cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Inner and Internal Areas in the European Cohesion Policies
Creators: name: Scanu, Giuseppe
name: Donato, Carlo
name: Mariotti, Gavino
name: Madau, Caterina
name: Camerada, Veronica
name: Battino, Silvia
name: Podda, Cinzia
name: Lampreu, Salvatore
Publisher: name: Bollettino della Società Geografica Italiana
Year: 2020

description: Taking as its point of reference the growth objectives of the Horizon 2020 project, the present study aims to present a new approach to identify policies for local development that are useful for promoting territorial cohesion in areas that represent spatial and/or functional peripheries. Beginning from a precise conceptualisation of these zones, based on definitions of inner and internal areas, the study first assesses the results that have been achieved with the funds that have been spent so far. It then focuses on specific indicators – mapped on the NUTS 2 and 3 levels to the end of applying the STeMA-TIA model – which are relevant to those factors of Smart, Sustainable and Inclusive Growth considered important for both geographical categories. Quantitative and qualitative analysis of these indicators, supported by pertinent graphic representations, produced a picture of local conditions which allowed us to pinpoint those objectives which still must be achieved and to identify developmental axes which should be given priority for the implementation of even more ‘localised’ policies. In presenting a reading that is fundamentally geographical and economic, based on place evidence, these findings have further relevance when referred to the analysis conducted on the Region of Sardinia, which was carried out by means of scrutiny of the main strategic documents adopted for the 2014-2020 programming cycle. This analysis led to policy recommendations for the efficient implementation of measures funded by EU cohesion policies.
description: Bollettino della Società Geografica Italiana, Series 14 Vol 2 Special Issue (2019)
The Ubiquitin-Interacting Motifs Target the Endocytic Adaptor Protein Epsin for Ubiquitination
Creators: name: Oldham, Carla
name: Hanes, Richard
name: Mohney, Robert
name: O'Bryan, John
name: Miller, Stephanie
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: The covalent attachment of ubiquitin to proteins is an evolutionarily conserved signal for rapid protein degradation. However, additional cellular functions for ubiquitination are now emerging, including regulation of protein trafficking and endocytosis [1]. For example, recent genetic studies suggested a role for ubiquitination in regulating epsin, a modular endocytic adaptor protein that functions in the assembly of clathrin-coated vesicles [2, 3]; however, biochemical evidence for this notion has been lacking. Epsin consists of an epsin NH2-terminal homology (ENTH) domain that promotes the interaction with phospholipids [4], several AP2 binding sites [5], two clathrin binding sequences [6], and several Eps15 homology (EH) domain binding motifs [3]. Interestingly, epsin also possesses several recently described ubiquitin-interacting motifs (UIMs) that have been postulated to bind ubiquitin [7]. Here, we demonstrate that epsin is predominantly monoubiquitinated and resistant to proteasomal degradation. The UIMs are necessary for epsin ubiquitination but are not the site of ubiquitination. Finally, we demonstrate that the isolated UIMs from both epsin and an unrelated monoubiquitinated protein, Eps15 [8], are sufficient to promote ubiquitination of a chimeric glutathione-S-transferase (GST)-UIM fusion protein. Thus, our data suggest that UIMs may serve as a general signal for ubiquitination.
Auxin Action in a Cell-Free System
Creators: name: Estelle, Mark
name: Jones, Alan
name: Dharmasiri, Sunethra
name: Dharmasiri, Nihal
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: The plant hormone auxin regulates diverse aspects of plant growth and development [1]. Despite its importance, the mechanisms of auxin action remain poorly understood. In particular, the identities of the auxin receptor and other signaling proteins are unknown. Recent studies have shown that auxin acts by promoting the degradation of a family of transcriptional regulators called the Aux/IAA proteins 2, 3 and 4. These proteins interact with another large family of plant-specific transcription factors called Auxin Response Factors (ARF) and negatively regulate their activity [5]. Auxin stimulates Aux/IAA degradation by promoting the interaction between a ubiquitin protein ligase (E3) called SCFTIR1 and the Aux/IAA protein [2]. In this report, we demonstrate that auxin promotes the interaction between the Aux/IAA proteins and SCFTIR1 in a soluble extract free of membranes, indicating that this auxin response is mediated by a soluble receptor. In addition, we show that the response is not dependent on protein phosphorylation or dephosphorylation but rather is prevented by an inhibitor of peptidyl-prolyl isomerases.
