cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Phage Therapy of Mycobacterium Infections: Compassionate Use of Phages in 20 Patients With Drug-Resistant Mycobacterial Disease
Creators: name: Schooley R.T.
name: Worth A.
name: Robinson P.D.
name: McMullan B.J.
name: Spencer H.
name: Hatfull G.F.
name: Freeman K.G.
name: Nick J.A.
name: Khatami A.
name: Cristinziano M.
name: Soothill J.
name: Ip W.
name: Davidson R.M.
name: Wark P.
name: Haidar G.
name: Benson C.A.
name: Malmivaara K.
name: Solomon D.A.
name: Skurnik M.
name: Belessis Y.
name: Dedrick R.M.
name: Gainey A.
name: Michalik D.E.
name: Jacobs-Sera D.
name: Tupayachi Ortiz M.G.
name: Little J.S.
name: Smith B.E.
name: Iredell J.
name: George C.R.R.
name: Cohen K.A.
name: Brown A.W.
name: Moscatelli A.
name: Van Duin D.
name: Polenakovik H.M.
name: Garcia C.B.
Publisher: name: Oxford University Press
Year: 2023

description: Background: Nontuberculous Mycobacterium infections, particularly Mycobacterium abscessus, are increasingly common among patients with cystic fibrosis and chronic bronchiectatic lung diseases. Treatment is challenging due to intrinsic antibiotic resistance. Bacteriophage therapy represents a potentially novel approach. Relatively few active lytic phages are available and there is great variation in phage susceptibilities among M. abscessus isolates, requiring personalized phage identification. Methods: Mycobacterium isolates from 200 culture-positive patients with symptomatic disease were screened for phage susceptibilities. One or more lytic phages were identified for 55 isolates. Phages were administered intravenously, by aerosolization, or both to 20 patients on a compassionate use basis and patients were monitored for adverse reactions, clinical and microbiologic responses, the emergence of phage resistance, and phage neutralization in serum, sputum, or bronchoalveolar lavage fluid. Results: No adverse reactions attributed to therapy were seen in any patient regardless of the pathogen, phages administered, or the route of delivery. Favorable clinical or microbiological responses were observed in 11 patients. Neutralizing antibodies were identified in serum after initiation of phage delivery intravenously in 8 patients, potentially contributing to lack of treatment response in 4 cases, but were not consistently associated with unfavorable responses in others. Eleven patients were treated with only a single phage, and no phage resistance was observed in any of these. Conclusions: Phage treatment of Mycobacterium infections is challenging due to the limited repertoire of therapeutically useful phages, but favorable clinical outcomes in patients lacking any other treatment options support continued development of adjunctive phage therapy for some mycobacterial infections.
Fritz Largiadèr, 1863-1939
Creators: name: Largiadèr, Anton
Publisher: name: Zentralbibliothek Zürich
Year: 1939
Subjects: subject: 920 Biografien, Genealogie, Insignien
subject: 537 Elektrizität, Elektronik
subject: Nachruf
subject: Chur
subject: Zürich

description: Sonderabdruck aus der "Neuen Zürcher Zeitung" vom 17. Dezember 1939, Nrn. 2142 und 2143
Additional file 1: of Conditional deletion of E11/podoplanin in bone protects against load-induced osteoarthritis
Creators: name: Staines, Katherine
name: Ekele Ikpegbu
name: Tรถrnqvist, Anna
name: Dillon, Scott
name: Javaheri, Behzad
name: Anish Amin
name: Clements, Dylan
name: Buttle, David
name: Pitsillides, Andrew
name: Farquharson, Colin
Publisher: name: Figshare
Year: 2019
Subjects: subject: Space Science
subject: Medicine
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Table S1. Percentage Identity Matrix for E11. (DOCX 13 kb)
Additional file 3 of The antimicrobial effect of a novel peptide LL-1 on Escherichia coli by increasing membrane permeability
Creators: name: Zhou, Lingling
name: Lian, Kaiqi
name: Wang, Mengting
name: Jing, Xueyi
name: Zhang, Yuanchen
name: Cao, Jinling
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 60506 Virology

description: Additional file 3: Table S1. Minimum inhibitory concentration (μg/mL) of the LL-1 against microorganisms.
Learning Spatio-Temporal Specifications for Dynamical Systems
Creators: name: Alsalehi, Suhail
name: Aasi, Erfan
name: Weiss, Ron
name: Belta, Calin
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (cs.LG)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Robotics (cs.RO)
subject: Systems and Control (eess.SY)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: I.5.3, I.5.4, B.1.0

