cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Mechanisms of change in psychological mood and anxiety interventions for autistic people: A systematic scoping review
Creators: name: Mandy, William
name: Pender, Richard
name: Crane, Laura
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Psychiatry and Psychology
subject: Medicine and Health Sciences
subject: Public Health
subject: Social and Behavioral Sciences
subject: Health Services Research
subject: Clinical Psychology
subject: Psychology
subject: FOS: Psychology

description: This paper aims to systematically scope the literature on psychological and psychosocial interventions for autistic people across the lifespan, with a particular focus on the implicit and explicit mechanisms of change that have been targeted for depression and/or anxiety, and the therapeutic techniques that have been applied to address these.
CRISPLD2 Is a Target of Progesterone Receptor and Its Expression Is Decreased in Women with Endometriosis
Creators: name: Fazleabas, Asgerally T.
name: Young, Steven L.
name: Yoo, Jung-Yoon
name: Ha, Un-Hwan
name: Shin, Heesung
name: Jeong, Jae-Wook
name: Choi, Won-Seok
name: Ferguson, Susan D.
name: Kim, Tae Hoon
name: Lessey, Bruce A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Endometriosis, defined as the presence of endometrial cells outside of the uterine cavity, is a major cause of infertility and pelvic pain, afflicting more than 10% of reproductive age women. Endometriosis is a chronic inflammatory disease and lipopolysaccharide promotes the proliferation and invasion of endometriotic stromal cells. Cysteine-rich secretory protein LCCL domain-containing 2 (CRISPLD2) has high affinity for lipopolysaccharide and plays a critical role in defense against endotoxin shock. However, the function of CRISPLD2 has not been studied in endometriosis and uterine biology. Herein, we examined the expression of CRISPLD2 in endometrium from patients with and without endometriosis using immunohistochemistry. The expression of CRISPLD2 was higher in the secretory phase in human menstrual cycle compared to proliferative phase. The expression of CRISPLD2 was significantly decreased in the endometrium of women with endometriosis in the early secretory phase compared to women without endometriosis. The increase of CRISPLD2 expression at the early secretory and dysregulation of its expression in endometriosis suggest progesterone (P4) regulation of CRISPLD2. To investigate whether CRISPLD2 is regulated by P4, we examined the expression of the CRISPLD2 in the uteri of wild-type and progesterone receptor knock out (PRKO) mice. The expression of CRISPLD2 was significantly increased after P4 treatment in the wild-type mice. However, CRISPLD2 expression was significantly decreased in the (PRKO) mice treated with P4. During early pregnancy, the expression of CRISPLD2 was increased in decidua of implantation and post-implantation stages. CRISPLD2 levels were also increased in cultured human endometrial stromal cells during in vitro decidualization. These results suggest that the CRISPLD2 is a target of the progesterone receptor and may play an important role in pathogenesis of endometriosis.
Hysteresis in phase-field models with thermal memory
Creators: name: Gilardi, Gianni
name: Krejčí, Pavel
name: Sprekels, Jürgen
Publisher: name: Weierstrass Institute
Year: 1999
Subjects: subject: Phase transitions
subject: hysteresis operators
subject: phase-field models
subject: heat conduction with memory
subject: integrodifferential equations
subject: 35K55
subject: 80A22
subject: 47H30

description: Phase-field systems as mathematical models for phase transitions have drawn increasing attention in recent years. However, while capable of capturing many of the experimentally observed phenomena, they are only of restricted value in modelling hysteresis effects occurring during phase transition processes. To overcome this shortcoming, a new approach has recently been proposed by the last two authors which is based on the mathematical theory of hysteresis operators developed in the past fifteen years. In this paper this approach is extended to cases where the material exhibits an additional thermal memory, i.e., where the heat flux contains a time convolution of the spatial gradient of temperature. It is shown that the corresponding system of field equations admits a unique strong solution that depends continuously on the data of the system.
Data_of_study_You never get a second chance First impressions of physicians depend on their body postures
Creators: name: Grün, Felix C.
name: Westfal, Viola
name: Heibges, Maren
name: Feufel, Markus A.
Publisher: name: Technische Universität Berlin
Year: 2021
Subjects: subject: 100 Philosophie und Psychologie
subject: psychology
subject: posture
subject: doctor patient interaction
subject: doctor patient relationship

description: In this study, we focus on the impact of posture on patients’ first impressions of a physician. In contrast to previous studies, we not only focus on physicians’ leadership skills, but just as much on their interpersonal and communicative skills. In an online survey, we obtained ratings of 167 participants assessing 4 sets of photographs. Each included pictures of 4 physicians (2 females) in two open or closed positions. We measured the physician’s skills, introducing items focussing on leadership, physician’s typical professional roles (derived from the CanMEDS framework), and the Shared Decision Making (SDM) process. The results show that male physicians were rated more positively in open postures. Female physicians received similar ratings, but only for leadership and medical expertise. Communicative and interpersonal skills received less favourable evaluations concerning open than closed postures. Our findings show that body postures shape the first impressions of a physician. In addition, these effects differ based on physician gender, which may be related to gender stereotypes and warrants further research.
