cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Rolling out of agro-ecology practices in Lukudzi Section, Ntcheu, Malawi: A case study
Creators: name: Kabambe, Vernon H
name: Chamdimba, Bridget
name: Phiri, Jechner
name: Kabambe, Vernon H
name: Chamdimba, Bridget
name: Phiri, Jechner
Publisher: name: Unknown
Year: 2022
Subjects: Crop Production/Industries

description: This bulletin has been prepared by the Malawi Agro-Ecological Intensification (AEI) hub as a case study to highlight how AEI practices are being rolled out in Chibale Model Village, Likudzi Section, Manjawila Extension planning Area (EPA) in Ntcheu district. The efforts are led by public extension service, using multi-model extension approach-es and multi-stakeholder collaboration to harness synergy. FAO (2018) suggested ten elements of agro-ecology as analytical tools to help in identifying important properties of agro-ecological systems and approaches and also relevant considerations in developing enabling environments for agro-ecology. The ten elements also serve as guide to policy makers, practitioners and stakeholders in planning, managing and evaluating agro-ecological transitions. Thus the same FAO’s (2018) ten elements have been used as basis for appraisal. The review shows that all ten elements are being promoted in the area, with variation in intensity and scale, and also some more directly and others more indi-rectly. We identified areas needing more emphasis as market linkages, and responsible local governance to enable protection of resources in the field such as plant material used as cover in CA systems and long duration crops such as pigeon peas and cassava, from uncontrolled fires and free ranging animals. Through farmer field schools farmers are generating evidence of the use of neem leaf powder as organic treatment for notorious fall army worm infestation in maize. This is commendable and is worth scaling out.
title: Aktuelle Versorgungswege im Gesundheitswesen bei der Behandlung von Patienten mit Rhinosinusitis
Creators: name: Park, Jonas
name: Stijn, Bogaert
name: Van Ackeren, Konstantin
name: Dazert, Stefan
name: Bachert, Claus
name: Kostev, Karel
name: Seidel, David
Publisher: name: German Medical Science GMS Publishing House
Year: 2019
Subjects: subject: 610 Medical sciences; Medicine

description: Einleitung: Ziel der vorliegenden Studie war es, die Überweisungsmuster von Rhinosinusitispatienten in Hausarztpraxen und HNO-Praxen in Deutschland im Hinblick auf bestehende Empfehlungen zu analysieren. Methoden: Die Stichprobe umfasste Patienten aus 940 Hausarztpraxen und 106 HNO-Praxen, die[zum vollständigen Text gelangen Sie über die oben angegebene URL]
description: Jahrestagung der Vereinigung Westdeutscher Hals-Nasen-Ohren-Ärzte
title: Die Prophylaxe venöser Thromboembolien nach operativen Eingriffen in der HNO-Heilkunde – Erste Ergebnisse eines neu konzipierten Algorithmus
Creators: name: Kanaan, Oliver
name: Mattheis, Stefan
name: Hansen, Stefan
name: Hussain, Timon
name: Lang, Stephan
name: Höing, Benedikt
Publisher: name: German Medical Science GMS Publishing House
Year: 2019
Subjects: subject: 610 Medical sciences; Medicine

description: Einleitung: 2017 veröffentlichten wir ein neues Konzept zur Thromboseprophylaxe operativ behandelter Patienten in der Kopf-Hals-Chirurgie. Ziel der aktuellen Studie ist es, anhand einer retrospektiven Analyse die Auswirkung der veränderten Indikationsstellung zu untersuchen und den neu implementierten[zum vollständigen Text gelangen Sie über die oben angegebene URL]
description: Jahrestagung der Vereinigung Westdeutscher Hals-Nasen-Ohren-Ärzte
Metaxya contamanensis Tuomisto & G. G. Cardenas, Kew Bull.
Creators: name: Kessler, Michael
name: Smith, Alan R.
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Cyatheales
Metaxyaceae
Metaxya
Metaxya contamanensis

description: Metaxya contamanensis Tuomisto & G.G.Cárdenas, Kew Bull. 71(5): 11–14, f. 5E, 6; map 1. 2016.
 Range: — Peru and Bolivia (BE, CO, LP) along the eastern base of the Andes.
 Ecology: —Fairly common; terrestrial in humid forests, often close to streams or on waterlogged soils; to 800 m.
description: Published as part of Kessler, Michael & Smith, Alan R., 2018, Prodromus of a fern flora for Bolivia. XXII. Metaxyaceae, pp. 95-96 in Phytotaxa 344 (1) on page 96, DOI: 10.11646/phytotaxa.344.1.16, http://zenodo.org/record/13720611
title: Soot Prediction in a Model Aero-Engine Combustor using a Quadrature-based Method of Moments
Creators: name: Çokuslu, Ömer H.
name: Hasse, Christian
name: Geigle, Klaus-Peter
name: Ferraro, Federica
Publisher: name: American Institute of Aeronautics and Astronautics, Inc.
Year: 2022

