a 28-day pre-discontinuation control period was lower than the cohort estimate (IRR= 0.79, CI 0.76, 0.83).

Conclusion: A significant proportion of nursing home residents with dementia who use statins when they progress to advanced stage disease discontinue use. Hospitalization outcomes following discontinuation differ depending on method of estimation.
Epitaxial hexagonal boron nitride on Ir(111): A work function template
Creators: name: Schulz, Fabian
name: Drost, Robert
name: Hämäläinen, Sampsa K.
name: Demonchaux, Thomas
name: Seitsonen, Ari P.
name: Liljeroth, Peter
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Hexagonal boron nitride (h-BN) is a prominent member in the growing family of two-dimensional materials with potential applications ranging from being an atomically smooth support for other 2D materials to templating growth of molecular layers. We have studied the structure of monolayer h-BN grown by chemical vapour deposition on Ir(111) by low-temperature scanning tunneling microscopy (STM) and spectroscopy (STS) experiments and state-of-the-art density functional theory (DFT) calculations. The lattice-mismatch between the h-BN and Ir(111) surface results in the formation of a moiré superstructure with a periodicity of $\sim$29 Å and a corrugation of $\sim$0.4 Å. By measuring the field emission resonances above the h-BN layer, we find a modulation of the work function within the moiré unit cell of $\sim$0.5 eV. DFT simulations for a 13-on-12 h-BN/Ir(111) unit cell confirm our experimental findings and allow us to relate the change in the work function to the subtle changes in the interaction between boron and nitrogen atoms and the underlying substrate atoms within the moiré unit cell. Hexagonal boron nitride on Ir(111) combines weak topographic corrugation with a strong work function modulation over the moiré unit cell. This makes h-BN/Ir(111) a potential substrate for electronically modulated thin film and hetero-sandwich structures.
description: 8 pages, 5 figures
title: A Multicenter Phase 2 Study Incorporating High-Dose Rituximab into the CODOX-M/IVAC Regimen for Untreated Burkitt’s Lymphoma (BL): Examination of Correlative Serum and CSF Rituximab Levels
Creators: name: Evens, Andrew
name: Islam, Nahida
name: Carson, Kenneth
name: Browning, Victoria
name: Nabhan, Chadi
name: Jovanovic, Borko
name: Barr, Paul M.
name: Caimi, Paoli
name: Gregory, Stephanie A.
name: Kolesar, Jill M.
name: Gordon, Leo I.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Background: Two-year survival rates for adult BL remain

Methods: Twenty-five BL patients were enrolled. Patients had low-risk (LR) or high-risk (HR) disease; LR patients received 3 CODOX-M cycles, while HR had 4 alternating CODOX-M/IVAC cycles (Mead et al. Blood 2009). Rituximab (500mg/m2) was given x 2 doses each cycle. Correlative analyses of paired serum and CSF Rituximab levels were obtained for cycles 1+3 at 24+72 hours.

Results: There were 20 HR and 5 LR patients and median age was 44 years (range, 23-70). 3 HR and 1 LR patient were HIV+, while 15% of HR patients had CNS disease. Additionally, 35% of HR patients had bulk >10 cm and 40% had bone marrow involvement. Myelosuppression and mucositis appeared comparable with prior CODOX-M/IVAC data. The overall remission rate after 2 cycles was 100% with 67% complete remission. At 34-month median follow-up, 2-year PFS and OS rates for all patients were 86% and 86%, respectively (LR 2-year PFS and OS: both 100%; HR 2-year PFS and OS: both 82%). Further, the 2-year PFS and OS for HR, HIV-negative patients were 91% and 91%, respectively (disease-specific survival 100%). Two patients died from progressive disease (both HIV+ HR). The median serum and CSF rituximab levels for these patients were compared with patients without relapse (Table 1). Interestingly, cycle 1, 24-hour serum Rituximab levels were significantly higher among patients without relapse compared with the two patients who relapsed/died (P=0.042). Cycle 3, 24-hour Rituximab levels were of borderline significance (P=0.06).