Nuf2 and Hec1 Are Required for Retention of the Checkpoint Proteins Mad1 and Mad2 to Kinetochores
Creators: name: Fang, Guowei
name: Hickey, Jennifer
name: Howell, Bonnie
name: Canman, Julie
name: Salmon, E.D.
name: DeLuca, Jennifer
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Members of the Ndc80/Nuf2 complex have been shown in several systems to be important in formation of stable kinetochore-microtubule attachments and chromosome alignment in mitosis 1, 2, 3, 4, 5, 6, 7, 8 and 9. In HeLa cells, we have shown that depletion of Nuf2 by RNA interference (RNAi) results in a strong prometaphase block with an active spindle checkpoint, which correlates with low but detectable Mad2 at kinetochores that have no or few stable kinetochore microtubules [5]. Another RNAi study in HeLa cells reported that Hec1 (the human Ndc80 homolog) is required for Mad1 and Mad2 binding to kinetochores and that kinetochore bound Mad2 does not play a role in generating and maintaining the spindle assembly checkpoint [6]. Here, we show that depletion of either Nuf2 or Hec1 by RNAi in HeLa cells results in reduction of both proteins at kinetochores and in the cytoplasm. Mad1 and Mad2 concentrate at kinetochores in late prophase/early prometaphase but become depleted by 5-fold or more over the course of the prometaphase block, which is Mad2 dependent. The reduction of Mad1 and Mad2 is reversible upon spindle depolymerization. Our observations support a model in which Nuf2 and Hec1 function to prevent microtubule-dependent stripping of Mad1 and Mad2 from kinetochores that have not yet formed stable kinetochore-microtubule attachments.
Methodological Approach for a New Economic Geography of the Territorial Cohesion in Europe and Italy
Creators: name: Prezioso, Maria
Publisher: name: Bollettino della Società Geografica Italiana
Year: 2020

description: In this time, the Territorial Impact Assessment (TIA) is the best process to support the development of global/local sustainable policies. It identifies territorial/spatial problems and objectives (by several ex ante and ex post steps), the main political/programming scenarios and options measuring impacts on economic, environmental, cultural and social fields. It outlines advantages and disadvantages for each policy option and examines all possible synergies and trade-offs on the base of the territorial context (geographical diversity). In order to study the integration of the Cohesion Policy objectives 2020 and post within the Italian development programs (national and regional), the evaluation of Territorial Cohesion in Italian regions by TIA was applied. The STeMA-TIA model has been devised to support an integrated strategic vision of general, territorialised and sectoral policies at NUT1, 2 and 3 decision-making levels. This assessment tool was created as part of the territorial dimension evaluation of the European Strategies. In the context of ongoing research (PRIN 2015), the method and the ex ante application are illustrated in the following in supporting of attended results of first step, which was critically discussed at European level, too.
description: Bollettino della Società Geografica Italiana, Series 14 Vol 2 Special Issue (2019)
The physical state of selected cold clumps
Creators: name: Parikka, A.
name: Juvela, M.
name: Pelkonen, V. -M.
name: Malinen, J.
name: Harju, J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Context. he study of prestellar cores is essential to understanding the initial stages of star formation. With $Herschel$ more cold clumps have been detected than ever before. For this study we have selected 21 cold clumps from 20 $Herschel$ fields observed as a follow-up on original $Planck$ detections. We have observed these clumps in $^{13}$CO (1-0), C$^{18}$O (1-0), and N$_2$H$^+$ (1-0) lines. Aims. Our aim is to find out if these cold clumps are prestellar. We have examined to what extent independent analysis of the dust and the molecular lines lead to similar conclusions about the masses of these objects. Methods. We calculate the clump masses and densities from the dust continuum and molecular line observations and compare these to each other and to the virial and Bonnor-Ebert masses calculated for each clump. Finally we examine two of the fields with radiative transfer models to estimate CO abundances. Results. When excitation temperatures could be estimated, the column densities derived from molecular line observations were comparable to those from dust continuum data. The median column density estimates are 4.2$\times 10^{21}$cm$^{-2}$ and 5.5$\times 10^{21}$cm$^{-2}$ for the line and dust emission data, respectively. The calculated abundances, column densities, volume densities, and masses all have large uncertainties and one must be careful when drawing conclusions. Abundance of $^{13}$CO was found in modeling the two clumps in the field G131.65$+$9.75 to be close to the usual value of 10$^{-6}$. The abundance ratio of $^{13}$CO and C$^{18}$O was $\sim$10. Molecular abundances could only be estimated with modeling, relying on dust column density data. Conclusions. The results indicate that most cold clumps, even those with dust color temperatures close to 11 K, are not necessarily prestellar.
description: Accepted to A&A
The Contribution of E2F-Regulated Transcription to Drosophila PCNA Gene Function
Creators: name: Duronio, Robert
name: Bonnette, Peter
name: Thacker, Stephen
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: E2F proteins control cell cycle progression by predominantly acting as either activators or repressors of transcription [1]. How the antagonizing activities of different E2Fs are integrated by cis-acting control regions into a final transcriptional output in an intact animal is not well understood. E2F function is required for normal development in many species [2–7], but it is not completely clear for which genes E2F-regulated transcription provides an essential biological function. To address these questions, we have characterized the control region of the Drosophila PCNA gene. A single E2F binding site within a 100-bp enhancer is necessary and sufficient to direct the correct spatiotemporal program of G1-S-regulated PCNA expression during development. This dynamic program requires both E2F-mediated transcriptional activation and repression, which, in Drosophila, are thought to be carried out by two distinct E2F proteins [2, 3, 8–11]. Our data suggest that functional antagonism between these different E2F proteins can occur in vivo by competition for the same binding site. An engineered PCNA gene with mutated E2F binding sites supports a low level of expression that can partially rescue the lethality of PCNA null mutants. Thus, E2F regulation of PCNA is dispensable for viability, but is nonetheless important for normal Drosophila development.
