cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of Effects of an online program including mindfulness, exercise therapy and patient education compared to online exercise therapy and patient education for people with Patellofemoral Pain: protocol for a randomized clinical trial
Creators: name: Priore, Liliam Barbuglio Del
name: Perez, Vitoria Ozores
name: Briani, Ronaldo Valdir
name: Farinelli, Lucca Andre Liporoni Bego
name: da Silva, Júlia de Cássia Pinto
name: Martins, Odisséia Marli Gimenes
name: Lopes, Fábio Arruda
name: Amorim, Anita Barros
name: Pappas, Evangelos
name: de Azevedo, Fábio Mícolis
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Supplementary Material 1
Cyclic thrombocytopenia associated with estradiol: a case report
Creators: name: Pang, Ningbo
name: Li, Yingwei
name: Zhou, Kangxi
name: Liu, Chunliang
name: Yan, Rong
name: Sun, Chenglin
name: Xiao, Weiling
name: Ruan, Changgeng
name: Zhai, Zhimin
name: Dai, Kesheng
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Science Policy
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences

description: Cyclic thrombocytopenia (CTP) is a rare blood disorder characterized by periodic fluctuations in platelet counts. CTP usually appears in pre-menopausal women, and these fluctuations of platelets are in phase with the menstrual cycle. CTP is a heterogeneous disease, and the pathogenic mechanism is still unclear. Therefore, it harbors great significance for exploring the association of fluctuations in platelet counts with hormonal-cycle. Firstly, we washed human platelets from healthy volunteers following the Declaration of Helsinki. Flow cytometer was employed to measure the mitochondrial inner transmembrane potential (ΔΨm) depolarization, PS exposure, P-selectin expression, and GPIIb/IIIa activation in platelets. In addition, western blot detected the related protein expression. The corresponding assay kit measured the caspase-3 and PDE3A activity. Finally, flow cytometry determined mouse platelets labeled with calcein. We find a reverse relationship between the platelet count and serum estradiol (E2) level in a CTP patient. We demonstrated that E2 induces platelet apoptosis in vitro and platelet clearance in vivo. We further discovered that E2 activates phosphodiesterase 3A, which inhibits protein kinase A (PKA), leading to PKA-mediated platelet apoptosis. Activation of PKA protected platelets from E2-induced thrombocytopenia and elevated the number of mice circulatory platelets. We find that E2 induces platelet apoptosis and clearance through PDE3A-mediated PKA inhibition. Activation of PKA rescues E2-induced thrombocytopenia in mice. Thus, our study reveals a pathogenesis of E2-related CTP and suggests promising therapeutic strategies for the disease.
Opportunities for agricultural water management interventions in the Nariarlé Basin, Burkina Faso
Creators: name: Bruin, Annemarieke De
name: Cambridge, Howard
name: Stein, Christian
name: Korodjouma Ouattara
name: Souleymane  Pare
Publisher: name: Gates Open Research
Year: 2019

description: Opportunities for agricultural water management interventions in the Nariarlé Basin, Burkina Faso
Additional file 2 of Artificial intelligence-supported lung cancer detection by multi-institutional readers with multi-vendor chest radiographs: a retrospective clinical validation study
Creators: name: Ueda, Daiju
name: Yamamoto, Akira
name: Shimazaki, Akitoshi
name: Walston, Shannon Leigh
name: Matsumoto, Toshimasa
name: Izumi, Nobuhiro
name: Tsukioka, Takuma
name: Komatsu, Hiroaki
name: Inoue, Hidetoshi
name: Kabata, Daijiro
name: Nishiyama, Noritoshi
name: Miki, Yukio
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer

description: Additional File 2. Supplementary Fig. 1. Metric definitions for cases and lesions
Additional file 2 of Effects of an online program including mindfulness, exercise therapy and patient education compared to online exercise therapy and patient education for people with Patellofemoral Pain: protocol for a randomized clinical trial
Creators: name: Priore, Liliam Barbuglio Del
name: Perez, Vitoria Ozores
name: Briani, Ronaldo Valdir
name: Farinelli, Lucca Andre Liporoni Bego
name: da Silva, Júlia de Cássia Pinto
name: Martins, Odisséia Marli Gimenes
name: Lopes, Fábio Arruda
name: Amorim, Anita Barros
name: Pappas, Evangelos
name: de Azevedo, Fábio Mícolis
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Supplementary Material 2
Generalized cluster states from Hopf algebras: non-invertible symmetry and Hopf tensor network representation
Creators: name: Jia, Zhian
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: Quantum Algebra (math.QA)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: Cluster states are crucial resources for measurement-based quantum computation (MBQC). It exhibits symmetry-protected topological (SPT) order, thus also playing a crucial role in studying topological phases. We present the construction of cluster states based on Hopf algebras. By generalizing the finite group valued qudit to a Hopf algebra valued qudit and introducing the generalized Pauli-X operator based on the regular action of the Hopf algebra, as well as the generalized Pauli-Z operator based on the irreducible representation action on the Hopf algebra, we develop a comprehensive theory of Hopf qudits. We demonstrate that non-invertible symmetry naturally emerges for Hopf qudits. Subsequently, for a bipartite graph termed the cluster graph, we assign the identity state and trivial representation state to even and odd vertices, respectively. Introducing the edge entangler as controlled regular action, we provide a general construction of Hopf cluster states. To ensure the commutativity of the edge entangler, we propose a method to construct a cluster lattice for any triangulable manifold. We use the 1d cluster state as an example to illustrate our construction. As this serves as a promising candidate for SPT phases, we construct the gapped Hamiltonian for this scenario and provide a detailed discussion of its non-invertible symmetries. We demonstrate that the 1d cluster state model is equivalent to the quasi-1d Hopf quantum double model with one rough boundary and one smooth boundary. We also discuss the generalization of the Hopf cluster state model to the Hopf ladder model through symmetry topological field theory. Furthermore, we introduce the Hopf tensor network representation of Hopf cluster states by integrating the tensor representation of structure constants with the string diagrams of the Hopf algebra, which can be used to solve the Hopf cluster state model.
description: v1: 41 pages; v2: 46 pages, several typos are corrected, a more detailed discussion of non-invertible symmetry is provided; v3: typos are corrected, more discussion on Hopf symmetries added
Computing the Girth of a Planar Graph in Linear Time
Creators: name: Chang, Hsien-Chih
name: Lu, Hsueh-I
Publisher: name: arXiv
Year: 2011
Subjects: subject: Data Structures and Algorithms (cs.DS)
subject: FOS: Computer and information sciences

description: The girth of a graph is the minimum weight of all simple cycles of the graph. We study the problem of determining the girth of an n-node unweighted undirected planar graph. The first non-trivial algorithm for the problem, given by Djidjev, runs in O(n^{5/4} log n) time. Chalermsook, Fakcharoenphol, and Nanongkai reduced the running time to O(n log^2 n). Weimann and Yuster further reduced the running time to O(n log n). In this paper, we solve the problem in O(n) time.
description: 20 pages, 7 figures, accepted to SIAM Journal on Computing
Does leukocytosis remain a predictive factor for survival outcomes in patients with acute promyelocytic leukemia receiving ATRA plus a chemotherapy-based regimen? A prospective multicenter analysis from TALWG
Creators: name: Kungwankiattichai, Smith
name: Owattanapanich, Weerapat
name: Rattanathammethee, Thanawat
name: Rattarittamrong, Ekarat
name: Chanswangphuwana, Chantiya
name: Polprasert, Chantana
name: Limvorapitak, Wasithep
name: Saengboon, Supawee
name: Niparuck, Pimjai
name: Puavilai, Teeraya
name: Julamanee, Jakrawadee
name: Saelue, Pirun
name: Wanitpongpun, Chinadol
name: Prayongratana, Kannadit
name: Sriswasdi, Chantarapa
name: Nakhakes, Chajchawan
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Hematology

description: Acute promyelocytic leukemia (APL) is a distinct subtype of acute myeloid leukemia (AML) with a unique clinical presentation and prognosis. This study aimed to investigate the epidemiology, clinical characteristics, treatments, and clinical outcomes of Thai APL patients dominantly treated with all-trans-retinoic acid (ATRA) combined with a chemotherapy-based therapy. This was an eight-year prospective, observational study from nine academic hospitals in the Thai Acute Leukemia Working Group (TALWG) of the Thai Society of Hematology, which included newly diagnosed Thai APL patients, aged 18 years or older. The web-based registration collected baseline charateristic, and clinical outcomes. From 992 newly diagnosed AML patients, 79 APL patients were enrolled in this study. Almost all subjects were de novo APL (94.9%), while the others were therapy-related APL. The commonest clinical presentation was disseminated intravascular coagulation (38%). One-third of the patients were categorized as high risk according to the initial WBC. Almost all patients received ATRA combined with idarubicin regimen. The complete response rate was as high as 95.7%, which translated into excellent four-year overall survival (OS) (75.6%) and four-year leukemia-free survival (LFS) (75.4%). The multivariate analysis demonstrated that the older age and WBC count >20 × 109/L conferred a significantly unfavorable OS with the hazard ratios of 3.03 (95% confidence interval [CI]: 1.14–8.05) and 4.18 (95%CI: 1.69–10.35), respectively. Similarly, these two parameters remained independent of the poor prognosis factors for LFS. This report confirmed that APL had a favorable prognosis. However, advanced age and high WBC count >20 × 109/L contributed to a worse outcome. APL; acute promyelocytic leukemia; ATRA; all-transretinoic acid; CR; complete remission; DS; differentiation syndrome; ECOG; Eastern Cooperative Oncology Group; ED; early death; HR; hazard ratio; IQR; interquartile range; LFS; leukemia-free survival; OS; overall survival; WBC; white blood cell.
Additional file 3 of Effects of an online program including mindfulness, exercise therapy and patient education compared to online exercise therapy and patient education for people with Patellofemoral Pain: protocol for a randomized clinical trial
Creators: name: Priore, Liliam Barbuglio Del
name: Perez, Vitoria Ozores
name: Briani, Ronaldo Valdir
name: Farinelli, Lucca Andre Liporoni Bego
name: da Silva, Júlia de Cássia Pinto
name: Martins, Odisséia Marli Gimenes
name: Lopes, Fábio Arruda
name: Amorim, Anita Barros
name: Pappas, Evangelos
name: de Azevedo, Fábio Mícolis
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Supplementary Material 3
Un théorème de l'application ouverte sur les corps valués algébriquement clos
Creators: name: Moret-Bailly, Laurent
Publisher: name: arXiv
Year: 2010
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14B25, 12J10

