cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Cardiac Motion Analysis Based on Optical Flow on Real-Time Three-Dimensional Ultrasound Data
Creators: name: Duan, Qi
name: Angelini, Elsa D.
name: Gerard, Olivier
name: Costa, Kevin D.
name: Holmes, Jeffrey W.
name: Homma, Shunichi
name: Laine, Andrew F.
Publisher: name: Columbia University
Year: 2006
Subjects: Biomedical engineering

description: With relatively high frame rates and the ability to acquire volume data sets with a stationary transducer, 3D ultrasound systems, based on matrix phased array transducers, provide valuable three-dimensional information, from which quantitative measures of cardiac function can be extracted. Such analyses require segmentation and visual tracking of the left ventricular endocardial border. Due to the large size of the volumetric data sets, manual tracing of the endocardial border is tedious and impractical for clinical applications. Therefore the development of automatic methods for tracking three-dimensional endocardial motion is essential. In this study, we evaluate a four-dimensional optical flow motion tracking algorithm to determine its capability to follow the endocardial border in three dimensional ultrasound data through time. The four-dimensional optical flow method was implemented using three-dimensional correlation. We tested the algorithm on an experimental open-chest dog data set and a clinical data set acquired with a Philips' iE33 three-dimensional ultrasound machine. Initialized with left ventricular endocardial data points obtained from manual tracing at end-diastole, the algorithm automatically tracked these points frame by frame through the whole cardiac cycle. Finite element surfaces were fitted through the data points obtained by both optical flow tracking and manual tracing by an experienced observer for quantitative comparison of the results. Parameterization of the finite element surfaces was performed and maps displaying relative differences between the manual and semi-automatic methods were compared. The results showed good consistency with less than 10% difference between manual tracing and optical flow estimation on 73% of the entire surface. In addition, the optical flow motion tracking algorithm greatly reduced processing time (about 94% reduction compared to human involvement per cardiac cycle) for analyzing cardiac function in three-dimensional ultrasound data sets. A displacement field was computed from the optical flow output, and a framework for computation of dynamic cardiac information is introduced. The method was applied to a clinical data set from a heart transplant patient and dynamic measurements agreed with known physiology as well as experimental results.
Minimal coupling in oscillator models of quantum dissipation
Creators: name: Kohler, Heiner
name: Sols, Fernando
Publisher: name: arXiv
Year: 2012
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The dissipative harmonic oscillator has two representations. In the first representation the central oscillator couples with its position to an oscillator bath. In the second one it couples with its momentum to the bath. Both representations are related by a unitary transformation. If the central oscillator couples with its position and momentum to two independent baths, no such unitary transformation exists. We discuss two possible models of this type and their physical relevance.
title: The Ecology and Conservation of the Red Uakari Monkey on the Yavari River, Peru
Creators: name: Bowler, Mark
Publisher: name: University of Kent
Year: 2021

description: The behaviour, ecology and conservation of the red uakari monkey Cacajao calvus ucaya/ii was studied on the Yavari River in northeastern Peru. The Lago Preto study site has four major habitats comprising terra firme, seasonally-flooded varzea, floodplain aguajal palm-swamp and upland aguajal palm-swamp forests that are very different in tree species composition. Productivity studies demonstrated that varzea and aguaja/ habitats were very seasonal in their fruit production, while terra firme showed less seasonal variation. Uakaris ate mainly unripe seeds for two thirds of the year, but ate large quantities of ripe pulp when Mauritia flexuosa palm fruits were available. Mauritia flexuosa was the most important species for red uakaris, making up 20% of the diet. Mauritia flexuosa was also important because it was available at times when other items were scarce. The abundance of uakaris at different sites on the Yavarf River was not correlated with the abundance of other primates, but was negatively correlated with seed-eating rodents. Uakaris ranged over at least 1200ha at Lago Preto, foraging in terra firme, varzea and aguajal forests depending on the availability of resources in these habitats. Uakari group sizes varied depending on habitat type, and fluctuating group sizes appear to be related to the distribution of food resources. Adult male uakaris were most commonly next to other adult males, and often performed aggressive displays with other males. Uakari calls varied with the context of behaviour. The adaptive significance of the uakari's red face can be explained by both ecological and behavioural adaptations. Uakaris in the Yavarf-Ucayali interfluvium are under threat from logging, hunting and non-timber plantresource extraction. The effects of logging on the Yavarf will depend largely on the tree species extracted. Currently most valuable species are extracted, the impact is expected to be low, but this could change if less valuable timber is felled. The extraction of Mauritia f/exuosa palm fruits for market sale is rare on the Yavarf but on more populous rivers may affect uakari populations. Hunting is the biggest threat to uakari populations on the Yavari and logging operations are likely to lead to an increase in the hunting of primates. Managing hunting is the priority for red uakari conservation throughout their range. The red uakari monkey is being used as a flagship species in a number of new and proposed reserves. The distribution and density of uakari monkeys within these areas is barely known. The ecological behavioural and distributional information obtained in this thesis will help these reserves determine the conservation requirements for the uakari monkeys.
title: Validating the German Short Basic Psychological Need Satisfaction and Frustration Scale in Individuals with Depression
Creators: name: Heissel, Andreas
name: Sanchez, Alba
name: Anou Pietrek
name: Bergau, Theresa
name: Stielow, Christiane
name: Rapp, Michael A.
name: Van der Kaap-Deeder, Jolene
Publisher: name: Universität Potsdam
Year: 2023
Subjects: subject: 610 Medizin und Gesundheit