Additional file 8 of TMBur: a distributable tumor mutation burden approach for whole genome sequencing
Creators: name: Titmuss, Emma
name: Corbett, Richard D.
name: Davidson, Scott
name: Abbasi, Sanna
name: Williamson, Laura M.
name: Pleasance, Erin D.
name: Shlien, Adam
name: Renouf, Daniel J.
name: Jones, Steven J. M.
name: Laskin, Janessa
name: Marra, Marco A.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer

description: Additional file 8: Figure S1. Impact of tumor fraction and sequencing depth on variant calling. F1 scores, recall and precision for SNV and indel calling for varying tumor and normal coverage, and tumor fraction. Values for variant callers Mutect2 and Strelka2 are indicated by orange and green lines respectively. Figure S2. Correlation between TMB estimates and predictive value of indels. Scatter plot showing the Spearman correlation between TMB estimates from subsets of the genome. Points in red show those who are not in the same threshold group (≥ 10/< 10/Mb), and the number of samples differing between each comparison is indicated in red text (top right of each square). R values are indicated in the bottom right of each square.
ADABIYOTDA XUSUSAN CHOʻLPON IJODIDA KLEOPATRA TIMSOLI
Creators: name: Yorbulova, Dildora
Publisher: name: Zenodo
Year: 2023

description: Ushbu maqolada tarixiy shaxs, Misr malikasi va fir'avni hisoblangan Kleopatra timsolining adabiyotga tabdili, jadid adabiyoti yorqin vakili hisoblangan Abdulhamid Sulaymon o'g'li Cho'lpon kichik nasriy asarlaridan biri "Kleopatra" hikoyasi tahlili berilgan.
Additional file 1 of Gender differences in psychiatric outpatients: a before and during COVID-19 pandemic study in general hospitals from China
Creators: name: He, Wenli
name: Xu, Danhong
name: Wang, Jiafeng
name: Shen, Yuze
name: Lin, Zheng
name: Ruan, Liemin
name: Chen, Qiaozhen
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Neuroscience
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1: Table S1. Diagnostic classification. Table S2. Gender composition of age, diagnosis and year at the level of person-time of diagnosis and treatment. Table S3. Gender composition of age, diagnosis and year at the level of patient number. Table S4. Gender composition of age, diagnosis and year at the level of first-visit patient number. Table S5. Gender difference by age groups in 2019 and 2020. Table S6. Gender difference by diagnostic categories in 2019 and 2020
A Computational Model Incorporating Neural Stem Cell Dynamics Reproduces Glioma Incidence across the Lifespan in the Human Population
Creators: name: Bauer, Roman
name: Kaiser, Marcus
name: Stoll, Elizabeth
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cell Behavior (q-bio.CB)
subject: Biological Physics (physics.bio-ph)
subject: Tissues and Organs (q-bio.TO)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: Glioma is the most common form of primary brain tumor. Demographically, the risk of occurrence increases until old age. Here we present a novel computational model to reproduce the probability of glioma incidence across the lifespan. Previous mathematical models explaining glioma incidence are framed in a rather abstract way, and do not directly relate to empirical findings. To decrease this gap between theory and experimental observations, we incorporate recent data on cellular and molecular factors underlying gliomagenesis. Since evidence implicates the adult neural stem cell as the likely cell-of-origin of glioma, we have incorporated empirically-determined estimates of neural stem cell number, cell division rate, mutation rate and oncogenic potential into our model. We demonstrate that our model yields results which match actual demographic data in the human population. In particular, this model accounts for the observed peak incidence of glioma at approximately 80 years of age, without the need to assert differential susceptibility throughout the population. Overall, our model supports the hypothesis that glioma is caused by randomly-occurring oncogenic mutations within the neural stem cell population. Based on this model, we assess the influence of the (experimentally indicated) decrease in the number of neural stem cells and increase of cell division rate during aging. Our model provides multiple testable predictions, and suggests that different temporal sequences of oncogenic mutations can lead to tumorigenesis. Finally, we conclude that four or five oncogenic mutations are sufficient for the formation of glioma.
Methods for climate change risk assessments: An international knowledge review (D1.1a)
Creators: name: Aall, C.
name: Menk, L.
name: M. Meyer
name: B. Dale
name: D. Lückerath
name: E. Nyadzi
name: E. Rome
name: F. Rudolf
name: H. Goosen
name: K. André
name: K. Harris
name: L. Becker
name: L. Fulco
name: M. Benzie
name: M. Zebisch
name: M. Hanssen Korsbrekke
name: M. K. Jansen
name: N. Durmaz
name: S. Kienberger
name: S. Terzi
name: U. Lehr
name: Å. Gerger Swartling
name: E. Leander
Publisher: name: Zenodo
Year: 2020
Subjects: Climate change adaptation

description: The report identifies knowledge gaps on analysing climate change risks relating to the use of the impact chain framework, user-interface and stakeholder involvement, socio-economic scenarios and societal exposure to climate change and transboundary climate change impacts. The identified knowledge gaps are reformulated into several research questions to be addressed in the succeeding case-studies of the UNCHAIN project.