Security as a campaign issue: programmatic mobilization in Burkina Faso’s 2020 elections
Creators: name: Saidou, Abdoul Karim
name: Bertrand, Eloïse
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: Computational Biology

description: Despite recent research suggesting that African parties engage with substantive issues more than was previously thought, the nature of issue mobilization and the drivers of programmatic appeals on the continent remain under-explored. This article analyses how presidential candidates addressed the issue of security during the 2020 election campaign in Burkina Faso – a country faced by a growing armed insurgency since 2016 – in order to understand the nature of these substantive appeals. Based upon the analysis of candidates’ manifestos, Facebook pages, media appearances, as well as direct observation of campaign meetings held in the thirteen regional capitals, we find that the crisis context favoured the mobilization of substantive issues related to security during the campaign. Furthermore, though all candidates addressed security in valence terms, opposition candidates also claimed controversial sub-issues in an attempt to use a broader range of campaign strategies than the incumbent. Finally, a specific question (whether to negotiate with armed groups or not) became a salient programmatic cleavage during the campaign, which can be explained by strategic choices made by opposition parties and the incumbent that contributed to the emergence of credible, coherent, and polarized policy options, providing real programmatic substance to the electoral campaign.
Turing patterns in multiplex networks
Creators: name: Asllani, Malbor
name: Busiello, Daniel M.
name: Carletti, Timoteo
name: Fanelli, Duccio
name: Planchon, Gwendoline
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The theory of patterns formation for a reaction-diffusion system defined on a multiplex is developed by means of a perturbative approach. The intra-layer diffusion constants act as small parameter in the expansion and the unperturbed state coincides with the limiting setting where the multiplex layers are decoupled. The interaction between adjacent layers can seed the instability of an homogeneous fixed point, yielding self-organized patterns which are instead impeded in the limit of decoupled layers. Patterns on individual layers can also fade away due to cross-talking between layers. Analytical results are compared to direct simulations.
Additional file 4 of Key factors predicting suspected severe malaria case management and health outcomes: an operational study in the Democratic Republic of the Congo
Creators: name: Okitawutshu, Jean
name: Signorell, Aita
name: Kalenga, Jean-Claude
name: Mukomena, Eric
name: Delvento, Giulia
name: Burri, Christian
name: Mwaluke, Fatou
name: Buj, Valentina
name: Sangare, Moulaye
name: Luketa, Sylvie
name: Brunner, Nina
name: Lee, Tristan
name: Hetzel, Manuel
name: Lengeler, Christian
name: Tshefu, Antoinette
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Neuroscience
subject: Biotechnology
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 4: Table S1. Number of deaths among community enrolment during post-RAS per iCCM general danger signs and DRC-specific iCCM danger signs. N = 2281.
Cubic-quintic nonlinearity in superfluid Bose-Bose mixtures in optical lattices: Heavy solitary waves, barrier-induced criticality, and current-phase relations
Creators: name: Danshita, Ippei
name: Yamamoto, Daisuke
name: Kato, Yasuyuki
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We study superfluid (SF) states of strongly interacting Bose-Bose mixtures with equal mass and intra-component interaction in optical lattices both in the presence and absence of a barrier potential (BP). We show that the SF order parameters obey the two-component nonlinear Schroedinger equation (NLSE) with not only cubic but also quintic nonlinearity in the vicinity of the first-order transitions to the Mott insulators with even fillings. In the case of no BP, we analyze solitary-wave (SW) solutions of the cubic-quintic NLSE. When the SF state changes from a ground state to a metastable one, a standard dark SW turns into a bubble-like dark SW, which has a non-vanishing density dip and no pi phase kink even in the case of a standing SW. It is shown that the former and latter SW are dynamically unstable against an out-of-phase fluctuation and an in-phase fluctuation, respectively, and the dynamical instabilities are weakened when one approaches the transition point. We find that the size and the inertial mass of the SW diverge at the first-order transition point. We suggest that the divergence of the inertial mass may be detected through measurement of the relation between the velocity and the phase jump of the SW. In the presence of BP, we reveal that when the barrier strength exceeds a certain critical value, the SF state that was metastable without the barrier is destabilized towards complete disjunction of the SF. The presence of the critical BP strength indicates that the strong BP qualitatively changes the criticality near the metastability limit of the SF state. We derive critical behaviors of the density, the compressibility, and the critical current near the metastability limit induced by the BP. It is also found that the relation between the supercurrent and the phase jump across the BP exhibits a peculiar behavior, owing to the non-topological nature of the bubble-like SW.
description: 25 pages, 19 figures
Data Sharing Reveals Complexity in the Westward Spread of Domestic Animals across Neolithic Turkey
Creators: name: Pöllath, Nadja
name: Kansa, Sarah Whitcher
name: Demirergi, Arzu
name: Russell, Nerissa
name: Carruthers, Denise
name: Helmer, Daniel
name: Peters, Joris
name: Buitenhuis, Hijlke
name: Würtenberger, Doris
name: Galik, Alfred
name: Pawłowska, Kamilla
name: Kansa, Eric
name: De Cupere, Bea
name: Mulville, Jacqui
name: Twiss, Katheryn
name: Arbuckle, Benjamin S.
