cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Osteoarthritis in England: Incidence Trends From National Health Service Hospital Episode Statistics
Creators: name: Russell, R.
name: Hillstrom, R.
name: Morgan, O.J.
name: Ellis, S.J.
name: Golightly, Y.M.
name: Hannan, M.T.
name: Deland, J.T., III
name: Hillstrom, H.J.
Publisher: name: John Wiley and Sons Inc
Year: 2019

description: Objective: It is typical in epidemiological research of osteoarthritis (OA) to collect data for the hand, hip, and knee. However, little population-based data exist for this disease in the foot. Thus, we addressed patterns of OA for the foot compared with the hand, hip, and knee spanning 2000/2001 to 2017/2018 in England. Methods: Secondary-care data from 3 143 928 patients with OA of the foot, hand, hip, and knee were derived from the National Health Service (NHS) Hospital Episode Statistics (HES) database. Distribution, population prevalence, and incidence of joint-specific OA were stratified by age and sex. Results: OA incidence increased significantly at the foot [3.8% (95% confidence interval [CI] 3.0, 4.6)], hand [10.9% (10.1, 11.7)], hip [3.8% (2.9, 4.7)], and knee [2.9% (2.2, 3.6)] per year from 2000/2001 to 2017/2018. A higher proportion of women were diagnosed with OA, whereas greater incidence in men was estimated for the hand and hip. Foot OA presented comparable diagnosis numbers to the hand. More recently during 2012/2013 to 2017/2018, a significant rise in hip OA was estimated among younger adults, whereas knee OA decreased across all age groups. Incidence of OA in the foot and hand were particularly significant among the 75 or older age group, though bimodal age distributions were observed for both sites. Conclusion: The significant increase in secondary care records for OA in England underscores the importance of exploring possible causative factors and identifying groups most at risk. Further detailed data may be particularly important for the hip, which represents significant incidence among younger adults. Greater incidence of OA in the foot compared with the knee emphasizes the need for well-conducted epidemiological research in this area. Monitoring the performance of surgical outcomes at the population-level for this frequently affected yet understudied site could have substantial potential to reduce the socioeconomic burden it represents to the NHS.
Additional file 4 of Determination of double- and single-stranded DNA breaks in bovine sperm is predictive of their fertilizing capacity
Creators: name: Ribas-Maynou, Jordi
name: Delgado-Bermúdez, Ariadna
name: Mateo-Otero, Yentel
name: Viñolas, Estel
name: Hidalgo, Carlos O.
name: Ward, W. Steven
name: Yeste, Marc
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Additional file 4: Table S3. Correlations between sperm DNA fragmentation, chromatin decondensation and sperm quality and functionality parameters for the second period of incubation.
Orotic Acid Decarboxylation in Water and Nonpolar Solvents: A Potential Role for Desolvation in the Action of OMP Decarboxylase
Creators: name: Wolfenden, Richard
name: Lewis, Charles A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: OMP decarboxylase (ODCase) generates a very large rate enhancement without the assistance of metals or other cofactors. The uncatalyzed decarboxylation of 1-methylorotate in water is shown to involve the monoanion, although uncharged 1-methylorotic acid is decarboxylated at a similar rate. To measure the extent to which the rate of the nonenzymatic decarboxylation of orotate derivatives might be enhanced by their removal from solvent water, the 1-phosphoribosyl moiety of OMP was replaced by 1-substituents that would allow it to enter less polar solvents. When the tetrabuytlyammonium salt of 1-cyclohexylorotate was transferred from water to a series of dipolar aprotic solvents, its rate of decarboxylation increased markedly, varying with the relative ability of each solvent to release the substrate in the ground state from stabilization by solvent water acting as a proton donor. These findings are consistent with the view that separation of the substrate from solvent water may contribute, at least to a limited extent, to the rate enhancement produced by ODCase. This enzyme's active site, like that of another cofactorless enzyme recently shown to produce a rate enhancement of similar magnitude (uroporphyrinogen decarboxylase), is equipped with an ammonium group positioned in such a way as to balance the electrostatic charge of the carboxylate group of the substrate and later supply a proton to the incipient carbanion in a relatively waterless environment.
Supernovae from direct collisions of white dwarfs and the role of helium shell ignition
Creators: name: Papish, Oded