description: Learning dynamical systems properties from data provides important insights that help us understand such systems and mitigate undesired outcomes. In this work, we propose a framework for learning spatio-temporal (ST) properties as formal logic specifications from data. We introduce SVM-STL, an extension of Signal Signal Temporal Logic (STL), capable of specifying spatial and temporal properties of a wide range of dynamical systems that exhibit time-varying spatial patterns. Our framework utilizes machine learning techniques to learn SVM-STL specifications from system executions given by sequences of spatial patterns. We present methods to deal with both labeled and unlabeled data. In addition, given system requirements in the form of SVM-STL specifications, we provide an approach for parameter synthesis to find parameters that maximize the satisfaction of such specifications. Our learning framework and parameter synthesis approach are showcased in an example of a reaction-diffusion system.
description: 12 pages, submitted to L4DC 2021
Additional file 1 of Process evaluation of a systemic intervention to identify and support partner violence survivors in a multi-specialty health system
Creators: name: Jackson, Emma C.
name: Renner, Lynette M.
name: Flowers, Nyla I.
name: Logeais, Mary E.
name: Clark, Cari Jo
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1. Process Evaluation Questions.
Transmission of Carbapenem-Resistant Klebsiella pneumoniae in US Hospitals
Creators: name: Kalayjian R.C.
name: Novick E.
name: Ostrowsky B.
name: Komarow L.
name: Chen L.
name: Gallagher J.C.
name: Luterbach C.L.
name: Van Duin D.
name: Arias C.A.
name: Kaye K.S.
name: Desai S.
name: Fowler V.G., Jr.
name: Lautenbach E.
name: Wortmann G.
name: Farrell J.J.
name: Hill C.
name: Eilertson B.
name: Bonomo R.A.
name: Hanson B.
name: Kreiswirth B.N.
name: Pagkalinawan S.
name: McCarty T.
Publisher: name: Oxford University Press
Year: 2023

description: Background: Carbapenem-resistant Klebsiella pneumoniae (CRKp) is the most prevalent carbapenem-resistant Enterobacterales in the United States. We evaluated CRKp clustering in patients in US hospitals. Methods: From April 2016 to August 2017, 350 patients with clonal group 258 CRKp were enrolled in the Consortium on Resistance Against Carbapenems in Klebsiella and other Enterobacteriaceae, a prospective, multicenter, cohort study. A maximum likelihood tree was constructed using RAxML. Static clusters shared ≤21 single-nucleotide polymorphisms (SNP) and a most recent common ancestor. Dynamic clusters incorporated SNP distance, culture timing, and rates of SNP accumulation and transmission using the R program TransCluster. Results: Most patients were admitted from home (n = 150, 43%) or long-term care facilities (n = 115, 33%). Urine (n = 149, 43%) was the most common isolation site. Overall, 55 static and 47 dynamics clusters were identified involving 210 of 350 (60%) and 194 of 350 (55%) patients, respectively. Approximately half of static clusters were identical to dynamic clusters. Static clusters consisted of 33 (60%) intrasystem and 22 (40%) intersystem clusters. Dynamic clusters consisted of 32 (68%) intrasystem and 15 (32%) intersystem clusters and had fewer SNP differences than static clusters (8 vs 9; P =. 045; 95% confidence interval [CI]: -4 to 0). Dynamic intersystem clusters contained more patients than dynamic intrasystem clusters (median [interquartile range], 4 [2, 7] vs 2 [2, 2]; P =. 007; 95% CI: -3 to 0). Conclusions: Widespread intrasystem and intersystem transmission of CRKp was identified in hospitalized US patients. Use of different methods for assessing genetic similarity resulted in only minor differences in interpretation.
Additional file 8 of Promoter conservation in HDACs points to functional implications
Creators: name: Boltz, Toni
name: Khuri, Sawsan
name: Wuchty, Stefan
Publisher: name: Figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: : Figure S7 Evolutionary conservation of transcription factor binding sites in HDAC11 promoter sequences in different organisms. (DOCX 3544 kb)
Additional file 1 of Mechanical consequences at the tendon-bone interface of different medial row knotless configurations and lateral row tension in a simulated rotator cuff repair
Creators: name: Maia Dias, Carlos
name: Gonçalves, Sérgio B.
name: Completo, António
name: da Silva, Manuel Ribeiro
name: de Campos Azevedo, Clara
name: Mineiro, Jorge
name: Ferreira, Frederico
name: Folgado, João
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Additional file 1: Table S1. Statistical power analysis performed using G power software for comparisons of the dependent variables between groups. Considered acceptable statistical power if power > 0,75; Alpha error probability = 0,05.
Most probable transition paths in piecewise-smooth stochastic differential equations
Creators: name: Hill, Kaitlin
name: Zanetell, Jessica
name: Gemmer, John A
Publisher: name: arXiv
Year: 2021
Subjects: subject: Dynamical Systems (math.DS)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 37H10, 37J45

description: We develop a path integral framework for determining most probable paths in a class of systems of stochastic differential equations with piecewise-smooth drift and additive noise. This approach extends the Freidlin-Wentzell theory of large deviations to cases where the system is piecewise-smooth and may be non-autonomous. In particular, we consider an $n-$dimensional system with a switching manifold in the drift that forms an $(n-1)-$dimensional hyperplane and investigate noise-induced transitions between metastable states on either side of the switching manifold. To do this, we mollify the drift and use $Γ-$convergence to derive an appropriate rate functional for the system in the piecewise-smooth limit. The resulting functional consists of the standard Freidlin-Wentzell rate functional, with an additional contribution due to times when the most probable path slides in a crossing region of the switching manifold. We explore implications of the derived functional through two case studies, which exhibit notable phenomena such as non-unique most probable paths and noise-induced sliding in a crossing region.
description: 38 pages, 9 figures
title: (Un-)Sinn der Verbandsmitgliedschaft
Creators: name: Buntz, Anja
Publisher: name: Hochschule für angewandte Wissenschaften Kempten
Year: 2024
Subjects: subject: 33 Wirtschaft