name: Martin, Louise
name: Gourichon, Lionel
name: Marciniak, Arkadiusz
name: Frame, Sheelagh
name: Çakırlar, Canan
name: Atici, Levent
name: Orton, David
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: This study presents the results of a major data integration project bringing together primary archaeozoological data for over 200,000 faunal specimens excavated from seventeen sites in Turkey spanning the Epipaleolithic through Chalcolithic periods, c. 18,000-4,000 cal BC, in order to document the initial westward spread of domestic livestock across Neolithic central and western Turkey. From these shared datasets we demonstrate that the westward expansion of Neolithic subsistence technologies combined multiple routes and pulses but did not involve a set ‘package’ comprising all four livestock species including sheep, goat, cattle and pig. Instead, Neolithic animal economies in the study regions are shown to be more diverse than deduced previously using quantitatively more limited datasets. Moreover, during the transition to agro-pastoral economies interactions between domestic stock and local wild fauna continued. Through publication of datasets with Open Context (opencontext.org), this project emphasizes the benefits of data sharing and web-based dissemination of large primary data sets for exploring major questions in archaeology (Alternative Language Abstract S1).
Decisions among the Undecided: Implicit Attitudes Predict Future Voting Behavior of Undecided Voters
Creators: name: Lundberg, Kristjen B.
name: Payne, B. Keith
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Implicit attitudes have been suggested as a key to unlock the hidden preferences of undecided voters. Past research, however, offered mixed support for this hypothesis. The present research used a large nationally representative sample and a longitudinal design to examine the predictive utility of implicit and explicit attitude measures in the 2008 U.S. presidential election. In our analyses, explicit attitudes toward candidates predicted voting better for decided than undecided voters, but implicit candidate attitudes were predictive of voting for both decided and undecided voters. Extending our examination to implicit and explicit racial attitudes, we found the same pattern. Taken together, these results provide convergent evidence that implicit attitudes predict voting about as well for undecided as for decided voters. We also assessed a novel explanation for these effects by evaluating whether implicit attitudes may predict the choices of undecided voters, in part, because they are neglected when people introspect about their confidence. Consistent with this idea, we found that the extremity of explicit but not implicit attitudes was associated with greater confidence. These analyses shed new light on the utility of implicit measures in predicting future behavior among individuals who feel undecided. Considering the prior studies together with this new evidence, the data seem to be consistent that implicit attitudes may be successful in predicting the behavior of undecided voters.
Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes
Creators: name: Sjostrom, Travis
name: Daligault, Jerome
Publisher: name: arXiv
Year: 2014
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We have developed and implemented a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation of density functional theory (DFT). The results for hydrogen and aluminum are in very good agreement with Kohn-Sham (orbital-based) DFT and path integral Monte Carlo (PIMC) for microscopic features such as the electron density as well as equation of state. The present approach does not scale with temperature and hence extends to higher temperatures than is accessible in Kohn-Sham method and lower temperatures than is accessible by PIMC, while being significantly less computationally expensive than either of those two methods
description: 7 pages
Deficiency of RAMP1 Attenuates Antigen-Induced Airway Hyperresponsiveness in Mice
Creators: name: Oswald, Erin
name: Caron, Kathleen M.
name: Wetzel-Strong, Sarah E.
name: Hua, Xiaoyang
name: Krummel, Matthew F.
name: Li, Manyu
name: Tilley, Stephen L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Asthma is a chronic inflammatory disease affecting the lung, characterized by breathing difficulty during an attack following exposure to an environmental trigger. Calcitonin gene-related peptide (CGRP) is a neuropeptide that may have a pathological role in asthma. The CGRP receptor is comprised of two components, which include the G-protein coupled receptor, calcitonin receptor-like receptor (CLR), and receptor activity-modifying protein 1 (RAMP1). RAMPs, including RAMP1, mediate ligand specificity in addition to aiding in the localization of receptors to the cell surface. Since there has been some controversy regarding the effect of CGRP on asthma, we sought to determine the effect of CGRP signaling ablation in an animal model of asthma. Using gene-targeting techniques, we generated mice deficient for RAMP1 by excising exon 3. After determining that these mice are viable and overtly normal, we sensitized the animals to ovalbumin prior to assessing airway resistance and inflammation after methacholine challenge. We found that mice lacking RAMP1 had reduced airway resistance and inflammation compared to wildtype animals. Additionally, we found that a 50% reduction of CLR, the G-protein receptor component of the CGRP receptor, also ameliorated airway resistance and inflammation in this model of allergic asthma. Interestingly, the loss of CLR from the smooth muscle cells did not alter the airway resistance, indicating that CGRP does not act directly on the smooth muscle cells to drive airway hyperresponsiveness. Together, these data indicate that signaling through RAMP1 and CLR plays a role in mediating asthma pathology. Since RAMP1 and CLR interact to form a receptor for CGRP, our data indicate that aberrant CGRP signaling, perhaps on lung endothelial and inflammatory cells, contributes to asthma pathophysiology. Finally, since RAMP-receptor interfaces are pharmacologically tractable, it may be possible to develop compounds targeting the RAMP1/CLR interface to assist in the treatment of asthma.