description: Numerical simulations of aero-engine combustors are extremely challenging due to the complex multiscale and multiphysics phenomena involved. Currently, reliable modeling and prediction of soot particle formation produced during incomplete hydrocarbon combustion is one of the major issues in combustion research. The next generation of gas turbines for more sustainable aircraft engines must meet strict limitations for soot particle mass and size distribution. Therefore, a comprehensive understanding of the processes leading to soot particle formation and its precise prediction in practical combustion systems is crucial. In this work, a recently developed detailed soot model, the Split-based Extended Quadrature Method of Moments (S-EQMOM), is applied to simulate a model aero-engine combustor, experimentally investigated by the German Aerospace Center (DLR). In previous studies, the S-EQMOM demonstrated good prediction capability in predicting soot particle oxidation, important to account for the reduction of soot particles. Here, the model is evaluated at elevated pressure conditions. Large eddy simulations are performed using flamelet-based tabulated chemistry with artificially thickened flame (ATF) approach coupled with the S-EQMOM. The simulation results are analyzed for both the gas phase and soot solid phase and compared with the experimental data. Velocity and temperature fields are well predicted. Soot formation is underestimated by the simulation, but qualitatively in good agreement with the experimental data.
An axiomatic basis for quantum mechanics
Creators: name: Cassinelli, Gianni
name: Lahti, Pekka
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences
subject: 81Pxx

description: In this paper we use the framework of generalized probabilistic theories to present two sets of basic assumptions, called axioms, for which we show that they lead to the Hilbert space formulation of quantum mechanics. The key results in this derivation are the co-ordinatization of generalized geometries and a theorem of Solér which characterizes Hilbert spaces among the orthomodular spaces. A generalized Wigner theorem is applied to reduce some of the assumptions of the theorem of Solér to the theory of symmetry in quantum mechanics. Since this reduction is only partial we also point out the remaining open questions.
description: 39 pages
Both Trait and State Mindfulness Predict Lower Aggressiveness via Anger Rumination: a Multilevel Mediation Analysis
Creators: name: Eisenlohr-Moul, Tory A.
name: Peters, Jessica R.
name: Pond, Richard S.
name: DeWall, C. Nathan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Trait mindfulness, or the capacity for nonjudgmental, present-centered attention, predicts lower aggression in cross-sectional samples, an effect mediated by reduced anger rumination. Experimental work also implicates state mindfulness (i.e., fluctuations around one's typical mindfulness) in aggression. Despite evidence that both trait and state mindfulness predict lower aggression, their relative impact and their mechanisms remain unclear. Higher trait mindfulness and state increases in mindfulness facets may reduce aggression-related outcomes by (1) limiting the intensity of anger, or (2) limiting rumination on anger experiences. The present study tests two hypotheses: First, that both trait and state mindfulness contribute unique variance to lower aggressiveness, and second, that the impact of both trait and state mindfulness on aggressiveness will be uniquely partially mediated by both anger intensity and anger rumination. 86 participants completed trait measures of mindfulness, anger intensity, and anger rumination, then completed diaries for 35 days assessing mindfulness, anger intensity, anger rumination, anger expression, and self-reported and behavioral aggressiveness. Using multilevel zero-inflated regression, we examined unique contributions of trait and state mindfulness facets to daily anger expression and aggressiveness. We also examined the mediating roles of anger intensity and anger rumination at both trait and state levels. Mindfulness facets predicted anger expression and aggressiveness indirectly through anger rumination after controlling for indirect pathways through anger intensity. Individuals with high or fluctuating aggression may benefit from mindfulness training to reduce both intensity of and rumination on anger.
title: Cochleaimplantation bei Kindern mit SSD – unsere Erfahrungen
Creators: name: Arnolds, Judith
name: Lang, Stephan
name: Arweiler-Harbeck, Diana
Publisher: name: German Medical Science GMS Publishing House
Year: 2019
Subjects: subject: 610 Medical sciences; Medicine

description: Einleitung: Während sich die CI-Versorgung einseitig postlingual ertaubter Erwachsener mittlerweile durchgesetzt hat [ref:1], [ref:2], ist die Studienlage zur CI-Versorgung bei einseitig prä- und perilingual ertaubten Kindern noch gering. Tavora-Vieira und Rajan berichten[zum vollständigen Text gelangen Sie über die oben angegebene URL]
description: Jahrestagung der Vereinigung Westdeutscher Hals-Nasen-Ohren-Ärzte
Making Friends with Yourself: A Mixed Methods Pilot Study of a Mindful Self-Compassion Program for Adolescents
Creators: name: Bluth, Karen
name: Gaylord, Susan A.
name: Mullarkey, Michael C.
name: Campo, Rebecca A.
name: Hobbs, Lorraine
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The aims of this mixed-method pilot study were to determine the feasibility, acceptability, and preliminary psychosocial outcomes of “Making Friends with Yourself: A Mindful Self-Compassion Program for Teens” (MFY), an adaptation of the adult Mindful Self-Compassion program. Thirty-four students age 14–17 enrolled in this waitlist controlled crossover study. Participants were randomized to either the waitlist or intervention group and administered online surveys at baseline, after the first cohort participated in the intervention, and after the waitlist crossovers participated in the intervention. Attendance and retention data were collected to determine feasibility, and audiorecordings of the 6-week class were analyzed to determine acceptability of the program. Findings indicated that MFY is a feasible and acceptable program for adolescents. Compared to the waitlist control, the intervention group had significantly greater self-compassion and life satisfaction and significantly lower depression than the waitlist control, with trends for greater mindfulness, greater social connectedness and lower anxiety. When waitlist crossovers results were combined with that of the first intervention group, findings indicated significantly greater mindfulness and self-compassion, and significantly less anxiety, depression, perceived stress and negative affect post-intervention. Additionally, regression results demonstrated that self-compassion and mindfulness predicted decreases in anxiety, depression, perceived stress, and increases in life satisfaction post-intervention. MFY shows promise as a program to increase psychosocial wellbeing in adolescents through increasing mindfulness and self-compassion. Further testing is needed to substantiate the findings.
Tangent spaces of bundles and of filtered diffeological spaces
Creators: name: Christensen, J. Daniel
name: Wu, Enxin
Publisher: name: arXiv
Year: 2015
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 57P99, 58A05

