cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Trends and Determinants of Antiretroviral Therapy Patient Monitoring Practices in Kenya and Uganda
Creators: name: Ng, Marie
name: Gakidou, Emmanuela
name: DeCenso, Brendan
name: Njuguna, Pamela
name: Burstein, Roy
name: Achan, Jane
name: Odeny, Thomas A.
name: Masters, Samuel H.
name: Duber, Herbert C.
name: Gasasira, Anne
name: Okiro, Emelda A.
name: Kisia, Caroline
name: Roberts, D. Allen
name: Ikilezi, Gloria
name: Dansereau, Emily
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: IntroductionPatients receiving antiretroviral therapy (ART) require routine monitoring to track response to treatment and assess for treatment failure. This study aims to identify gaps in monitoring practices in Kenya and Uganda.MethodsWe conducted a systematic retrospective chart review of adults who initiated ART between 2007 and 2012. We assessed the availability of baseline measurements (CD4 count, weight, and WHO stage) and ongoing CD4 and weight monitoring according to national guidelines in place at the time. Mixed-effects logistic regression models were used to analyze facility and patient factors associated with meeting monitoring guidelines.ResultsFrom 2007 to 2012, at least 88% of patients per year in Uganda had a recorded weight at initiation, while in Kenya there was a notable increase from 69% to 90%. Patients with a documented baseline CD4 count increased from 69% to about 80% in both countries. In 2012, 83% and 86% of established patients received the recommended quarterly weight monitoring in Kenya and Uganda, respectively, while semiannual CD4 monitoring was less common (49% in Kenya and 38% in Uganda). Initiating at a more advanced WHO stage was associated with a lower odds of baseline CD4 testing. On-site CD4 analysis capacity was associated with increased odds of CD4 testing at baseline and in the future.DiscussionSubstantial gaps were noted in ongoing CD4 monitoring of patients on ART. Although guidelines have since changed, limited laboratory capacity is likely to remain a significant issue in monitoring patients on ART, with important implications for ensuring quality care.
In silico study identifies peptide inhibitors that negate the effect of non-synonymous mutations in major drug targets of SARS-CoV-2 variants
Creators: name: Prasad, Roshny
name: Ajith, Harikrishnan
name: Chandrakumaran, Naveen Kumar
name: Khangar, Pawan Dnyaneshwar
name: Mohan, Anand
name: Nelson-Sathi, Shijulal
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Since its advent in December 2019, SARS-CoV-2 has diverged into multiple variants with differing levels of virulence owing to the accumulation of mutations in its genome. The structural changes induced by non-synonymous mutations in major drug targets of the virus are known to alter the binding of potential antagonistic inhibitors. Here, we analyzed the effects of non-synonymous mutations in major targets of SARS-CoV-2 in response to potential peptide inhibitors. We screened 12 peptides reported to have anti-viral properties against RBD and 5 peptides against Mpro of SARS-CoV-2 variants using molecular docking and simulation approaches. The mutational landscape of RBD among SARS-CoV-2 variants had 21 non-synonymous mutations across 18 distinct sites. Among these, 14 mutations were present in the RBM region directly interacting with the hACE2 receptor. However, Only 3 non-synonymous mutations were observed in Mpro. We found that LCB1 - a de novo-synthesized peptide has the highest binding affinity to RBD despite non-synonymous mutations in variants and engages key residues of RBD-hACE2 interaction such as K417, E484, N487, and N501. Similarly, an antimicrobial peptide; 2JOS, was identified against Mpro with high binding affinity as it interacts with key residues in dimerization sites such as E166 and F140 crucial for viral replication. MD simulations affirm the stability of RBD-LCB1 and Mpro-2JOS complexes with an average RMSD of 1.902 and 2.476 respectively. We ascertain that LCB1 and 2JOS peptides are promising inhibitors to combat emerging variants of SARS-CoV-2 and thus warrant further investigations using in-vitro and in-vivo analysis. Communicated by Ramaswamy H. Sarma
Trends and Determinants of Oral Anti-Diabetic Initiation in Youth with Suspected Type 2 Diabetes
Creators: name: Brookhart, Maurice Alan
name: Girman, Cynthia J.
name: Cai, Mona
name: Jain, Nina
name: Stürmer, Til
name: Kappelman, Michael D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ObjectiveTo evaluate trends and identify predictors of treatment initiation of oral anti-diabetic drugs (OAD) in youth.Patients and MethodsWe identified a select population of children, ages 8–18 years, with at least 13 months of continuous health plan coverage within the years 2001–2012 in a large US commercial insurance claims database. New use of an OAD was defined as the first claim for an outpatient dispensing following a 12-month wash out period. Treatment incidence was estimated monthly over the study period, and stratified by age, gender, geographic region, and provider specialty.ResultsThe median size of the source population during the study period was 2.2 million children. A total of 13,824 initiators (mean monthly incidence of 4.6 (95% CI = 3.6, 5.5) per 100,000 youths) were identified. Initiators were more likely to be females, age 15–18, from the southern region, and have visited a family practitioner (versus a general pediatrician) prior to initiation. Time trends demonstrate a 43% increase in initiation from 2002–2012, with a gradual decrease starting from early 2008.ConclusionIncidence of filled OAD medications in youth increased over time, especially for patients treated by family practitioners. Additional research is needed into factors influencing prescribing by family practitioners and pediatricians.
Trends in Health Care Access/Experiences: Differential Gains across Sexuality and Sex Intersections before and after Marriage Equality
Creators: name: Turpin, Rodman E.
name: Williams, Natasha D.
name: Akré, Ellesse-Roselee L.
name: Boekeloo, Bradley O.
name: Fish, Jessica N.
Publisher: name: MDPI
Year: 2022
Subjects: LGBT
healthcare
national
barriers
services
time series