description: Die Masterthesis greift das Thema Verbände in der Beratungsbranche auf und die damit zusammenhängenden Gesichtspunkte einer Mitgliedschaft. Die Arbeit befasst sich daher stark mit dem Nutzen einer Mitgliedschaft.
title: First Principles Investigations of Hydrogen Adsorption on Carbon-Supported Metal Catalysts
Creators: name: Sihag, Amita
Publisher: name: University of Liverpool Repository
Year: 2023

description: Hydrogen is well established as a renewable and clean alternative to conventional fossil fuels and is a potential solution to the global energy crisis. With the ever-rising demand for hydrogen in numerous industries worldwide, there is a clear need for more efficient hydrogen storage methods. In this dissertation, ab-initio density functional theory calculations were performed to extensively investigate both well-ordered and amorphous carbon-based materials for hydrogen adsorption and further metal decoration for possible enhancement in their performance. It was observed that although pristine graphene does not favour spontaneous dissociation and adsorption of hydrogen atoms due to a stable sp2 hybridized structure, local distortions due to defects can cause a change in hybridization to dissociate and adsorb hydrogen spontaneously on certain two-fold coordinated carbon sites. Similarly, the presence of different bonding environments in amorphous carbon structures play an active role in hydrogen adsorption. Hydrogen interacts stronger with two-fold coordinated carbon atoms as compared to three- and four-fold coordinated carbon. High migration barriers for hydrogen atoms on carbon supports make them unlikely to spontaneously spread over the surfaces. To achieve further enhancement, the interaction of metal clusters (Pt and Ni) with these surfaces were considered. It was observed that hydrogen adsorption strength on the carbon atoms of graphene and amorphous carbon increases due to the presence of metal clusters. In addition, the metal support interaction is found to increase with the presence of vacancy defects in the vicinity, which leads to lower energy barriers for hydrogen migration from the metal cluster to the surface. Hydrogen adsorption in a dissociative form on all these surfaces shows a higher saturation limit in the case of Pt clusters as compared to Ni. Overall, metal clusters adsorbed on the carbon supports were proven beneficial for hydrogen adsorption and are crucial to designing efficient materials for H-storage.
Recent progress of fabrication, characterization, and applications of anodic aluminum oxide (AAO) membrane: A review
Creators: name: Manzoor, Saher
name: Ashraf, M. Waseem
name: Tayyaba, Shahzadi
name: Hossain, M. Khalid
Publisher: name: arXiv
Year: 2021
Subjects: subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: The progress of membrane technology with the development of membranes with controlled parameters led to porous membranes. These membranes can be formed using different methods and have numerous applications in science and technology. Anodization of aluminum in this aspect is an electro-synthetic process that changes the surface of the metal through oxidation to deliver an anodic oxide layer. This process results in a self-coordinated, exceptional cluster of round and hollow formed pores with controllable pore widths, periodicity, and thickness. After the initial introduction, the paper proceeds with a brief overview of anodizing process. That engages anodic aluminum oxide (AAO) layers to be used as formats in various nanotechnology applications without the necessity for expensive lithographical systems. This review article surveys the current status of the investigation on AAO membranes. A comprehensive analysis is performed on AAO membranes in applications; filtration, sensors, drug delivery, template-assisted growth of various nanostructures. Their multiple usages in nanotechnology have also been discussed to gather nanomaterials and devices or unite them into specific applications, such as nano-electronic gadgets, channel layers, and clinical platforms tissue designing. From this review, the fact that the specified enhancement of properties of AAO can be done by varying geometric parameters of AAO has been highlighted. No review paper focused on a detailed discussion of applications of AAO with prospects and challenges. This review paper represents the formation, properties, applications with objective consideration of the prospects and challenges of AAO applications. The prospects may appeal to researchers to promote the development of unique membranes with functionalization and controlled geometric parameters and check the feasibility of the AAO membranes in nano-devices.
description: 36 pages, 19 figures, 8 tables
Additional file 1 of Study design and baseline characteristics of a population-based prospective cohort study of dementia in Japan: the Japan Prospective Studies Collaboration for Aging and Dementia (JPSC-AD)
Creators: name: Ninomiya, Toshiharu
name: Nakaji, Shigeyuki
name: Maeda, Tetsuya
name: Yamada, Masahito
name: Mimura, Masaru
name: Nakashima, Kenji
name: Mori, Takaaki
name: Takebayashi, Minoru
name: Ohara, Tomoyuki
name: Hata, Jun
name: Kokubo, Yoshihiro
name: Uchida, Kazuhiro
name: Taki, Yasuyuki
name: Kumagai, Shuzo
name: Yonemoto, Koji
name: Yoshida, Hisako
name: Muto, Kaori
name: Yukihide Momozawa
name: Akiyama, Masato
name: Kubo, Michiaki
name: Ikeda, Manabu
name: Kanba, Shigenobu
name: Kiyohara, Yutaka
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Neuroscience
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1: Table S1. Instruments to measure blood pressure, electrocardiogram, and handgrip strength. Table S2. Measurement methods by item. Table S3. The baseline characteristics for 5,257 subjects at three research sites (Nakajima Town, Nakayama Town, and Hisayama Town). Table S4. Age-specific prevalence of dementia at baseline among 5,257 subjects at three research sites (Nakajima Town, Nakayama Town, and Hisayama Towna); participation rate: 85%), where surveys by home visit or visits to nursing homes or other facilities (e.g., long-stay hospitals) were conducted in addition to the surveys at the health centres or hospital. Figure S1. Organization of the Japan Prospective Studies Collaboration for Aging and Dementia (JPSC-AD).
title: Human immunodeficiency virus (HIV) and the condom : a study of the knowledge, attitudes and behaviour of population groups at increased risk of HIV infection
Creators: name: Ssembatya-Lule, Godfrey Charles
Publisher: name: University of Glasgow
Year: 1991