Eupatrella bijani Wiles 1999
Creators: name: Smit, Harry
name: Pešić, Vladimir
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Actinedida
Eupatrellidae
Eupatrella
Eupatrella bijani

description: Eupatrella bijani Wiles, 1999
(Figs. 3A–E)
New records. 0/2/0, Liwagu River at crossing with summit, Mt Kinabalu, Borneo, Malaysia, 6°01.868 N, 116°32.912 E, alt. 1919 m asl., 11-ix-2012; 0/1/0, Small stream Layang Layang, Mt Kinabalu, 6° 0 2.711 N 116° 33.627 E, alt. 2697 m asl, 12-ix-2012.
Description. Female (male unknown): As the original description lacks figures of chelicerae and gnathosoma, we give additional figures and measurements based on two females from Borneo (a larger, mature, and a juvenile [indicated by larger sclerite pores and a weaker sclerotization, see Figs. 3A–B]).
Measurements (mature specimen, in parentheses juvenile; [in square parentheses measurements from Wiles 1999])—Idiosoma (ventral view: Fig. 3B) length 1390–1584 (1013) [460], width 988–1206 (700) [300]; distance between anterior tip of Cx-I and posterior margin of Cx-IV 759 (650); gonopore length/width 205 (194) [200]/166 (159). Capitulum length 258 (244) [141]; chelicera total length 489 (483), basal segment length 319 (305), claw length 185 (194), basal segment/claw length ratio 1.7 (1.57); Palp (Fig. 3E): total length 415 [325], dorsal length/ height, dorsal length/height ratio: P1, 55/35, 1.6 [46/-, -]; P2, 85/51, 1.68 (89/52, 1.7) [65/-, -]; P3, 69/51.5, 1.34 (71/53, 1.34) [54/-, -]; P4, 157/37, 4.2 (152/40, 3.8) [130/-, -]; P5, 49/16, 3.0 (48/28, 2.65) [30/-, -]; length P2/P4 ratio 0.54 (0.59) [0.5]. Legs: dorsal length of I-leg-2–5: 131 (116), 116 (116) [78], 159 (158) [130], 180 (177) [95], 208 (197) [147]; dorsal length of IV-leg: 131 (131), 119 (116), 144 (144) [78], 297 (294) [260], 272 (269) [217], 259 (250) [183].
Remarks. The two female specimens from this study match the general morphology of Eupatrella bijani Wiles, 1999, described from S. Bersih, a tributary of the River Belalong in Brunei Darussalem. Wiles’ (1999) measurements of idiosoma (length 460, width 300) are in contradiction compared with the specimens in our study, but also with the gonopore length (200) in the original description. While the idiosoma size of our specimens exceed by more than 100% dimensions given by Wiles (1999), the gonopore length is in good agreement with the original description. Most probably the measurements of idiosoma in Wiles (1999) are mistaken by a factor of about two.
Distribution. Borneo (Wiles 1999, present study).
description: Published as part of Smit, Harry & Pešić, Vladimir, 2014, Water mites from Mount Kinabalu and the Crocker Range, Borneo, Malaysia (Acari: Hydrachnidia), with the description of 34 new species, pp. 1-71 in Zootaxa 3876 (1) on page 9, DOI: 10.11646/zootaxa.3876.1.1, http://zenodo.org/record/287281
Supplementary figures from Phylogenomics of weevils revisited: data curation and modelling compositional heterogeneity
Creators: name: Li, Yan-Da
name: Engel, Michael S.
name: Tihelka, Erik
name: Cai, Chenyang
Publisher: name: The Royal Society
Year: 2023
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences

description: Supplementary Figures S1–S34
title: Δραστικές ουσίες με αναπλαστική- επουλωτική δράση.
title: Active substances with regenerative-healing effect.
