cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Consensus methods in patellofemoral pain and patellofemoral osteoarthritis : how rigorous are they? : a scoping review
Creators: name: Blazey, Paul
Publisher: name: University of British Columbia
Year: 2024

description: Background: Consensus-methods are used to gain agreement when evidence is absent or conflicting. Due to its complex nature patellofemoral pain (PFP) research has often utilized consensus-methods to make best-practice recommendations in the absence of conclusive scientific evidence. There has been little scrutiny of which consensus methods have been used to reach agreement, or the rigor with which they have been applied. Objective: Primary objective was to map the methods used to gain and/or measure consensus within PFP or patellofemoral OA (PF-OA), and develop a novel framework through which to assess the rigor of consensus development methods. My secondary objective was to assess whether consensus statements within PFP/PF-OA have had research-impact or impact on policy. Design: Online databases were searched from inception to May 2022 to identify consensus-, or position-statements, or clinical practice guidelines that have used consensus-methods. A novel deductive framework was applied to map the methods used against potential measures of rigor in consensus development. Results: 22 statements were identified. Three groups (14% of consensus-developers reported the experience of panelists, and two (9% defined the panels desired level of expertise. One group (5%) included a patient on their panel. Medical doctors (N=11 – 50%), orthopaedic surgeons (N=11 – 50%) and physical therapists (N=8 – 36%) were the professions most frequently represented and the USA (N=16 – 73%) was the most frequently represented country. 80% of statements (8 of the 10 who had clear gender information) included more men than women. Seven (32%) reported using an established method of consensus measurement/development, and six (27%) reported using systematic methods to inform consensus process or identify relevant evidence gaps in the existing research. Citations of published consensus statements ranged from 11 to 1778, Altmetrics from 4 to 529, and policy-citations from 0 to 23. Conclusions: Consensus statements on PFP and PF-OA have largely failed to use recognized methods of consensus development (e.g. Delphi, RAND-UCLA, Nominal Group Technique, Expert Lens) to generate their recommendations. Panels have lacked diversity (geographic, gender, and professional). Systematic methods have rarely been used to identify evidence gaps and consensus-developers have failed to consistently define and measure what consensus is among their panels.
A circular order on edge-coloured trees and RNA m-diagrams
Creators: name: Marsh, Bethany
name: Schroll, Sibylle
Publisher: name: arXiv
Year: 2010
Subjects: subject: Combinatorics (math.CO)
subject: Representation Theory (math.RT)
subject: Biomolecules (q-bio.BM)
subject: FOS: Mathematics
subject: FOS: Biological sciences
subject: 05C05, 05A15 (Primary) 13F60, 68R10 (Secondary)

description: We study a circular order on labelled, m-edge-coloured trees with k vertices, and show that the set of such trees with a fixed circular order is in bijection with the set of RNA m-diagrams of degree k, combinatorial objects which can be regarded as RNA secondary structures of a certain kind. We enumerate these sets and show that the set of trees with a fixed circular order can be characterized as an equivalence class for the transitive closure of an operation which, in the case m=3, arises as an induction in the context of interval exchange transformations.
description: 15 pages, 7 figures. New title. Shortened version, presenting the results more efficiently
Additional file 1 of Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana
Creators: name: Akram, Jannat
name: Siddique, Riffat
name: Shafiq, Muhammad
name: Tabassum, Bushra
name: Manzoor, Muhammad Tariq
name: Javed, Muhammad Arshad
name: Anwar, Samia
name: Nisa, Bader Un
name: Saleem, Muhammad Hamzah
name: Javed, Bilal
name: Malik, Tabarak
name: Mustafa, Abd El-Zaher M. A.
name: Ali, Baber
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1.
A Cartan type identity for isoparametric hypersurfaces in symmetric spaces
Creators: name: Koike, Naoyuki
Publisher: name: arXiv
Year: 2010
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53C40, 53C35

description: In this paper, we obtain a Cartan type identity for curvature-adapted isoparametric hypersurfaces in symmetric spaces of compact type or non-compact type. This identity is a generalization of Cartan-D'Atri's identity for curvature-adapted(=amenable) isoparametric hypersurfaces in rank one symmetric spaces. Furthermore, by using the Cartan type identity, we show that certain kind of curvature-adapted isoparametric hypersurfaces in a symmetric space of non-compact type are principal orbits of Hermann actions.
description: 20pages
On p-adic lattices and Grassmannians
Creators: name: Kreidl, Martin
Publisher: name: arXiv
Year: 2010
Subjects: subject: Number Theory (math.NT)
subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 08B25, 13A50, 14G17, 14L15, 14L30, 18A35