description: Background: Sexual minority adults experience several health care access inequities compared to their heterosexual peers; such inequities may be affected by LGBTQ+ legislation, such as the 2015 national marriage equality ruling. Methods: Using population-based data (n = 28,463) from the Association of American Medical Colleges biannual Consumer Survey of Health Care Access, we calculated trend ratios (TR) for indicators of health care access (e.g., insurance coverage, delaying or forgoing care due to cost) and satisfaction (e.g., general satisfaction, being mistreated due to sexual orientation) from 2013 to 2018 across sexuality and sex. We also tested for changes in trends related to the 2015 marriage equality ruling using interrupted time series trend interactions (TRInt). Results: The largest increases in access were observed in gay men (TR = 2.42, 95% CI 1.28, 4.57). Bisexual men had decreases in access over this period (TR = 0.47, 95% CI 0.22, 0.99). Only gay men had a significant increase in the health care access trend after U.S. national marriage equality (TRInt = 5.59, 95% CI 2.00, 9.18), while other sexual minority groups did not. Conclusions: We found that trends in health care access and satisfaction varied significantly across sexualities and sex. Our findings highlight important disparities in how federal marriage equality has benefited sexual minority groups.
R-mode frequencies of slowly rotating relativistic neutron stars with realistic equations of state
Creators: name: Idrisy, Ashikuzzaman
name: Owen, Benjamin J.
name: Jones, David I.
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The frequencies of r-mode oscillations of rotating neutron stars can be useful for guiding and interpreting gravitational wave and electromagnetic observations. The frequencies of slowly rotating, barotropic, and non-magnetic Newtonian stars are well known, but subject to various corrections. After making simple estimates of the relative strengths of these corrections we conclude that relativistic corrections are likely to be the most important. For this reason we extend the formalism of K. H. Lockitch, J. L. Friedman, and N. Andersson [Phys. Rev. D 68, 124010 (2003)], who consider relativistic polytropes, to the case of realistic equations of state. This formulation results in perturbation equations which are solved using a spectral method. We find that for realistic equations of state the r-mode frequency ranges from 1.39 to 1.57 times the spin frequency of the star when the relativistic compactness parameter (M/R) is varied over the astrophysically motivated interval 0.11 to 0.31. The results presented here are relevant to the design of gravitational wave and electromagnetic r-mode searches, and following a successful r-mode detection could help constrain the high density equation of state.
description: 16 pages, 5 figures
Trends and Patterns of Urodynamic Studies in U.S. Males, 2000–2012
Creators: name: Wu, Jennifer M.
name: Jonsson Funk, Michele
name: Conover, Mitchell M
name: Borawski, Kristy M.
name: Kinlaw, Alan C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ObjectiveTo evaluate trends in urodynamic procedures in the U.S. males from 2000–2012 and determine if a 2010 decline in reimbursement was associated with decreased utilization.Subjects and methodsWe analyzed 2000–2012 administrative healthcare claims from Truven Health’s Marketscan Database and evaluated males ≥18 years of age. We identified cystometrograms and any concurrent procedures using procedure billing codes. Covariates included age, year of cystometrogram, region and associated diagnosis codes. We estimated standardized cystometrogram utilization rates per 10,000 person-years (PY). We used age, region, and calendar year adjusted Poisson regression models to estimate the independent effect of calendar year and region.ResultsDuring 127,558,186 PY of observation, we identified 153,168 cystometrograms for an overall utilization rate of 12.0 per 10,000 PY (95% CI 11.9–12.1). Cystometrogram utilization increased with age, peaking at age 85 with a rate of 77.7 per 10,000 PY (95% CI 74.7–80.7). Adjusted cystometrogram utilization rate ratios show that compared to a referent of 2000–2004, utilization was significantly higher in each year 2005 to 2011 among all patients and in 2012 among patients ≥ 65. Standardized utilization rates peaked in 2008 at 12.4 per 10,000 PY (95% CI 12.2–12.6), remained elevated until 2010, then decreased slightly in 2011 and substantially in 2012 to 8.5 per 10,000 PY (95% CI 8.4–8.7).ConclusionsUtilization of urodynamic procedures increased until 2010 and decreased thereafter. Utilization was greatest among men older than 65.
Homogeneous coloured multipartite graphs
Creators: name: Lockett, Deborah C
name: Truss, John K
Publisher: name: arXiv
Year: 2014
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics

description: We classify the countable homogeneous coloured multipartite graphs with any finite number of parts. By Fraisse's Theorem this amounts to classifying the families F of pairwise non-embeddable finite coloured multipartite graphs for which the class Forb(F) of multipartite graphs which forbid these is an amalgamation class. We show that once we understand such families F in the quadripartite case, things do not become any more complicated for larger numbers of parts.
description: 27 pages
Integration of VIIRS Observations with GEDI-Lidar Measurements to Monitor Forest Structure Dynamics from 2013 to 2020 across the Conterminous United States
Creators: name: Rishmawi, Khaldoun
name: Huang, Chengquan
name: Schleeweis, Karen
name: Zhan, Xiwu
Publisher: name: MDPI
Year: 2022
Subjects: VIIRS-NOAA 20
GEDI Ecosystem LiDAR
vegetation 3D structure
random forest regression models
airborne discrete return LiDAR
accuracy assessment

description: Consistent and spatially explicit periodic monitoring of forest structure is essential for estimating forest-related carbon emissions, analyzing forest degradation, and supporting sustainable forest management policies. To date, few products are available that allow for continental to global operational monitoring of changes in canopy structure. In this study, we explored the synergy between the NASA’s spaceborne Global Ecosystem Dynamics Investigation (GEDI) waveform LiDAR and the Visible Infrared Imaging Radiometer Suite (VIIRS) data to produce spatially explicit and consistent annual maps of canopy height (CH), percent canopy cover (PCC), plant area index (PAI), and foliage height diversity (FHD) across the conterminous United States (CONUS) at a 1-km resolution for 2013–2020. The accuracies of the annual maps were assessed using forest structure attribute derived from airborne laser scanning (ALS) data acquired between 2013 and 2020 for the 48 National Ecological Observatory Network (NEON) field sites distributed across the CONUS. The root mean square error (RMSE) values of the annual canopy height maps as compared with the ALS reference data varied from a minimum of 3.31-m for 2020 to a maximum of 4.19-m for 2017. Similarly, the RMSE values for PCC ranged between 8% (2020) and 11% (all other years). Qualitative evaluations of the annual maps using time series of very high-resolution images further suggested that the VIIRS-derived products could capture both large and “more” subtle changes in forest structure associated with partial harvesting, wind damage, wildfires, and other environmental stresses. The methods developed in this study are expected to enable multi-decadal analysis of forest structure and its dynamics using consistent satellite observations from moderate resolution sensors such as VIIRS onboard JPSS satellites.
Understanding the High Prevalence of HIV and Other Sexually Transmitted Infections among Socio-Economically Vulnerable Men Who Have Sex with Men in Jamaica
Creators: name: Weir, Sharon S.
name: Hobbs, Marcia M.
name: Byfield, Lovette
name: Figueroa, J. Peter
name: Cooper, Carol Jones
name: Edwards, Jessie K.
name: Eastman, Shashauna
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ObjectivesThis study estimates HIV prevalence among men who have sex with men (MSM) in Jamaica and explores social determinants of HIV infection among MSM.DesignAn island-wide cross-sectional survey of MSM recruited by peer referral and outreach was conducted in 2011. A structured questionnaire was administered and HIV/STI tests done. We compared three groups: MSM who accepted cash for sex within the past 3 months (MSM SW), MSM who did not accept cash for sex (MSM non-SW), and MSM with adverse life events (ever raped, jailed, homeless, victim of violence or low literacy).ResultsHIV prevalence among 449 MSM was 31.4%, MSM SW 41.1%, MSM with adverse life events 38.5%, 17 transgender MSM (52.9%), and MSM non-SW without adverse events 21.0%. HIV prevalence increased with age and number of adverse life events (test for trend P < 0.001), as did STI prevalence (P = 0.03). HIV incidence was 6.7 cases/100 person-years (95% CI: 3.74, 12.19). HIV prevalence was highest among MSM reporting high-risk sex; MSM SW who had been raped (65.0%), had a STI (61.2%) and who self identified as female (55.6%). Significant risk factors for HIV infection common to all 3 subgroups were participation in both receptive and insertive anal intercourse, high-risk sex, and history of a STI. Perception of no or little risk, always using a condom, and being bisexual were protective.ConclusionHIV prevalence was high among MSM SW and MSM with adverse life events. Given the characteristics of the sample, HIV prevalence among MSM in Jamaica is probably in the range of 20%. The study illustrates the importance of social vulnerability in driving the HIV epidemic. Programs to empower young MSM, reduce social vulnerability and other structural barriers including stigma and discrimination against MSM are critical to reduce HIV transmission.
ALUPower: Data Dependent Power Consumption in GPUs - Research Data
Creators: name: Lucas, Jan
name: Juurlink, Ben
Publisher: name: Technische Universität Berlin
Year: 2016
Subjects: subject: 004 Datenverarbeitung; Informatik
subject: data dependent power
subject: GPU
subject: Power modelling