description: Prevention will likely remain the world's primary weapon against HIV for at least the next decade, and educational measures are the best available preventive alternative here in the United Kingdom and in other parts of the world.
Pay-it-forward gonorrhea and chlamydia testing among men who have sex with men and male STD patients in China: the PIONEER pragmatic, cluster randomized controlled trial protocol
Creators: name: Tucker J.D.
name: Wang T.
name: Hlatshwako T.G.
name: Holly M.E.
name: Tang W.
name: Yang L.
name: Wang C.
name: Marley G.
name: Ramaswamy R.
name: Van Duin D.
name: Gray K.
name: Zheng H.
name: Wu D.
name: Tan R.K.J.
name: Sylvia S.S.
name: Luo D.
name: Sun M.
name: Sheng Q.
Publisher: name: BioMed Central Ltd
Year: 2023

description: Background: Gonorrhea and chlamydia are the most common sexually transmitted diseases (STDs) among men who have sex with men (MSM) in China. Previous studies have shown pay-it-forward (PIF) interventions to be associated with a substantial increase in gonorrhea and chlamydia test uptake compared to standard-of-care. We propose a 'pay-it-forward' gonorrhea and chlamydia testing randomized controlled trial (PIONEER). The trial would evaluate the effectiveness of two pay-it-forward strategies in promoting testing uptake compared to the standard of care (in which men pay for their tests out-of-pocket) among MSM and male STD patients in China. Methods: PIONEER will be a three-armed, pragmatic cluster randomized controlled trial (RCT), conducted across 12 clinics (six MSM-led and six public STD clinics) to compare the effectiveness of three implementation strategies. Each facility will be randomized to a standard pay-it-forward intervention of gonorrhea/ chlamydia testing with minimal encouragement for testing, a community-engaged pay-it-forward arm, or a control arm where men pay for their tests out-of-pockets. The primary outcome will be dual gonorrhea/chlamydia test uptake. Secondary outcomes will include syphilis testing, amount donated in pay-it-forward, number of positive gonorrhea and chlamydia tests, and measures of antimicrobial resistance. A sequential transformative mixed methods design will be used to evaluate the implementation process in type 2 effectiveness-implementation hybrid design. Data sources will include survey on acceptability, and feelings and attitudes towards the interventions among participants; testing and treatment uptake data from clinic records, WeChat records, and qualitative data to gain insights into men's perceptions and attitudes towards the pay-it-forward, mechanisms driving uptake, and donating behaviors. Implementers and organizers will be interviewed about fidelity and adherence to protocol, sustainability of pay-it-forward intervention, and barriers and facilitators of implementing the intervention. Discussion: PIONEER will substantially increase gonorrhea/chlamydia testing among MSM in China, providing an innovative and new financial mechanism to sustain STD screening among sexual minorities in low- and middle-income countries. This study will answer compelling scientific questions about how best to implement pay-it-forward and the individual and organizational characteristics that moderate it. Trial registration: The study with identification number NCT05723263 has been registered on clinicaltrials.gov/.
Additional file 2 of Mechanical consequences at the tendon-bone interface of different medial row knotless configurations and lateral row tension in a simulated rotator cuff repair
Creators: name: Maia Dias, Carlos
name: Gonçalves, Sérgio B.
name: Completo, António
name: da Silva, Manuel Ribeiro
name: de Campos Azevedo, Clara
name: Mineiro, Jorge
name: Ferreira, Frederico
name: Folgado, João
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Additional file 2: Supplementary table S2. Statistical power analysis performed using G power software for comparisons of tension variation within groups.
Quantum criticality driven by the cavity coupling in Rabi-dimer model
Creators: name: Cheng, Shujie
name: Xu, Heguang
name: Liu, Xueying
name: Xianlong, Gao
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The superradiant phase transition (SPT) controlled by the interacting strength between the two-level atom and the photons has been a hot topic in the Rabi model and the Rabi-dimer model. The latter describes two Rabi cavities coupled with an inter-cavity hopping parameter. Moreover, the SPT in the Rabi-dimer model is found to be the same universal class that in the Rabi model by investigating the correlation-length critical exponent. In this paper, we are concerned about whether the inter-cavity hopping parameter between two Rabi cavities (i.e., the Rabi-dimer model) will induce the SPT and to which the universal class of the phase transition belongs. We analytically derive the phase boundary of the SPT and investigate the ground-state properties of the system. We uncover that the inter-cavity induced SPT can be apparently understood from the ground-state energy and the ground-state photon population, as well as the ground-state expectation value of the squared anti-symmetric mode. From the scaling analysis of the fidelity susceptibility, we numerically verify that the SPT driven by the cavity coupling belongs to the same universal class as the one driven by the atom-cavity interaction. Our work enriches the studies on the SPT and its critical behaviors in the Rabi-dimer model.
description: 11 pages, 6 figures
Torrenticola (Torrenticola) microdentifera Cook 1967
Creators: name: Pešić, Vladimir
name: Chatterjee, Tapas
name: Bordoloi, Sabitry
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Trombidiformes
Torrenticolidae
Torrenticola
Torrenticola microdentifera