description: Let K be an algebraically closed valued field, and let f:X--->Y be a universally open morphism of K-schemes of finite type. We show that the induced map on K-rational points is open for the topologies deduced from the absolute value of K. ------ Soit K un corps valué algébriquement clos, et soit f:X--->Y un morphisme universellement ouvert de K-schémas de type fini. On montre que l'application de X(K) dans Y(K) induite par f est ouverte pour les topologies déduites de la valeur absolue sur K.
description: 7 pages, in French. Some minor changes after referee's report. Accepted for publication in Mathematica Scandinavica
A novel wide-bandwidth linear inductive differential position sensor
Creators: name: Reinholz, Devin
Publisher: name: University of British Columbia
Year: 2022

description: Linear inductive differential position sensors such as the linear variable differential transformer (LVDT) and the differential variable reluctance transducer (DVRT) are used extensively in a variety of applications due to their rugged, inexpensive design and compact size. Both the LVDT and DVRT are proficient at measuring the position of slow moving, or stationary objects, but become progressively more inaccurate as the speed of the object being measured increases. The variable reluctance differential solenoid transducer (VRDST) was recently developed, and shown to be capable of concurrently performing a measurement that is accurate at low speeds and a measurement that is accurate at high speeds. The VRDST was able to combine these two measurements using a complementary filter to create a single wide-bandwidth measurement. However, the large cost and small stroke-to-length ratio of the VRDST limits its practical viability. This thesis presents a novel variation of the VRDST called the ironless-stator variable reluctance differential solenoid transducer (ISVRDST). The ISVRDST removes the ferromagnetic stator used by the VRDST to reduce the overall size and cost of the sensor. Finite element analysis (FEA) and analytical simulations are used to design the ISVRDST and predict its performance. A proof-of-concept prototype is fabricated and used to experimentally validate the analytical models and simulation results as well as compare its performance against the VRDST prototype. The ISVRDST is shown to be capable of robustly utilizing the complementary filter measurement pioneered by the VRDST, while having a 3.5 times larger stroke-to-length ratio, a 6.8 times larger stroke-to-width ratio, and while costing over 100 times less. Additionally, the ISVRDST is compared against the LVDT and DVRT and is found to have a comparable size, cost and performance while having a measurement bandwidth over 250 times larger.
DarkDNS: Revisiting the Value of Rapid Zone Update
Creators: name: Sommese, Raffaele
name: Akiwate, Gautam
name: Affinito, Antonia
name: Müller, Moritz
name: Jonker, Mattijs
name: Claffy, KC
Publisher: name: arXiv
Year: 2024
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: Malicious actors exploit the DNS namespace to launch spam campaigns, phishing attacks, malware, and other harmful activities. Combating these threats requires visibility into domain existence, ownership and nameservice activity that the DNS protocol does not itself provide. To facilitate visibility and security-related study of the expanding gTLD namespace, ICANN introduced the Centralized Zone Data Service (CZDS) that shares daily zone file snapshots of new gTLD zones. However, a remarkably high concentration of malicious activity is associated with domains that do not live long enough make it into these daily snapshots. Using public and private sources of newly observed domains, we discover that even with the best available data there is a considerable visibility gap in detecting short-lived domains. We find that the daily snapshots miss at least 1% of newly registered and short-lived domains, which are frequently registered with likely malicious intent. In reducing this critical visibility gap using public sources of data, we demonstrate how more timely access to TLD zone changes can provide valuable data to better prevent abuse. We hope that this work sparks a discussion in the community on how to effectively and safely revive the concept of sharing Rapid Zone Updates for security research. Finally, we release a public live feed of newly registered domains, with the aim of enabling further research in abuse identification.
description: Accepted at IMC2024, Madrid
Additional file 4 of Effects of an online program including mindfulness, exercise therapy and patient education compared to online exercise therapy and patient education for people with Patellofemoral Pain: protocol for a randomized clinical trial
Creators: name: Priore, Liliam Barbuglio Del
name: Perez, Vitoria Ozores
name: Briani, Ronaldo Valdir
name: Farinelli, Lucca Andre Liporoni Bego
name: da Silva, Júlia de Cássia Pinto
name: Martins, Odisséia Marli Gimenes
name: Lopes, Fábio Arruda
name: Amorim, Anita Barros
name: Pappas, Evangelos
name: de Azevedo, Fábio Mícolis
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Supplementary Material 4
A search for light dark matter in XENON10 data
Creators: name: Angle, J.
name: Aprile, E.
name: Arneodo, F.
name: Baudis, L.
name: Bernstein, A.
name: Bolozdynya, A.
name: Brusov, P.
name: Coelho, L. C. C.
name: Dahl, C. E.
name: DeViveiros, L.
name: Ferella, A. D.
name: Fernandes, L. M. P.
name: Fiorucci, S.
name: Gaitskell, R. J.
name: Giboni, K. L.
name: Gomez, R.
name: Hasty, R.
name: Kastens, L.
name: Kwong, J.
name: Lopes, J. A. M.
name: Madden, N.
name: Manalaysay, A.
name: Manzur, A.
name: McKinsey, D. N.
name: Monzani, M. E.
name: Ni, K.
name: Oberlack, U.
name: Orboeck, J.
name: Plante, G.
name: Santorelli, R.
name: Santos, J. M. F. dos
name: Shagin, P.
name: Shutt, T.
name: Sorensen, P.
name: Schulte, S.
name: Winant, C.
name: Yamashita, M.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We report results of a search for light (<10 GeV) particle dark matter with the XENON10 detector. The event trigger was sensitive to a single electron, with the analysis threshold of 5 electrons corresponding to 1.4 keV nuclear recoil energy. Considering spin-independent dark matter-nucleon scattering, we exclude cross sections σ_n>3.5x10^{-42} cm^2, for a dark matter particle mass m_χ=8 GeV. We find that our data strongly constrain recent elastic dark matter interpretations of excess low-energy events observed by CoGeNT and CRESST-II, as well as the DAMA annual modulation signal.
description: Manuscript identical to v2 (published version) but also contains erratum. Note v3==v2 but without \linenumbers
Bioinformatics analysis of the endoplasmic reticulum stress-related prognostic model and immune cell infiltration in acute myeloid leukemia
Creators: name: Pan, Mengya
name: Zhou, Junjie
name: Jiao, Changqing
name: Ge, Jian
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Hematology