The Minus End-Directed Motor Kar3 Is Required for Coupling Dynamic Microtubule Plus Ends to the Cortical Shmoo Tip in Budding Yeast
Creators: name: Maddox, Paul
name: Satterwhite, Lisa
name: Bloom, Kerry
name: Stemple, Jennifer
name: Salmon, E.D
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: The budding yeast shmoo tip is a model system for analyzing mechanisms coupling force production to microtubule plus-end polymerization/depolymerization. Dynamic plus ends of astral microtubules interact with the shmoo tip in mating yeast cells, positioning nuclei for karyogamy [1]. We have used live-cell imaging of GFP fusions to identify proteins that couple dynamic microtubule plus ends to the shmoo tip. We find that Kar3p, a minus end-directed kinesin motor protein, is required, whereas the other cytoplasmic motors, dynein and the kinesins Kip2p and Kip3p, are not. In the absence of Kar3p, attached microtubule plus ends released from the shmoo tip when they switched to depolymerization. Furthermore, microtubules in cells expressing kar3-1, a mutant that results in rigor binding to microtubules [2], were stabilized specifically at shmoo tips. Imaging of Kar3p-GFP during mating revealed that fluorescence at the shmoo tip increased during periods of microtubule depolymerization. These data are the first to localize the activity of a minus end-directed kinesin at the plus ends of microtubules. We propose a model in which Kar3p couples depolymerizing microtubule plus ends to the cell cortex and the Bim1p-Kar9p protein complex maintains attachment during microtubule polymerization. In support of this model, analysis of Bim1p-GFP at the shmoo tip results in a localization pattern complementary to that of Kar3p-GFP.
Additional file 1 of Process quality of type 2 diabetes mellitus care and association with patient perceived attributes of family doctor service in urban general practices, Beijing, China
Creators: name: Wang, Feiyue
name: Wei, Yun
name: Wang, Meirong
name: Pan, Zhaolu
name: Jin, Guanghui
name: Lu, Xiaoqin
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1: Supplementary Table 1. Sources of guidelines and indicators from key institutions reviewed. Supplementary Table 2. Modification of the indicators in domains of monitoring and health counseling.
Association between recorded medication reviews in primary care and adequate drug treatment management – a cross-sectional study
Creators: name: López, Naldy Parodi
name: Svensson, Staffan A.
name: Wallerstedt, Susanna M.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: Medicine
Pharmacology
Biotechnology
Cancer
Science Policy

description: To investigate the association between a recorded procedure code for a medication review and adequate drug treatment management, and to explore factors associated with this code. Cross-sectional study; two primary health care centres, in Region Västra Götaland, Sweden. A total of 302 consecutive patients (≥65 years old, 59% female; median number of drugs: six) requiring a non-urgent consultation with a physician in October–November 2017. Adequate drug treatment management (treatment that did not require any further action), determined in consensus by two specialists in family medicine blinded to the medication review code. Adequate drug treatment management was, overall, less common in those with a recorded medication review over the last year: 63% versus 73% (p = 0.047). This negative association was evident among patients aged 65–74 years: 49% versus 74% (p = 0.003), but absent in those ≥75 years old: 67% versus 70% (p = 0.77). Recommendations from consensus included the search for additional information to be able to make a decision regarding initiation or withdrawal of a drug (n = 53), withdrawal of a drug (n = 41), or ordering a laboratory test (n = 25). Factors associated with a recorded procedure code included age above the remuneration limit of 75 years (odds ratio: 9.8; 95% confidence interval 5.0–19), type 2 diabetes (3.0 (1.5–6.2)), hypertension (2.4 (1.2–4.8)), and depression (2.5 (1.02–6.0)). The presence of a recorded medication review was not positively associated with adequate drug treatment management but was associated with the age limit for remuneration, and some chronic diseases.Key pointsTo improve drug treatment in older people in primary care, a remuneration system linked to recorded medication reviews has been introduced.In this study, fewer patients with than without a recorded medication review (63% versus 73%) had adequate drug treatment management.A recorded medication review was ten times more common in those ≥75 years, that is, the age limit for remuneration.Recorded codes for medication reviews were also common in those with type 2 diabetes, hypertension, and depression. To improve drug treatment in older people in primary care, a remuneration system linked to recorded medication reviews has been introduced. In this study, fewer patients with than without a recorded medication review (63% versus 73%) had adequate drug treatment management. A recorded medication review was ten times more common in those ≥75 years, that is, the age limit for remuneration. Recorded codes for medication reviews were also common in those with type 2 diabetes, hypertension, and depression.