name: Perets, Hagai B.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Models for supernovae (SNe) arising from thermonuclear explosions of white dwarfs (WDs) have been extensively studied over the last few decades, mostly focusing on the single degenerate (accretion of material of a WD) and double degenerate (WD-WD merger) scenarios. In recent years it was suggested that WD-WD direct collisions provide an additional channel for such explosions. Here we extend the studies of such explosions, and explore the role of Helium-shells in affecting the thermonuclear explosions. We study both the impact of low-mass helium ($\sim0.01$ M$_{\odot})$ shells, as well as high mass shells ($\ge0.1$ M$_{\odot}$). We find that detonation of the massive helium layers precede the detonation of the WD Carbon-Oxygen (CO) bulk during the collision and can change the explosive evolution and outcomes for the cases of high mass He-shells. In particular, the He-shell detonation propagates on the WD surface and inefficiently burns material prior to the CO detonation that later follows in the central parts of the WD. Such evolution leads to larger production of intermediate elements, producing large yields of $^{44}{\rm Ti}$ and $^{48}{\rm Cr}$ relative to the pure CO-CO WD collisions. Collisions of WDs with a low-mass He-shell do not give rise to helium detonation, but helium burning does precede the CO bulk detonation. Such collisions produce a high velocity, low-mass of ejected burned material enriched with intermediate elements, with smaller changes to the overall explosion outcomes. The various effects arising from the contribution of low/high mass He layers change the kinematics and the morphological structure of collision-induced SNe and may thereby provide unique observational signatures for such SNe, and play a role in the chemical enrichment of galaxies and the production of intermediate elements and positrons from their longer-term decay.
description: Final version. Accepted for publication in ApJ
Stability Property of Numerical Cherenkov Radiation and its Application to Relativistic Shock Simulations
Creators: name: Ikeya, Naoki
name: Matsumoto, Yosuke
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: We studied the stability property of numerical Cherenkov radiation in relativistic plasma flows employing particle-in-cell simulations. Using the implicit finite-difference time-domain method to solve Maxwell equations, we found that nonphysical instability was greatly inhibited with a Courant-Friedrichs-Lewy (CFL) number of 1.0. The present result contrasts with recently reported results (Vay, J. L., et al. 2011, J. Comp. Phys, 230, 5908; Godfrey. B., & Vay, J. L. 2013, J. Comp. Phys, 243, 260; Xu, X., et al. 2013, Comput. Phys. Commun, 184, 2503) in which magical CFL numbers in the range 0.5-0.7 were obtained with explicit field solvers. In addition, we found employing higher-order shape functions and an optimal implicitness factor further suppressed long-wavelength modes of the instability. The findings allowed the examination of the long-term evolution of a relativistic collisionless shock without the generation of nonphysical wave excitations in the upstream. This achievement will allow us to investigate particle accelerations in relativistic shocks associated with, for example, gamma-ray bursts.
description: 12 pages, 8 figures
Protein Nuclear Magnetic Resonance under Physiological Conditions †
Creators: name: Miklos, Andrew C.
name: Wang, Gui-Fang
name: Zigoneanu, Imola G.
name: Pielak, Gary J.
name: Schlesinger, Alexander P.
name: Li, Conggang
name: Slade, Kristin M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Almost everything we know about protein biophysics comes from studies on purified proteins in dilute solution. Most proteins, however, operate inside cells where the concentration of macromolecules can be >300 mg per mL. Although reductionism-based approaches have served protein science well for over a century, biochemists now have the tools to study proteins under these more physiologically-relevant conditions. We review a part of this burgeoning post-reductionist landscape by focusing on high-resolution protein NMR spectroscopy, the only method that provides atomic-level information over an entire protein under the crowded conditions found in cells.
Structure and Function of Vps15 in the Endosomal G Protein Signaling Pathway ,
Creators: name: Betts, Laurie
name: Sondek, John E.
name: Heenan, Erin J.
name: Temple, Brenda R.
name: Vanhooke, Janeen L.
name: Dohlman, Henrik G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: G protein-coupled receptors mediate cellular responses to a wide variety of stimuli, including taste, light and neurotransmitters. In the yeast Saccharomyces cerevisiae, activation of the pheromone pathway triggers events leading to mating. The view had long been held that the G protein-mediated signal occurs principally at the plasma membrane. Recently, it has been shown that the G protein α subunit Gpa1 can promote signaling at endosomes and requires two components of the sole phosphatidylinositol-3-kinase in yeast, Vps15 and Vps34. Vps15 contains multiple WD repeats and also binds to Gpa1 preferentially in the GDP-bound state; these observations led us to hypothesize that Vps15 may function as a G protein β subunit at the endosome. Here we show an X-ray crystal structure of the Vps15 WD domain that reveals a seven-bladed propeller resembling that of typical Gβ subunits. We show further that the WD domain is sufficient to bind Gpa1 as well as to Atg14, a potential Gγ protein that exists in a complex with Vps15. The Vps15 kinase domain together with the intermediate domain (linking the kinase and WD domains) also contributes to Gpa1 binding, and is necessary for Vps15 to sustain G protein signaling. These findings reveal that the Vps15 Gβ-like domain serves as a scaffold to assemble Gpa1 and Atg14, whereas the kinase and intermediate domains are required for proper signaling at the endosome.
Public Health Interventions for Osteoarthritis - updates on the Osteoarthritis Action Alliance's efforts to address the 2010 OA Public Health Agenda Recommendations
Creators: name: Callahan, L.F.
name: Ambrose, K.R.
name: Altpeter, M.
name: Golightly, Y.M.
name: Nelson, A.E.
name: Albright, A.L.
name: Huffman, K.F.
name: Weisner, S.E.
Publisher: name: NLM (Medline)
Year: 2019