description: Acute myeloid leukemia (AML) is the most common malignant hematological disease originating from hematopoietic stem cells. Endoplasmic reticulum stress (ERs) has been reported to be involved in multiple tumor-related biological processes. However, the prognostic role of ERs-related genes in AML has not been fully investigated. The TCGA-LAML RNA-seq dataset was downloaded from the UCSC Xena website as the training cohort. Univariate Cox regression analysis was used to identify 42 ER stress-related genes associated with prognosis. Then, a ERs risk score prognostic model was established through LASSO regression analysis. AML patients were divided into high- and low-risk groups according to the median risk score. The Kaplan-Meier survival curve, time ROC curve analysis and univariate and multivariate independent prognostic analyses were presented for the high- and low-risk groups. Moreover, we verified the ERs risk model in the TARGET-AML and GSE37642 datasets. Next, we performed immune cell infiltration analysis, immune checkpoint gene expression analysis and drug sensitivity analysis. We found 42 ER stress-related genes with prognostic significance, and a prognostic model consisting of 13 genes was constructed and verified. The survival rate of AML patients in the low-risk group was better than that in the high-risk group. The tumor microenvironment and immune cell infiltration results showed that immune cell infiltration was correlated with the survival status of patients. This research identified a ERs risk model with significant prognostic value. These genes are expected to be potential prognostic biomarkers in AML, providing a new theoretical basis for disease management.
Additional file 3 of Artificial intelligence-supported lung cancer detection by multi-institutional readers with multi-vendor chest radiographs: a retrospective clinical validation study
Creators: name: Ueda, Daiju
name: Yamamoto, Akira
name: Shimazaki, Akitoshi
name: Walston, Shannon Leigh
name: Matsumoto, Toshimasa
name: Izumi, Nobuhiro
name: Tsukioka, Takuma
name: Komatsu, Hiroaki
name: Inoue, Hidetoshi
name: Kabata, Daijiro
name: Nishiyama, Noritoshi
name: Miki, Yukio
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer

description: Additional File 3. Supplementary Fig. 2. Eligibility of chest radiographs for test dataset
Moeglin's theorem and Goldie rank polynomials in Cartan type A
Creators: name: Brundan, Jonathan
Publisher: name: arXiv
Year: 2010
Subjects: subject: Representation Theory (math.RT)
subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics
subject: 17B35