titleType: AlternativeTitle
Creators: name: Δόσπρα, Μαρία
Publisher: name: Πανεπιστήμιο Δυτικής Αττικής
Year: 2023
Subjects: Επούλωση
Βιταμίνη Α

description: Στην παρούσα εργασία διερευνήθηκαν βιβλιογραφικά ουσίες με τεκμηριωμένη επουλωτική δράση. Για κάθε μία από τις ουσίες αυτές διερευνήθηκαν οι πηγές προέλευσής τους, η δομή τους και οι φυσικοχημικές τους ιδιότητες, μελέτες όπου αποδεικνύεται η δράση τους, μελέτες αποτελεσματικότητας τελικών προϊόντων στα οποία περιέχονται καθώς και οι διάφορες εφαρμογές τους. Οι ουσίες αυτές είναι με την σειρά: α) η βιταμίνη Α, μια λιποδιαλυτή βιταμίνη με κύριο παράγωγο την ρετινόλη και το β καροτένιο, εκ των οποίων μεγαλύτερο ενδιαφέρον σε εφαρμογές που αφορούν το δέρμα έχει η ρετινόλη. Βοηθάει την επούλωση λόγω της αντιφλεγμονώδους και αντιμικροβιακής της δράσης ενώ παράλληλα είναι απαραίτητη στην ομαλή λειτουργία του ανοσοποιητικού και προάγει την αντίσταση σε μολύνσεις. β) Η βιταμίνη D, μια προ-ορμόνη με δύο κύριες μορφές στον ανθρώπινο οργανισμό, την D2 και την D3. Εμπλέκεται στην κυτταρική διαίρεση και διαφοροποίηση και στηρίζει το ανοσοποιητικό. Ο υποδοχέας της παίζει σημαντικό ρόλο στην επούλωση. γ) Η βιταμίνη Ε, μια λιποδιαλυτή, φυτικής προέλευσης ομάδα 8 ενώσεων που δρα επηρεάζοντας την ανοσολογική και την αντιοξειδωτική απόκριση. δ) Το εικοσιπεντανοϊκό οξύ (EPA), ένα ωμέγα-3 πολυακόρεστο λιπαρό οξύ, πρόδρομος του DHA, που έχει κυρίως αντιφλεγμονώδη δράση. ε) Το κολλαγόνο, μία δομική πρωτεΐνη με 29 ταυτοποιημένους τύπους, που αποτελεί κλειδί στην επουλωτική διαδικασία. στ) Η παπαΐνη, μια πρωτεάση κυστεΐνης που δρα αφαιρώντας τον νεκρό ιστό και διεγείροντας έμμεσα τον κυτταρικό πολλαπλασιασμό. Συγχρόνως έχει και αντιφλεγμονώδη δράση. Τέλος ζ) η πρόπολη, μια ουσία αποτελούμενη κυρίως από ρητίνη και βάλσαμο, με αντιοξειδωτική, αντιφλεγμονώδη και αντιμικροβιακή δράση.
Depressive Symptoms, HIV Medication Adherence, and HIV Clinical Outcomes in Tanzania: A Prospective, Observational Study
Creators: name: Belenky, Nadya M.
name: Itemba, Dafrosa
name: Whetten, Kathryn
name: Maro, Venance
name: Pence, Brian W.
name: Cole, Stephen R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Depressive symptoms have been shown to independently affect both antiretroviral therapy (ART) adherence and HIV clinical outcomes in high-income countries. We examined the prospective relationship between depressive symptoms and adherence, virologic failure, and suppressed immune function in people living with HIV/AIDS in Tanzania. Data from 403 study participants who were on stable ART and engaged in HIV clinical care were analyzed. We assessed crude and adjusted associations of depressive symptoms and ART adherence, both at baseline and at 12 months, using logistic regression. We used logistic generalized estimating equations to assess the association and 95% confidence intervals (CI) between depressive symptoms and both virologic failure and suppressed immune function. Ten percent of participants reported moderate or severe depressive symptoms at baseline and 31% of participants experienced virologic failure (>150 copies/ml) over two years. Depressive symptoms were associated with greater odds of reported medication nonadherence at both baseline (Odds Ratio [OR] per 1-unit increase = 1.18, 95% CI [1.12, 1.24]) and 12 months (OR = 1.08, 95% CI [1.03, 1.14]). By contrast, increases in depressive symptom score were inversely related to both virologic failure (OR = 0.93, 95% CI [0.87, 1.00]) and immune system suppression (OR = 0.88, 95% CI [0.79, 0.99]), though the association between depressive symptoms and clinical outcomes was less precise than for the association with nonadherence. Findings indicate a positive association between depressive symptoms and nonadherence, and also an inverse relationship between depressive symptoms and clinical outcomes, possibly due to informative loss to follow-up.
Constraining the Sub-AU-Scale Distribution of Hydrogen and Carbon Monoxide Gas around Young Stars with the Keck Interferometer
Creators: name: Eisner, J. A.
name: Hillenbrand, L. A.
name: Stone, Jordan M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present Keck Interferometer observations of T Tauri and Herbig Ae/Be stars with a spatial resolution of a few milliarcseconds and a spectral resolution of ~2000. Our observations span the K-band, and include the Br gamma transition of Hydrogen and the v=2-0 and v=3-1 transitions of carbon monoxide. For several targets we also present data from Keck/NIRSPEC that provide higher spectral resolution, but a seeing-limited spatial resolution, of the same spectral features. We analyze the Br gamma emission in the context of both disk and infall/outflow models, and conclude that the Br gamma emission traces gas at very small stellocentric radii, consistent with the magnetospheric scale. However some Br gamma-emitting gas also seems to be located at radii of >0.1 AU, perhaps tracing the inner regions of magnetically launched outflows. CO emission is detected from several objects, and we generate disk models that reproduce both the KI and NIRSPEC data well. We infer the CO spatial distribution to be coincident with the distribution of continuum emission in most cases. Furthermore the Br gamma emission in these objects is roughly coincident with both the CO and continuum emission. We present potential explanations for the spatial coincidence of continuum, Br gamma, and CO overtone emission, and explore the implications for the low occurrence rate of CO overtone emission in young stars. Finally, we provide additional discussion of V1685 Cyg, which is unusual among our sample in showing large differences in emitting region size and spatial position as a function of wavelength.