Conclusions: The integration of Rituximab into CODOX-M/IVAC was associated with excellent survival rates, especially for HIV-negative BL. Further investigation of the predictive value of serum Rituximab levels is warranted.
title: Framing Hospital Engagement for the Recruitment of a Birth Cohort for the NCS: Lessons Learned for Ensuring Collaboration in Worcester County
Creators: name: Felice, Marianne E.
name: Moore Simas, Tiffany A.
name: Sepavich, Deidre M.
name: Brenckle, Linda
name: McLaughlin, Thomas J.
name: Aupont, Onesky
Publisher: name: eScholarship@UMMS
Year: 2013

description: In 2011, three designated NCS Study Centers began preparatory work for field implementation of a planned recruitment strategy called Provider Based Sampling (PBS). In each PBS primary sampling unit, three hospitals were selected to test the feasibility of recruiting a cohort of 125 women and their babies around delivery time. The selected hospitals for Worcester account for nearly 80% of County births and can be categorized into three distinct facility types and patient catchment areas: an academic medical center; a university-affiliated but independent community hospital; and a private for-profit community hospital with market share competitor of the academic medical center.

Methods: We used tailored negotiations and engagement strategies to gain the cooperation and engagement of targeted hospitals/birthing centers.

Preliminary Conclusions: The lessons learned from this exercise are:
• Time to gain hospital engagement and clearance to initiate study activities ranges anywhere from 2 weeks to 2 months and depends largely upon the type of the institution, the profile of the Negotiator, and the nature of the scope of work.
• A greater likelihood of hospital engagement in the NCS seems to be associated with the depth of existing relationships between the Study Center and targeted hospitals.
• Thoughtful interactions and timely discussions with the key institutional stakeholders (either individually or in groups) are important to achieve collaboration and engagement.
• Balancing sensitivity to clinical cultures and settings while preserving research integrity is essential for study implementation in busy hospital/clinical environments.
• Planning for site compensation and/or the ability to support local clerical staff to help with study activities must be considered as a means to facilitate negotiations and site engagement.
• Adequate resources must be planned for successful implementation and execution of research activities in settings (e.g community hospitals) unfamiliar with research activities.
• Involvement of nursing personnel is crucial for successful implementation of any protocol.
title: Setting Proper Matrices for Accelerometry-based Physical Activity Measures in Older Women
Creators: name: Duckham, Rachel
name: Crouter, Scott
name: Churchill, Linda C.
name: Kane, Kevin J.
name: Franklin, Patricia D.
name: Li, Wenjun
Publisher: name: eScholarship@UMMS
Year: 2013

description: BACKGROUND: Accelerometers to objectively measure physical activity (PA) among adults and youth are widespread, with few studies in the older population. Optimal PA cut-points in older adults who are often frail and/or have limited function still remain unclear.

PURPOSE: To compare the level of PA in older women with lower extremity problems using existing PA cut-points.

METHODS: Women (N=89) aged 65 to 85 years were instructed to wear an Actigraph accelerometer for seven consecutive days. Wear-time and activities away from the home were recorded daily. Questionnaires were used to assess participant sociodemographic attributes, lower extremity and comorbid conditions. PA was defined using cut-points identified in the literature (Freedson, Copeland (one axis) and Carr (vector)). Weekly minutes of sedentary, light, moderate and vigorous activity was compared among age groups, and those with or without lower extremity problems affecting walking.

RESULTS: Preliminary data of 72 women with valid accelerometry measures (> 6 consecutive days of >8 hours of daily wearing time). According to the Freedson cut-points, average weekly minutes of light, moderate and vigorous PA were 4,674 (612, 8,520), 24.0 (range 0, 1,050) and 6.6 (range: 0, 330), respectively. Application of Copeland and Carr cut-points yielded similar patterns. Such patterns were persistent when the analysis was stratified by age group (=75y) and whether having any lower extremity problem affecting walking.