description: We use the theory of finite W-algebras associated to nilpotent orbits in the Lie algebra g = gl_N(C) to give another proof of Moeglin's theorem about completely prime primitive ideals in the enveloping algebra U(g). We also make some new observations about Joseph's Goldie rank polynomials in Cartan type A.
description: final version; minor changes and some additions to bibliography; 32 pages
Additional file 5 of Effects of an online program including mindfulness, exercise therapy and patient education compared to online exercise therapy and patient education for people with Patellofemoral Pain: protocol for a randomized clinical trial
Creators: name: Priore, Liliam Barbuglio Del
name: Perez, Vitoria Ozores
name: Briani, Ronaldo Valdir
name: Farinelli, Lucca Andre Liporoni Bego
name: da Silva, Júlia de Cássia Pinto
name: Martins, Odisséia Marli Gimenes
name: Lopes, Fábio Arruda
name: Amorim, Anita Barros
name: Pappas, Evangelos
name: de Azevedo, Fábio Mícolis
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Supplementary Material 5
Additional file 4 of Artificial intelligence-supported lung cancer detection by multi-institutional readers with multi-vendor chest radiographs: a retrospective clinical validation study
Creators: name: Ueda, Daiju
name: Yamamoto, Akira
name: Shimazaki, Akitoshi
name: Walston, Shannon Leigh
name: Matsumoto, Toshimasa
name: Izumi, Nobuhiro
name: Tsukioka, Takuma
name: Komatsu, Hiroaki
name: Inoue, Hidetoshi
name: Kabata, Daijiro
name: Nishiyama, Noritoshi
name: Miki, Yukio
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer

description: Additional File 4. Supplementary Fig. 3. Example of a case in which a physician mistakenly changed their decision from true positive to false negative due to the false negative output of the CAD
Atlantic Adventures with ATLAS Show
Creators: name: Paterson, Emma
Publisher: name: Zenodo
Year: 2019
Subjects: public engagement

description: There are 2 parts to 'Atlantic Adventures with ATLAS'.

1. PowerPoint file with embedded videos

2. PDF file which contains an explanation of the show, a kit list, script and video transcript.

This show was developed to explain the ATLAS project and the work of people involved in it. It starts with a brief introduction to how and why oceans are important, then moves on to how scientists and engineers work at sea. There are discussions around the technology used for exploration of the deep-sea and the challenges posed by deep water. It also features an introduction to cold-water corals, how they feed and how bottom trawling for fish damages them. The show finishes with information about marine protected areas and a compilation video from various ATLAS cruises (expeditions at sea).
SDSS-V Local Volume Mapper (LVM): A Glimpse into Orion
Creators: name: Kreckel, K.
name: Egorov, O. V.
name: Egorova, E.
name: Blanc, G. A.
name: Drory, N.
name: Kounkel, M.
name: Mendez-Delgado, J. E.
name: Roman-Zuniga, C. G.
name: Sanchez, S. F.
name: Stringfellow, G. S.
name: Stutz, A. M.
name: Zari, E.
name: Barrera-Ballesteros, J. K.
name: Bizyaev, D.
name: Brownstein, J. R.
name: Congiu, E.
name: Fernandez-Trincado, J. G.
name: Garcia, P.
name: Hillenbrand, L.
name: Ibarra-Medel, H. J.
name: Jin, Y.
name: Johnston, E. J.
name: Jones, A. M.
name: Kim, J. Serena
name: Kollmeier, J. A.
name: Kong, S.
name: Krishnarao, D.
name: Kumari, N.
name: Li, J.
name: Long, K.
name: Mata-Sanchez, A.
name: Mejia-Narvaez, A.
name: Popa, S. A.
name: Rix, H-W
name: Sattler, N.
name: Serna, J.
name: Singh, A.
name: Sanchez-Gallego, J. R.
name: Wofford, A.
name: Wong, T.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The Orion Molecular Cloud complex, one of the nearest (D = 406 pc) and most extensively studied massive star-forming regions, is ideal for constraining the physics of stellar feedback, but its ~12 deg diameter on the sky requires a dedicated approach to mapping ionized gas structures within and around the nebula. The Sloan Digital Sky Survey (SDSS-V) Local Volume Mapper (LVM) is a new optical integral field unit (IFU) that will map the ionized gas within the Milky Way and Local Group galaxies, covering 4300 deg^2 of the sky with the new LVM Instrument. We showcase optical emission line maps from LVM covering 12 deg^2 inside of the Orion belt region, with 195,000 individual spectra combined to produce images at 0.07 pc (35.3") resolution. This is the largest IFU map made (to date) of the Milky Way, and contains well-known nebulae (the Horsehead Nebula, Flame Nebula, IC 434, and IC 432), as well as ionized interfaces with the neighboring dense Orion B molecular cloud. We resolve the ionization structure of each nebula, and map the increase in both the [SII]/Ha and [NII]/Ha line ratios at the outskirts of nebulae and along the ionization front with Orion B. [OIII] line emission is only spatially resolved within the center of the Flame Nebula and IC 434, and our ~0.1 pc scale line ratio diagrams show how variations in these diagnostics are lost as we move from the resolved to the integrated view of each nebula. We detect ionized gas emission associated with the dusty bow wave driven ahead of the star sigma Orionis, where the stellar wind interacts with the ambient interstellar medium. The Horsehead Nebula is seen as a dark occlusion of the bright surrounding photo-disassociation region. This small glimpse into Orion only hints at the rich science that will be enabled by the LVM.
description: 13 pages, 10 figures, accepted for publication in A&A
Additional file 5 of Artificial intelligence-supported lung cancer detection by multi-institutional readers with multi-vendor chest radiographs: a retrospective clinical validation study
Creators: name: Ueda, Daiju
name: Yamamoto, Akira
name: Shimazaki, Akitoshi
name: Walston, Shannon Leigh
name: Matsumoto, Toshimasa
name: Izumi, Nobuhiro
name: Tsukioka, Takuma
name: Komatsu, Hiroaki
name: Inoue, Hidetoshi
name: Kabata, Daijiro
name: Nishiyama, Noritoshi
name: Miki, Yukio
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer

description: Additional File 5. Supplementary Fig. 4. Other examples of cases in which physicians correctly changed their decision from false negative to true positive due to the true positive output of the CAD
Additional file 1 of PIK3CA mutation in endometriotic epithelial cells promotes viperin-dependent inflammatory response to insulin
Creators: name: Wilson, Mike R.
name: Harkins, Shannon
name: Reske, Jake J.
name: Siwicki, Rebecca A.
name: Adams, Marie
name: Bae-Jump, Victoria L.
name: Teixeira, Jose M.
name: Chandler, Ronald L.
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer

description: Supplementary Material 1
Facing Emotions: Between- and Within-Session Changes in Facial Expression During Psychological Treatment for Depression
Creators: name: Hadar Fisher
name: Reiss, Philip
Publisher: name: Open Science Framework
Year: 2023
Subjects: subject: Social and Behavioral Sciences

description: The current study harnessed a computational approach to explore whether experiencing negative emotions during psychological treatment is related to subsequent changes in these emotions. Facial expressions were automatically extracted from 175 sessions of 58 patients with MDD. Within sessions, a U-shaped trajectory of change in valence was observed where patients expressed an increase in negative emotions in the middle of the session. Between sessions, a consistent increase in valence was observed. A trajectory of within-session decrease followed by an increase in valence was positively associated with greater perceived positive emotions and subsequent decreases in depressive symptoms.
Additional file 1 of Psychosocial demands and resources for working time organization in GP practices. Results from a team-based ethnographic study in Germany
Creators: name: Preiser, Christine
name: Tsarouha, Elena
name: Weltermann, Birgitta
name: Junne, Florian
name: Seifried-Dübon, Tanja
name: Hartmann, Sigrid
name: Bleckwenn, Markus
name: Rieger, Monika A.
name: Rind, Esther
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: Additional file 1.
On the many Dirichlet Laplacians on a non-convex polygon and their approximations by point interactions
Creators: name: Posilicano, Andrea
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mathematical Physics (math-ph)
subject: Analysis of PDEs (math.AP)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: By Birman and Skvortsov it is known that if $\Omegasf$ is a planar curvilinear polygon with $n$ non-convex corners then the Laplace operator with domain $H^2(\Omegasf)\cap H^1_0(\Omegasf)$ is a closed symmetric operator with deficiency indices $(n,n)$. Here we provide a Kre\uın-type resolvent formula for any self-adjoint extensions of such an operator, i.e. for the set of self-adjoint non-Friedrichs Dirichlet Laplacians on $\Omegasf$, and show that any element in this set is the norm resolvent limit of a suitable sequence of Friedrichs-Dirichlet Laplacians with $n$ point interactions.
description: Slightly revised version. Accepted for publication in Journal of Functional Analysis
Comparative analysis of annotation tools in grouping cell types from single-cell RNA sequencing data
Creators: name: Kshirsagar, Meghana
name: Vaidya, Gauri
Publisher: name: F1000 Research Limited
Year: 2023