description: We show that a diffeological bundle gives rise to an exact sequence of internal tangent spaces. We then introduce two new classes of diffeological spaces, which we call weakly filtered and filtered diffeological spaces, whose tangent spaces are easier to understand. These are the diffeological spaces whose categories of pointed plots are (weakly) filtered. We extend the exact sequence one step further in the case of a diffeological bundle with filtered total space and base space. We also show that the tangent bundle $T^H X$ defined by Hector is a diffeological vector space over $X$ when $X$ is filtered or when $X$ is a homogeneous space, and therefore agrees with the dvs tangent bundle introduced by the authors in a previous paper.
description: v3: new results and improvements to exposition; 14 pages; this version to appear in Proceedings of the AMS
title: Follow-up-Ergebnisse eines neu entwickelten Biofeedback Programms zum Gesichtsmuskeltraining für Patienten mit Fazialisparese
Creators: name: Bernd, Eva
name: Holtmann, Laura
name: Mattheis, Stefan
name: Kukuk, Markus
name: Lang, Stephan
name: Schlüter, Anke
Publisher: name: German Medical Science GMS Publishing House
Year: 2019
Subjects: subject: 610 Medical sciences; Medicine

description: Einleitung: Patienten mit einer Fazialisparese sind sowohl in ihrer Lebensqualität als auch funktionell stark eingeschränkt. Neben der leitliniengerechten Therapie mit Cortison ist ein intensives Gesichtsmuskeltraining die Therapie der Wahl, solange kein irreversibler Nervenschaden vorliegt.[zum vollständigen Text gelangen Sie über die oben angegebene URL]
description: Jahrestagung der Vereinigung Westdeutscher Hals-Nasen-Ohren-Ärzte
Mindfulness in Parenting and Coparenting
Creators: name: McKee, Laura G.
name: Gonzalez, Michelle
name: Jones, Deborah J.
name: Anton, Margret
name: Parent, Justin
name: Forehand, Rex
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Mindfulness has been established as a critical psychosocial variable for the well-being of individuals; however, less is understood regarding the role of mindfulness within the family context of parents, coparents, and children. This study tested a model examining the process by which parent dispositional mindfulness relates to parenting and coparenting relationship quality through mindful parenting and coparenting. Participants were 485 parents (59.2% mothers) from three community samples of families with youth across three developmental stages: young childhood (3 – 7 yrs.; n = 164), middle childhood (8 – 12 yrs.; n = 161), and adolescence (13 – 17 yrs.; n = 160). Path analysis using maximum likelihood estimation was employed to test primary hypotheses. The proposed model demonstrated excellent fit. Findings across all three youth development stages indicated both direct effects or parent dispositional mindfulness, as well as indirect effects through mindful parenting and mindful coparenting, with parenting and coparenting relationship quality. Implications for intervention and prevention efforts are discussed.
Reading List: Researcher Needs in Digital Humanities
Creators: name: LIBER Digital Humanities Working Group
name: Ames, Sarah
Publisher: name: Zenodo
Year: 2020

description: This summer the ‘Building Relationships’ strand of the LIBER Digital Humanities Working Group has been exploring the theme of ‘researcher needs in digital humanities’, asking how libraries know what these needs are, and how we can meet them. This has involved considering area such as potential engagement activities for digital humanities services; how libraries work with and collaborate with researchers; skills training required by the research community; and the challenges of meeting these needs. This resource list brings together some of the articles recommended by members of the Building Relationships subgroup, which help to navigate these questions.
TRANSFORMUOJANTIS UNIVERSITETŲ BIBLIOTEKŲ IR KITŲ ATMINTIES INSTITUCIJŲ VAIDMUO ATVIRAJAME IR PILIEČIŲ MOKSLE BALTIJOS ŠALYSE
Creators: name: Pranckutė, Aistė
Publisher: name: Zenodo
Year: 2022
Subjects: Libocs, citizen science, academic libraries, open science