description: It is well-known that the coset spaces G(k((z)))/G(k[[z]]), for a reductive group G over a field k, carry the geometric structure of an inductive limit of projective k-schemes. This k-ind-scheme is known as the affine Grassmannian for G. From the point of view of number theory it would be interesting to obtain an analogous geometric interpretation of quotients of the form G(W(k)[1/p])/G(W(k)), where p is a rational prime, W denotes the ring scheme of p-typical Witt vectors, k is a perfect field of characteristic p and G is a reductive group scheme over W(k). The present paper is an attempt to describe which constructions carry over from the function field case to the p-adic case, more precisely to the situation of the p-adic affine Grassmannian for the special linear group G=SL_n. We start with a description of the R-valued points of the p-adic affine Grassmannian for SL_n in terms of lattices over W(R), where R is a perfect k-algebra. In order to obtain a link with geometry we further construct projective k-subvarieties of the multigraded Hilbert scheme which map equivariantly to the p-adic affine Grassmannian. The images of these morphisms play the role of Schubert varieties in the p-adic setting. Further, for any reduced k-algebra R these morphisms induce bijective maps between the sets of R-valued points of the respective open orbits in the multigraded Hilbert scheme and the corresponding Schubert cells of the p-adic affine Grassmannian for SL_n.
description: 36 pages. This is a thorough revision, in the form accepted by Math. Zeitschrift, of the previously published preprint "On p-adic loop groups and Grassmannians"
BioExcel-2 Deliverable 2.1 – State of the Art and Initial Roadmap
Creators: name: Hospital, Adam
name: Soiland-Reyes, Stian
name: Gelpí, Josep Lluís
name: Andrio, Pau
name: Lezzi, Daniele
name: Butcher, Sarah
name: Niewielska, Ania
name: Westermaier, Yvonne
Publisher: name: Zenodo
Year: 2019
Subjects: Tools
Workflows
Workflow managers
Hardware infrastructures
Container technologies

description: This deliverable is presented as a follow-up to the BioExcel-1 D2.1 deliverable, describing the new state of the art of technologies, methods and tools applicable to the computational biomolecular field, and presenting a roadmap for WP2 in the first period (18 months) of the BioExcel-2 project. A current situation section briefly summarizes the work done in BioExcel- 1 on the development of the BioExcel building blocks (biobb) library following a collection of software development best practices, success stories reached for a set of workflows built using this library, and finding and using BioExcel workflows through the BioExcel Cloud Portal. The state of the art of technologies, tools and methods presented in the BioExcel-1 D2.1 is reviewed, briefly describing new hardware and software infrastructures that have been gaining popularity in the recent years, such as software containers or Jupyter notebooks. Workflow managers, especially the ones focused on the HPC and exascale supercomputers are also reviewed, presenting a collaboration with the Molecular Science Software Institute (MolSSI). New, still ongoing initiatives closely related to the BioExcel expertise are introduced, including workflows and MD trajectories data repositories. The set of available modules used on the solution-oriented workflows built for the first period of the project will be updated in this new period. A new list of proposed tools to be wrapped into the BioExcel building block library is presented, including advanced and modern functionalities such as biased MD simulations and High Performance Data Analytics (HPDA). The final section of the deliverable describes the immediate future roadmap for the WP2, divided in the different tasks presented in the DoA: Application building blocks for computational biomolecular simulations Definition, development and specification of workflow prototypes and demonstrators Optimization of Workflows for Exascale computing Convergence of HPC and HPDA Provisioning and maintaining a workflow environment For each of the tasks, a set of objectives and corresponding milestones for the first period of the project (18 months) are introduced. An extension and update on this roadmap will be presented in the D2.3 - First release of demonstration workflows in PM18.
Additional file 1 of COVID-19 vaccination strategies in settings with limited rollout capacity: a mathematical modelling case study in Sierra Leone
Creators: name: Bilgin, Gizem Mayis
name: Lokuge, Kamalini
name: Jabbie, Ernest
name: Munira, Syarifah Liza
name: Glass, Kathryn
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: S1. Model Structure. S1.1. Modelling transmission. S1.2. Fitting to the basic reproduction number. S1.3. Tracking the effective reproduction number. S1.4. Modification of severe outcome projections with high-risk group. S2. Parameter Estimates. S2.1. Parameters associated with transmission. S2.2. Vaccine effectiveness. S2.3. Infection-derived immunity. S2.4. Severe outcome projections. S2.5. Characterising high-risk groups. S3. Model Fit. S4. Sensitivity Analysis. S4.1. Outbreak of a new immune-escape variant. S4.2. Prioritisation of a double-dose vaccine. S4.3. Prioritisation of a larger number of doses. S4.4. Increased vaccine hesitancy in pregnant women. S4.5. Reduced vaccine effectiveness in older adults. S4.6. Reduced vaccine effectiveness in older adults and adults with comorbidities. S4.7. Increased or decreased risk of high-risk groups. S4.8. Influence of pre-existing infection-derived immunity.
Additional file 1 of The effect of growth hormone on the metabolome of follicular fluid in patients with diminished ovarian reserve
Creators: name: He, Fan
name: Wang, Fang
name: Yang, Yang
name: Yuan, Zhi
name: Sun, Chengguang
name: Zou, Heng
name: Chen, Huijia
name: Yi, Hongliang
name: Gao, Shan Hu
name: Zhang, Shen
name: Hu, Lina
name: Han, Ting-li
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 1: Table S1. The area under the receiver operating characteristic curve (AUC), p-value, q-value and peak intensity of identified metabolites.
Additional file 1 of Food insecurity, COVID-19 and diets in Fiji – a cross-sectional survey of over 500 adults
Creators: name: Webster, Jacqui
name: Moala, Anasaini
name: McKenzie, Briar
name: Santos, Joseph Alvin
name: Palu, Aliyah
name: Deo, Alvina
name: Lolohea, Susana
name: Sanif, Mohammed
name: Naivunivuni, Penaia
name: Kumar, Shajal
name: Vimatemate, Emosi
name: Tawakilai, Helen
name: Seru, Litiana
name: Woodward, Mark
name: Patay, Dori
name: Nand, Devina
name: Kama, Ateca
name: Reeve, Erica
name: Waqa, Gade
name: Bell, Colin
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: Mental Health