description: Satisfaction and frustration of the needs for autonomy, competence, and relatedness, as assessed with the 24-item Basic Psychological Need Satisfaction and Frustration Scale (BPNSFS), have been found to be crucial indicators of individuals’ psychological health. To increase the usability of this scale within a clinical and health services research context, we aimed to validate a German short version (12 items) of this scale in individuals with depression including the examination of the relations from need frustration and need satisfaction to ill-being and quality of life (QOL). This cross-sectional study involved 344 adults diagnosed with depression (Mage (SD) = 47.5 years (11.1); 71.8% females). Confirmatory factor analyses indicated that the short version of the BPNSFS was not only reliable, but also fitted a six-factor structure (i.e., satisfaction/frustration X type of need). Subsequent structural equation modeling showed that need frustration related positively to indicators of ill-being and negatively to QOL. Surprisingly, need satisfaction did not predict differences in ill-being or QOL. The short form of the BPNSFS represents a practical instrument to measure need satisfaction and frustration in people with depression. Further, the results support recent evidence on the importance of especially need frustration in the prediction of psychopathology.
description: Zweitveröffentlichungen der Universität Potsdam : Humanwissenschaftliche Reihe; 837
Additional file 1 of Age-specific difference in the association between prediabetes and subclinical atherosclerosis: an analysis of a chinese prospective cohort study
Creators: name: Cao, Qiuyu
name: Xin, Zhuojun
name: He, Ruixin
name: Wang, Tiange
name: Xu, Min
name: Lu, Jieli
name: Dai, Meng
name: Zhang, Di
name: Chen, Yuhong
name: Zhao, Zhiyun
name: Wang, Shuangyuan
name: Lin, Hong
name: Wang, Weiqing
name: Ning, Guang
name: Bi, Yufang
name: Xu, Yu
name: Li, Mian
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Geology
subject: FOS: Earth and related environmental sciences
subject: Environmental Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Developmental Biology

description: Additional file 1. This additional file provided Additional tables in the paper.
Victims, villains, and cheats: A thematic analysis of disability representation in Albertan newspapers during the COVID-19 pandemic.
Creators: name: McLennan, Kate
Publisher: name: Cumming School of Medicine
Year: 2022
Subjects: disability
media
COVID-19