description: Osteoarthritis (OA) is a painful joint disease affecting more than 32.5 million adults in the US and over 350 million adults worldwide. The prevalence is expected to rise continually over the next several decades with significant impacts to societal health and economic costs as well as individuals' daily activities and quality of life. In 2008, the Centers for Disease Control and Prevention (CDC) and the Arthritis Foundation (AF) led a collaborative effort to address approaches to reduce the burden of OA via public health interventions, policies (systems and environmental), and communication strategies. This collaboration resulted in the National Public Health Agenda for OA (OA Agenda), which was vetted by more than 75 stakeholder organisations and released in 2010. The OA Agenda listed ten recommendations focused on public health interventions for OA including weight management, physical activity, self-management education, and injury prevention, and policies, systems, communication, research and evaluation. In 2011, the CDC and AF mobilised the OA Action Alliance (OAAA), a national coalition of organisations concerned with mitigating the public health impact of OA, to operationalise the recommendations set forth in the OA Agenda. Since then, the OAAA has grown to include more than 110 organisations that work collectively to increase awareness about the prevention and management of OA, provide educational resources, and expand access to evidence-based programmes for target audiences including individuals with OA, community-based organisations, healthcare systems and providers, and policymakers. This review highlights the OAAA's progress to date in addressing the OA Agenda recommendations; successes and challenges in delivery of effective communication, programmes, and resources; and future implications.
Age and genetic relationships among CB, CH and CR chondrites
Creators: name: Wölfer, Elias
name: Budde, Gerrit
name: Kleine, Thorsten
Publisher: name: arXiv
Year: 2023
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: The carbonaceous Bencubbin-like (CB), high-metal (CH), and Renazzo-like (CR) chondrites are metal-rich chondrites that have been suggested to be genetically linked and are sometimes grouped together as the CR chondrite clan. Of these, the CB and CH chondrites are thought to have formed in an impact-generated vapor-melt plume from material that may be isotopically akin to CR chondrites. We report Mo, Ti, Cr, and Hf-W isotopic data for CB and CH chondrites in order to determine their formation time, to assess whether these chondrites are genetically related, and to evaluate their potential link to CR chondrites. An internal Hf-W isochron for the CH chondrite Acfer 182 yields an age of 3.8 +- 1.2 Ma after the formation of Ca-Al-rich inclusions (CAIs), which is indistinguishable from the mean Hf-W model age for CB metal of 3.8 +- 1.3 Ma. The Mo isotopic data for CB and CH chondrites indicate that both contain some of the same metal and silicate components, which themselves are isotopically distinct. As such, the different Mo isotopic compositions of bulk CB and CH chondrites reflect their distinct metal-to-silicate ratios. CR metal exhibits the same Mo isotopic composition as CB and CH metal, but CR silicates have distinct Mo and Ti isotopic compositions compared to CB and CH silicates, indicating that CB/CH chondrites may be genetically related to CR metal, but not to CR silicates. Together, the new isotopic data are consistent with formation of CB and CH chondrites in different regions of a common impact-generated vapor- melt plume and suggest that the CB and CH metal may derive from a metal-rich precursor genetically linked to CR chondrites. The Hf-W systematics of CH and CB chondrites indicate that the impact occurred at 3.8 +- 0.8 Ma after the formation of Ca-Al-rich inclusions and, hence, up to ~1 Ma earlier than previously inferred based on Pb- Pb chronology.
description: 54 pages, 8 figures, 5 tables
Additional file 1 of Comparative analysis of stress-induced calcium signals in the crop species barley and the model plant Arabidopsis thaliana
Creators: name: Giridhar, Maya
name: Meier, Bastian
name: Imani, Jafargholi
name: Kogel, Karl-Heinz
name: Peiter, Edgar
name: Vothknecht, Ute C.
name: Chigri, Fatima
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 1. Figures S1 to Figures S9
Structure-Based Design, Synthesis, and Biochemical and Pharmacological Characterization of Novel Salvinorin A Analogues as Active State Probes of the κ-Opioid Receptor
Creators: name: Parker, Carol E.
name: Zjawiony, Jordan K.
name: Roth, Bryan L.
name: Yan, Feng
name: Mocanu, Viorel
name: Wetsel, William C.
name: Dicheva, Nedyalka
name: Allen, John A.
name: Westkaemper, Richard B.
name: Mosier, Philip D.
name: Bikbulatov, Ruslan V.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Salvinorin A, the most potent naturally occurring hallucinogen, has gained increasing attention since the κ-opioid receptor (KOR) was identified as its principal molecular target by us (Roth et al, PNAS, 2002). Here we report the design, synthesis and biochemical characterization of novel, irreversible, salvinorin A-derived ligands suitable as active state probes of the KOR. Based on prior substituted cysteine accessibility and molecular modeling studies, C3157.38 was chosen as a potential anchoring point for covalent labeling of salvinorin A-derived ligands. Automated docking of a series of potential covalently-bound ligands suggested that either a haloacetate moiety or other similar electrophilic groups could irreversibly bind with C3157.38. 22-thiocyanatosalvinorin A (RB-64) and 22-chlorosalvinorin A (RB-48) were both found to be extraordinarily potent and selective KOR agonists in vitro and in vivo. As predicted based on molecular modeling studies, RB-64 induced wash-resistant inhibition of binding with a strict requirement for a free cysteine in or near the binding pocket. Mass spectrometry (MS) studies utilizing synthetic KOR peptides and RB-64 supported the hypothesis that the anchoring residue was C3157.38 and suggested one biochemical mechanism for covalent binding. These studies provide direct evidence for the presence of a free cysteine in the agonist-bound state of KOR and provide novel insights into the mechanism by which salvinorin A binds to and activates KOR.
Keynote: IS THERE A NEW NORMAL?
Creators: name: Shah, David
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: This keynote presentation was presented at the Foresight Centre, University of Liverpool, 17-18 November 2009.