description: Accepted for publication in MNRAS
Detection of Antibodies against Turkey Astrovirus in Humans
Creators: name: Kayali, Ghazi
name: Meliopoulos, Victoria A.
name: Schultz-Cherry, Stacey
name: Oshansky, Christine M.
name: Burnham, Andrew
name: Gray, Gregory C.
name: Beck, Melinda A.
name: Thomas, Paul G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Astroviruses are a leading cause of gastroenteritis in mammals and birds worldwide. Although historically thought to be species-specific, increasing evidence suggests that astroviruses may cross species barriers. In this report, we used enzyme-linked immunosorbent assays to screen sera from three distinct human cohorts involved in influenza studies in Memphis, TN or Chapel Hill, NC, and Midwestern poultry abattoir workers for antibodies to turkey astrovirus type 2 (TAstV-2). Surprisingly, 26% of one cohort’s population was TAstV-2 positive as compared to 0 and 8.9% in the other cohorts. This cohort was composed of people with exposure to turkeys in the Midwestern United States including abattoir workers, turkey growers, and non-occupationally exposed participants. The odds of testing positive for antibodies against turkey astrovirus among abattoir workers were approximately 3 times higher than the other groups. These studies suggest that people with contact to turkeys can develop serological responses to turkey astrovirus. Further work is needed to determine if these exposures result in virus replication and/or clinical disease.
Development of a Composite Measure of Product Adherence, Protocol Compliance, and Semen Exposure Using DNA and Protein Biomarkers for Topical HIV Prevention Studies
Creators: name: Doncel, Gustavo F.
name: Jacot, Terry A.
name: Thurman, Andrea
name: Archer, David F.
name: Kashuba, Angela D. M.
name: Nelson, Ashley
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: BackgroundPoor and inconsistent use of study products has hindered clinical HIV prevention studies. It is important to be able to monitor product adherence and protocol compliance in order to determine microbicide efficacy and safety more accurately. Current methods for monitoring adherence are subjective, non-specific, or invasive. Herein, we present a composite, objective measure of product adherence and protocol compliance to assess vaginal insertion, semen exposure and drug expulsion utilizing DNA, protein, and drug isolated directly from returned, vaginally used gel applicators.MethodsDNA, vaginal cells, and residual tenofovir were isolated from vaginally inserted applicators. Vaginal and semen biomarkers were amplified using a multiplex PCR to determine vaginal insertion. Vaginal cells were fixed followed by cytokeratin 4 immunocytochemistry to confirm DNA assessment of vaginal insertion. Tenofovir was extracted and quantitated through LC-MS/MS.ResultsDNA isolated from vaginally inserted applicators were positive for vaginal bacteria DNA and the control eukaryotic gene, amelogenin, while manually handled, “sham”, applicators were negative for both. Semen exposure was independently determined by simultaneous amplification of one or both Y-chromosomal genes, SRY and TSPY4. Vaginal insertion determination by DNA analysis was further confirmed by positive cytokeratin 4 (CK4) immunocytochemistry of vaginal cells remaining on the gel applicators. On the contrary, sham applicators provided very few cells when swabbed, and they were all negative for CK4. CK4 was not found in epidermal cells from the hand. Drug expulsion was detected through quantitation of residual gel present on the surface of returned applicators. Sham applicators had no detectable tenofovir.ConclusionUtilizing a composite, triple marker based panel of DNA, protein, and drug present on the surface of returned vaginal gel applicators, it is possible to determine, objectively and non-invasively, product adherence, protocol compliance, and semen exposure in microbicide trials.
MPEC 2023-D62 : 2023 DQ
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
subject: 2023 DQ

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.
Discrete Molecular Dynamics Can Predict Helical Prestructured Motifs in Disordered Proteins
Creators: name: Szöllősi, Dániel
name: Kalmár, Lajos
name: Tompa, Péter
name: Han, Kyou-Hoon
name: Hegedűs, Tamás
name: Dokholyan, Nikolay V.
name: Horváth, Tamás
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Intrinsically disordered proteins (IDPs) lack a stable tertiary structure, but their short binding regions termed Pre-Structured Motifs (PreSMo) can form transient secondary structure elements in solution. Although disordered proteins are crucial in many biological processes and designing strategies to modulate their function is highly important, both experimental and computational tools to describe their conformational ensembles and the initial steps of folding are sparse. Here we report that discrete molecular dynamics (DMD) simulations combined with replica exchange (RX) method efficiently samples the conformational space and detects regions populating α-helical conformational states in disordered protein regions. While the available computational methods predict secondary structural propensities in IDPs based on the observation of protein-protein interactions, our ab initio method rests on physical principles of protein folding and dynamics. We show that RX-DMD predicts α-PreSMos with high confidence confirmed by comparison to experimental NMR data. Moreover, the method also can dissect α-PreSMos in close vicinity to each other and indicate helix stability. Importantly, simulations with disordered regions forming helices in X-ray structures of complexes indicate that a preformed helix is frequently the binding element itself, while in other cases it may have a role in initiating the binding process. Our results indicate that RX-DMD provides a breakthrough in the structural and dynamical characterization of disordered proteins by generating the structural ensembles of IDPs even when experimental data are not available.