description: Media coverage of disability is dominated by stereotypes and disempowering narratives. These narratives negatively impact disabled people’s self-perception, and how others treat them. Disability representations in news media influence how the public defines issues disabled people face. In turn, these beliefs influence proposed policy solutions, healthcare interventions, and funding decisions. Health-related risks, and risks to funding and quality of life that disabled people faced during COVID-19 made the impact of these beliefs even more oppressive. This study explored representations of disability in Albertan newspaper during the COVID-19 pandemic. This aim was met through four objectives: to identify disability terminology used, to identify representation of disabled people in interviews, to identify themes, and to identify frames used to present information. This study used a qualitative design. The Factiva database was systematically searched for news articles that contained two disability search terms and were published in Alberta during the first 18 months of the pandemic. A sample of 56 articles met the inclusion criteria and content, thematic, and framing analyses were conducted. Person-first terminology was used in most articles followed by identity-first language, severely handicapped, and special needs. Less than a third of interviewees were disabled and only one was labelled as being developmentally disabled. Thematic analysis resulted in five themes: (1) Dehumanization, (2) Erasure, (3) Unworthy Diseases, (4) Empowerment- A Contradictory Promise, and (5) Dis/armed. Framing analysis found nine dominant frames, including disability is medical and disability is a burden, and two counter frames, including disability rights are human rights. The findings of this study indicate that disabled people in Alberta face numerous human rights issues, and the medical and social pathology models of disability are dominant in news media. Future research should explore disability language in Alberta’s policies and explore disability representation on social media.
Evaluating Descriptive and Predictive Spatial Models of Emergency Medical Services Demand During Extreme Heat Events in Austin, TX
Creators: name: Mandalapu, Akhil
Publisher: name: The University of Texas at Austin
Year: 2023
Subjects: Extreme heat
emergency medical services
epidemiology
climate change
urban informatics
urban planning
environmental justice

description: Extreme heat events are becoming increasingly common. With extreme heat exposure often necessitating prompt emergency medical service (EMS) response, the situation is critical as a rapid response is necessary to prevent severe disability or death. However, limited EMS capacity requires reallocation of resources to meet the increased demand for EMS. Although prior literature suggests a slight positive association between heat and EMS demand, studies have not investigated the spatial patterns of EMS demand during extreme heat. This study compares predictive models of EMS demand during extreme heat events across space. First, an unsupervised clustering approach was utilized to characterize EMS demand spatially to identify clusters with similar EMS demand and heat vulnerability characteristics. Finally, linear regression and geographically weighted regression (GWR) models were evaluated in predicting the spatial demand of EMS.
MOBAK Posuzování a rozvoj základních pohybových kompetencí
Creators: name: Scheuer, Claude
name: Heck, Sandra
name: Vlček, Petr
name: Vrbas, Jaroslav
name: Vašíčková, Jana
Publisher: name: Zenodo
Year: 2021
Subjects: motor competence
children
teacher
support toolkit
assessment
promotion

description: V rámci projektu BMC-EU (Základní pohybové kompetence v Evropě) byla na bázi koncepce základních pohybových kompetencí a výsledků sběru dat vytvořena testová sada pro učitele tělesné výchovy, která využívá běžně dostupné pomůcky, jež jsou v tělocvičně k dispozici. Účelem této sady a přiloženého uživatelského manuálu je nabídnout variabilní didaktický přístup k výuce a vzdělávacímu obsahu tělesné výchovy. V první fázi projektu byla vytvořena testová sada pro diagnostiku základních pohybových kompetencí žáků, aby se hodnocením silných a slabých stránek žáků v dané oblasti vytvořil základ pro možnou intervenci. Na základě tohoto souboru testů byly vyvinuty podklady ve formě vzorové sady didaktických materiálů, připravených k implementaci v konkrétních vzdělávacích situacích, jejichž účelem je rozvoj základních pohybových kompetencí žáků. Předložená sada nástrojů a pomůcek obsahuje manuál pro aplikaci souboru testů a pokyny pro interpretaci výsledků testů MOBAK (Motorische Basiskompetenzen), rámcový popis testové sady MOBAK, glosář a vzorovou podpůrnou sadu nástrojů a pomůcek s materiály pro učitele tělesné výchovy ve formě karet MOBAK. Karty MOBAK popisují činnosti dle principu variace (rozličnosti podnětů) a jsou založeny na přístupu orientovaném na kompetence. V průběhu systematického zajišťování kvality vyvstává stále více otázka, jakých výsledků žáci dosahují v oblasti tělesné výchovy. Ústředními vzdělávacími cíli tělesné výchovy jsou základní pohybové kompetence, které dětem umožňují hrát aktivní roli v pohybově aktivním životním stylu. Nezbytným předpokladem systematického zvyšování základních pohybových kompetencí je tzv. cílená diagnostika. Popisem úrovně pohybových kompetencí dětí se získají informace, které pomáhají učitelům přizpůsobit své výukové strategie individuálním potřebám dětí. Jako nástroj k posouzení základních pohybových kompetencí může být použita testová sada MOBAK, která je použitelná u dětí a dospívajících různého věku.
description: Project "Basic Motor Competencies in Europe – Assessment and Promotion" (BMC-EU); Funder: European Commission - Erasmus+ Programme of the European Union; Programme: Erasmus+ Sport: Collaborative Partnerships - 2017; Reference: 590777-EPP-1-2017-1-DE-SPO-SCP; Timeline: January 2018 - December 2019; Project Sheet: https://ec.europa.eu/programmes/erasmus-plus/projects/eplus-project-details/#project/590777-EPP-1-2017-1-DE-SPO-SCP
House of Graphs: a database of interesting graphs
Creators: name: Brinkmann, Gunnar
name: Coolsaet, Kris
name: Goedgebeur, Jan
name: Melot, Hadrien
Publisher: name: arXiv
Year: 2012
Subjects: subject: Combinatorics (math.CO)
subject: Discrete Mathematics (cs.DM)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: In this note we present House of Graphs (http://hog.grinvin.org) which is a new database of graphs. The key principle is to have a searchable database and offer -- next to complete lists of some graph classes -- also a list of special graphs that already turned out to be interesting and relevant in the study of graph theoretic problems or as counterexamples to conjectures. This list can be extended by users of the database.
description: 8 pages; added a figure
Evaluation of a Multi-Scale Enhancement Protocol for Digital Mammography
Creators: name: Mekle, Ralf
name: Laine, Andrew F.
name: Smith, Suzanne
Publisher: name: Columbia University
Year: 2001
Subjects: Biomedical engineering
Contrast-enhanced magnetic resonance imaging
Breast--Radiography