Anaphase Spindle Mechanics Prevent Mis-Segregation of Merotelically Oriented Chromosomes
Creators: name: Cameron, Lisa
name: Cimini, Daniela
name: Salmon, E.D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Merotelic kinetochore orientation is a kinetochore misattachment in which a single kinetochore is attached to microtubules from both spindle poles instead of just one. It can be favored in specific circumstances [1–5], is not detected by the mitotic checkpoint, and induces lagging chromosomes in anaphase [6, 7]. In mammalian cells, it occurs at high frequency in early mitosis [5], but few anaphase cells show lagging chromosomes [5]. We developed live-cell imaging methods to determine whether and how the mitotic spindle prevents merotelic kinetochores from producing lagging chromosomes. We found that merotelic kinetochores entering anaphase never lost attachment to the spindle poles; they remained attached to both microtubule bundles, but this did not prevent them from segregating correctly. The two microtubule bundles usually showed different fluorescence intensities, the brighter bundle connecting the merotelic kinetochore to the correct pole. During anaphase, the dimmer bundle lengthened much more than the brighter bundle as spindle elongation occurred. This resulted in correct segregation of the merotelically oriented chromosome. We propose a model based on the ratios of microtubules to the correct versus incorrect pole for how anaphase spindle dynamics and microtubule polymerization at kinetochores prevent potential segregation errors deriving from merotelic kinetochore orientation.
MPEC 2023-T251 : DAILY ORBIT UPDATE (2023 October 15)
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2023
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
Topological phases with long-range interactions
Creators: name: Gong, Zhe-Xuan
name: Maghrebi, Mohammad F.
name: Hu, Anzi
name: Wall, Michael L.
name: Foss-Feig, Michael
name: Gorshkov, Alexey V.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Atomic Physics (physics.atom-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Topological phases of matter are primarily studied in systems with short-range interactions. In nature, however, non-relativistic quantum systems often exhibit long-range interactions. Under what conditions topological phases survive such interactions, and how they are modified when they do, is largely unknown. By studying the symmetry-protected topological phase of an antiferromagnetic spin-1 chain with $1/r^α$ interactions, we show that two very different outcomes are possible, depending on whether or not the interactions are frustrated. While non-frustrated long-range interactions can destroy the topological phase for $α\lesssim3$, the topological phase survives frustrated interactions for all $α>0$. Our conclusions are based on strikingly consistent results from large-scale matrix-product-state simulations and effective-field-theory calculations, and we expect them to hold for more general interacting spin systems. The models we study can be naturally realized in trapped-ion quantum simulators, opening the prospect for experimental investigation of the issues confronted here.
description: Accepted version. See the supplemental information on the APS website
Additional file 1 of [18F]FE-PE2I PET is a feasible alternative to [123I]FP-CIT SPECT for dopamine transporter imaging in clinically uncertain parkinsonism
Creators: name: Marner, Lisbeth
name: Korsholm, Kirsten
name: Anderberg, Lasse
name: Lonsdale, Markus N.
name: Jensen, Mads Radmer
name: Brødsgaard, Eva
name: Denholt, Charlotte L.
name: Gillings, Nic
name: Law, Ian
name: Friberg, Lars
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Neuroscience
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1 Table S1: STARD checklist. Contains the STARD checklist
Dark Matter with multi-annihilation channels and AMS-02 positron excess and antiproton
Creators: name: Chen, Yu-Heng
name: Cheung, Kingman
name: Tseng, Po-Yan
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: AMS-02 provided the unprecedented statistics in the measurement of the positron fraction from cosmic rays. That may offer a unique opportunity to distinguish the positron spectrum coming from various dark matter (DM) annihilation channels, if DM is the source of this positron excess. Therefore, we consider the scenario that the DM can annihilate into leptonic, quark, and massive gauge boson channels simultaneously with floating branching ratios to test this hypothesis. We also study the impacts from MAX, MED, MIN, and DC diffusion models as well as from isothermal, NFW, and Einasto DM density profiles on our results. We found two parameter regions that can satisfy both AMS-02 $\frac{e^+}{e^++e^-}$ and $\bar{p}/p$ datasets at 95\% CL. i) Under the NFW-MIN combination with $M_χ\subset[10,30]$ TeV. ii) Under the Einasto-DC combination with $M_χ\subset[500,1500]$ GeV.