description: Torrenticola (Torrenticola) microdentifera Cook, 1967
Records from the study area: Maharashtra—Cook (1967); Prasad (1974); Pešić & Ranga Reddy (2009).
Remarks: Torrenticola microdentifera is similar to T. ungeri (Palaearctic), and the difference between the species (Cook 1967) is related to the absence of well developed tubercles of P- 4 in T. microdentifera. According to Wiles (1997a), this character is known to be variable and T. microdentifera is probably a synonym of T. ungeri.
Habitat: Streams; benthos and hyporheic interstital.
Distribution: India.
description: Published as part of Pešić, Vladimir, Chatterjee, Tapas & Bordoloi, Sabitry, 2010, A checklist of the water mites (Acari: Hydrachnidia) of India, with new records and description of one new species, pp. 1-54 in Zootaxa 2617 (1) on page 15, DOI: 10.11646/zootaxa.2617.1.1, http://zenodo.org/record/197964
Utility of Urine Cultures During Febrile Neutropenia Workup in Hematopoietic Stem Cell Transplantation Recipients Without Urinary Symptoms
Creators: name: Sena A.
name: Lachiewicz A.
name: Moore D.T.
name: van Duin D.
name: Tran M.
name: Andermann T.M.
name: Bartelt L.A.
name: Ptachcinski J.
name: Friedland A.
name: Trepte M.
name: Shaw R.
name: Palmer S.
name: Grgic T.
Publisher: name: Oxford University Press
Year: 2023

description: The utility of obtaining screening urine cultures for febrile neutropenia (FN) during hematopoietic stem cell transplant (HCT) is unknown. In 667 adult HCT patients with FN, only 40 (6%) were found with bacteriuria. Antibiotics were modified in 3 patients (0.4%) based on urine cultures and none developed urinary-associated infectious complications.
title: Языковая подготовка к курсу «Фармакология»
Creators: name: ELS IPR BOOKS
Publisher: name: Ай Пи Ар Медиа
Year: 2023

description: Цель учебного пособия — формирование навыков чтения и монологической речи у иностранных студентов-медиков. Издание включает тексты по фармакологии на русском языке, систему заданий к ним с англо-русским комментарием, контрольную работу, тестовые задания и задания для самостоятельной работы. Тематика, содержание текстов и лексико-грамматических заданий подчинены задачам обучения иностранных студентов-медиков языку специальности. Учебное пособие предназначено для студентов медицинских вузов, изучающих русский язык как иностранный.
Triadic analysis of affiliation networks
Creators: name: Brunson, Jason Cory
Publisher: name: arXiv
Year: 2015
Subjects: subject: Combinatorics (math.CO)
subject: Social and Information Networks (cs.SI)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences
subject: 91D30 (Primary) 05C82 (Secondary)

description: Triadic closure has been conceptualized and measured in a variety of ways, most famously the clustering coefficient. Existing extensions to affiliation networks, however, are sensitive to repeat group attendance, which manifests in bipartite models as biclique proliferation. Whereas this sensitivity does not reflect common interpretations of triadic closure in social networks, this paper proposes a measure of triadic closure in affiliation networks designed to control for it. To avoid arbitrariness, the paper introduces a triadic framework for affiliation networks, within which a range of measures can be defined; it then presents a set of basic axioms that suffice to narrow this range to the one measure. An instrumental assessment compares the proposed and two existing measures for reliability, validity, redundancy, and practicality. All three measures then take part in an investigation of three empirical social networks, which illustrates their differences.
description: 33 pages, 16 figures, 5 tables
Data For mTAPS
Creators: name: Liu, Jinchu
name: Xi, Kun
name: Zhu, Lizhe
Publisher: name: Zenodo
Year: 2024