description: We have carried out a receiver operating characteristics (ROC) study for the enhancement of mammographic features in digitized mammograms. The study evaluated the benefits of multi-scale enhancement methods in terms of diagnostic performance of radiologists. The enhancement protocol relied on multi-scale expansions and non-linear enhancement functions. Dyadic spline wavelet functions (first derivative of a cubic spline) were used together with a sigmoidal non-linear enhancement function. We designed a computer interface on a softcopy display and performed an ROC study with three radiologists, who specialized in mammography. Clinical cases were obtained from a national mammography database of digitized radiographs prepared by the University of South Florida (USF) and Harvard Medical School. Our study focused on dense mammograms, i.e. mammograms of density 3 and 4 on the American College of Radiology (ACR) breast density rating, which are the most difficult cases in screening, were selected. To compare the performance of radiologists with and without using multi-scale enhancement, two groups of 30 cases each were diagnosed. Each group contained 15 cases of cancerous and 15 cases of normal mammograms. Conventional ROC analysis was applied, and the resulting ROC curves indicated improved diagnostic performance when radiologists used multi-scale non-linear enhancement.
Microfluidic technologies for rapid, high-throughput screening and selection of monoclonal antibodies from single cells
Creators: name: Singhal, Anupam
Publisher: name: University of British Columbia
Year: 2013

description: This thesis describes the development of novel microfluidic technologies for rapid, high-­‐throughput screening and selection of monoclonal antibodies (mAbs) from single cells. Microfluidic devices were used to compartmentalize single antibody-­‐ secreting cells (ASCs) in small-­‐volume chambers (i.e. hundreds of picoliters to nanoliters) in order to concentrate secreted mAbs for measurement of antigen binding kinetics and affinities using a novel microfluidic fluorescence bead assay. Microfluidic single-­‐cell antibody screening was performed on ASCs harvested from antigen-­‐ immunized mice and purified by fluorescence-­‐activated cell sorting (FACS). Following microfluidic selection of ASCs producing antigen-­‐specific mAbs, ASCs were sequentially recovered from the microfluidic device and subjected to single-­‐cell RT-­‐PCR to amplify the antibody-­‐encoding heavy and light chain genes. Antibody genes for selected high-­‐ affinity mAbs are sequenced and cloned into expression vectors for recombinant production in mammalian cell lines. Nearly 200 high-­‐affinity mouse mAbs to the model antigen hen egg lysozyme (HEL) were selected as a validation of this technology, representing a ten-­‐fold increase in the number of high affinity anti-­‐HEL mAbs previously selected using single-­‐cell micro-­‐technologies and the traditional hybridoma approach. Microfluidic single-­‐cell mAb screening also yielded important insights into affinity maturation, immuno-­‐dominance, and antibody stereotypy in the adaptive immune system. By circumventing time-­‐consuming limiting dilution and clonal expansion in the hybridoma approach, microfluidic single-­‐cell screening will enable selection of mAbs from other animal species (e.g. rabbits, humans) for both therapeutic and research applications.
Coarse to Fine Segmentation of Stargardt Rings Using an Expert Guided Dual Ellipse Model
Creators: name: Lee, Noah
name: Laine, Andrew F.
name: Smith, R. Theodore
Publisher: name: Columbia University
Year: 2008
Subjects: Biomedical engineering