description: Existing architectural power models for GPUs count activities such as executing floating point or integer instructions, but do not consider the data values processed. While data value dependent power consumption can often be neglected when performing architectural simulations of high performance Out-of-Order (OoO) CPUs, in our related paper we show that this approach is invalid for estimating the power consumption of GPUs. The throughput processing approach of GPUs reduces the amount of control logic and shifts the area and power budget towards functional units and register files. This makes accurate estimations of the power consumption of functional units even more crucial than in OoO CPUs. Using measurements from actual GPUs, we have shown that the processed data values influence the energy consumption of GPUs significantly. This file provides the open research data for this paper, including the coefficients employed by our power model.
Using Community-Based Participatory Research Principles to Develop More Understandable Recruitment and Informed Consent Documents in Genomic Research
Creators: name: Garcia, Beverly
name: Schisler, Jonathan C.
name: Skinner, Harlyn G.
name: Patterson, Cam
name: Ammerman, Alice
name: DeMarco, Molly
name: Calancie, Larissa
name: Vu, Maihan B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: BackgroundHeart Healthy Lenoir is a transdisciplinary project aimed at creating long-term, sustainable approaches to reduce cardiovascular disease risk disparities in Lenoir County, North Carolina using a design spanning genomic analysis and clinical intervention. We hypothesized that residents of Lenoir County would be unfamiliar and mistrustful of genomic research, and therefore reluctant to participate; additionally, these feelings would be higher in African-Americans.MethodologyTo test our hypothesis, we conducted qualitative research using community-based participatory research principles to ensure our genomic research strategies addressed the needs, priorities, and concerns of the community. African-American (n = 19) and White (n = 16) adults in Lenoir County participated in four focus groups exploring perceptions about genomics and cardiovascular disease. Demographic surveys were administered and a semi-structured interview guide was used to facilitate discussions. The discussions were digitally recorded, transcribed verbatim, and analyzed in ATLAS.ti.Results and SignificanceFrom our analysis, key themes emerged: transparent communication, privacy, participation incentives and barriers, knowledge, and the impact of knowing. African-Americans were more concerned about privacy and community impact compared to Whites, however, African-Americans were still eager to participate in our genomic research project. The results from our formative study were used to improve the informed consent and recruitment processes by: 1) reducing misconceptions of genomic studies; and 2) helping to foster participant understanding and trust with the researchers. Our study demonstrates how community-based participatory research principles can be used to gain deeper insight into the community and increase participation in genomic research studies. Due in part to these efforts 80.3% of eligible African-American participants and 86.9% of eligible White participants enrolled in the Heart Healthy Lenoir Genomics study making our overall enrollment 57.8% African-American. Future research will investigate return of genomic results in the Lenoir community.
E²MC: Entropy Encoding Based Memory Compression for GPUs
Creators: name: Lal, Sohan
name: Lucas, Jan
name: Juurlink, Ben
Publisher: name: Technische Universität Berlin
Year: 2017
Subjects: subject: 004 Datenverarbeitung; Informatik
subject: memory compression
subject: GPUs
subject: Huffman compression
subject: memory bandwidth
subject: energy efficiency

description: Modern Graphics Processing Units (GPUs) provide much higher off-chip memory bandwidth than CPUs, but many GPU applications are still limited by memory bandwidth. Unfortunately, off-chip memory bandwidth is growing slower than the number of cores and has become a performance bottleneck. Thus, optimizations of effective memory bandwidth play a significant role for scaling the performance of GPUs. Memory compression is a promising approach for improving memory bandwidth which can translate into higher performance and energy efficiency. However, compression is not free and its challenges need to be addressed, otherwise the benefits of compression may be offset by its overhead. We propose an entropy encoding based memory compression (E2MC) technique for GPUs, which is based on the well-known Huffman encoding. We study the feasibility of entropy encoding for GPUs and show that it achieves higher compression ratios than state-of-the-art GPU compression techniques. Furthermore, we address the key challenges of probability estimation, choosing an appropriate symbol length for encoding, and decompression with low latency. The average compression ratio of E2MC is 53% higher than the state of the art. This translates into an average speedup of 20% compared to no compression and 8% higher compared to the state of the art. Energy consumption and energy-delay product are reduced by 13% and 27%, respectively. Moreover, the compression ratio achieved by E2MC is close to the optimal compression ratio given by Shannon's source coding theorem.
High-Rate Crystal/Polycrystal Dislocation Dynamics
Creators: name: Armstrong, Ronald W.
Publisher: name: MDPI
Year: 2022
Subjects: split-Hopkinson pressure bar measurements
shock waves in plate impact and gas-gun impact measurements
shock-front dislocation model generators
dislocation mechanics parameters
constitutive equation predictions
strain rate sensitivity parameters

description: The present report builds upon work recently published on crystal and polycrystal dislocation mechanics behaviors assessed, in part, in split-Hopkinson pressure bar (SHPB) and shock loading investigations. A connection between the flow stress dependencies on strain rate in the different tests had been established in the previous report, whereas additional results are assessed here for (1) relationship of the measurements to a nano-scale prismatic dislocation structure proposed to be generated at a propagating shock front and (2) further relationships between the modeled structure and corresponding thermal stress and strain rate sensitivity computations, including new evaluations of the engineering rate sensitivity parameter, m = [∆lnσ/∆ln(dε/dt)]T. A comparison is made of m values approaching 1.0 for simulated dislocation mechanics results computed for tantalum crystals. Other (lower) m value comparisons involve recently determined higher shock stress measurements made on copper material at higher temperatures.
Wealth distribution of simple exchange models coupled with extremal dynamics
Creators: name: Bagatella-Flores, N.
name: Rodriguez-Achach, M.
name: Coronel-Brizio, H. F.
name: Hernandez-Montoya, A. R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Physics and Society (physics.soc-ph)
subject: General Finance (q-fin.GN)
subject: FOS: Physical sciences
subject: FOS: Economics and business