Determining efficient temperature sets for the simulated tempering method
Creators: name: Valentim, A.
name: da Luz, M. G. E.
name: Fiore, Carlos E.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: In statistical physics, the efficiency of tempering approaches strongly depends on ingredients such as the number of replicas $R$, reliable determination of weight factors and the set of used temperatures, ${\mathcal T}_R = \{T_1, T_2, \ldots, T_R\}$. For the simulated tempering (SP) in particular -- useful due to its generality and conceptual simplicity -- the latter aspect (closely related to the actual $R$) may be a key issue in problems displaying metastability and trapping in certain regions of the phase space. To determine ${\mathcal T}_R$'s leading to accurate thermodynamics estimates and still trying to minimize the simulation computational time, here it is considered a fixed exchange frequency scheme for the ST. From the temperature of interest $T_1$, successive $T$'s are chosen so that the exchange frequency between any adjacent pair $T_r$ and $T_{r+1}$ has a same value $f$. By varying the $f$'s and analyzing the ${\mathcal T}_R$'s through relatively inexpensive tests (e.g., time decay toward the steady regime), an optimal situation in which the simulations visit much faster and more uniformly the relevant portions of the phase space is determined. As illustrations, the proposal is applied to three lattice models, BEG, Bell-Lavis, and Potts, in the hard case of extreme first-order phase transitions, always giving very good results, even for $R=3$. Also, comparisons with other protocols (constant entropy and arithmetic progression) to choose the set ${\mathcal T}_R$ are undertaken. The fixed exchange frequency method is found to be consistently superior, specially for small $R$'s. Finally, distinct instances where the prescription could be helpful (in second-order transitions and for the parallel tempering approach) are briefly discussed.
description: 10 pages, 14 figures
Disrupted Brain Functional Network in Internet Addiction Disorder: A Resting-State Functional Magnetic Resonance Imaging Study
Creators: name: Xu, Jianrong
name: Yap, Pew-Thian
name: Wu, Guorong
name: Zhao, Zhimin
name: Shi, Feng
name: Price, True
name: Zhou, Yan
name: Du, Yasong
name: Wee, Chong-Yaw
name: Shen, Dinggang
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Internet addiction disorder (IAD) is increasingly recognized as a mental health disorder, particularly among adolescents. The pathogenesis associated with IAD, however, remains unclear. In this study, we aim to explore the encephalic functional characteristics of IAD adolescents at rest using functional magnetic resonance imaging data. We adopted a graph-theoretic approach to investigate possible disruptions of functional connectivity in terms of network properties including small-worldness, efficiency, and nodal centrality on 17 adolescents with IAD and 16 socio-demographically matched healthy controls. False discovery rate-corrected parametric tests were performed to evaluate the statistical significance of group-level network topological differences. In addition, a correlation analysis was performed to assess the relationships between functional connectivity and clinical measures in the IAD group. Our results demonstrate that there is significant disruption in the functional connectome of IAD patients, particularly between regions located in the frontal, occipital, and parietal lobes. The affected connections are long-range and inter-hemispheric connections. Although significant alterations are observed for regional nodal metrics, there is no difference in global network topology between IAD and healthy groups. In addition, correlation analysis demonstrates that the observed regional abnormalities are correlated with the IAD severity and behavioral clinical assessments. Our findings, which are relatively consistent between anatomically and functionally defined atlases, suggest that IAD causes disruptions of functional connectivity and, importantly, that such disruptions might link to behavioral impairments.
WORKSHOP: Single cell RNAseq analysis in R
Creators: name: Williams, Sarah
name: Barugahare, Adele
name: Harrison, Paul
name: Perlaza Jimenez, Laura
name: Matigan, Nicholas
name: Murigneux, Valentine
name: Antczak, Magdalena
name: Winter, Uwe
Publisher: name: Zenodo
Year: 2023
Subjects: bioinformatics
transcriptomics
single cell RNA-seq
Seurat
R statistical software

description: This record includes training materials associated with the Australian BioCommons workshop 'Single cell RNAseq analysis in R'. This workshop took place over two, 3.5 hour sessions on 26 and 27 October 2023.
Event description
Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using Seurat - an R package for QC, analysis, and exploration of single-cell RNAseq data. 
We will discuss the 'why' behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data.