description: Computer aided diagnosis in the medical image domain requires adaptive knowledge-based models to handle uncertainty, ambiguity, and noise. We propose an expert guided coupled dual ellipse model in a coarse to fine energy minimization framework. In our approach we enforce subspace model constraints by fusing domain knowledge and model information to guide the segmentation process on the fly. We apply our method to the task of retinal Stargardt segmentation a disease that manifests itself in a ring like structure around the macula. Quantitative evaluations on synthetic and real data sets show the performance of our framework. Experimental results demonstrate that our framework performance well with an area under the ROC curve of 0.93.
Compressing Random Microstructures via Stochastic Wang Tilings
Creators: name: Novák, Jan
name: Kučerová, Anna
name: Zeman, Jan
Publisher: name: arXiv
Year: 2012
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: This paper presents a stochastic Wang tiling based technique to compress or reconstruct disordered microstructures on the basis of given spatial statistics. Unlike the existing approaches based on a single unit cell, it utilizes a finite set of tiles assembled by a stochastic tiling algorithm, thereby allowing to accurately reproduce long-range orientation orders in a computationally efficient manner. Although the basic features of the method are demonstrated for a two-dimensional particulate suspension, the present framework is fully extensible to generic multi-dimensional media.
description: 4 pages, 6 figures, v2: minor changes as suggested by reviewers, v3: corrected two typos in the revised version
Automatic 4-D Registration in Dynamic MR Renography
Creators: name: Song, Ting
name: Lee, Vivian S.
name: Rusinek, Henry
name: Kaur, Manmeen
name: Laine, Andrew F.
Publisher: name: Columbia University
Year: 2005
Subjects: Biomedical engineering

description: Dynamic contrast-enhanced 4-D MR renography has the potential for broad clinical applications, but suffers from respiratory motion that limits analysis and interpretation. Since each examination yields at least over 10 20 serial 3-D images of the abdomen, manual registration is prohibitively labor-intensive. Besides in-plane motion and translation, out-of-plane motion and rotation are observed in the image series. In this paper, a novel robust and automated technique for removing out-of-plane translation and rotation with sub-voxel accuracy in 4-D dynamic MR images is presented. The method was evaluated on simulated motion data derived directly from a clinical patient's data. The method was also tested on 24 clinical patient kidney data sets. Registration results were compared with a mutual information method, in which differences between manually co-registered time-intensity curves and tested time-intensity curves were compared. Evaluation results showed that our method agreed well with these ground truth data.
Supplementary figures and analyses from The specious interaction of time and numerosity perception
Creators: name: Togoli, Irene
name: Fornaciai, Michele
name: Bueti, Domenica
Publisher: name: The Royal Society
Year: 2021
Subjects: subject: Neuroscience
subject: 170299 Cognitive Science not elsewhere classified
subject: FOS: Psychology
subject: 60801 Animal Behaviour
subject: FOS: Biological sciences

description: Information about the power analysis performed for Exp. 2, analysis of precision measures, and supplementary figures S1-S5
A symplectic proof of a theorem of Franks
Creators: name: Collier, Brian
name: Kerman, Ely
name: Reiniger, Benjamin M.
name: Turmunkh, Bolor
name: Zimmer, Andrew
Publisher: name: arXiv
Year: 2011
Subjects: subject: Symplectic Geometry (math.SG)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics

description: A celebrated theorem in two-dimensional dynamics due to John Franks asserts that every area preserving homeomorphism of the sphere has either two or infinitely many periodic points. In this work we reprove Franks' theorem under the additional assumption that the map is smooth. Our proof uses only tools from symplectic topology and thus differs significantly from all previous proofs. A crucial role is played by the results of Ginzburg and Kerman concerning resonance relations for Hamiltonian diffeomorpisms.
description: 15 pages. Minor changes. Final version to appear in Compositio Mathematica
SOPHIE velocimetry of Kepler transit candidates IV. KOI-196b: a non-inflated hot-Jupiter with a high albedo
Creators: name: Santerne, A.
name: Bonomo, A. S.
name: Hébrard, G.
name: Deleuil, M.
name: Moutou, C.
name: Almenara, J. -M.
name: Bouchy, F.
name: Díaz, R. F.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We report the discovery of a new hot-Jupiter, KOI-196b, transiting a solar-type star with an orbital period of 1.855558 days\pm0.6s thanks to public photometric data from the Kepler space mission and new radial velocity observations obtained by the SOPHIE spectrograph mounted on the 1.93-m telescope at the Observatoire de Haute-Provence, France. The planet KOI-196b, with a radius of 0.841\pm0.032 Rjup and a mass of 0.49\pm0.09 Mjup, orbits a G2V star with R* = 0.996\pm0.032 Rsun, M*= 0.94\pm0.09 Msun, [Fe/H] = -0.10\pm0.16 dex, Teff= 5660\pm100 K and an age of 7.7\pm3.4 Gy. KOI-196b is one the rare close-in hot-Jupiters with a radius smaller than Jupiter suggesting a non-inflated planet. The high precision of the Kepler photometry permits us to detect the secondary transit with a depth of 64 +10/-12 ppm as well as the optical phase variation. We find a geometric albedo of Ag = 0.30\pm0.08 which is higher than most of the transiting hot-Jupiters with a measured Ag. Assuming no heat recirculation, we find a day-side temperature of Tday = 1930\pm80 K. KOI-196b seems to be one of the rare hot-Jupiters located in the short-period hot-Jupiter desert.
description: 9 pages, 10 figures, accepted in A&A
A novel registration method for retinal images based on local features
Creators: name: Chen, Jian
name: Smith, R. Theodore
name: Tian, Jie
name: Laine, Andrew F.
Publisher: name: Columbia University
Year: 2008
Subjects: Biomedical engineering

description: Sometimes it is very hard to automatically detect the bifurcations of vascular network in retinal images so that the general feature based registration methods will fail to register two images. In order to solve this problem, we developed a novel local feature based retinal image registration method. We first detect the corner points instead of bifurcations since corner points are sufficient and uniformly distributed in the overlaps. Second, a novel highly distinctive local feature is extracted around each corner point. These local features are invariant to rotation and contrast, and partially invariant to scaling. Third, a bilateral matching technique is applied to identify the corresponding features between two images. Finally a second order polynomial transformation is used to register two images. Experimental results show that our method is very robust and compute efficient to register retinal images even of very low quality.
Rise of azimuthal anisotropies as a signature of the Quark-Gluon-Plasma in relativistic heavy-ion collisions
Creators: name: Konchakovski, V. P.
name: Bratkovskaya, E. L.
name: Cassing, W.
name: Toneev, V. D
name: Voronyuk, V.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: The azimuthal anisotropies of the collective transverse flow of hadrons are investigated in a large range of heavy-ion collision energy within the Parton-Hadron-String Dynamics (PHSD) microscopic transport approach which incorporates explicit partonic degrees of freedom in terms of strongly interacting quasiparticles (quarks and gluons) in line with an equation-of-state from lattice QCD as well as dynamical hadronization and hadronic dynamics in the final reaction phase. The experimentally observed increase of the elliptic flow $v_2$ with bombarding energy is successfully described in terms of the PHSD approach in contrast to a variety of other kinetic models based on hadronic interactions. The analysis of higher-order harmonics $v_3$ and $v_4$ shows a similar tendency of growing deviations between partonic and purely hadronic models with increasing bombarding energy. This signals that the excitation functions of azimuthal anisotropies provide a sensitive probe for the underling degrees of freedom excited in heavy-ion collisions.
description: 4 pages, 3 figures, title changed
Global circadian transcript profile of mouse skeletal muscle entrained by inverted feeding
Creators: name: 旻典 李(Min-Dian Li)
Publisher: name: CNGB
Year: 2023
Subjects: Raw sequence reads
Transcriptome or Gene expression
Multiisolate
Model organism