description: Straipsnyje pateikiama tyrimo "Universitetų bibliotekų ir kitų atminties institucijų transformuojantis vaidmuo atvirajame ir piliečių moksle Baltijos šalyse", kuris buvo atliktas įgyvendinant "Erasmus+" programos antrosios bendrosios programos strateginės partnerystės projektą "Universitetų bibliotekos, stiprinančios akademinės bendruomenės ir visuomenės ryšį per piliečių mokslą Baltijos šalyse - LibOCS", ataskaitos santrauka. Visą ataskaitą anglų kalba ir šios ataskaitos santraukas projekto partnerių nacionalinėmis kalbomis rasite projekto medžiagos kolekcijoje Zenodo talpykloje https://zenodo.org/communities/libocs/ The article provides a summary of the study report on “The Transformative Role of University Libraries and other Memory Institutions for Citizen Science and Open Science in the Baltics”, which was conducted during Erasmus+ program second framework strategic partnering project “University libraries strengthening the academia-society connection through citizen science in the Baltics – LibOCS”. The full report and summaries of this report in project partners' national languages are available under project materials collection on Zenodo.https://zenodo.org/communities/libocs/
description: Erasmus+ KA2 Strategic Partnerships program Project number: 2021-1-EE01-KA220-HED-000031125. Project name: University libraries strengthening the academia-society connection through citizen science in the Baltics (LibOCS), https://www.libocs.ut.ee/
Generalised Smarr Formula and the Viscosity Bound for Einstein-Maxwell-Dilaton Black Holes
Creators: name: Liu, Hai-Shan
name: Lu, H.
name: Pope, C. N.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study the shear viscosity to entropy ratio $η/S$ in the boundary field theories dual to black hole backgrounds in theories of gravity coupled to a scalar field, and generalisations including a Maxwell field and non-minimal scalar couplings. Motivated by the observation in simple examples that the saturation of the $η/S\ge 1/(4π)$ bound is correlated with the existence of a generalised Smarr relation for the planar black-hole solutions, we investigate this in detail for the general black-hole solutions in these theories, focusing especially on the cases where the scalar field plays a non-trivial role and gives rise to an additional parameter in the space of solutions. We find that a generalised Smarr relation holds in all cases, and in fact it can be viewed as the bulk gravity dual of the statement of the saturation of the viscosity to entropy bound. We obtain the generalised Smarr relation, whose existence depends upon a scaling symmetry of the planar black-hole solutions, by two different but related methods, one based on integrating the first law of thermodynamics, and the other based on the construction of a conserved Noether charge.
description: Latex, 36 pages, references added, typos corrected, to appear in PRD
Reproducibility of the NEPTUNE descriptor-based scoring system on whole-slide images and histologic and ultrastructural digital images
Creators: name: Gillespie, Brenda W
name: Nast, Cynthia
name: Troost, Jonathan P
name: Song, Peter
name: Hodgin, Jeffrey
name: Barisoni, Laura
name: Meehan, Shane M
name: Chang, Anthony
name: Palmer, Matthew
name: Bagnasco, Serena
name: Hewitt, Stephen M
name: Gibson, Debbie
name: Chien, Hui-Ping
name: Merlino, Lino
name: Gasim, Adil
name: Avila-Casado, Carmen
name: Holzman, Lawrence
name: Gaut, Joseph
name: Rosenberg, Avi
name: Liensziewski, Chrysta
name: Kretzler, Matthias
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The multicenter Nephrotic Syndrome Study Network (NEPTUNE) digital pathology scoring system employs a novel and comprehensive methodology to document pathologic features from whole-slide images, immunofluorescence and ultrastructural digital images. To estimate inter- and intra-reader concordance of this descriptor-based approach, data from 12 pathologists (eight NEPTUNE and four non-NEPTUNE) with experience from training to 30 years were collected. A descriptor reference manual was generated and a webinar-based protocol for consensus/cross-training implemented. Intra-reader concordance for 51 glomerular descriptors was evaluated on jpeg images by seven NEPTUNE pathologists scoring 131 glomeruli three times (Tests I, II, and III), each test following a consensus webinar review. Inter-reader concordance of glomerular descriptors was evaluated in 315 glomeruli by all pathologists; interstitial fibrosis and tubular atrophy (244 cases, whole-slide images) and four ultrastructural podocyte descriptors (178 cases, jpeg images) were evaluated once by six and five pathologists, respectively. Cohen’s kappa for inter-reader concordance for 48/51 glomerular descriptors with sufficient observations was moderate (0.40<kappa ≤0.60) for 17 and good (0.60<kappa ≤0.80) for 8, for 52% with moderate or better kappas. Clustering of glomerular descriptors based on similar pathologic features improved concordance. Concordance was independent of years of experience, and increased with webinar cross-training. Excellent concordance was achieved for interstitial fibrosis and tubular atrophy. Moderate-to-excellent concordance was achieved for all ultrastructural podocyte descriptors, with good-to-excellent concordance for descriptors commonly used in clinical practice, foot process effacement, and microvillous transformation. NEPTUNE digital pathology scoring system enables novel morphologic profiling of renal structures. For all histologic and ultrastructural descriptors tested with sufficient observations, moderate-to-excellent concordance was seen for 31/54 (57%). Descriptors not sufficiently represented will require further testing. This study proffers the NEPTUNE digital pathology scoring system as a model for standardization of renal biopsy interpretation extendable outside the NEPTUNE consortium, enabling international collaborations.
An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer
Creators: name: Erdmann-Gilmore, Petra
name: Smith, Richard D.
name: Slebos, Robbert
name: Sun, Shisheng
name: Zhang, Zhen
name: Zhang, Hui
name: Liu, Tao
name: Tang, Zuojian
name: Grover, Himanshu
name: Kinsinger, Christopher R.
name: Zhou, Jian-Ying
name: Rodland, Karen D.
name: Teubl, Jennifer
name: Askenazi, Manor
name: Liebler, Daniel C.
name: Payne, Samuel
name: Ellis, Matthew J.
name: Maher, Christopher A.
name: Xie, Ling
name: Townsend, R. Reid
name: Rodriguez, Henry
name: Davies, Sherri R.
name: Perou, Charles M.
name: Cao, Song
name: Gunawardena, Harsha P.
name: Tabb, David L.
name: Fenyo, David
name: Ruggles, Kelly V.
name: Chan, Daniel
name: Mertins, Philipp
name: Chen, Xian
name: Clauser, Karl R.
name: Wang, Xuya
name: Ding, Li
name: Li, Shunqiang
name: McLellan, Michael D.
name: Hoadley, Katherine A.
name: Carr, Steven A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Improvements in mass spectrometry (MS)-based peptide sequencing provide a new opportunity to determine whether polymorphisms, mutations, and splice variants identified in cancer cells are translated. Herein, we apply a proteogenomic data integration tool (QUILTS) to illustrate protein variant discovery using whole genome, whole transcriptome, and global proteome datasets generated from a pair of luminal and basal-like breast-cancer-patient-derived xenografts (PDX). The sensitivity of proteogenomic analysis for singe nucleotide variant (SNV) expression and novel splice junction (NSJ) detection was probed using multiple MS/MS sample process replicates defined here as an independent tandem MS experiment using identical sample material. Despite analysis of over 30 sample process replicates, only about 10% of SNVs (somatic and germline) detected by both DNA and RNA sequencing were observed as peptides. An even smaller proportion of peptides corresponding to NSJ observed by RNA sequencing were detected (<0.1%). Peptides mapping to DNA-detected SNVs without a detectable mRNA transcript were also observed, suggesting that transcriptome coverage was incomplete (∼80%). In contrast to germline variants, somatic variants were less likely to be detected at the peptide level in the basal-like tumor than in the luminal tumor, raising the possibility of differential translation or protein degradation effects. In conclusion, this large-scale proteogenomic integration allowed us to determine the degree to which mutations are translated and identify gaps in sequence coverage, thereby benchmarking current technology and progress toward whole cancer proteome and transcriptome analysis.
Model Weights for hBN Detection
Creators: name: Ramezani, Fereshteh
name: Whitaker, Bradley M.
Publisher: name: Zenodo
Year: 2023
Subjects: model weights; hexagonal boron nitride; computer vision