This workshop is presented by the Australian BioCommons, Queensland Cyber Infrastructure Foundation (QCIF) and the Monash Genomics and Bioinformatics Platform with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
Lead trainers: Sarah Williams, Adele Barugahare, Paul Harrison, Laura Perlaza Jimenez
Facilitators: Nick Matigan, Valentine Murigneux, Magdalena (Magda) Antczak
Infrastructure provision: Uwe Winter
Coordinator: Melissa Burke
Training materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:

Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
scRNAseq_Schedule (PDF): A breakdown of the topics and timings for the workshop
Materials shared elsewhere:
This workshop follows the tutorial 'scRNAseq Analysis in R with Seurat'
https://swbioinf.github.io/scRNAseqInR_Doco/index.html
Slides used to introduce key topics are available via GitHub
https://github.com/swbioinf/scRNAseqInR_Doco/tree/main/slides
This material is based on the introductory Guided Clustering Tutorial tutorial from Seurat.
It is also drawing from a similar workshop held by Monash Bioinformatics Platform Single-Cell-Workshop, with material here.
Reflections on COP26 for Africa and Zambia: where to next?
Creators: name: Tomei, Julia
name: Mubanga, Mulima
name: Tesfamichael, Meron
name: Somavilla, Lucas
name: Miedzinski, Michal
name: Mulugetta, Yacob
Publisher: name: Zenodo
Year: 2022
Subjects: COP26
COP27
climate
policy
development

description: COP26 concluded with the 197 parties agreeing to the 'Glasgow Climate Pact'. The package of decisions included strengthened efforts to curb greenhouse gas emissions and returning to COP27 in Egypt with more ambitious emissions reductions targets. This is with the aim of closing the gap to limit global warming to under 1.5°C from the current trajectory of 2.4°C. Drawing on an online workshop held in December 2021, this policy brief discusses the implications of the Glasgow Climate Pact for Africa and Zambia in particular. It highlights key policy areas of interest, including finance, mitigation and adaptation, collaboration, and climate policy implementation challenges, before setting out important issues for Africa that will need to be debated as we look towards COP27 in Egypt in November 2022.
description: This material has been produced under the Climate Compatible Growth (CCG) programme, which brings together leading research organizations and is led out of the STEER centre, Loughborough University. CCG is funded by UK aid from the UK government. However, the views expressed herein do not necessarily reflect the UK government's official policies.
Iris Biometric System using a hybrid approach
Creators: name: Sarin, Abhimanyu
name: Nayak, Dr. Jagadish
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences
subject: 47G20

description: Iris Recognition Systems are ocular- based biometric devices used primarily for security reasons. The complexity and the randomness of the Iris, amongst various other factors, ensure that this biometric system is inarguably an exact and reliable method of identification. The algorithm is responsible for automatic localization and segmentation of boundaries using circular Hough Transform, noise reductions, image enhancement and feature extraction across numerous distinct images present in the database. This paper delves into the various kinds of techniques required to approximate the pupillary and limbic boundaries of the enrolled iris image, captured using a suitable image acquisition device and perform feature extraction on the normalized iris image with the help of Haar Wavelets to encode the input data into a binary string format. These techniques were validated using images from the CASIA database, and various other procedures were also tried and tested.
description: 11 pages, 11 pictures, Computer Science & Information Technology-CSCP 2014
Does Global Progress on Sanitation Really Lag behind Water? An Analysis of Global Progress on Community- and Household-Level Access to Safe Water and Sanitation
Creators: name: Elliott, Mark
name: Bartram, Jamie
name: Cumming, Oliver
name: Overbo, Alycia
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Safe drinking water and sanitation are important determinants of human health and wellbeing and have recently been declared human rights by the international community. Increased access to both were included in the Millennium Development Goals under a single dedicated target for 2015. This target was reached in 2010 for water but sanitation will fall short; however, there is an important difference in the benchmarks used for assessing global access. For drinking water the benchmark is community-level access whilst for sanitation it is household-level access, so a pit latrine shared between households does not count toward the Millennium Development Goal (MDG) target. We estimated global progress for water and sanitation under two scenarios: with equivalent household- and community-level benchmarks. Our results demonstrate that the “sanitation deficit” is apparent only when household-level sanitation access is contrasted with community-level water access. When equivalent benchmarks are used for water and sanitation, the global deficit is as great for water as it is for sanitation, and sanitation progress in the MDG-period (1990–2015) outstrips that in water. As both drinking water and sanitation access yield greater benefits at the household-level than at the community-level, we conclude that any post–2015 goals should consider a household-level benchmark for both.
Precision studies of v_n fluctuations
Creators: name: Gorda, Tyler
name: Romatschke, Paul
Publisher: name: arXiv
Year: 2014
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The power spectrum of heavy ion collisions is investigated by studying initial state fluctuations on top of a smooth hydrodynamic flow. In particular, the stability of the location of the first minimum of the power spectrum and the dependence of the hydrodynamic response v_n / epsilon_n on n and on eta / s are discussed. In our study we develop a new Green's function method for the analytic hydrodynamic flow by S. Gubser and make use of a fully non-linear hydrodynamics code. We find that there will be no well-defined first minimum of the response for n < 10, due to the fact that all minima in that region are found to be sensitive to the location of the initial perturbations. Also, we find that the often proposed form of the hydrodynamical response, that ln ( v_n / epsilon_n ) depend quadratically on n and linearly on eta / s, should not hold once many events have been averaged over.
description: 24 pages, 6 figures