description: 25 pages, 11 figures
Weekend / holiday effect on stroke mortality in regional Australia: A ten-year retrospective study
Creators: name: He, Fan
name: Mnatzaganian, George
name: Rutherford, David
name: Njovu, Michael
name: Blackberry, Irene
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 32
subject: Biomedical and clinical sciences
classificationCode: 3202
subject: Clinical sciences
classificationCode: 3209
subject: Neurosciences
subject: FOS: Clinical medicine

description: Background: There is a deficiency in the evidence from rural and regional centres in Australia on the weekend effect following presentation with acute stroke. Objective: To estimate the association between admission over a weekend/holiday and all-cause mortality 3-day, 7-day, 14-day, 1-month, 3-month, 6-month, and 12-month following acute stroke. Methods: The records of stroke patients admitted to a main regional hospital in Australia from 2010 to 2020 were linked with the National Death Index. Time to death following ischaemic, haemorrhagic, and total stroke at different time points was modelled using Weibull, Exponential, or Gompertz regression based on best model fit determined by Akaike's information criterion. Results: Of 1669 patients, 1273 (76.3%) were admitted on a weekday, and 396 (23.7%) on a weekend/ or holiday. After adjusting for age, sex, and Charlson Comorbidity Index, stroke type and country of birth, admissions over a weekend/holiday following total stroke were significantly associated with an increased risk of dying within three days from admission [hazard ratio (HR): 1.59, 95% confidence interval: 1.01-2.50]. In haemorrhagic stroke, increased risk of death was significantly higher at three days (HR: 2.19, 95% confidence interval: 1.17-4.08), 14 days (HR: 1.73, 95% confidence interval: 1.02-2.93), and 1 month (HR: 1.82, 95% confidence interval: 1.09-3.03) following admission on the weekend/ or holiday compared to those admitted during the weekdays. Conclusions: This study reports a short-term adverse weekend/holiday effect following admission for haemorrhagic stroke or total stroke. No significant weekend/holiday effect was found in ischaemic stroke.
Distinct types of eigenvector localization in networks
Creators: name: Pastor-Satorras, Romualdo
name: Castellano, Claudio
Publisher: name: arXiv
Year: 2015
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Social and Information Networks (cs.SI)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: The spectral properties of the adjacency matrix provide a trove of information about the structure and function of complex networks. In particular, the largest eigenvalue and its associated principal eigenvector are crucial in the understanding of nodes centrality and the unfolding of dynamical processes. Here we show that two distinct types of localization of the principal eigenvector may occur in heterogeneous networks. For synthetic networks with degree distribution $P(q) \sim q^{-γ}$, localization occurs on the largest hub if $γ>5/2$; for $γ<5/2$ a new type of localization arises on a mesoscopic subgraph associated with the shell with the largest index in the $K$-core decomposition. Similar evidence for the existence of distinct localization modes is found in the analysis of real-world networks. Our results open a new perspective on dynamical processes on networks and on a recently proposed alternative measure of node centrality based on the non-backtracking matrix.
description: Final version: 16 pages, 8 figures. Open access article available online at http://www.nature.com/articles/srep18847
Additional file 2 of [18F]FE-PE2I PET is a feasible alternative to [123I]FP-CIT SPECT for dopamine transporter imaging in clinically uncertain parkinsonism
Creators: name: Marner, Lisbeth
name: Korsholm, Kirsten
name: Anderberg, Lasse
name: Lonsdale, Markus N.
name: Jensen, Mads Radmer
name: Brødsgaard, Eva
name: Denholt, Charlotte L.
name: Gillings, Nic
name: Law, Ian
name: Friberg, Lars
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Neuroscience
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 2 Table S2: Disagreement between [123I]FP-CIT SPECT and [18F]FE-PE2I PET. Table of patients classified different
Atypical Mechanism of Regulation of the Wrch-1 Rho Family Small GTPase
Creators: name: Cox, Adrienne
name: Berzat, Anastacia
name: Der, Channing
name: Shutes, Adam
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Rho family GTPases are GDP/GTP-regulated molecular switches that regulate signaling pathways controlling diverse cellular processes [1, 2, 3]. Wrch-1 was identified as a Wnt-1 regulated Cdc42 homolog, upregulated by Wnt1 signaling in Wnt1-transformed mouse mammary cells [4], and was able to promote formation of filopodia and activate the PAK serine/threonine kinase. Wrch-1 shares significant sequence and functional similarity with the Cdc42 small GTPase. However, Wrch-1 possesses a unique N-terminal 46 amino acid sequence extension that contains putative Src homology 3 (SH3) domain-interacting motifs. We determined the contribution of the N terminus to Wrch-1 regulation and activity. We observed that Wrch-1 possesses properties that distinguish it from Cdc42 and other Rho family GTPases. Unlike Cdc42, Wrch-1 possesses an extremely rapid, intrinsic guanine nucleotide exchange activity. Although the N terminus did not influence GTPase or GDP/GTP cycling activity in vitro, N-terminal truncation of Wrch-1 enhanced its ability to interact with and activate PAK and to cause growth transformation. The N terminus associated with the Grb2 SH3 domain-containing adaptor protein, and this association increased the levels of active Wrch-1 in cells. We propose that Grb2 overcomes N-terminal negative regulation to promote Wrch-1 effector interaction. Thus, Wrch-1 exhibits an atypical model of regulation not seen in other Rho family GTPases.