description: Punctuated Equilibrium (PE) states that after long periods of evolutionary quiescence, species evolution can take place in short time intervals, where sudden differentiation makes new species emerge and some species extinct. In this paper, we introduce and study the effect of punctuated equilibrium on two different asset exchange models: The yard sale model (YS, winner gets a random fraction of a poorer player's wealth) and the theft and fraud model (TF, winner gets a random fraction of the loser's wealth). The resulting wealth distribution is characterized using the Gini index. In order to do this, we consider PE as a perturbation with probability $ρ$ of being applied. We compare the resulting values of the Gini index at different increasing values of $ρ$ in both models. We found that in the case of the TF model, the Gini index reduces as the perturbation $ρ$ increases, not showing dependence with the agents number. While for YS we observe a phase transition which happens around $ρ_c=0.79$. For perturbations $ρ
description: 15 pages, 5 figures. An Econophysics paper
Efficient HEVC Decoder for Heterogeneous CPU with GPU Systems
Creators: name: Wang, Biao
name: Alvarez-Mesa, Mauricio
name: Chi, Chi Ching
name: Juurlink, Ben
name: Souza, Diego F. De
name: Ilic, Aleksandar
name: Roma, Nuno
name: Sousa, Leonel
Publisher: name: Technische Universität Berlin
Year: 2016
Subjects: subject: 004 Datenverarbeitung; Informatik
subject: HEVC Decoder
subject: GPUs

description: The High Efficiency Video Coding (HEVC) standard provides higher compression efficiency than other video coding standards but at the cost of increased computational load, which makes it hard to achieve real-time encoding/decoding of high-resolution, high-quality video sequences. In this paper, we investigate how Graphics Processing Units (GPUs) can be employed to accelerate HEVC decoding. GPUs are known to provide massive processing capability for throughput computing kernels, but the HEVC entropy decoding kernel cannot be executed efficiently on GPUs. We therefore propose a complete HEVC decoding solution for heterogeneous CPU+GPU systems, in which the entropy decoder is executed on the CPU and the remaining kernels on the GPU. Furthermore, the decoder is pipelined such that the CPU and the GPU can decode different frames in parallel. The proposed CPU+GPU decoder achieves an average frame rate of 150 frames per second for Ultra HD 4K video sequences when four CPU cores are used with an NVIDIA GeForce Titan X GPU.
Validity and Reliability of the Brazilian Version of the Rapid Estimate of Adult Literacy in Dentistry – BREALD-30
Creators: name: Junkes, Monica C.
name: Ferreira, Fernanda M.
name: Fraiz, Fabian C.
name: Lee, Jessica Y.
name: Paiva, Saul M.
name: Sardenberg, Fernanda
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ObjectiveThe aim of the present study was to translate, perform the cross-cultural adaptation of the Rapid Estimate of Adult Literacy in Dentistry to Brazilian-Portuguese language and test the reliability and validity of this version.MethodsAfter translation and cross-cultural adaptation, interviews were conducted with 258 parents/caregivers of children in treatment at the pediatric dentistry clinics and health units in Curitiba, Brazil. To test the instrument's validity, the scores of Brazilian Rapid Estimate of Adult Literacy in Dentistry (BREALD-30) were compared based on occupation, monthly household income, educational attainment, general literacy, use of dental services and three dental outcomes.ResultsThe BREALD-30 demonstrated good internal reliability. Cronbach’s alpha ranged from 0.88 to 0.89 when words were deleted individually. The analysis of test-retest reliability revealed excellent reproducibility (intraclass correlation coefficient = 0.983 and Kappa coefficient ranging from moderate to nearly perfect). In the bivariate analysis, BREALD-30 scores were significantly correlated with the level of general literacy (rs = 0.593) and income (rs = 0.327) and significantly associated with occupation, educational attainment, use of dental services, self-rated oral health and the respondent’s perception regarding his/her child's oral health. However, only the association between the BREALD-30 score and the respondent’s perception regarding his/her child's oral health remained significant in the multivariate analysis.ConclusionThe BREALD-30 demonstrated satisfactory psychometric properties and is therefore applicable to adults in Brazil.
Test of mock up coils with dummy cable
Creators: name: I.FAST WP8 members
Publisher: name: Zenodo
Year: 2024