Futurescan: Mapping the Territory
Edited by Sally Wade and Kerry WaltonFebruary 2011ISBN: 978 1 907382 30 7
Valuing Stillbirths: Valuing Stillbirths
Creators: name: Phillips, John
name: Millum, Joseph
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Estimates of the burden of disease assess the mortality and morbidity that affect a population by producing summary measures of health such as quality-adjusted life years (QALYs) and disability-adjusted life years (DALYs). These measures typically do not include stillbirths (fetal deaths occurring during the later stages of pregnancy or during labor) among the negative health outcomes they count. Priority setting decisions that rely on these measures are therefore likely to place little value on preventing the more than three million stillbirths that occur annually worldwide. In contrast, neonatal deaths, which occur in comparable numbers, have a substantial impact on burden of disease estimates and are commonly seen as a pressing health concern. In this paper we argue in favor of incorporating unintended fetal deaths that occur late in pregnancy into estimates of the burden of disease. Our argument is based on the similarity between late-term fetuses and newborn infants and the assumption that protecting newborns is important. We respond to four objections to counting stillbirths: (1) that fetuses are not yet part of the population and so their deaths should not be included in measures of population health; (2) that valuing the prevention of stillbirths will undermine women’s reproductive rights; (3) that including stillbirths implies that miscarriages (fetal deaths early in pregnancy) should also be included; and (4) that birth itself is in fact ethically significant. We conclude that our proposal is ethically preferable to current practice and, if adopted, is likely to lead to improved decisions about health spending.
Spin-structures and proper group actions
Creators: name: Hochs, Peter
name: Mathai, Varghese
Publisher: name: arXiv
Year: 2014
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics

description: We generalise Atiyah and Hirzebruch's vanishing theorem for actions by compact groups on compact Spin-manifolds to possibly noncompact groups acting properly and cocompactly on possibly noncompact Spin-manifolds. As corollaries, we obtain some vanishing results for $\hat A$-type genera.
description: 10 pages, revised
Dynamically weighted clustering with noise set
Creators: name: Shen, Yijing
name: Sun, Wei
name: Li, Ker Chau
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Motivation: Various clustering methods have been applied to microarray gene expression data for identifying genes with similar expression profiles. As the biological annotation data accumulated, more and more genes have been organized into functional categories. Functionally related genes may be regulated by common cellular signals, thus likely to be co-expressed. Consequently, utilizing the rapidly increasing functional annotation resources such as Gene Ontology (GO) to improve the performance of clustering methods is of great interest. On the opposite side of clustering, there are genes that have distinct expression profiles and do not co-express with other genes. Identification of these scattered genes could enhance the performance of clustering methods.Results: We developed a new clustering algorithm, Dynamically Weighted Clustering with Noise set (DWCN), which makes use of gene annotation information and allows for a set of scattered genes, the noise set, to be left out of the main clusters. We tested the DWCN method and contrasted its results with those obtained using several common clustering techniques on a simulated dataset as well as on two public datasets: the Stanford yeast cell-cycle gene expression data, and a gene expression dataset for a group of genetically different yeast segregants.Conclusion: Our method produces clusters with more consistent functional annotations and more coherent expression patterns than existing clustering techniques.Contact: yshen@stat.ucla.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Futurescan - Acknowledgements
Creators: name: Wade, Sally
name: Walton, Kerry
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: Acknowledgements for the Association of Fashion and Textile Courses (FTC) conference and post-conference publication Futurescan: Mapping the Territory.