description: Supplementary Material 1: Alignment of study reporting with “The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies”
Infinite presentability of groups and condensation
Creators: name: Bieri, Robert
name: de Cornulier, Yves
name: Guyot, Luc
name: Strebel, Ralph
Publisher: name: arXiv
Year: 2010
Subjects: subject: Group Theory (math.GR)
subject: FOS: Mathematics
subject: Primary 20F16, Secondary 20E18, 20F05, 20E05, 20E06, 20J06

description: We describe various classes of infinitely presented groups that are condensation points in the space of marked groups. A well-known class of such groups consists of finitely generated groups admitting an infinite minimal presentation. We introduce here a larger class of condensation groups, called infinitely independently presentable groups, and establish criteria which allow one to infer that a group is infinitely independently presentable. In addition, we construct examples of finitely generated groups with no minimal presentation, among them infinitely presented groups with Cantor-Bendixson rank 1, and we prove that every infinitely presented metabelian group is a condensation group.
description: 32 pages, no figure. 1->2 Major changes (the 13-page first version, authored by Y.C. and L.G., was entitled "On infinitely presented soluble groups") 2->3 some changes including cuts in Section 4
Examining excitability : from electrophysiology to mesoscale calcium imaging
Creators: name: Wang, Yundi
Publisher: name: University of British Columbia
Year: 2023

description: Preclinical drug discovery relies on the identification of appropriate target compounds and usage of effective animal model screening tests. In this work excitability across systems as well as spatial and temporal scales were evaluated to understand long QT syndrome (LQTS) therapeutic targets and develop a behavioral assay that could sensitively characterize motor phenotype onset in a Huntington Disease (HD) mouse model. Case I: The pairing of the tetrameric voltage-gated potassium channel, KCNQ1, with an accessory β-subunit, KCNE1, gives rise to the slow delayed cardiac rectifier current (IKs), known to play an important role in the physiological shortening of the cardiac action potential. With loss-of-function mutations in both subunits found to be associated with LQTS, enhancing IKs has been identified as a therapeutic approach. Here, the NSAID, mefenamic acid, was found to dose- and rate-dependently activate IKs. More KCNE1-saturated IKs channel complexes had a greater response to mefenamic acid treatment. KCNE1 residue K41 was identified as critical for mefenamic acid action, suggesting a potential binding site. Case II: HD is a dominantly inherited neurodegenerative disease with characteristic motor symptoms. Animal models with increasingly better face and construct validity have been developed to understand HD pathophysiology. Although HD gross motor defects have been extensively characterized, less is known about forelimb motor deficits. Using a high-throughput alternating reward/non-reward water-reaching task, HD forelimb movement defects and associated aberrant cortical activity were examined. HD heterozygous-zQ175 mice displayed an event sequence defect at ~5.5 months with progressive forelimb deficits starting at ~6 months. Cortical activity associated with water-reaching increased over time in HD but not wildtype mice. Gross motor defects characterized using the tapered beam and rotarod tasks, as well as post-hoc striatal immunostaining, confirmed HD pathology at ~8 months. Overall, at the nanoscale level, a biophysical and pharmacological characterization of mefenamic acid’s effect on IKs highlighted a binding site and the potential of the NSAID to act as a precursor compound for LQTS therapeutic development. At the mesoscale level, a water-reaching task was developed and used to characterize HD phenotype demonstrating the potential of the behavioral task to examine therapeutic efficacy and intervention windows.
Commuting Simplicity and Closure Constraints for 4D Spin Foam Models
Creators: name: Han, Muxin
name: Thiemann, Thomas
Publisher: name: arXiv
Year: 2010
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Spin Foam Models are supposed to be discretised path integrals for quantum gravity constructed from the Plebanski-Holst action. The reason for there being several models currently under consideration is that no consensus has been reached for how to implement the simplicity constraints. Indeed, none of these models strictly follows from the original path integral with commuting B fields, rather, by some non standard manipulations one always ends up with non commuting B fields and the simplicity constraints become in fact anomalous which is the source for there being several inequivalent strategies to circumvent the associated problems. In this article, we construct a new Euclidian Spin Foam Model which is constructed by standard methods from the Plebanski-Holst path integral with commuting B fields discretised on a 4D simplicial complex. The resulting model differs from the current ones in several aspects, one of them being that the closure constraint needs special care. Only when dropping the closure constraint by hand and only in the large spin limit can the vertex amplitudes of this model be related to those of the FK Model but even then the face and edge amplitude differ. Curiously, an ad hoc non-commutative deformation of the $B^{IJ}$ variables leads from our new model to the Barrett-Crane Model in the case of Barbero-Immirzi parameter goes to infinity.
description: 41 pages, 4 figures
Additional file 1 of Engaging communities to inform the development of a diverse cohort of cancer survivors: formative research for the eat move sleep study (EMOVES)
Creators: name: Andemeskel, Ghilamichael
name: Palmer, Nynikka R.
name: Pasick, Rena
name: Van Blarigan, Erin L.
name: Kenfield, Stacey A.
name: Graff, Rebecca E.
name: Shaw, Michael
name: Yu, Wil
name: Sanchez, Mayte
name: Hernandez, Roberto
name: Washington, Samuel L.
name: Shariff-Marco, Salma
name: Rhoads, Kim F.
name: Chan, June M.
Publisher: name: figshare
Year: 2023
Subjects: Medicine
Biological Sciences not elsewhere classified
Science Policy