Chromosome Fragmentation after Induction of a Double-Strand Break Is an Active Process Prevented by the RMX Repair Complex
Creators: name: Bloom, Kerry
name: Resnick, Michael
name: Stemple, Jennifer
name: Vitriol, Eric
name: Lobachev, Kirill
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Chromosome aberrations are common outcomes of exposure to DNA-damaging agents or altered replication events and are associated with various diseases and a variety of carcinomas, including leukemias, lymphomas, sarcomas, and epithelial tumors 1 and 2. The incidence of aberrations can be greatly increased as a result of defects in DNA repair pathways [3]. Although there is considerable information about the molecular events associated with the induction and repair of a double-strand break (DSB), little is known about the events that ultimately lead to translocations or deletions through the formation of chromosome breaks or the dissociation of broken ends. We describe a system for visualizing DNA ends at the site of a DSB in living cells. After induction of the break, DNA ends flanking the DSB site in wild-type cells remained adjacent. Loss of a functional RMX complex (Rad50/Mre11/Xrs2) or a mutation in the Rad50 Zn-hook structure resulted in DNA ends being dispersed in approximately 10%–20% of cells. Thus, the RMX complex holds broken ends together and counteracts mitotic spindle forces that can be destructive to damaged chromosomes.
Antibiotic prescribing in Danish general practice in the elderly population from 2010 to 2017
Creators: name: Jensen, Maria Louise Veimer
name: Aabenhus, Rune Munck
name: Holzknecht, Barbara Juliane
name: Bjerrum, Lars
name: Jensen, Jette Nygaard
name: Siersma, Volkert
name: Córdoba, Gloria
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: This study aimed to describe prescription of antibiotics to the elderly population in general practice in Denmark from 2010–2017. This is a national register-based observational study. General practice, Denmark The main outcome measure was prescriptions/1,000 inhabitants/day (PrID) in relation to year, age and sex, indication, and antibiotic agent. In this study, we included inhabitants of Denmark, ≥65 years of age between 01st July 2010–30th June 2017. A total of 5,168,878 prescriptions were included in the study. Antibiotic prescriptions decreased from 2.2 PrID to 1.7 (-26.9%, CI95% [-31.1;-22.4]) PrID during the study. The decrease in PrID was most noticeable among 65–74-year-olds (-25%). The ≥85-year-olds were exposed to twice as many PrID than the 65–74-year-olds, but only accounted for 20% of the total use. Urinary tract infection (UTI) was the most common indication for antibiotic prescription and increased with advancing age. The most commonly prescribed antibiotics were pivmecillinam and phenoxymethylpenicillin. Prescribing with no informative indication was present in one third of all cases. The prescription of antibiotics in the elderly population in general practice decreased from 2010 to 2017. The oldest age group was exposed twice as frequently to antibiotic prescriptions as the 65–74-year-olds. The smallest reduction was observed for the ≥85-year-olds, suggesting targeting interventions at this group.Key PointsHigh antibiotic use among elderly is well known and studies indicate mis- and overuse within this population. Our study shows.The prescription rate is decreasing within all age groups of the elderly population.The ≥85-year-olds receive twice as many prescriptions/1000/day as the 65–74-years-olds. High antibiotic use among elderly is well known and studies indicate mis- and overuse within this population. Our study shows. The prescription rate is decreasing within all age groups of the elderly population. The ≥85-year-olds receive twice as many prescriptions/1000/day as the 65–74-years-olds.
A Hierarchical Framework for State Space Matrix Inference and Clustering
Creators: name: Zuo, Chandler
name: Chen, Kailei
name: Hewitt, Kyle
name: Bresnick, Emery
name: Keles, Sunduz
Publisher: name: arXiv
Year: 2015
Subjects: subject: Methodology (stat.ME)
subject: Applications (stat.AP)
subject: FOS: Computer and information sciences

description: In recent years, a large number of genomic and epigenomic studies have been focusing on the integrative analysis of multiple experimental datasets measured over a large number of observational units. The objectives of such studies include not only inferring a hidden state of activity for each unit over individual experiments, but also detecting highly associated clusters of units based on their inferred states. In this paper, we develop the MBASIC (Matrix Based Analysis for State-space Inference and Clustering) framework. MBASIC consists of two parts: state-space mapping and state-space clustering. In state-space mapping, it maps observations onto a finite state-space, representing the activation states of units across conditions. In state-space clustering, MBASIC incorporates a finite mixture model to cluster the units based on their inferred state-space profiles across all conditions. Both the state-space mapping and clustering can be simultaneously estimated through an Expectation-Maximization algorithm. MBASIC flexibly adapts to a large number of parametric distributions for the observed data, as well as the heterogeneity in replicate experiments. In our data-driven simulation studies, MBASIC showed significant accuracy in recovering both the underlying state-space variables and clustering structures. We applied MBASIC to two genome research problems using large numbers of datasets from the ENCODE project. In both studies, MBASIC showed higher levels of raw data fidelity than analyzing these data with a two-step approach using ENCODE results on transcription factor occupancy data.