description: The identification of differentially expressed immune related genes in immune cells and subtypes holds huge potential in predicting prognosis and survival of immunotherapy treatment outcomes. Gene expression profiling can help to identify the patterns of genes expressed in major immune cells amongst cohorts of patients at different stages of cancer which can generate new biological hypotheses. There exists a number of platforms and libraries that allow investigation of gene regulation in cell populations such as 10x Genomics, Seurat Workflow etc. Various prognostic models such as tumor progression , survival analysis can be designed using machine learning approaches from gene signature patterns. However, the accuracy of the models largely depend on the tools used for cell annotation. This research makes a comparative analysis of the popular annotation tools in grouping cell populations and validates the tools on the biomarkers identified in different cell populations.
title: The Spectrum of Slip Behaviors of a Granular Fault Gouge Analogue Governed by Rate and State Friction
Creators: name: Rudolf, Michael
name: Rosenau, Matthias
name: Oncken, Onno
Publisher: name: Wiley
Year: 2023

description: Currently, it is unknown how seismic and aseismic slip influences the recurrence and magnitude of earthquakes. Modern seismic hazard assessment is therefore based on statistics combined with numerical simulations of fault slip and stress transfer. To improve the underlying statistical models we conduct low velocity shear experiments with glass micro‐beads as fault gouge analogue at confining stresses of 5–20 kPa. As a result, we show that characteristic slip events emerge, ranging from fast and large slip to small scale oscillating creep and stable sliding. In particular, we observe small scale slip events that occur immediately before large scale slip events for a specific set of experiments. Similar to natural faults we find a separation of scales by several orders of magnitude for slow events and fast events. Enhanced creep and transient dilatational events pinpoint that the granular analogue is close to failure. From slide‐hold‐slide tests, we find that the rate‐and‐state properties are in the same range as estimates for natural faults and fault rocks. The fault shows velocity weakening characteristics with a reduction of frictional strength between 0.8% and 1.3% per e‐fold increase in sliding velocity. Furthermore, the slip modes that are observed in the normal shear experiments are in good agreement with analytical solutions. Our findings highlight the influence of micromechanical processes on macroscopic fault behavior. The comprehensive data set associated with this study can act as a benchmark for numerical simulations and improve the understanding of observations of natural faults.
Guide: How to organize Mobilization and Mutual Learning Processes - Public Engagement in Science.
Creators: name: Barbosa, Luisa
name: Revuelta, Gema
Publisher: name: Zenodo
Year: 2019
Subjects: public engagement, MML, mobilization and mutual learning,

description: The following document describes Mobilization and Mutual Learning (MML) actions, whose objective is to learn through dialogue. It intends to be a guide for research projects partners to implement their own MML and broaden their research activities to include other sectors of the society. The plan establishes a set of steps to organize an MML action: either a World café, a Focus Group or a Reverse Science Café.
Additional file 1 of Insights into the capability of the lignocellulolytic enzymes of Penicillium parvum 4-14 to saccharify corn bran after alkaline hydrogen peroxide pretreatment
Creators: name: Long, Liangkun
name: Wang, Wei
name: Liu, Zhen
name: Lin, Yuanxin
name: Wang, Jing
name: Lin, Qunying
name: Ding, Shaojun
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: Plant Biology
subject: Computational Biology

description: Additional file 1: Figure S1. Structural model of corn bran arabinoxylan.
Cosmological Constant from Decoherence
Creators: name: Kiefer, Claus
name: Queisser, Friedemann
name: Starobinsky, Alexei A.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We address the issue why a cosmological constant (dark energy) possesses a small positive value instead of being zero. Motivated by the cosmic landscape picture, we mimic the dark energy by a scalar field with potential wells and show that other degrees of freedom interacting with it can localize this field by decoherence in one of the wells. Dark energy can then acquire a small positive value. We also show that the additional degrees of freedom enhance the tunneling rate between the wells. The consideration is performed in detail for the case of two wells and then extended to a large number of wells.
description: 39 pages, 2 figures, final version
Additional file 2 of Psychosocial demands and resources for working time organization in GP practices. Results from a team-based ethnographic study in Germany
Creators: name: Preiser, Christine
name: Tsarouha, Elena
name: Weltermann, Birgitta
name: Junne, Florian
name: Seifried-Dübon, Tanja
name: Hartmann, Sigrid
name: Bleckwenn, Markus
name: Rieger, Monika A.
name: Rind, Esther
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: Additional file 2.
General theory for localizing the where and when of entropy production meets single-molecule experiments
Creators: name: Degünther, Julius
name: van der Meer, Jann
name: Seifert, Udo
Publisher: name: arXiv
Year: 2024
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Physical sciences

description: The laws of thermodynamics apply to biophysical systems on the nanoscale as described by the framework of stochastic thermodynamics. This theory provides universal, exact relations for quantities like work, which have been verified in experiments where a fully resolved description allows direct access to such quantities. Complementary studies consider partially hidden, coarse-grained descriptions, in which the mean entropy production typically is not directly accessible but can be bounded in terms of observable quantities. Going beyond the mean, we introduce a fluctuating entropy production that applies to individual trajectories in a coarse-grained description under time-dependent driving. Thus, this concept is applicable to the broad and experimentally significant class of driven systems in which not all relevant states can be resolved. We provide a paradigmatic example by studying an experimentally verified protein unfolding process. As a consequence, the entire distribution of the coarse-grained entropy production rather than merely its mean retains spatial and temporal information about the microscopic process. In particular, we obtain a bound on the distribution of the physical entropy production of individual unfolding events.
Character Varieties and the Moduli of Quiver Representations
Creators: name: Florentino, Carlos
name: Lawton, Sean
Publisher: name: arXiv
Year: 2011
Subjects: subject: Geometric Topology (math.GT)
subject: Algebraic Geometry (math.AG)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics
subject: 14L30 (Primary) 14P25, 14D20, 16G20 (Secondary)