description: In order to verify the developed technologies, tools and techniques for the manufacturing of the high-temperature superconductor canted cosine theta magnet prototype, a mock-up coil with only 6 turns was wound. This document presents the developed infrastructure and techniques, and the manufacturing/winding of the mock-up coil. The document also gives a brief overview of the tests which have led to the presented solution.
Loss of Coastal Wetlands in Lake Burullus, Egypt: A GIS and Remote-Sensing Study
Creators: name: Keshta, Amr E.
name: Riter, J. C. Alexis
name: Shaltout, Kamal H.
name: Baldwin, Andrew H.
name: Kearney, Michael
name: Sharaf El-Din, Ahmed
name: Eid, Ebrahem M.
Publisher: name: MDPI
Year: 2022
Subjects: sea-level rise
land-use management
coastal wetlands
Landsat 8
submerged aquatic vegetation

description: Lake Burullus is the second largest lake at the northern edge of the Nile Delta, Egypt, and has been recognized as an internationally significant wetland that provides a habitat for migrating birds, fish, herpetofauna, and mammals. However, the lake is experiencing severe human impacts including drainage and conversion to agricultural lands and fish farms. The primary goal of this study was to use multispectral, moderate-spatial-resolution (30 m2) Landsat satellite imagery to assess marsh loss in Lake Burullus, Egypt, in the last 35 years (1985–2020). Iterative Self-Organizing Data Analyses (ISODATA) unsupervised techniques were applied to the Landsat 5 Thematic Mapper (TM) and Landsat 8 Operational Land Imager–Thermal Infrared Sensor (OLI–TIRS) satellite images for classification of the Lake Burullus area into four main land-use classes: water, marsh, unvegetated land surfaces (roads, paths, sand sheets and dunes), and agricultural lands and fish farms. The overall classification accuracy was estimated to be 96% and the Kappa index was 0.95. Our results indicated that there is a substantial loss (44.8% loss) in the marsh aerial coverage between 1985 and 2020. The drainage and conversion of wetlands into agricultural lands and/or fish farms is concentrated primarily in the western and southern part of the lake where the surface area of the agricultural lands and/or fish farms doubled (103.2% increase) between 2000 and 2020. We recommend that land-use-policy makers and environmental government agencies raise public awareness among the local communities of Lake Burullus of the economic and environmental consequences of the alarming loss of marshland, which will likely have adverse effects on water quality and cause a reduction in the invaluable wetland-ecosystem services.
Visinets: A Web-Based Pathway Modeling and Dynamic Visualization Tool
Creators: name: Gomez, Shawn
name: Spychala, Pawel
name: Weinreb, Gabriel E.
name: Spychala, Jozef
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: In this report we describe a novel graphically oriented method for pathway modeling and a software package that allows for both modeling and visualization of biological networks in a user-friendly format. The Visinets mathematical approach is based on causal mapping (CMAP) that has been fully integrated with graphical interface. Such integration allows for fully graphical and interactive process of modeling, from building the network to simulation of the finished model. To test the performance of Visinets software we have applied it to: a) create executable EGFR-MAPK pathway model using an intuitive graphical way of modeling based on biological data, and b) translate existing ordinary differential equation (ODE) based insulin signaling model into CMAP formalism and compare the results. Our testing fully confirmed the potential of the CMAP method for broad application for pathway modeling and visualization and, additionally, showed significant advantage in computational efficiency. Furthermore, we showed that Visinets web-based graphical platform, along with standardized method of pathway analysis, may offer a novel and attractive alternative for dynamic simulation in real time for broader use in biomedical research. Since Visinets uses graphical elements with mathematical formulas hidden from the users, we believe that this tool may be particularly suited for those who are new to pathway modeling and without the in-depth modeling skills often required when using other software packages.
A homological upper bound on critical probabilities for hyperbolic percolation
Creators: name: Delfosse, Nicolas
name: Zémor, Gilles
Publisher: name: arXiv
Year: 2014
Subjects: subject: Probability (math.PR)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics

description: We study bond percolation for a family of infinite hyperbolic graphs. We relate percolation to the appearance of homology in finite versions of these graphs. As a consequence, we derive an upper bound on the critical probabilities of the infinite graphs.
Quantum Coherences and Classical Inhomogeneities as Equivalent Thermodynamics Resources
Creators: name: Smith, Andrew
name: Sinha, Kanupriya
name: Jarzynski, Christopher
Publisher: name: MDPI
Year: 2022
Subjects: quantum thermodynamics
quantum coherence
work extraction