Futurescan: Mapping the Territory
Edited by Sally Wade and Kerry WaltonFebruary 2011ISBN: 978 1 907382 30 7
The selected contributions and research papers for this publication were presented at the Foresight Centre, University of Liverpool, 17-18 November 2009.
METAL: fast and efficient meta-analysis of genomewide association scans
Creators: name: Willer, Cristen J.
name: Li, Yun
name: Abecasis, Gonçalo R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Summary: METAL provides a computationally efficient tool for meta-analysis of genome-wide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. METAL provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a variety of input file formats.Availability and implementation: METAL, including source code, documentation, examples, and executables, is available at http://www.sph.umich.edu/csg/abecasis/metal/Contact: goncalo@umich.edu
Prevalence of Foot Pain Across an International Consortium of Population-Based Cohorts
Creators: name: Golightly, Y.M.
name: Gill, T.K.
name: Dufour, A.
name: Bowen, C.J.
name: Hill, C.L.
name: Thomas, M.J.
name: Rathod-Mistry, T.
name: Roddy, E.
name: Menz, H.B.
name: Arden, N.K.
name: Gates, L.S.
name: Hannan, M.T.
Publisher: name: John Wiley and Sons Inc.
Year: 2019

description: Objective: Despite the potential burden of foot pain, some of the most fundamental epidemiologic questions surrounding the foot remain poorly explored. The prevalence of foot pain has proven to be difficult to compare across existing studies due to variations in case definitions. The objective of this study was to investigate the prevalence of foot pain in several international population-based cohorts using original data and to explore differences in the case definitions used. Methods: Foot pain variables were examined in 5 cohorts: the Chingford 1000 Women Study, the Johnston County Osteoarthritis Project, the Framingham Foot Study, the Clinical Assessment Study of the Foot, and the North West Adelaide Health Study. One question about foot pain was chosen from each cohort based on its similarity to the American College of Rheumatology pain question. Results: The precise definition of foot pain varied between the cohorts. The prevalence of foot pain ranged from 13% to 36% and was lowest in the cohort in which the case definition specific to pain was used, compared to the 4 remaining cohorts in which a definition included components of pain, aching, or stiffness. Foot pain was generally more prevalent in women and obese individuals and generally increased with age, with the prevalence being much lower in younger participants (ages 20–44 years). Conclusion: Foot pain is common and is associated with female sex, older age, and obesity. Estimates of the prevalence of foot pain are likely to be affected by the case definition used. Therefore, in future population studies, the use of consistent measures of data collection must be considered.
Futurescan - Editor Biographies
Creators: name: Wade, Sally
name: Walton, Kerry
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: Editor Biographies for Association of Fashion and Textile Courses (FTC) conference and post-conference publication Futurescan: Mapping the Territory.
Futurescan: Mapping the Territory
Edited by Sally Wade and Kerry WaltonFebruary 2011ISBN: 978 1 907382 30 7
The selected contributions and research papers from this publication were presented at the Foresight Centre, University of Liverpool, 17-18 November 2009.
Poisson factor models with applications to non-normalized microRNA profiling
Creators: name: Dittmer, Dirk P.
name: Chugh, Pauline E.
name: Eberle, R.
name: Shen, Haipeng
name: Lee, Seonjoo
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Motivation: Next-generation (NextGen) sequencing is becoming increasingly popular as an alternative for transcriptional profiling, as is the case for micro RNAs (miRNA) profiling and classification. miRNAs are a new class of molecules that are regulated in response to differentiation, tumorigenesis or infection. Our primary motivating application is to identify different viral infections based on the induced change in the host miRNA profile. Statistical challenges are encountered because of special features of NextGen sequencing data: the data are read counts that are extremely skewed and non-negative; the total number of reads varies dramatically across samples that require appropriate normalization. Statistical tools developed for microarray expression data, such as principal component analysis, are sub-optimal for analyzing NextGen sequencing data.
title: Armenians in Strasbourg and Berlin: Engagement, Institutions, Diaspora
Creators: name: Tavitian, Nicolas
Publisher: name: The Open University
Year: 2025

description: The thesis explores how diverse routes to engagement help shape, sustain and transform the Armenian diaspora in Strasbourg and Berlin. The Armenian diaspora in these cities has involved both historical and recent migrations from various countries of origin. The most recent waves of migration from the Republic of Armenia and other post-Soviet countries have contributed to significant transformations in these particular locations of the diaspora. These cities are therefore characteristic of a transforming Armenian diaspora, which is still poorly understood.

I build on theories of diasporas being grounded in shared practices and narratives of identity, in which diasporic institutions play a key role. The thesis expands on the concept of ‘diaspora dynamics’, providing empirical evidence that illustrates how differing positionings and orientations 
lead to conditional and negotiated engagement with diasporic institutions.

Based on 72 in-depth, narrative interviews carried out in Berlin and Strasbourg, I find that very diverse family migration histories and trajectories shape how Armenians engage with the diasporic community and institutions along three distinctive routes. The three routes identified are: first, 
directly engaging with familiar Armenian institutions based on a diasporic orientation acquired before migration; second, engaging through newly evolving migrant social networks; and, third, engaging via collective identity mobilising, driven by aspirations towards recognition of key identity-related narratives. Over time, these routes intersect and, in turn, (re)shape diasporic institutions, as well as the narratives of identity and community that they embody and the diasporic practices and projects they stand for.