CONCLUSION: The existing cut-points for PA are ineffective in differentiation of active and inactive older. Age-appropriate cut-points for PA need to be established in older adults. Due to the lack of time spent in moderate/vigorous PA, health promotions may consider focusing on decreasing sedentary time and increasing time spent in light PA rather than promoting 150 minutes per week of moderate/vigorous PA in older adults.
Co-selection of metal and antibiotic resistance in the gut microbial community of the Mummichog fish (Fundulus heteroclitus)
Creators: name: Lloyd, Nicole A.
Publisher: name: No Publisher Supplied
Year: 2018

description: Microbial resistance to antibiotics is one of the most pressing health care concerns we are currently facing.  Antibiotic resistance can be selected for by metals through the process known as co-selection.  Co-selection occurs through two primary mechanisms: i) co-resistance, when genes encoding both are located together in the genome and ii), cross-resistance, when the same mechanism provides resistance to both (e.g. efflux pump proteins).  This thesis describes co-selection in the gut microbiota of a forage feeder fish, the mummichog (Fundulus heteroclitus).   By comparing gut microbiota from fish from a mercury contaminated site and a relatively clean site, we established the mummichog gut as a reservoir of antibiotic and mercury resistant microbiota.  We further examined three representative isolates with interesting antibiotic and metal resistant profiles.  Genome analyses revealed few instance of co-resistance, and instead, presented various chromosomally-encoded resistance genes, including some of public health concern, (i.e. a blaOXA carbapenemase), and contributions from cross-resistance. All three organisms contained a large number of efflux pump proteins, including multiple RND efflux pump operons.  Testing of the strains shows that RND efflux pumps may be involved in resistance to several classes of drugs. A transcriptomic study is in progress to understand the regulation of arsenate resistance and the potential involvement of RND efflux pumps under metal stress. Together, this work describes the abundance and inventory of antibiotic resistance genes and mechanisms in the mummichog gut microbiome and establishes the fish gut as a reservoir of such genes.  This work further adds to the understanding of the role of RND efflux pumps in resistance to antibiotics, which is critical in understanding multi-drug resistance in Gram negative bacteria.
"If I Had All the Time in the World": Ophthalmologists' Perceptions of Anchoring Bias Mitigation in Clinical AI Support
Creators: name: Bach, Anne Kathrine Petersen
name: Nørgaard, Trine Munch
name: Brok, Jens Christian
name: van Berkel, Niels
Publisher: name: arXiv
Year: 2023
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Clinical needs and technological advances have resulted in increased use of Artificial Intelligence (AI) in clinical decision support. However, such support can introduce new and amplify existing cognitive biases. Through contextual inquiry and interviews, we set out to understand the use of an existing AI support system by ophthalmologists. We identified concerns regarding anchoring bias and a misunderstanding of the AI's capabilities. Following, we evaluated clinicians' perceptions of three bias mitigation strategies as integrated into their existing decision support system. While clinicians recognised the danger of anchoring bias, we identified a concern around the impact of bias mitigation on procedure time. Our participants were divided in their expectations of any positive impact on diagnostic accuracy, stemming from varying reliance on the decision support. Our results provide insights into the challenges of integrating bias mitigation into AI decision support.
description: CHI '23
Direct simulation of critical Casimir forces
Creators: name: Hobrecht, Hendrik
name: Hucht, Alfred
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We present a new Monte Carlo method to calculate Casimir forces acting on objects in a near-critical fluid, considering the two basic cases of a wall and a sphere embedded in a two-dimensional Ising medium. During the simulation, the objects are moved through the system with appropriate statistical weights, and consequently are attracted or repelled from the system boundaries depending on the boundary conditions. The distribution function of the object position is utilized to obtain the residual free energy, or Casimir potential, of the configuration as well as the corresponding Casimir force. The results are in perfect agreement with known exact results. The method can easily be generalized to more complicated geometries, to higher dimensions, and also to colloidal suspensions with many particles.
description: 6 pages, 6 figures
DOLOMITIZATION RELATED TO FRACTURE POROSITY EVOLUTION: A CASE STUDY IN PERMIAN RATBURI CARBONATE OUTCROP, YAT PHO SILA THONG DOLOMITE QUARRY KRABI, SOUTHERN THAILAND
Creators: name: Maradona Mansyur
Publisher: name: Department of Geology, Chulalongkorn University
Year: 2012
Subjects: Carbonate, Permian, Dolomitization, Fractures

description: Bulletin of Earth Sciences of Thailand (BEST), 5, 2, 58-67