description: Additional file 1. GRIPP2 Long Form checklist.
Functional connectivity of the human hypothalamus using meta-analytic connectivity modeling
Creators: name: Bottenhorn, Katherine L.
name: Robinson, Jennifer L.
Publisher: name: Zenodo
Year: 2014
Subjects: human hypothalamus
neuroimaging meta-analysis

description: The human hypothalamus is an intersection between neural systems, implicated in numerous processes and disorders related to homeostasis. We examined the functional connectivity of the human hypothalamus using robust meta-analytic connectivity modeling methods, capitalizing on the rigorous coding structure of the BrainMap neuroimaging database. We applied a replicable method of region of interest (ROI) generation using multi-image analysis graphical user interface (Mango), which loads specific regions defined in Talairach brain space. Bilateral, left and right hypothalamic ROIs were generated. We searched for studies that included activation of the each ROI using Sleuth to query the BrainMap database, imposing additional search criteria to limit our results to studies including healthy subjects. Activation likelihood estimate (ALE) analysis was performed on coordinates returned by our search to provide information about the convergence of coactivated regions. Using Mango, we performed behavioral analysis on these regions. Coactivation with bilateral hypothalamus was identified in 17 regions of the brain including frontal, temporal, and limbic regions. Coactivation with the right hypothalamus was identified in limbic and temporal regions. The left hypothalamus displayed coactivation with frontal, temporal, and limbic regions. Four behavioral domains were represented within the clusters of coactivation, including emotion in regions associated with cognition. Our results reveal distinct patterns of functional connectivity between the hypothalamus and regions of cognitive and emotional processes. The hypothalamus is intimately involved with autonomic and neuroendocrine responses and connectivity patterns may reveal potential regions of intervention for disorders in which it is implicated such as posttraumatic stress disorder. Future research should use resting state and diffusion tensor imaging to extend our understanding of the neural connectivity of this structure.
Dualities and Identities for Entanglement-Assisted Quantum Codes
Creators: name: Lai, Ching-Yi
name: Brun, Todd A.
name: Wilde, Mark M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Information Theory (cs.IT)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: The dual of an entanglement-assisted quantum error-correcting (EAQEC) code is the code resulting from exchanging the original code's information qubits with its ebits. To introduce this notion, we show how entanglement-assisted (EA) repetition codes and accumulator codes are dual to each other, much like their classical counterparts, and we give an explicit, general quantum shift-register circuit that encodes both classes of codes.We later show that our constructions are optimal, and this result completes our understanding of these dual classes of codes. We also establish the Gilbert-Varshamov bound and the Plotkin bound for EAQEC codes, and we use these to examine the existence of some EAQEC codes. Finally, we provide upper bounds on the block error probability when transmitting maximal-entanglement EAQEC codes over the depolarizing channel, and we derive variations of the hashing bound for EAQEC codes, which is a lower bound on the maximum rate at which reliable communication over Pauli channels is possible with the use of pre-shared entanglement.
description: 24 pages, 3 figures, to be published in Quantum Information Processing. A new section about EA hashing bound is included in the new version
Additional file 1 of Oral microbiome contributes to the failure of orthodontic temporary anchorage devices (TADs)
Creators: name: Zhao, Ningrui
name: Zhang, Qian
name: Guo, Yanning
name: Cui, Shengjie
name: Tian, Yajing
name: Zhang, Yidan
name: Zhou, Yanheng
name: Wang, Xuedong
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: The most abundant genera and phyla in 16S rRNA gene sequencing.
Co-Higgs bundles on P^1
Creators: name: Rayan, Steven
Publisher: name: arXiv
Year: 2010
Subjects: subject: Algebraic Geometry (math.AG)
subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 14D20, 14H60, 14D22