The thesis contributes to an understanding of diaspora not solely as the result of migration, but as the outcome of diaspora dynamics at work in the specific localities and nations where diasporans live. A better understanding of these processes can inform the work of both policymakers and 
diaspora practitioners.
Relationship of joint hypermobility with ankle and foot radiographic osteoarthritis and symptoms in a community-based cohort
Creators: name: Jordan, J.M.
name: Hannan, M.T.
name: Schwartz, T.A.
name: Cleveland, R.J.
name: Renner, J.B.
name: Golightly, Y.M.
name: Nelson, A.E.
name: Goode, A.P.
name: Hillstrom, H.J.
name: Flowers, P.
name: Kraus, V.B.
Publisher: name: John Wiley and Sons Inc.
Year: 2019

description: Objective. To explore associations of joint hypermobility (a condition where range of motion is greater than normal) with ankle and foot radiographic osteoarthritis (OA) and symptoms in a large community-based cohort of African American and white adults ages 55-94 years old. Methods. Ankle and foot radiographs and joint hypermobility data (Beighton score for joint hypermobility criteria) were available for 848 participants (from 2003 to 2010) in this cross-sectional study. General joint hypermobility was defined as a Beighton score ≥4 (range 0-9); knee hypermobility was defined as hyperextension of at least 1 knee. Standing anteroposterior and lateral foot radiographs were read with standard atlases for Kellgren-Lawrence grade, osteophytes, and joint space narrowing (JSN) at the tibiotalar joint, and for osteophytes and JSN to define OA at 5 foot joints. Ankle or foot symptoms were self-reported. Separate person-based logistic regression models were used to estimate associations of ankle and foot OA and symptom outcomes with hypermobility measures, adjusting for age, sex, race, body mass index, and history of ankle/foot injury. Results. This sample cohort included 577 women (68%) and 280 African Americans (33%). The mean age of the participants was 71 years, with a mean body mass index of 31 kg/m2. The general joint hypermobility of the participants was 7% and knee hypermobility was 4%. Having a history of ankle injury was 11.5%, and foot injury was 3.8%. Although general joint hypermobility was not associated with ankle and foot outcomes, knee hypermobility was associated with ankle symptoms, foot symptoms, and talonavicular OA (adjusted odds ratios of 4.4, 2.4, and 3.0, respectively). Conclusion. Knee joint hypermobility may be related to talonavicular OA and to ankle and foot symptoms.
Iterative Subsampling in Solution Path Clustering of Noisy Big Data
Creators: name: Marchetti, Yuliya
name: Zhou, Qing
Publisher: name: arXiv
Year: 2014
Subjects: subject: Methodology (stat.ME)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: We develop an iterative subsampling approach to improve the computational efficiency of our previous work on solution path clustering (SPC). The SPC method achieves clustering by concave regularization on the pairwise distances between cluster centers. This clustering method has the important capability to recognize noise and to provide a short path of clustering solutions; however, it is not sufficiently fast for big datasets. Thus, we propose a method that iterates between clustering a small subsample of the full data and sequentially assigning the other data points to attain orders of magnitude of computational savings. The new method preserves the ability to isolate noise, includes a solution selection mechanism that ultimately provides one clustering solution with an estimated number of clusters, and is shown to be able to extract small tight clusters from noisy data. The method's relatively minor losses in accuracy are demonstrated through simulation studies, and its ability to handle large datasets is illustrated through applications to gene expression datasets. An R package, SPClustering, for the SPC method with iterative subsampling is available at http://www.stat.ucla.edu/~zhou/Software.html.
description: 17 pages, 7 figures
Additional file 1 of Association between exposure to family planning messages on different mass media channels and the utilization of modern contraceptives among young women in Sierra Leone: insights from the 2019 Sierra Leone Demographic Health Survey
Creators: name: Sserwanja, Quraish
name: Turimumahoro, Patricia
name: Nuwabaine, Lilian
name: Kamara, Kassim
name: Musaba, Milton W.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Science Policy

description: Additional file 1. Rural-Urban stratification of exposure to family planning messages and utilization of modern contraceptives among young women in Sierra Leone.
REFLECT, UNDERSTAND AND PLAN; AN INTEGRATED LEARNING PORTFOLIO
Creators: name: Squires, Paul
name: Redmore, Nicola
name: Tinker, Amanda
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: This research paper was presented at Futurescan: Mapping the Territory, Foresight Centre, University of Liverpool, 17-18 November 2009.

Futurescan: Mapping the Territory
Edited by Sally Wade and Kerry WaltonFebruary 2011ISBN: 978 1 907382 30 7
Sociodemographic and clinical correlates of physical therapy utilization in adults with symptomatic knee osteoarthritis
Creators: name: Callahan, L.F.
name: Goode, A.
name: Hill, C.
name: Huffman, K.
name: Pathak, A.
name: Cooke, J.
name: Allen, K.D.
name: Iversen, M.D.
name: Schwartz, T.A.
name: Heideken, J.
name: Golightly, Y.M.
Publisher: name: Oxford University Press
Year: 2018