description: Parameter files, input files, and output files: Built-up complex XYZ coordinates for MD simulations (protein.pdb), the topology files for MetEn and T4L-L99A systems (.top), the input coordinates for MD simulations (protein.pdb), the input (.mdp) and output (.log and .gro) files of MD simulations, the biasing force and CV defining files for umbrella sampling simulations (.dat).
Counting Objects by Diffused Index: geometry-free and training-free approach
Creators: name: Tang, Mengyi
name: Yashtini, Maryam
name: Kang, Sung Ha
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Numerical Analysis (math.NA)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: I.4.9; I.4.6; I.5.5
subject: 65Z05(Primary), 65S05(Secondary)

description: Counting objects is a fundamental but challenging problem. In this paper, we propose diffusion-based, geometry-free, and learning-free methodologies to count the number of objects in images. The main idea is to represent each object by a unique index value regardless of its intensity or size, and to simply count the number of index values. First, we place different vectors, refer to as seed vectors, uniformly throughout the mask image. The mask image has boundary information of the objects to be counted. Secondly, the seeds are diffused using an edge-weighted harmonic variational optimization model within each object. We propose an efficient algorithm based on an operator splitting approach and alternating direction minimization method, and theoretical analysis of this algorithm is given. An optimal solution of the model is obtained when the distributed seeds are completely diffused such that there is a unique intensity within each object, which we refer to as an index. For computational efficiency, we stop the diffusion process before a full convergence, and propose to cluster these diffused index values. We refer to this approach as Counting Objects by Diffused Index (CODI). We explore scalar and multi-dimensional seed vectors. For Scalar seeds, we use Gaussian fitting in histogram to count, while for vector seeds, we exploit a high-dimensional clustering method for the final step of counting via clustering. The proposed method is flexible even if the boundary of the object is not clear nor fully enclosed. We present counting results in various applications such as biological cells, agriculture, concert crowd, and transportation. Some comparisons with existing methods are presented.
Knowledge Matters: Radiology Report Generation with General and Specific Knowledge
Creators: name: Yang, Shuxin
name: Wu, Xian
name: Ge, Shen
name: Zhou, Shaohua Kevin
name: Xiao, Li
Publisher: name: arXiv
Year: 2021
Subjects: subject: Image and Video Processing (eess.IV)
subject: Computation and Language (cs.CL)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: Automatic radiology report generation is critical in clinics which can relieve experienced radiologists from the heavy workload and remind inexperienced radiologists of misdiagnosis or missed diagnose. Existing approaches mainly formulate radiology report generation as an image captioning task and adopt the encoder-decoder framework. However, in the medical domain, such pure data-driven approaches suffer from the following problems: 1) visual and textual bias problem; 2) lack of expert knowledge. In this paper, we propose a knowledge-enhanced radiology report generation approach introduces two types of medical knowledge: 1) General knowledge, which is input independent and provides the broad knowledge for report generation; 2) Specific knowledge, which is input dependent and provides the fine-grained knowledge for report generation. To fully utilize both the general and specific knowledge, we also propose a knowledge-enhanced multi-head attention mechanism. By merging the visual features of the radiology image with general knowledge and specific knowledge, the proposed model can improve the quality of generated reports. Experimental results on two publicly available datasets IU-Xray and MIMIC-CXR show that the proposed knowledge enhanced approach outperforms state-of-the-art image captioning based methods. Ablation studies also demonstrate that both general and specific knowledge can help to improve the performance of radiology report generation.
description: Medical Image Analysis
Impact of childhood malnutrition and intestinal microbiota on MDR infections
Creators: name: Bartelt L.A.
name: van Duin D.
name: Holowka T.
Publisher: name: Oxford University Press
Year: 2023