description: Co-Higgs bundles are Higgs bundles in the sense of Simpson, but with Higgs fields that take values in the tangent bundle instead of the cotangent bundle. Given a vector bundle on P^1, we find necessary and sufficient conditions on its Grothendieck splitting for it to admit a stable Higgs field. We characterize the rank-2, odd-degree moduli space as a universal elliptic curve with a globally-defined equation. For ranks r=2,3,4, we explicitly verify the conjectural Betti numbers emerging from the recent work of Chuang, Diaconescu, Pan, and Mozgovoy on the ADHM formula. We state the result for r=5.
description: 18 pages, 1 table. This version of the paper matches the published version. This version features expanded remarks, corrections, and two new sections on Betti numbers of moduli spaces that do not appear in the original preprint. (References to the original preprint should be unaffected, as all of its results are preserved in the new version.)
Additional file 1 of Adjunct prednisone in community-acquired pneumonia: 180-day outcome of a multicentre, double-blind, randomized, placebo-controlled trial
Creators: name: Blum, Claudine A.
name: Roethlisberger, Eva A.
name: Cesana-Nigro, Nicole
name: Winzeler, Bettina
name: Rodondi, Nicolas
name: Blum, Manuel R.
name: Briel, Matthias
name: Mueller, Beat
name: Christ-Crain, Mirjam
name: Schuetz, Philipp
Publisher: name: figshare
Year: 2023
Subjects: Medicine
Cancer
Virology
Computational Biology

description: Additional file 1: Supplemental Table S1. Baseline characteristics of per-protocol population. Supplemental Table S2. Overview of primary and secondary endpoints per-protocol. Supplemental Table S3. Subgroup analyses per-protocol for the primary endpoint mortality. Supplemental Table S4. Subgroup analyses per-protocol for the secondary endpoint recurrence. Supplemental Table S5. Subgroup analyses per-protocol for the secondary endpoint secondary infection. Supplemental Table S6. Overview of disease activity scores of intention-to-treat population. Supplemental Figure F1. Trial flow chart per-protocol. Supplemental Figure F2. Kaplan-Meier-curve of time to death per-protocol.
On the curvature of vortex moduli spaces
Creators: name: Bökstedt, Marcel
name: Romão, Nuno M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mathematical Physics (math-ph)
subject: Algebraic Topology (math.AT)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We use algebraic topology to investigate local curvature properties of the moduli spaces of gauged vortices on a closed Riemann surface. After computing the homotopy type of the universal cover of the moduli spaces (which are symmetric powers of the surface), we prove that, for genus g>1, the holomorphic bisectional curvature of the vortex metrics cannot always be nonnegative in the multivortex case, and this property extends to all Kaehler metrics on certain symmetric powers. Our result rules out an established and natural conjecture on the geometry of the moduli spaces.
description: 25 pages; final version, to appear in Math. Z
Additional file 1 of Challenges regarding informed consent in recruitment to clinical research: a qualitative study of clinical research nurses’ experiences
Creators: name: Godskesen, Tove
name: Björk, Joar
name: Juth, Niklas
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Science Policy
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Research checklist. Consolidated criteria forreporting qualitative studies (COREQ): 32-item checklist.
From Low-Distortion Norm Embeddings to Explicit Uncertainty Relations and Efficient Information Locking
Creators: name: Fawzi, Omar
name: Hayden, Patrick
name: Sen, Pranab
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Computational Complexity (cs.CC)
subject: Metric Geometry (math.MG)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: F.1.1; E.4