description: Background. Physical therapy is essential for conservative management of symptomatic knee osteoarthritis (OA). However, physical therapy utilization data are limited for knee OA. Objective. The purpose of this study is to identify correlates of physical therapy utilization among adults with symptomatic knee OA. Design. The design consisted of secondary analysis using baseline data from a randomized controlled trial of 350 adults with physician-diagnosed symptomatic knee OA. Methods. Patients completed baseline surveys regarding demographics, pain, function, medical history, and prior physical therapy utilization for symptomatic knee OA. Multivariable logistic regression identified correlates of physical therapy utilization, with models adjusted for body mass index and age. Interactions of race and sex with all other characteristics were evaluated. Results. One hundred and eighty-one patients (52%) reported prior physical therapy utilization. Factors independently associated with increased odds of physical therapy utilization were female sex (odds ratio [OR] =3.06, 95% CI = 1.58-5.93), bachelor degree or higher degree (OR = 2.44, 95% CI = 1.15-5.16), prior knee injury (OR = 1.86, 95% CI = 1.08-3.19), and duration of knee OA symptoms (OR = 2.16, 95% CI = 1.09-4.29 for > 5-10 years; OR = 2.11, 95% CI = 1.10-4.04 for > 10 years). Whites who had received a joint injection were > 3 times as likely to have utilized physical therapy (OR = 3.69, 95% CI = 1.94-7.01); this relationship did not exist for non-whites who had received joint injections. Limitations. A sample enrolled in an exercise study may limit generalizability. Self-report of physical therapy may misclassify utilization. It cannot be determined whether lack of utilization resulted from lack of referral or from patients choosing not to attend physical therapy. Conclusion. Physical therapy is underutilized to manage symptomatic knee OA. Women and those with a bachelor degree or higher degree, prior knee injury, and longer duration of knee OA symptoms were more likely to have used therapy previously. Differences by race in the link between joint injection and physical therapy utilization may reflect a reduced likelihood of referral and decreased use of health interventions for symptomatic knee OA among non-whites, or both.
Temperature and doping dependence of normal state spectral properties in a two-orbital model for ferropnictides
Creators: name: Flores, J. D. Querales
name: Ventura, C. I.
name: Citro, R.
name: Rodríguez-Núñez, J. J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Using a second-order perturbative Green's functions approach we determined the normal state single-particle spectral function $A(\vec{k},ω)$ employing a minimal effective model for iron-based superconductors. The microscopic model, used before to study magnetic fluctuations and superconducting properties, includes the two effective tight-binding bands proposed by S.Raghu et al. [Phys. Rev. B 77, 220503 (R) (2008)], and intra- and inter-orbital local electronic correlations, related to the Fe-3d orbitals. Here, we focus on the study of normal state electronic properties, in particular the temperature and doping dependence of the total density of states, $A(ω)$, and of $A(\vec{k},ω)$ in different Brillouin zone regions, and compare them to the existing angle resolved photoemission spectroscopy (ARPES) and previous theoretical results in ferropnictides. We obtain an asymmetric effect of electron and hole doping, quantitative agreement with the experimental chemical potential shifts as a function of doping, as well as spectral weight redistributions near the Fermi level as a function of temperature consistent with the available experimental data. In addition, we predict a non-trivial dependence of the total density of states with the temperature, exhibiting clear renormalization effects by correlations. Interestingly, investigating the origin of this predicted behaviour by analyzing the evolution with temperature of the k-dependent self-energy obtained in our approach, we could identify a number of specific Brillouin zone points, none of them probed by ARPES experiments yet, where the largest non-trivial effects of temperature on the renormalization are present.
description: Manuscript accepted in Physics Letters A on Feb. 25, 2016
Protziella hutchinsoni Lundblad 1934
Creators: name: Pešić, Vladimir
name: Chatterjee, Tapas
name: Bordoloi, Sabitry
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Trombidiformes
Hydryphantidae
Protziella
Protziella hutchinsoni

description: Protziella hutchinsoni Lundblad, 1934
Records from the study area: Kashmir—Lundblad (1934).
Habitat: Mountain springs.
Distribution: India, Afghanistan.
description: Published as part of Pešić, Vladimir, Chatterjee, Tapas & Bordoloi, Sabitry, 2010, A checklist of the water mites (Acari: Hydrachnidia) of India, with new records and description of one new species, pp. 1-54 in Zootaxa 2617 (1) on page 7, DOI: 10.11646/zootaxa.2617.1.1, http://zenodo.org/record/197964
LOST IN TRANSLATION: BUILDING GLOBAL COMMUNITIES THROUGH INTERNATIONAL WORKSHOP DELIVERY - BEIJING, CHINA 2009
Creators: name: Jones, Lucy
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: This research paper was presented at Futurescan: Mapping the Territory, Foresight Centre, University of Liverpool, 17-18 November 2009.