description: The global burden of infection from MDR organisms (MDROs) disproportionately affects children residing in low- and middle-income countries and those with increased healthcare exposure. These populations have high rates of malnutrition making them increasingly vulnerable to infection with intestinal-derived pathogens. Malnourished children experience increased incidence of intestinal carriage and invasive infection with intestinal-derived MDROs including ESBL- and carbapenemase-producing Enterobacterales. However, the relationship between malnutrition and MDRO infection remains to be clearly defined. Impairment in intestinal barrier function and innate and adaptive immunity in malnutrition increases the risk for infection with intestinal-derived pathogens, and there is an increasing appreciation of the role of the intestinal microbiota in this process. Current evidence from human studies and animal models suggests that diet and the intestinal microbiota influence each other to determine nutritional status, with important implications for infectious outcomes. These insights are crucial to developing microbiota-targeted strategies aimed at reversing the growing burden of MDRO infections in malnourished populations worldwide.
Improving heavy Dirac neutrino prospects at future hadron colliders using machine learning
Creators: name: Feng, Jie
name: Li, Mingqiu
name: Yan, Qi-Shu
name: Zeng, Yu-Pan
name: Zhang, Hong-Hao
name: Zhang, Yongchao
name: Zhao, Zhijie
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: In this work, by using the machine learning methods, we study the sensitivities of heavy pseudo-Dirac neutrino $N$ in the inverse seesaw at the high-energy hadron colliders. The production process for the signal is $pp \to \ell N \to 3 \ell + E_T^{\rm miss}$, while the dominant background is $p p \to W Z \to 3 \ell + E_T^{\rm miss}$. We use either the Multi-Layer Perceptron or the Boosted Decision Tree with Gradient Boosting to analyse the kinematic observables and optimize the discrimination of background and signal events. It is found that the reconstructed $Z$ boson mass and heavy neutrino mass from the charged leptons and missing transverse energy play crucial roles in separating the signal from backgrounds. The prospects of heavy-light neutrino mixing $|V_{\ell N}|^2$ (with $\ell = e,\,μ$) are estimated by using machine learning at the hadron colliders with $\sqrt{s}=14$ TeV, 27 TeV, and 100 TeV, and it is found that $|V_{\ell N}|^2$ can be improved up to ${\cal O} (10^{-6})$ for heavy neutrino mass $m_N = 100$ GeV and ${\cal O} (10^{-4})$ for $m_N = 1$ TeV.
description: 33 pages, 14 figures, 4 tables, more details and more references added, version published in JHEP
Additional file 3 of Mechanical consequences at the tendon-bone interface of different medial row knotless configurations and lateral row tension in a simulated rotator cuff repair
Creators: name: Maia Dias, Carlos
name: Gonçalves, Sérgio B.
name: Completo, António
name: da Silva, Manuel Ribeiro
name: de Campos Azevedo, Clara
name: Mineiro, Jorge
name: Ferreira, Frederico
name: Folgado, João
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Additional file 3: Supplementary Table S3. Mean Comparison between locked medial anchor (DP) and sliding medial anchors (SLDP) regarding contact force, area and pressure, peak force and MBR force in the repair box (25N lateral tension) - * reached statistical significance. Supplementary Table S4. Mean comparison between locked medial anchor (DP) and sliding medial anchors (SLDP) regarding contact force, area and pressure, peak force and MBR force in the repair box (50N lateral tension) - * reached statistical significance. Supplementary Table S5. Mean comparison between tape double-hole passage (DP) and single-hole passage (SP) regarding contact force, area and pressure, peak force and MBR force in the repair box (25N lateral tension) - * reached statistical significance. Supplementary Table S6. Mean comparison between tape double–hole passage (DP) and single-hole passage (SP) regarding contact force, area and pressure, peak force and MBR force in the repair box (50N lateral tension) - * reached statistical significance. Supplementary Table S7. Variation within each group if lateral row tension increases 100% - * reached statistical significance.
Insights into cation ordering of double perovskite oxides from machine learning and causal relations
Creators: name: Ghosh, Ayana
name: Palanichamy, Gayathri
name: Trujillo, Dennis P.
name: Shaikh, Monirul
name: Ghosh, Saurabh
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: This work investigates the origins of cation ordering of double perovskites using first-principles theory computations combined with machine learning (ML) and causal relations. We have considered various oxidation states of A, A', B, and B' from the family of transition metal ions to construct a diverse compositional space. A conventional framework employing traditional ML classification algorithms such as Random Forest (RF) coupled with appropriate features including geometry-driven and key structural modes leads to highly accurate prediction (~98%) of A-site cation ordering. We have evaluated the accuracy of ML models by entailing analyses of decision paths, assignments of probabilistic confidence bound, and finally introducing a direct non-Gaussian acyclic structural equation model to investigate causality. Our study suggests that the structural modes are the most important features for classifying layered, columnar and rock-salt ordering. For clear layered ordering, the charge difference between the A and A' is the most important feature which in turn depends on the B, B' charge separation. Based on the outputs from ML models, we have designed functional forms with these features to derive energy differences forming clear layered ordering. The trilinear coupling between tilt, rotation, and A-site antiferroelectric displacement in Landau free-energy expansion becomes the necessary condition behind the formation of A-site cation ordering.
Additional file 6 of Promoter conservation in HDACs points to functional implications
Creators: name: Boltz, Toni
name: Khuri, Sawsan
name: Wuchty, Stefan
Publisher: name: Figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: : Figure S5 Evolutionary conservation of transcription factor binding sites in HDAC8 promoter sequences in different organisms. (DOCX 3673 kb)
Socioeconomic disparities in the prevalence of multidrug resistance in Enterobacterales
Creators: name: Moody J.
name: Brown D.R.
name: Henderson H.I.
name: van Duin D.
name: Ruegsegger L.
Publisher: name: Cambridge University Press
Year: 2023