description: The existence of quantum uncertainty relations is the essential reason that some classically impossible cryptographic primitives become possible when quantum communication is allowed. One direct operational manifestation of these uncertainty relations is a purely quantum effect referred to as information locking. A locking scheme can be viewed as a cryptographic protocol in which a uniformly random n-bit message is encoded in a quantum system using a classical key of size much smaller than n. Without the key, no measurement of this quantum state can extract more than a negligible amount of information about the message, in which case the message is said to be "locked". Furthermore, knowing the key, it is possible to recover, that is "unlock", the message. In this paper, we make the following contributions by exploiting a connection between uncertainty relations and low-distortion embeddings of L2 into L1. We introduce the notion of metric uncertainty relations and connect it to low-distortion embeddings of L2 into L1. A metric uncertainty relation also implies an entropic uncertainty relation. We prove that random bases satisfy uncertainty relations with a stronger definition and better parameters than previously known. Our proof is also considerably simpler than earlier proofs. We apply this result to show the existence of locking schemes with key size independent of the message length. We give efficient constructions of metric uncertainty relations. The bases defining these metric uncertainty relations are computable by quantum circuits of almost linear size. This leads to the first explicit construction of a strong information locking scheme. Moreover, we present a locking scheme that is close to being implementable with current technology. We apply our metric uncertainty relations to exhibit communication protocols that perform quantum equality testing.
description: 60 pages, 5 figures. v4: published version
Additional file 1 of Impact of a disability-targeted microentrepreneurship programme in Kenya: study protocol for a randomised controlled trial of the InBusiness programme
Creators: name: Banks, Lena Morgon
name: Kepha, Stella
name: Zinke-Allmang, Anja
name: Gichuki, Paul M.
name: Scherer, Nathaniel
name: Mwandawiro, Charles
name: Carew, Mark
name: Njomo, Doris
name: Chen, Shanquan
name: Okoyo, Collins
name: Davey, Calum
name: Shakespeare, Tom
name: Pereira, Maria Antonella
name: Goyal, Divya
name: Kuper, Hannah
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1. SPIRIT checklist.
Fourier-Mukai functors in the supported case
Creators: name: Canonaco, Alberto
name: Stellari, Paolo
Publisher: name: arXiv
Year: 2010
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: We prove that exact functors between the categories of perfect complexes supported on projective schemes are of Fourier--Mukai type if the functor satisfies a condition weaker than being fully faithful. We also get generalizations of the results in the literature in the case without support conditions. Some applications are discussed and, along the way, we prove that the category of perfect supported complexes has a strongly unique enhancement.
description: 36 pages. Major revision and new results added. Accepted for publication in Compositio Math
Lightweight mitigation against transient cache side-channel attacks
Creators: name: He, Muchen
Publisher: name: University of British Columbia
Year: 2023

description: Today, nearly all modern devices, including smartphones, PCs, and cloud servers, benefit significantly from two architectural advancements that speed up computation. First, speculative execution allows the execution of instructions ahead of time; and second, cache memory store data close to the processor to reduce latency of memory operations. Unfortunately, these features also make compute systems vulnerable to security holes known as transient side-channel attacks. These attacks exploit predictive mechanisms and use mis-speculated instructions to modify the cache persistently as a side channel. Such attacks enables leakage of private data, such as cryptographic keys. Full-fledged mitigations against transient attacks have come at a significant performance cost. They either try to stop potential leakage at the source — where it is speculatively execution instructions — and penalize many “innocent” executions or laboriously restore past states in the memory hierarchy. This research focuses on mitigating the transient side-channel attacks while minimizing performance loss. Our approach combines significantly more efficient protection schemes inside the cache hardware, the destination, to stop potential leaks. We identify and leverage a specific memory access pattern to detect an ongoing cache side-channel attack and localize the protection to where it occurs. We propose FantôMiss, our mitigation strategy that allows cache state changes speculatively but also tracks the modified cache lines under speculation. Then, for subsequent accesses to those speculated cache lines, we generate fake cache misses that traverse the memory hierarchy that conceals speculative cache states, thereby closing the side-channel. Crucially, the increased latency is not imposed upon all load instructions but only on loads that read potential leak sources. As a result, FantôMiss significantly outperforms prior proposed mitigations, with execution-time overheads of just 0.5% and 1.6%(geometric-mean) across the PARSEC and SPEC benchmark suites.
Additional file 3 of Monitored anesthesia care and asleep-awake-asleep techniques combined with multiple monitoring for resection of gliomas in eloquent brain areas: a retrospective analysis of 225 patients
Creators: name: Li, San-Zhong
name: Su, Ning
name: Wu, Shuang
name: Fei, Xiao-Wei
name: He, Xin
name: Zhang, Jiu-Xiang
name: Wang, Xiao-Hui
name: Zhang, Hao-Peng
name: Bai, Xiao-Guang
name: Cheng, Guang
name: Fei, Zhou
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 3: Sup. Table 1. Intraoperative medication for complications. Sup. Table 2. Modified Rankin Scale.
How to make a clean separation between CMB E and B modes with proper foreground masking
Creators: name: Kim, Jaiseung
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We investigate the E/B decomposition of CMB polarization on a masked sky. In real space, operators of E and B mode decomposition involve only differentials of CMB polarization. We may, therefore in principle, perform a clean E/B decomposition from incomplete sky data. Since it is impractical to apply second derivatives to observation data, we usually rely on spherical harmonic transformation and inverse transformation, instead of using real-space operators. In spherical harmonic representation, jump discontinuities in a cut sky produces Gibbs phenomenon, unless a spherical harmonic expansion is made up to an infinitely high multipole. By smoothing a foreground mask, we may suppress the Gibbs phenomenon effectively in a similar manner to apodization of a foreground mask discussed in other works. However, we incur foreground contamination by smoothing a foreground mask, because zero-value pixels in the original mask may be rendered non-zero by the smoothing process. In this work, we investigate an optimal foreground mask, which ensures proper foreground masking and suppresses Gibbs phenomenon. We apply our method to a simulated map of the pixel resolution comparable to the Planck satellite. The simulation shows that the leakage power is lower than unlensed CMB B mode power spectrum of tensor-to-scalar ratio $r\sim 1\times10^{-7}$. We compare the result with that of the original mask. We find that the leakage power is reduced by a factor of $10^{6} \sim 10^{9}$ at the cost of a sky fraction $0.07$, and that the enhancement is highest at lowest multipoles. We confirm that all the zero-value pixels in the original mask remain zero in our mask. The application of this method to the Planck data will improve the detectability of primordial tensor perturbation.
description: v2: typos corrected, v3: matched with the published version (the clarity improved) v4: a typo corrected v5: a bibliography file error fixed
Additional file 1 of Contents of antenatal care services in Afghanistan: findings from the national health survey 2018
Creators: name: Stanikzai, Muhammad Haroon
name: Tawfiq, Essa
name: Jafari, Massoma
name: Wasiq, Abdul Wahed
name: Seddiq, Mohammad Khaled
name: Currie, Sheena
name: Sayam, Hadia
name: Baray, Ahmad Haroon
name: Saeedzai, Sayed Ataullah
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Cardiology