description: Circadian clocks in peripheral organs are entrained by feeding. Eating in the right time is crucial to maintain metabolic health, whereas eating in the wrong time increases the susceptibility to metabolic diseases. It is unknown how change of mealtime impacts circadian transcriptomes in peripheral organs and brain. Here, we presented global circadian transcript profile of mouse gastrocnemius muscle entrained by inverted feeding to compile an atlas for mechanistic insights into how feed-fast cycle regulates circadian biology.
Hexagonal QMF Banks and Wavelets
Creators: name: Schuler, Sergio
name: Laine, Andrew F.
Publisher: name: Columbia University
Year: 1998
Subjects: Biomedical engineering

description: In this chapter we shall lay bare the theory and implementation details of hexagonal sampling systems and hexagonal quadrature mirror filters (HQMF). Hexagonal sampling systems are of particular interest because they exhibit the tightest packing of all regular two-dimensional sampling systems and for a circularly band-limited waveform, hexagonal sampling requires 13.4 percent fewer samples than rectangular sampling. In addition, hexagonal sampling systems also lead to nonseparable quadrature mirror filters in which all basis functions are localized in space, spatial frequency and orientation. This chapter is organized in two sections. Section I describes the theoretical aspects of hexagonal sampling systems while Section II covers important implementation details.
Investigating the Effects of Probiotic Supplementation on the Gut-Brain Axis in Autism Spectrum Disorder
Creators: name: Pochakom, Angela
Publisher: name: Cumming School of Medicine
Year: 2022
Subjects: subject: Gut Microbiota
subject: Autism
subject: Behaviour
subject: Probiotics
subject: Metabolomics
subject: Mitochondria
subject: Gut-Brain Axis
subject: Education--Sciences
subject: Neuroscience
subject: Psychology--Developmental

description: Historically, the purpose of probiotic use in autism spectrum disorder (ASD) has been associated with alleviating co-morbid gastrointestinal symptoms. Recent studies have shown promise for the use of probiotics in modulating brain function to improve the behavioural symptoms of ASD through the microbiota-gut-brain axis. In the present study, we assessed the impact of two probiotic strains in mitigating autism-related symptomology in the BTBR T+ Itpr3tf/J mouse model of autism spectrum disorder (ASD). Male juvenile BTBR mice were randomized into 1) control, 2) Lr probiotic (1 x 109 CFU/mL Lacticaseibacillus rhamnosus HA-114), and 3) Ls probiotic groups (1 x 109 CFU/mL Ligilactobacillus salivarius HA-118) (n=18-21/group), receiving treatments in drinking water for 4-weeks. Gut microbiota profiling by 16S rRNA showed Lr, but not Ls supplementation, to increase microbial richness and phylogenetic diversity, with a rise in potential anti-inflammatory and butyrate-producing taxa. Assessing serum and brain metabolites, Lr and Ls supplementation produced distinct metabolic profiles, with Lr treatment elevating concentrations of potentially beneficial neuroactive compounds, such as 5-aminovaleric acid and choline. As mitochondrial dysfunction is often observed in ASD, we assessed mitochondrial oxygen consumption rates in the prefrontal cortex and hippocampus. No differences were observed for either treatment. Both Lr and Ls treatment reduced behavioural deficits in social novelty preference. However, no changes in hyperactivity, repetitive behaviour, and sociability were observed. Results show Lr to impart positive changes along the microbiota-gut-brain axis, exhibiting beneficial effects on selected behaviour, gut microbial diversity, and metabolism in BTBR mice.
Old drugs in a new light : investigating the gold Rheumatoid Arthritis medications as novel inhibitors of neuroinflammation
Creators: name: Madeira, Jocelyn Marie
Publisher: name: University of British Columbia
Year: 2012