description: Let G be a Lie group and Q a quiver with relations. In this paper, we define G-valued representations of Q which directly generalize G-valued representations of finitely generated groups. Although as G-spaces, the G-valued quiver representations are more general than G-valued representations of finitely generated groups, we show by collapsing arrows that their quotient spaces are equivalent. We then establish a general criterion for the moduli of G-valued quiver representations with relations to admit a strong deformation retraction to a compact quotient by pinching vertices on the quiver. This provides two different generalizations of main results in our previous work. Lastly, we establish quiver theoretic conditions for the moduli spaces of GL(n,C) and SL(n,C)-valued quiver representations to embed into traditional moduli spaces of quiver representations having constant dimension vector.
description: 37 pages; 5 figures; v3 has minor edits and added clarification
Energy requirements of grey whales
Creators: name: Agbayani, Selina Vivar
Publisher: name: University of British Columbia
Year: 2024

description: Eastern North Pacific grey whales (Eschrichtius robustus) rely on energy reserves obtained on their northern feeding grounds to complete their annual 17,000 km round-trip migration between the Arctic and Mexico. However, estimates of how much food is required to complete the annual migration is limited to adult whales of average size, and is not readily available across all age classes of males and females. I constructed an age-structured bioenergetics model using detailed information on the grey whale life cycle and migration timings to predict the energy requirements of different cohorts of grey whales. Results show that nursing calves require 24–35 L of milk daily in their first 9 to 10 months. Once weaned, juveniles require ~345 kg day⁻¹ of benthic invertebrates (4.5% of body weight), while the largest adult whales will need a minimum of ~870 kg day⁻¹ (4.3% of body weight) during the ~5 month (154 days) summer foraging season in the Arctic. In contrast, pregnant individuals need 1,630–1,969 kg of prey day⁻¹ (9.3–10.3% of body weight) during this same period to support foetal growth and store sufficient energy to produce milk once the calves are born in Mexico. Lactating whales returning to the Arctic with their calves will require 1,360–1,960 kg of prey day⁻¹ (8.2–8.9% of body weight) over the next 4.5 months to continue producing milk. My results can be combined with measured densities of benthic prey in the Arctic to assess and anticipate the likelihood of climate change or conspecific competition causing starvation-related mortality of grey whales in the future. My age-structured bioenergetics model is simple and flexible enough to adapt to any migratory species of interest, including rare, endangered species that may otherwise be considered data deficient.
Additional file 2 of Insights into the capability of the lignocellulolytic enzymes of Penicillium parvum 4-14 to saccharify corn bran after alkaline hydrogen peroxide pretreatment
Creators: name: Long, Liangkun
name: Wang, Wei
name: Liu, Zhen
name: Lin, Yuanxin
name: Wang, Jing
name: Lin, Qunying
name: Ding, Shaojun
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: Plant Biology
subject: Computational Biology

description: Additional file 2: Figure S2. Saccharification of CBAX1and CBAX2by different enzyme blends of P. parvum 4-14. Figure S3. Effect of metal ions on saccharification of CBAX1and CBAX2by E_CBAX1.
Additional file 1 of Competitive PCR with dual fluorescent primers enhances the specificity and reproducibility of genotyping animals generated from genome editing
Creators: name: Fu, Liezhen
name: Ma, Emily
name: Okada, Morihiro
name: Shibata, Yuki
name: Shi, Yun-Bo
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. Comparative analysis of regular PCR and competitive single-tube dual fluorescent PCR for genotyping small deletion mutant X. tropicalis animals generated via CRISPR/Cas9-mediated genome editing. Regular PCR with a single genotype-specific primer set in a PCR reaction often leads to non-specific amplification and inconclusive or false genotyping results. On the other hand, competitive single-tube PCR with a mixture of two genotype-specific fluorescent primers and a common primer inhibits non-specific amplification to allow accurate genotyping.
Additional file 1 of ‘Don’t forget the mouth!’: a process evaluation of a public oral health project in community-dwelling frail older people
Creators: name: Ho, Bach Van
name: van der Maarel-Wierink, Claar Debora
name: Rollman, Annemiek
name: Weijenberg, Roxane Anthea Francesca
name: Lobbezoo, Frank
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 1. General data of the towns.