description: Supplementary Material 1: Comparison of the baseline characteristics of the 186 women who did not report a specific service with women who received services
An integrated performance model learning and planning approach for optimal infrastructure facility maintenance under partial observability
Creators: name: Amin, Saurabh
Publisher: name: The University of Texas at Austin
Year: 2004
Subjects: Sequence classification
Reinforcement learning
Infrastructure inspection and maintenance

description: Infrastructure inspection and maintenance decision making is a stochastic and partially observable problem. This thesis presents a learning and decision-making approach for developing optimal joint inspection and maintenance policies for civil infrastructure facilities under performance model uncertainty and partially observable condition state. Joint inspection and maintenance decision making refers to the cost-effective policies that capture the interactions between the inspections, and the maintenance and rehabilitation decisions. Performance model uncertainty is the uncertainty about the actual facility deterioration model. Partially observation condition states imply that the true or latent condition of the facility is not captured by the measurement technology used for inspecting the facility due to measurement errors. The proposed approach models single facility inspection and maintenance decision-making problem as a partially observable Markov decision process. The data collected during the agency-facility interaction is used to learn the maximum likelihood estimate of performance model using the Baum-Welch algorithm. Both offline and online versions of the learning algorithm are presented. The probing-optimizing dichotomy, also known as exploration-exploitation dilemma, in choosing between the best strategy based on the past knowledge of deterioration and the strategy that provides information leading to better performance model is also illustrated. Once a set of performance models is learned, each of the models is quantitatively compared with the corresponding true model using an information theoretic measure known as asymmetric Kullback-Leibler divergence to determine its goodness. It is also shown that given a set of new observation sequences gathered after the model learning, each of the sequences or the entire set of sequences can be assigned the model that gives the least log-likelihood on that sequence or the set. This can help in classifying the facility deterioration into different deterioration modes like slow, medium, or fast. Finally, an exact algorithm for arriving at optimal inspection and maintenance decision-making policies is described. It is argued that the proposed approach scores over other recently developed adaptive control approaches in that it directly learns the best model from historical data instead of maintaining and updating beliefs over a set of pre-selected models. Furthermore, since the proposed learning approach is model-based, it makes more efficient use of costly data as compared to the model-less learning approaches. Keywords: Infrastructure Inspection and Maintenance, Baum-Welch Algorithm, Kullback-Liebler Divergence, Sequence Classification, Partially Observable Markov Decision Process, Reinforcement Learning.
Discussion of: Brownian distance covariance
Creators: name: Kosorok, Michael R.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Applications (stat.AP)
subject: FOS: Computer and information sciences