description: Quantum energy coherences represent a thermodynamic resource, which can be exploited to extract energy from a thermal reservoir and deliver that energy as work. We argue that there exists a closely analogous classical thermodynamic resource, namely, energy-shell inhomogeneities in the phase space distribution of a system’s initial state. We compare the amount of work that can be obtained from quantum coherences with the amount that can be obtained from classical inhomogeneities, and find them to be equal in the semiclassical limit. We thus conclude that coherences do not provide a unique thermodynamic advantage of quantum systems over classical systems, in situations where a well-defined semiclassical correspondence exists.
Epstein–Barr Virus MicroRNAs Are Evolutionarily Conserved and Differentially Expressed
Creators: name: Raab-Traub, Nancy
name: Schäfer, Alexandra
name: Cullen, Bryan R.
name: Cai, Xuezhong
name: Desrosiers, Ronald C.
name: Lu, Shihua
name: Edwards, Rachel
name: Bilello, John P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: The pathogenic lymphocryptovirus Epstein–Barr virus (EBV) is shown to express at least 17 distinct microRNAs (miRNAs) in latently infected cells. These are arranged in two clusters: 14 miRNAs are located in the introns of the viral BART gene while three are located adjacent to BHRF1. The BART miRNAs are expressed at high levels in latently infected epithelial cells and at lower, albeit detectable, levels in B cells. In contrast to the tissue-specific expression pattern of the BART miRNAs, the BHRF1 miRNAs are found at high levels in B cells undergoing stage III latency but are essentially undetectable in B cells or epithelial cells undergoing stage I or II latency. Induction of lytic EBV replication was found to enhance the expression of many, but not all, of these viral miRNAs. Rhesus lymphocryptovirus, which is separated from EBV by ≥13 million years of evolution, expresses at least 16 distinct miRNAs, seven of which are closely related to EBV miRNAs. Thus, lymphocryptovirus miRNAs are under positive selection and are likely to play important roles in the viral life cycle. Moreover, the differential regulation of EBV miRNA expression implies distinct roles during infection of different human tissues.
Landau-Zener evolution under weak measurement: Manifestation of the Zeno effect under diabatic and adiabatic measurement protocols
Creators: name: Novelli, Anna
name: Belzig, Wolfgang
name: Nitzan, Abraham
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The time evolution and the asymptotic outcome of a Landau-Zener-Stueckelberg-Majorana (LZ) process under continuous weak non-selective measurement is analyzed. We compare two measurement protocols in which the populations of either the adiabatic or the non-adiabatic levels are (continuously and weakly) monitored. The weak measurement formalism, described using a Gaussian Kraus operator, leads to a time evolution characterized by a Markovian dephasing process, which, in the non-adiabatic measurement protocol is similar to earlier studies of LZ dynamics in a dephasing environment. Casting the problem in the language of measurement theory makes it possible for us to compare diabatic and adiabatic measurement scenarios, to consider engineered dephasing as a control device and to examine the manifestation of the Zeno effect under the different measurement protocols. In particular, under measurement of the non- adiabatic populations, the Zeno effect is manifested not as a freezing of the measured system in its initial state, but rather as an approach to equal asymptotic populations of the two diabatic states. This behavior can be traced to the way by which the weak measurement formalism behaves in the strong measurement limit, with a built-in relationship between measurement time and strength.
description: 21 pages, 3 figures, submitted to New J. Phys
Using Timeliness in Tracking Infections †
Creators: name: Bastopcu, Melih
name: Ulukus, Sennur
Publisher: name: MDPI
Year: 2022
Subjects: timely infection tracking
age of information
timely tracking of multiple processes
Markovian infection spread model

description: We consider real-time timely tracking of infection status (e.g., COVID-19) of individuals in a population. In this work, a health care provider wants to detect both infected people and people who have recovered from the disease as quickly as possible. In order to measure the timeliness of the tracking process, we use the long-term average difference between the actual infection status of the people and their real-time estimate by the health care provider based on the most recent test results. We first find an analytical expression for this average difference for given test rates, infection rates and recovery rates of people. Next, we propose an alternating minimization-based algorithm to find the test rates that minimize the average difference. We observe that if the total test rate is limited, instead of testing all members of the population equally, only a portion of the population may be tested in unequal rates calculated based on their infection and recovery rates. Next, we characterize the average difference when the test measurements are erroneous (i.e., noisy). Further, we consider the case where the infection status of individuals may be dependent, which occurs when an infected person spreads the disease to another person if they are not detected and isolated by the health care provider. In addition, we consider an age of incorrect information-based error metric where the staleness metric increases linearly over time as long as the health care provider does not detect the changes in the infection status of the people. Through extensive numerical results, we observe that increasing the total test rate helps track the infection status better. In addition, an increased population size increases diversity of people with different infection and recovery rates, which may be exploited to spend testing capacity more efficiently, thereby improving the system performance. Depending on the health care provider’s preferences, test rate allocation can be adjusted to detect either the infected people or the recovered people more quickly. In order to combat any errors in the test, it may be more advantageous for the health care provider to not test everyone, and instead, apply additional tests to a selected portion of the population. In the case of people with dependent infection status, as we increase the total test rate, the health care provider detects the infected people more quickly, and thus, the average time that a person stays infected decreases. Finally, the error metric needs to be chosen carefully to meet the priorities of the health care provider, as the error metric used greatly influences who will be tested and at what test rate.
A Closer Look in the Mirror: An Investigation into the Association Between Visual Processing and Mirror Neuron System Activity in Autism Spectrum Disorder
Creators: name: RIDDIFORD, JACQUELINE ANNE
Publisher: name: Monash University
Year: 2023
Subjects: Social and affective neuroscience
Cognitive neuroscience