description: Trained weights for model described in the published manuscript: F. Ramezani et al., "Automatic detection of multilayer hexagonal boron nitride in optical images using deep learning-based computer vision," Scientific Reports, 2023.
Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry
Creators: name: Naldrett, Michael J.
name: Briggs, Steven P.
name: Kay, Steve A.
name: Hicks, Leslie M.
name: Nusinow, Dmitri A.
name: Bindbeutel, Rebecca
name: Huang, He
name: Alvarez, Sophie
name: Evans, Bradley S.
name: Shen, Zhouxin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Many species possess an endogenous circadian clock to synchronize internal physiology with an oscillating external environment. In plants, the circadian clock coordinates growth, metabolism and development over daily and seasonal time scales. Many proteins in the circadian network form oscillating complexes that temporally regulate myriad processes, including signal transduction, transcription, protein degradation and post-translational modification. In Arabidopsis thaliana, a tripartite complex composed of EARLY FLOWERING 4 (ELF4), EARLY FLOWERING 3 (ELF3), and LUX ARRHYTHMO (LUX), named the evening complex, modulates daily rhythms in gene expression and growth through transcriptional regulation. However, little is known about the physical interactions that connect the circadian system to other pathways. We used affinity purification and mass spectrometry (AP-MS) methods to identify proteins that associate with the evening complex in A. thaliana. New connections within the circadian network as well as to light signaling pathways were identified, including linkages between the evening complex, TIMING OF CAB EXPRESSION1 (TOC1), TIME FOR COFFEE (TIC), all phytochromes and TANDEM ZINC KNUCKLE/PLUS3 (TZP). Coupling genetic mutation with affinity purifications tested the roles of phytochrome B (phyB), EARLY FLOWERING 4, and EARLY FLOWERING 3 as nodes connecting the evening complex to clock and light signaling pathways. These experiments establish a hierarchical association between pathways and indicate direct and indirect interactions. Specifically, the results suggested that EARLY FLOWERING 3 and phytochrome B act as hubs connecting the clock and red light signaling pathways. Finally, we characterized a clade of associated nuclear kinases that regulate circadian rhythms, growth, and flowering in A. thaliana. Coupling mass spectrometry and genetics is a powerful method to rapidly and directly identify novel components and connections within and between complex signaling pathways.
Reading List: Text Recognition for Digital Collections
Creators: name: LIBER Digital Humanities Working Group
name: Wilms, Lotte
name: Lefferts, Marian
Publisher: name: Zenodo
Year: 2020