description: We discuss briefly the very interesting concept of Brownian distance covariance developed by Székely and Rizzo [Ann. Appl. Statist. (2009), to appear] and describe two possible extensions. The first extension is for high dimensional data that can be coerced into a Hilbert space, including certain high throughput screening and functional data settings. The second extension involves very simple modifications that may yield increased power in some settings. We commend Székely and Rizzo for their very interesting work and recognize that this general idea has potential to have a large impact on the way in which statisticians evaluate dependency in data. [arXiv:1010.0297]
description: Published in at http://dx.doi.org/10.1214/09-AOAS312B the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org). With Corrections
Additional file 1 of Reproductive decision making in women with medical comorbidities: a qualitative study
Creators: name: Kraus, Elena M.
name: Chavan, Niraj R.
name: Whelan, Victoria
name: Goldkamp, Jennifer
name: DuBois, James M.
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: Mental Health

description: Additional file 1.
Framing violence in times of peace talks : El Tiempo’s news coverage of massacres committed during the 1999–2002 Colombian government - FARC peace process
Creators: name: Merchan, Juan
Publisher: name: University of British Columbia
Year: 2023

description: This thesis examines the news coverage of El Tiempo, Colombia’s largest and most influential newspaper, on the massacres committed by the FARC guerilla and the AUC paramilitary during the 1999 - 2002 peace process between the Colombian government and the FARC. The study confirmed some observations from previous research concerning the Colombian news ecosystem and the news coverage of the Colombian armed conflict by conducting a framing analysis of El Tiempo's news stories, front-page headlines, and standfirsts that were published within five days after the massacres occurred. It also identified problematic patterns in the news reporting of the massacres, such as the presence of victim-blaming accusations made by official sources and armed groups and the poor journalistic fact verification of the events. This thesis contributes to the communications and journalism studies in three ways. Firstly, it examines the news coverage of Colombia’s most important newspaper during a significant time period in Colombia’s history: the 1999-2002 peace process. Secondly, the study expands the comprehension of how news production in Colombia operates in times of crisis. Finally, it demonstrates the research capabilities of KH-Coder, a text analysis software, and promotes its use in communications and journalism studies.
Theory of self-learning $Q$-matrix
Creators: name: Liu, Jingchen
name: Xu, Gongjun
name: Ying, Zhiliang
Publisher: name: arXiv
Year: 2010
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics

description: Cognitive assessment is a growing area in psychological and educational measurement, where tests are given to assess mastery/deficiency of attributes or skills. A key issue is the correct identification of attributes associated with items in a test. In this paper, we set up a mathematical framework under which theoretical properties may be discussed. We establish sufficient conditions to ensure that the attributes required by each item are learnable from the data.
description: Published in at http://dx.doi.org/10.3150/12-BEJ430 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm)
Successive normalization of rectangular arrays
Creators: name: Olshen, Richard A.
name: Rajaratnam, Bala
Publisher: name: arXiv
Year: 2010
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics

description: Standard statistical techniques often require transforming data to have mean $0$ and standard deviation $1$. Typically, this process of "standardization" or "normalization" is applied across subjects when each subject produces a single number. High throughput genomic and financial data often come as rectangular arrays where each coordinate in one direction concerns subjects who might have different status (case or control, say), and each coordinate in the other designates "outcome" for a specific feature, for example, "gene," "polymorphic site" or some aspect of financial profile. It may happen, when analyzing data that arrive as a rectangular array, that one requires BOTH the subjects and the features to be "on the same footing." Thus there may be a need to standardize across rows and columns of the rectangular matrix. There arises the question as to how to achieve this double normalization. We propose and investigate the convergence of what seems to us a natural approach to successive normalization which we learned from our colleague Bradley Efron. We also study the implementation of the method on simulated data and also on data that arose from scientific experimentation.
description: Published in at http://dx.doi.org/10.1214/09-AOS743 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org). With Corrections
Additional file 1 of A base substitution in OsphyC disturbs its Interaction with OsphyB and affects flowering time and chlorophyll synthesis in rice
Creators: name: Lin, Xiaoli
name: Huang, Yongping
name: Rao, Yuchun
name: Ouyang, Linjuan
name: Zhou, Dahu
name: Zhu, Changlan
name: Fu, Junru
name: Chen, Chunlian
name: Yin, Jianhua
name: Bian, Jianmin
name: He, Haohua
name: Zou, Guoxing
name: Xu, Jie
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 1.
Methodologies, strategies or practices for the development of clinical practice guidelines for rare, orphan or low prevalence diseases: Scoping review
Creators: name: Echeverry, Sandra Johanna
name: Matamoros, Fabio Alexander Sierra
name: Muñoz, Ani Julieth Cortes
Publisher: name: Open Science Framework
Year: 2023
Subjects: subject: Medicine and Health Sciences
subject: Methodology
subject: rare disease
subject: Guidelines

description: The objective of this scoping is to explore the methodologies, strategies or practices implemented by groups that develop clinical practice guidelines (CPG) for rare or low-prevalence diseases, especially with regard to the type and quality of existing evidence in these diseases and how it is generate the recommendations