description: We examined the association between multidrug resistance and socioeconomic status (SES), analyzing microbiological and ZIP-code-level socioeconomic data. Using generalized linear models, we determined that multidrug resistance is significantly and persistently more prevalent in samples taken from patients residing in low-income ZIP codes versus high-income ZIP codes in North Carolina.
A Surrogate-Assisted Controller for Expensive Evolutionary Reinforcement Learning
Creators: name: Wang, Yuxing
name: Zhang, Tiantian
name: Chang, Yongzhe
name: Liang, Bin
name: Wang, Xueqian
name: Yuan, Bo
Publisher: name: arXiv
Year: 2022
Subjects: subject: Neural and Evolutionary Computing (cs.NE)
subject: FOS: Computer and information sciences

description: The integration of Reinforcement Learning (RL) and Evolutionary Algorithms (EAs) aims at simultaneously exploiting the sample efficiency as well as the diversity and robustness of the two paradigms. Recently, hybrid learning frameworks based on this principle have achieved great success in various challenging robot control tasks. However, in these methods, policies from the genetic population are evaluated via interactions with the real environments, limiting their applicability in computationally expensive problems. In this work, we propose Surrogate-assisted Controller (SC), a novel and efficient module that can be integrated into existing frameworks to alleviate the computational burden of EAs by partially replacing the expensive policy evaluation. The key challenge in applying this module is to prevent the optimization process from being misled by the possible false minima introduced by the surrogate. To address this issue, we present two strategies for SC to control the workflow of hybrid frameworks. Experiments on six continuous control tasks from the OpenAI Gym platform show that SC can not only significantly reduce the cost of fitness evaluations, but also boost the performance of the original hybrid frameworks with collaborative learning and evolutionary processes.
A Systems-Based Analysis of Mono- and Combination Therapy for Carbapenem-Resistant Klebsiella pneumoniae Bloodstream Infections
Creators: name: van Duin D.
name: Nation R.L.
name: Rao G.G.
name: Doi Y.
name: Lin F.-C.
name: Hanafin P.O.
name: Piscitelli J.
name: Qiu H.
name: Cober E.
name: Kalayjian R.C.
name: Watkins R.R.
name: Luterbach C.
name: Salata R.A.
name: Kaye K.S.
name: Ilomaki J.
name: Bonomo R.A.
name: Landersdorfer C.B.
name: Sharma R.
Publisher: name: American Society for Microbiology
Year: 2022

description: Antimicrobial resistance is a global threat. As “proof-of-concept, ” we employed a system-based approach to identify patient, bacterial, and drug variables contributing to mortality in patients with carbapenem-resistant Klebsiella pneumoniae (CRKp) bloodstream infections exposed to colistin (COL) and ceftazidime-avibactam (CAZ/AVI) as mono- or combination therapies. Patients (n = 49) and CRKp isolates (n = 22) were part of the Consortium on Resistance Against Carbapenems in Klebsiella and other Enterobacteriaceae (CRACKLE-1), a multicenter, observational, prospective study of patients with carbapenem-resistant Enterobacterales (CRE) conducted between 2011 and 2016. Pharmacodynamic activity of mono- and combination drug concentrations was evaluated over 24 h using in vitro static time-kill assays. Bacterial growth and killing dynamics were estimated with a mechanism-based model. Random Forest was used to rank variables important for predicting.
Five Scenes from a Modern Prometheus - Magic Lantern Conference September 2018
Creators: name: Jolly, Martyn
name: Hunter, Alexander
name: DeCourcy, Elisa
name: Vickery, Karen
Publisher: name: Australian Association for the Advancement of Pacific Studies, Australian National University
Year: 2018

description: Two hundred years ago Mary Shelley wrote a very famous novel with the subtitle 'The Modern Prometheus'. Inspired by that anniversary we created a magic lantern show using two authentic 'dissolving view' magic lanterns from the 1880s, and over sixty different magic lantern slides. Some were photographic slides originally used to instruct students at a twentieth century London medical school, others were hand-painted, animated, mechanical slides, intended to make nineteenth century audiences laugh. We have imagined five new scenes for our Promethean creation, following the same anguished journey from electrical animation in a laboratory to disappearance in the icy wastes of the north, but with some new detours on the way. Karen Vickery supplied the moaning and groaning, Alexander Hunter the moody chords, and Elisa deCourcy and Martyn Jolly manipulated the antique lanterns and the original slides. Videography by Amr Tawfik
J. W. Newland's "Beautiful Scientific Exhibition of Dissolving Views" reinterpreted in 2021
Creators: name: Jolly, Martyn
name: DeCourcy, Elisa
name: Hunter, Alexander
name: Thoms, Rachael
Publisher: name: PhotoAccess, Canberra
Year: 2021

description: Magic lantern performance at Photo Access on 18 February 2021 as part of the launch of 'Empire, Early Photography and Spectacle: the global career of showman daguerreotypist J.W. Newland' (London: Routledge, 2021).
Additional file 1 of Personality and learning styles in relation to attitudes towards interprofessional education: a cross-sectional study on undergraduate medical students during their clinical courses
Creators: name: Olsson, Caroline
name: Lachmann, Hanna
name: Kalén, Susanne
name: Ponzer, Sari
name: Navarro, Cecilia Mellstrand
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1. Appendix 1: English Summary of Marke and Cesarecs Swedish version of Kolb’s Learning Style Inventory