description: 65 pages, 27 figures
Additional file 3 of [18F]FE-PE2I PET is a feasible alternative to [123I]FP-CIT SPECT for dopamine transporter imaging in clinically uncertain parkinsonism
Creators: name: Marner, Lisbeth
name: Korsholm, Kirsten
name: Anderberg, Lasse
name: Lonsdale, Markus N.
name: Jensen, Mads Radmer
name: Brødsgaard, Eva
name: Denholt, Charlotte L.
name: Gillings, Nic
name: Law, Ian
name: Friberg, Lars
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Neuroscience
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 3 Figure S1: PET versus SPECT. Figure of SBR of each patient
Phagocytosis of Apoptotic Cells Is Regulated by a UNC-73/TRIO-MIG-2/RhoG Signaling Module and Armadillo Repeats of CED-12/ELMO
Creators: name: Ravichandran, Kodi
name: Kinchen, Jason
name: deBakker, Colin
name: Haney, Lisa
name: Grimsley, Cynthia
name: Lu, Mingjian
name: Chou, Bin-Kuan
name: Wu, Yi-Chun
name: Cheng, Li-Chun
name: Klingele, Doris
name: Blangy, Anne
name: Hsu, Pei-Ken
name: Hengartner, Michael
name: Sondek, John
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Background: Phagocytosis of cells undergoing apoptosis is essential during development, cellular turnover, and wound healing. Failure to promptly clear apoptotic cells has been linked to autoimmune disorders. C. elegans CED-12 and mammalian ELMO are evolutionarily conserved scaffolding proteins that play a critical role in engulfment from worm to human. ELMO functions together with Dock180 (a guanine nucleotide exchange factor for Rac) to mediate Rac-dependent cytoskeletal reorganization during engulfment and cell migration. However, the components upstream of ELMO and Dock180 during engulfment remain elusive.Results: Here, we define a conserved signaling module involving the small GTPase RhoG and its exchange factor TRIO, which functions upstream of ELMO/Dock180/Rac during engulfment. Complementary studies in C. elegans show that MIG-2 (which we identify as the homolog of mammalian RhoG) and UNC-73 (the TRIO homolog) also regulate corpse clearance in vivo, upstream of CED-12. At the molecular level, we identify a novel set of evolutionarily conserved Armadillo (ARM) repeats within CED-12/ELMO that mediate an interaction with activated MIG-2/RhoG; this, in turn, promotes Dock180-mediated Rac activation and cytoskeletal reorganization.Conclusions: The combination of in vitro and in vivo studies presented here identify two evolutionarily conserved players in engulfment, TRIO/UNC73 and RhoG/MIG-2, and the TRIO → RhoG signaling module is linked by ELMO/CED-12 to Dock180-dependent Rac activation during engulfment. This work also identifies ARM repeats within CED-12/ELMO and their role in linking RhoG and Rac, two GTPases that function in tandem during engulfment.
Spindle Checkpoint Protein Dynamics at Kinetochores in Living Cells
Creators: name: Stewart, Scott
name: Moree, Ben
name: Howell, Bonnie
name: Farrar, Emily
name: Salmon, E.D
name: Fang, Guowei
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: BACKGROUND: To test current models for how unattached and untense kinetochores prevent Cdc20 activation of the anaphase-promoting complex/cyclosome (APC/C) throughout the spindle and the cytoplasm, we used GFP fusions and live-cell imaging to quantify the abundance and dynamics of spindle checkpoint proteins Mad1, Mad2, Bub1, BubR1, Mps1, and Cdc20 at kinetochores during mitosis in living PtK2 cells. RESULTS: Unattached kinetochores in prometaphase bound on average only a small fraction (estimated at 500-5000 molecules) of the total cellular pool of each spindle checkpoint protein. Measurements of fluorescence recovery after photobleaching (FRAP) showed that GFP-Cdc20 and GFP-BubR1 exhibit biphasic exponential kinetics at unattached kinetochores, with approximately 50% displaying very fast kinetics (t1/2 of approximately 1-3 s) and approximately 50% displaying slower kinetics similar to the single exponential kinetics of GFP-Mad2 and GFP-Bub3 (t1/2 of 21-23 s). The slower phase of GFP-Cdc20 likely represents complex formation with Mad2 since it was tension insensitive and, unlike the fast phase, it was absent at metaphase kinetochores that lack Mad2 but retain Cdc20 and was absent at unattached prometaphase kinetochores for the Cdc20 derivative GFP-Cdc20delta1-167, which lacks the major Mad2 binding domain but retains kinetochore localization. GFP-Mps1 exhibited single exponential kinetics at unattached kinetochores with a t1/2 of approximately 10 s, whereas most GFP-Mad1 and GFP-Bub1 were much more stable components. CONCLUSIONS: Our data support catalytic models of checkpoint activation where Mad1 and Bub1 are mainly resident, Mad2 free of Mad1, BubR1 and Bub3 free of Bub1, Cdc20, and Mps1 dynamically exchange as part of the diffuse wait-anaphase signal; and Mad2 interacts with Cdc20 at unattached kinetochores.