description: Autism is characterised by difficulties with social interaction. This thesis investigated whether differences in brain activity in autism might be explained by differences in what people with autism choose to look at in their social environment. Findings from this thesis showed that people with autism cast their gaze at different parts of a social scene compared to people without autism. However, these social attention differences were not related to differences in brain activity. These findings help us to understand brain differences in autism and provide a new direction for clinical neuroscience research.
A Two-Phase Innate Host Response to Alphavirus Infection Identified by mRNP-Tagging In Vivo
Creators: name: Beard, Clayton W.
name: Keene, Jack D.
name: Konopka, Jennifer L.
name: White, Laura J.
name: Thompson, Joseph M.
name: Johnston, Robert E.
name: Penalva, Luiz O.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: A concept fundamental to viral pathogenesis is that infection induces specific changes within the host cell, within specific tissues, or within the entire animal. These changes are reflected in a cascade of altered transcription patterns evident during infection. However, elucidation of this cascade in vivo has been limited by a general inability to distinguish changes occurring in the minority of infected cells from those in surrounding uninfected cells. To circumvent this inherent limitation of traditional gene expression profiling methods, an innovative mRNP-tagging technique was implemented to isolate host mRNA specifically from infected cells in vitro as well as in vivo following Venezuelan equine encephalitis virus (VEE) infection. This technique facilitated a direct characterization of the host defense response specifically within the first cells infected with VEE, while simultaneous total RNA analysis assessed the collective response of both the infected and uninfected cells. The result was a unique, multifaceted profile of the early response to VEE infection in primary dendritic cells, as well as in the draining lymph node, the initially targeted tissue in the mouse model. A dynamic environment of complex interactions was revealed, and suggested a two-step innate response in which activation of a subset of host genes in infected cells subsequently leads to activation of the surrounding uninfected cells. Our findings suggest that the application of viral mRNP-tagging systems, as introduced here, will facilitate a much more detailed understanding of the highly coordinated host response to infectious agents.
A semi-implicit finite element method for viscous lipid membranes
Creators: name: Rodrigues, Diego S.
name: Ausas, Roberto F.
name: Mut, Fernando
name: Buscaglia, Gustavo C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Numerical Analysis (math.NA)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 65N30, 65Z05, 76D07, 92C37

description: We propose a robust simulation method for phospholipid membranes. It is based on a mixed three-field formulation that accounts for tangential fluidity (Boussinesq-Scriven law), bending elasticity (Canham-Helfrich model) and inextensibility. The unknowns are the velocity, vector curvature and surface pressure fields, all of which are interpolated with linear continuous finite elements. The method is semi-implicit - it requires the solution of a single linear system per time step. Conditional time stability is observed, with a time step restriction that scales as the square of the mesh size. Mesh quality and refinement are maintained by adaptively remeshing. Another ingredient is a numerical force that emulates the action of an optical tweezer, allowing for virtual interaction with the membrane. Extensive relaxation experiments are reported. Comparisons to exact shapes reveal the orders of convergence for position (5/3), vector curvature (3/2), surface pressure (1) and bending energy (2). Tweezing experiments are also presented. Convergence to the exact dynamics of a cylindrical tether is confirmed. Further tests illustrate the robustness of the method (six tweezers acting simultaneously) and the significance of viscous effects on membrane deformation under external forces.
Correction: Type III Effector Activation via Nucleotide Binding, Phosphorylation, and Host Target Interaction
Creators: name: McNulty, Brian C.
name: Sondek, John
name: Singer, Alex U.
name: Nimchuk, Zachary
name: Musselwhite, Laura
name: Dangl, Jeffery L.
name: Desveaux, Darrell
name: Wu, Ai-Jiuan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: The Pseudomonas syringae type III effector protein avirulence protein B (AvrB) is delivered into plant cells, where it targets the Arabidopsis RIN4 protein (resistance to Pseudomonas maculicula protein 1 [RPM1]–interacting protein). RIN4 is a regulator of basal host defense responses. Targeting of RIN4 by AvrB is recognized by the host RPM1 nucleotide-binding leucine-rich repeat disease resistance protein, leading to accelerated defense responses, cessation of pathogen growth, and hypersensitive host cell death at the infection site. We determined the structure of AvrB complexed with an AvrB-binding fragment of RIN4 at 2.3 Å resolution. We also determined the structure of AvrB in complex with adenosine diphosphate bound in a binding pocket adjacent to the RIN4 binding domain. AvrB residues important for RIN4 interaction are required for full RPM1 activation. AvrB residues that contact adenosine diphosphate are also required for initiation of RPM1 function. Nucleotide-binding residues of AvrB are also required for its phosphorylation by an unknown Arabidopsis protein(s). We conclude that AvrB is activated inside the host cell by nucleotide binding and subsequent phosphorylation and, independently, interacts with RIN4. Our data suggest that activated AvrB, bound to RIN4, is indirectly recognized by RPM1 to initiate plant immune system function.
title: Georeferenced birthplaces of identified DTA authors
Creators: name: Lameli, Alfred
Publisher: name: Forschungszentrum Deutscher Sprachatlas
Year: 2024

description: The dataset provides geo-coordinates of the birthplaces of more than 900 authors of the German Text Archive. Birthplaces were identified using the services of the German National Library (DNB), but also other sources such as Wikipedia, and then geocoordinated. The dataset was created in the study by Lameli (2018). It is requested to refer to this study when using the dataset: Lameli, Alfred. 2018. The replacement of diminutive suffixes in the New High German Period – A time series analysis in word formation. In: Journal of Historical Linguistics 8(2), 273–316.