description: This reading list aims to highlight some publications worth reading for librarians that wish to learn more about the text recognition processes, new developments in the field and the impact of lower quality text recognition in digital collections.
Modelling high resolution Echelle spectrographs for calibrations: Hanle Echelle spectrograph, a case study
Creators: name: Chanumolu, Anantha
name: Jones, Damien
name: Thirupathi, Sivarani
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We present a modelling scheme that predicts the centroids of spectral line features for a high resolution Echelle spectrograph to a high accuracy. Towards this, a computing scheme is used, whereby any astronomical spectrograph can be modelled and controlled without recourse to a ray tracing program. The computations are based on paraxial ray trace and exact corrections added for certain surface types and Buchdahl aberration coefficients for complex modules. The resultant chain of paraxial ray traces and corrections for all relevant components is used to calculate the location of any spectral line on the detector under all normal operating conditions with a high degree of certainty. This will allow a semi-autonomous control using simple in-house, programming modules. The scheme is simple enough to be implemented even in a spreadsheet or in any scripting language. Such a model along with an optimization routine can represent the real time behaviour of the instrument. We present here a case study for Hanle Echelle Spectrograph. We show that our results match well with a popular commercial ray tracing software. The model is further optimized using Thorium Argon calibration lamp exposures taken during the preliminary alignment of the instrument. The model predictions matched the calibration frames at a level of 0.08 pixel. Monte Carlo simulations were performed to show the photon noise effect on the model predictions.
A Digital Humanities Reading List: Part 4, The Role of Libraries
Creators: name: LIBER Digital Humanities Working Group
name: Lingstadt, Kirsty
name: Ames, Sarah
Publisher: name: Zenodo
Year: 2018

description: Four teams, each with a specific focus, have assembled a list of must-read papers, articles and reports. The recommendations in this article (the fourth and last in the series) have been assembled by the team looking at the roles of libraries in digital humanities and awareness raising in academic libraries. The team is led by Kirsty Lingstadt of the University of Edinburgh and, for these recommendations, Sarah Ames of the University of Edinburgh has lent additional support.
Dynamical effects of spin-dependent interactions in low- and intermediate-energy heavy-ion reactions
Creators: name: Xu, Jun
name: Li, Bao-An
name: Shen, Wen-Qing
name: Xia, Yin
Publisher: name: arXiv
Year: 2015
Subjects: subject: Nuclear Theory (nucl-th)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: It is well known that non-central nuclear forces, such as the spin-orbital coupling and the tensor force, play important roles in understanding many interesting features of nuclear structures. However, their dynamical effects in nuclear reactions are poorly known since only the spin-averaged observables are normally studied both experimentally and theoretically. Realizing that spin-sensitive observables in nuclear reactions may carry useful information about the in-medium properties of non-central nuclear interactions, besides earlier studies using the time-dependent Hartree-Fock approach to understand effects of spin-orbital coupling on the threshold energy and spin polarization in fusion reactions, some efforts have been made recently to explore dynamical effects of non-central nuclear forces in intermediate-energy heavy-ion collisions using transport models. The focuses of these studies have been on investigating signatures of the density and isospin dependence of the form factor in the spin-dependent single-nucleon potential. Interestingly, some useful probes were identified in the model studies while so far there is still no data to compare with. In this brief review, we summarize the main physics motivations as well as the recent progress in understanding the spin dynamics and identifying spin-sensitive observables in heavy-ion reactions at intermediate energies. We hope the interesting, important, and new physics potentials identified in the spin dynamics of heavy-ion collisions will stimulate more experimental work in this direction.
description: invited review, 13 pages, 16 figures, minor modifications and references added, to appear in Frontiers of Physics
QuantFusion: Novel Unified Methodology for Enhanced Coverage and Precision in Quantifying Global Proteomic Changes in Whole Tissues
Creators: name: O'Brien, Jonathon
name: Wrobel, John A.
name: Li, Shunqiang
name: Xie, Ling
name: Davies, Sherri R.
name: Gunawardena, Harsha P.
name: Qaqish, Bahjat F.
name: Chen, Xian
name: Ellis, Matthew J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Single quantitative platforms such as label-based or label-free quantitation (LFQ) present compromises in accuracy, precision, protein sequence coverage, and speed of quantifiable proteomic measurements. To maximize the quantitative precision and the number of quantifiable proteins or the quantifiable coverage of tissue proteomes, we have developed a unified approach, termed QuantFusion, that combines the quantitative ratios of all peptides measured by both LFQ and label-based methodologies. Here, we demonstrate the use of QuantFusion in determining the proteins differentially expressed in a pair of patient-derived tumor xenografts (PDXs) representing two major breast cancer (BC) subtypes, basal and luminal. Label-based in-spectra quantitative peptides derived from amino acid-coded tagging (AACT, also known as SILAC) of a non-malignant mammary cell line were uniformly added to each xenograft with a constant predefined ratio, from which Ratio-of-Ratio estimates were obtained for the label-free peptides paired with AACT peptides in each PDX tumor. A mixed model statistical analysis was used to determine global differential protein expression by combining complementary quantifiable peptide ratios measured by LFQ and Ratio-of-Ratios, respectively. With minimum number of replicates required for obtaining the statistically significant ratios, QuantFusion uses the distinct mechanisms to “rescue” the missing data inherent to both LFQ and label-based quantitation. Combined quantifiable peptide data from both quantitative schemes increased the overall number of peptide level measurements and protein level estimates. In our analysis of the PDX tumor proteomes, QuantFusion increased the number of distinct peptide ratios by 65%, representing differentially expressed proteins between the BC subtypes. This quantifiable coverage improvement, in turn, not only increased the number of measurable protein fold-changes by 8% but also increased the average precision of quantitative estimates by 181% so that some BC subtypically expressed proteins were rescued by QuantFusion. Thus, incorporating data from multiple quantitative approaches while accounting for measurement variability at both the peptide and global protein levels make QuantFusion unique for obtaining increased coverage and quantitative precision for tissue proteomes.
title: Erstbeschreibung einer Myiasis des Tracheostomas in Deutschland
Creators: name: Badawi, Sascha
name: Rudack, Claudia
name: Beule, Achim-Georg
name: Spiekermann, Christoph
Publisher: name: German Medical Science GMS Publishing House
Year: 2019
Subjects: subject: 610 Medical sciences; Medicine