Futurescan: Mapping the Territory
Edited by Sally Wade and Kerry WaltonFebruary 2011ISBN: 978 1 907382 30 7
Mixing Histopathology Prototypes into Robust Slide-Level Representations for Cancer Subtyping
Creators: name: Butke, Joshua
name: Hashimoto, Noriaki
name: Takeuchi, Ichiro
name: Miyoshi, Hiroaki
name: Ohshima, Koichi
name: Sakuma, Jun
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Whole-slide image analysis via the means of computational pathology often relies on processing tessellated gigapixel images with only slide-level labels available. Applying multiple instance learning-based methods or transformer models is computationally expensive as, for each image, all instances have to be processed simultaneously. The MLP-Mixer is an under-explored alternative model to common vision transformers, especially for large-scale datasets. Due to the lack of a self-attention mechanism, they have linear computational complexity to the number of input patches but achieve comparable performance on natural image datasets. We propose a combination of feature embedding and clustering to preprocess the full whole-slide image into a reduced prototype representation which can then serve as input to a suitable MLP-Mixer architecture. Our experiments on two public benchmarks and one inhouse malignant lymphoma dataset show comparable performance to current state-of-the-art methods, while achieving lower training costs in terms of computational time and memory load. Code is publicly available at https://github.com/butkej/ProtoMixer.
description: The final authenticated publication is available online at https://doi.org/10.1007/978-3-031-45676-3_12
Neural responses to infants linked with behavioral interactions and testosterone in fathers
Creators: name: Grewen, Karen M.
name: Carp, Joshua
name: Kuo, Patty X.
name: Light, Kathleen C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Few fMRI studies have investigated the brain-behavioral basis of parenting in human fathers. Ten fathers were videotaped and gave salivary testosterone samples while interacting with their 2–4 month old infants, and viewed video clips of their own infant and an unfamiliar age-, ethnicity- and sex-matched other infant during an fMRI protocol. Infant stimuli activated a network of prefrontal and subcortical brain regions. Furthermore, a subset of these regions activated significantly more to own (OWN) than other (OTHER) infants. Finally, neural responses to OWN versus OTHER were linked with paternal sensitivity, paternal reciprocity, and testosterone. In sum, our results provide a novel perspective on the links between brain, behavior, and hormones in fathers.
THE INSPIRATION BOARD: VISUALLY EVIDENCING THE HERMENEUTIC CIRCLE
Creators: name: Lerpinere, Claire
Publisher: name: FUTURESCAN
Year: 2019
Subjects: subject: 120306 Textile and Fashion Design
subject: FOS: Arts (arts, history of arts, performing arts, music)

description: This research paper was presented at Futurescan: Mapping the Territory, Foresight Centre, University of Liverpool, 17-18 November 2009.

Futurescan: Mapping the Territory
Edited by Sally Wade and Kerry WaltonFebruary 2011ISBN: 978 1 907382 30 7
Novel electronic behavior driving NdNiO3 metal-insulator transition
Creators: name: Upton, M. H.
name: Choi, Yongseong
name: Liu, Jian
name: Meyers, D.
name: Middey, S.
name: Chakhalian, J.
name: Kim, Jong-Woo
name: Ryan, Philip J.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We present evidence that the metal-insulator transition (MIT) in a tensile strained NdNiO3 (NNO) film is facilitated by a redistribution of electronic density and neither requires Ni charge disproportionation nor symmetry change [1, 2]. Given epitaxial tensile strain in thin NNO films induces preferential occupancy of the $e_g$ $d_{x^2-y^2}$ orbital ($s_{3z^2-r^2}$) we propose the larger transfer integral of this orbital state with the O 2p mediates a redistribution of electronic density from the Ni atom. A decrease in Ni $d_{x^2-y^2}$ orbital occupation is directly observed by resonant inelastic x-ray scattering below the MIT temperature. Furthermore, an increase in Nd charge occupancy is measured by x-ray absorption at the Nd L3 edge. Both spin-orbit coupling and crystal field effects combine to break the degeneracy of the Nd 5d states shifting the energy of the Nd $e_g$ $d_{x^2-y^2}$ orbital towards the Fermi level allowing the A site to become an active acceptor during the MI transition. This work identifies the relocation of electrons from the Ni 3d to the Nd 5d orbitals across the MIT. We propose the insulating gap opens between the Ni 3d and O 2p resulting from Ni 3d electron localization mediated by charge loss. The transition seems neither purely Mott-Hubbard nor simple charge transfer.
description: http://dx.doi.org/10.1103/PhysRevLett.115.036401
Sensitization of Transforming Growth Factor-β Signaling by Multiple Peptides Patterned on DNA Nanostructures
Creators: name: Labean, Thomas H.
name: Pedersen, Ronnie O.
name: Loboa, Elizabeth G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: We report sensitization of a cellular signaling pathway by addition of functionalized DNA nanostructures. Signaling by transforming growth factor β (TGFβ) has been shown to be dependent on receptor clustering. By patterning a DNA nanostructure with closely spaced peptides that bind to TGFβ we observe increased sensitivity of NMuMG cells to TGFβ ligand. This is evidenced by translocation of secondary messenger proteins to the nucleus and stimulation of an inducible luciferase reporter at lower concentrations of TGFβ ligand. We believe this represents an important initial step towards realization of DNA as a self assembling and biologically compatible material for use in tissue engineering and drug delivery.