description: Einleitung: Myiasis bezeichnet den Befall von Gewebe mit Fliegenmaden, die sich vom Wirt ernähren. In der HNO-Heilkunde ist ein derartiger Befund selten. Somit ist dies nach bestem Wissen die erste Beschreibung einer Myiasis des Trachestomas in Deutschland. Methoden: Wir beschreiben den Kasus[zum vollständigen Text gelangen Sie über die oben angegebene URL]
description: Jahrestagung der Vereinigung Westdeutscher Hals-Nasen-Ohren-Ärzte
title: Nehmen die Nasennebenhöhlenmalignome zu?
Creators: name: Alzahr, Afif
name: Knof, Benedikt
Publisher: name: German Medical Science GMS Publishing House
Year: 2019
Subjects: subject: 610 Medical sciences; Medicine

description: Einleitung: Malignen Tumore der Nasennebenhöhlen machen in der aktuellen Literatur ca. 3 % aller Malignome im Kopf-Halsbereich aus. Sie treten überwiegend bei alten Patienten oder Kindern auf. Die Ursachen sind entweder beruflich bedingt (Holz/Chemikalien) oder unklar. NNH Malignome[zum vollständigen Text gelangen Sie über die oben angegebene URL]
description: Jahrestagung der Vereinigung Westdeutscher Hals-Nasen-Ohren-Ärzte
Kinome Profiling Identifies Druggable Targets for Novel Human Cytomegalovirus (HCMV) Antivirals
Creators: name: Lenarcic, Erik M.
name: Herring, Laura E.
name: Vincent, Heather A.
name: Arend, Kyle C.
name: McDonald, Ian M.
name: Gilbert, Thomas S. K.
name: Lazear, Eric
name: Rashid, Naim
name: Johnson, Gary L.
name: Moorman, Nathaniel J.
name: Graves, Lee M.
name: East, Michael P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Human cytomegalovirus (HCMV) is a significant cause of disease in immune-compromised adults and immune naïve newborns. No vaccine exists to prevent HCMV infection, and current antiviral therapies have toxic side effects that limit the duration and intensity of their use. There is thus an urgent need for new strategies to treat HCMV infection. Repurposing existing drugs as antivirals is an attractive approach to limit the time and cost of new antiviral drug development. Virus-induced changes in infected cells are often driven by changes in cellular kinase activity, which led us to hypothesize that defining the complement of kinases (the kinome), whose abundance or expression is altered during infection would identify existing kinase inhibitors that could be repurposed as new antivirals. To this end, we applied a kinase capture technique, multiplexed kinase inhibitor bead-mass spectrometry (MIB-MS) kinome, to quantitatively measure perturbations in >240 cellular kinases simultaneously in cells infected with a laboratory-adapted (AD169) or clinical (TB40E) HCMV strain. MIB-MS profiling identified time-dependent increases and decreases in MIB binding of multiple kinases including cell cycle kinases, receptor tyrosine kinases, and mitotic kinases. Based on the kinome data, we tested the antiviral effects of kinase inhibitors and other compounds, several of which are in clinical use or development. Using a novel flow cytometry-based assay and a fluorescent reporter virus we identified three compounds that inhibited HCMV replication with IC 50 values of 3 log decrease in virus replication. These results show the utility of MIB-MS kinome profiling for identifying existing kinase inhibitors that can potentially be repurposed as novel antiviral drugs.
title: Seltene Differentialdiagnose einer laryngealen Raumforderung
Creators: name: van Ackeren, Konstantin
name: Holtmann, Eva
name: Park, Jonas Jae-Hyun
name: Dazert, Stefan
Publisher: name: German Medical Science GMS Publishing House
Year: 2019
Subjects: subject: 610 Medical sciences; Medicine

description: Einleitung: Inflammatorische myofibroblastische Tumore (IMT) stellen eine sehr seltene Differentialdiagnose laryngealer Raumforderungen dar. Durch den initial häufig bestehenden Neoplasieverdacht sowie die teils heteromorphe Histologie kann diese ätiologisch noch ungeklärte Tumorentität[zum vollständigen Text gelangen Sie über die oben angegebene URL]
description: Jahrestagung der Vereinigung Westdeutscher Hals-Nasen-Ohren-Ärzte
title: Tinnitus suppression by use of lateral inhibition in cochlear implant patients
Creators: name: Savvas, Eleftherios
name: Heslinga, Katharina
name: Rudack, Claudia
Publisher: name: German Medical Science GMS Publishing House
Year: 2019
Subjects: subject: 610 Medical sciences; Medicine

description: Introduction: The purpose of this study is to examine the possibility of tinnitus manipulation on cochlear implant patients with preexisting tinnitus by use of frequency modulation by turning off the pitch-matched electrode in the cochlear implant. Methods: Individual prospective cohort study [for full text, please go to the a.m. URL]
description: Jahrestagung der Vereinigung Westdeutscher Hals-Nasen-Ohren-Ärzte
Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction
Creators: name: Zhang, Hui
name: Paulovich, Amanda G.
name: Townsend, R. Reid
name: Ellis, Matthew J. C.
name: Ma, Zihao
name: Kinsinger, Christopher R.
name: Zhang, Bing
name: Chen, Xian
name: Lieblerc, Daniel C.
name: Boja, Emily S.
name: Wang, Jing
name: Rodriguez, Henry
name: Chan, Daniel W.
name: Mertins, Philipp
name: Smith, Richard D.
name: McDermott, Jason E.
name: Mesri, Mehdi
name: Zhang, Zhen
name: Carr, Steven A.
name: Rodland, Karin D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this “guilt-by-association” (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies.
title: Erstbeschreibung einer Langerhanszellhistiozytose nach Adenotomie
Creators: name: Bastian, Tobias
name: Theurer, Sarah
name: Lang, Stephan
name: Bosch, Jan
Publisher: name: German Medical Science GMS Publishing House
Year: 2019
Subjects: subject: 610 Medical sciences; Medicine

description: Einleitung: Die Langerhanszellhistiozytose (LCH) ist ein komplexes Krankheitsbild, das durch eine Fehlentwicklung und –funktion der mononukleären Phagozyten gekennzeichnet ist. Es kann einzeln, solitär oder systemisch auftreten. Prinzipiell ist ein Befall jedes Organs möglich, [zum vollständigen Text gelangen Sie über die oben angegebene URL]
description: Jahrestagung der Vereinigung Westdeutscher Hals-Nasen-Ohren-Ärzte
title: Cervikaler Bandscheibenprolaps als seltene Differentialdiagnose bei zystischer epipharyngealer Raumforderung
Creators: name: Rosenstein, Michèle
name: Weber, Steffen
name: Neumann, Andreas
Publisher: name: German Medical Science GMS Publishing House
Year: 2019
Subjects: subject: 610 Medical sciences; Medicine

description: Einleitung: Berichtet wird über einen männlichen, 76-jährigen Patienten, der mit dem Befund einer epipharyngealen Raumforderung in unserer Klinik vorstellig wurde. Epipharyngeale Raumforderungen sind häufige Zufallsbefunde bei einer Panendoskopie, dabei handelt es sich gehäuft[zum vollständigen Text gelangen Sie über die oben angegebene URL]
description: Jahrestagung der Vereinigung Westdeutscher Hals-Nasen-Ohren-Ärzte
title: Auditive Phänomene
Creators: name: Marek, Astrid
Publisher: name: German Medical Science GMS Publishing House
Year: 2019
Subjects: subject: 610 Medical sciences; Medicine

description: Einleitung: Das bekannteste auditive Wahrnehmungsphänomen ist subjektiver Tinnitus, worunter eine Geräuschempfindung ohne vorausgegangenen akustischen Reiz verstanden wird. Untersucht wurden folgende Fragen: welche auditiven Wahrnehmungsphänomene sind in der Literatur beschrieben?[zum vollständigen Text gelangen Sie über die oben angegebene URL]
description: Jahrestagung der Vereinigung Westdeutscher Hals-Nasen-Ohren-Ärzte
A Digital Humanities Reading List: Part 2, Cooperation Between Libraries and Research Communities
Creators: name: LIBER Digital Humanities Working Group
name: O'Dwyer, Liam
Publisher: name: Zenodo
Year: 2018
Subjects: digital humanities

description: Four teams, each with a specific focus, have assembled a list of must-read papers, articles and reports. The recommendations in this article (the second in the series) have been assembled by the team in charge of Cooperation and Relationship Between Libraries and Research Communities, led by Liam O'Dwyer of Dublin City University.
Human Glucocorticoid Receptor β Regulates Gluconeogenesis and Inflammation in Mouse Liver
Creators: name: Cidlowski, John A.
name: Oakley, Robert H.
name: Xiao, Xiao
name: Cruz-Topete, Diana
name: He, Bo
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Whilein vitrostudies have demonstrated that a glucocorticoid receptor (GR) splice isoform, β-isoform of human GR (hGRβ), acts as a dominant-negative inhibitor of the classic hGRα and confers glucocorticoid resistance, thein vivofunction of hGRβ is poorly understood. To this end, we created an adeno-associated virus (AAV) to express hGRβ in the mouse liver under the control of the hepatocyte-specific promoter. Genome-wide expression analysis of mouse livers showed that hGRβ significantly increased the expression of numerous genes, many of which are involved in endocrine system disorders and the inflammatory response. Physiologically, hGRβ antagonized GRα's function and attenuated hepatic gluconeogenesis through downregulation of phosphoenolpyruvate carboxykinase (PEPCK) in wild-type (WT) mouse liver. Interestingly, however, hGRβ did not repress PEPCK in GR liver knockout (GRLKO) mice. In contrast, hGRβ regulates the expression of STAT1 in the livers of both WT and GRLKO mice. Chromatin immunoprecipitation (ChIP) and luciferase reporter assays demonstrated that hGRβ binds to the intergenic glucocorticoid response element (GRE) of the STAT1 gene. Furthermore, treatment with RU486 inhibited the upregulation of STAT1 mediated by hGRβ. Finally, our array data demonstrate that hGRβ regulates unique components of liver gene expressionin vivoby both GRα-dependent and GRα-independent mechanisms.