description: Several degenerative disorders of the central nervous system including Alzheimer’s and Parkinson’s diseases are characterized by chronic inflammation. The main contributors to this inflammation are glial cells, including microglia and astrocytes. Even though they are normally protective, disease specific stimuli can activate glial cells to start secreting neurotoxic molecules. There is no effective treatment for neurodegenerative diseases, though it is hypothesized that reducing neuroinflammation may diminish neuronal loss. Chronic use of non-steroidal anti-inflammatory drugs (NSAIDs) has been linked with lower incidence of neurodegenerative disorders, though mixed results have been obtained in clinical trials of NSAIDs when these drugs are used for treatment of established disease. Gold thiol compounds, including aurothiomalate, aurothioglucose, and auranofin, comprise another class of medications effective at reducing peripheral inflammation in rheumatoid arthritis patients. Their effects on neuroinflammation are unknown. In this thesis I demonstrate that 0.1 – 5 µM auranofin, but not the other gold thiol compounds, inhibits human microglia and astrocyte-mediated neurotoxicity in vitro. The anti-neurotoxic properties of auranofin are selective; treatment with auranofin does not inhibit expression or secretion of several cytokines by glia but does upregulate heme-oxygenase (HOX)-1. Interestingly, low micromolar concentrations of auranofin directly protect neuronal cells from toxicity induced by hydrogen peroxide or stimulated glial supernatants, possibly through the upregulation of HOX-1. Lastly, laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) was used to demonstrate that auranofin reaches low micromolar concentrations in mouse brains following daily oral administration for one week. Since auranofin can protect against neuroinflammation by inhibiting glial toxicity and is directly neuroprotective, it may be useful in neurodegenerative diseases where sustained inflammation contributes to disease progression including neuronal loss.
Born-Infeld with Higher Derivatives
Creators: name: Chemissany, Wissam
name: Kallosh, Renata
name: Ortin, Tomas
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We present new models of non-linear electromagnetism which satisfy the Noether-Gaillard-Zumino current conservation and are, therefore, self-dual. The new models differ from the Born-Infeld-type models in that they deform the Maxwell theory starting with terms like $λ(\partial F)^{4}$. We provide a recursive algorithm to find all higher order terms in the action of the form $λ^{n} \partial ^{4n} F^{2n+2} $, which are necessary for the U(1) duality current conservation. We use one of these models to find a self-dual completion of the $λ(\partial F)^{4}$ correction to the open string action. We discuss the implication of these findings for the issue of UV finiteness of ${\cal N}=8$ supergravity.
description: 10 pages, revtex4, no figures, 1 table, new reference added, minor typos corrected, accepted for publication in PRD
Transcriptional analysis of the response of nectarine fruit to low-temperature stress in cold storage
Creators: name: Gao, Yang
name: Jiao, Xuan
name: Gao, Zhen-feng
name: Feng, Zhi-hong
name: Hao, Li-Ping
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Plant Biology
subject: Computational Biology

description: Nectarine (Prunus persica var. nectarina) is a sub-tropical fruit tree with strong cold sensitivity. In this study, flesh of nectarine (Shuguang) was used to determine the difference in transcriptional data before and after chilling injury under storage. In addition, genes responses involved in nectarine acclimation to cold stress were also explored. Results of the current study showed that nectarine was found to be more susceptible to chilling injury during storage at 5°C than at 0°C, and differentially expressed genes (DEGs) were concentrated in the late stage of low-temperature storage where chilling injury symptoms appeared at the end of the experiment. The key genes related to low-temperature response were associated with post-harvest biological processes. DEGs were annotated on the metabolic pathways of cold regulation signal transduction, cold resistance physiological metabolism and cold resistance-related protein synthesis. Moreover, the expression of genes related to cold stress such as plant hormone signal transduction element such as Auxin-responsive protein, transcription factors responding to cold stress such as WRKY transcription factor and genes related to maintaining membrane stability and regulating physiological metabolism such as proline dehydrogenase was more pronounced when nectarine was stored at 5°C than at 0°C. Overall, these findings showed that alteration in chilling temperature has substantial impact on the transcription levels associated with cold resistance pathway during the low-temperature storage of nectarine and thus promotes chilling injury disorders in nectarine.
Robust yeast biocontainment system dependent on unnatural amino acid
Creators: name: 张惠铭(Zhanghuiming)
Publisher: name: CNGB
Year: 2023
Subjects: Raw sequence reads
Genome sequencing
Monoisolate
Other
Synthetic biology

description: Studying the escape mechanism of the amber suppressor tRNA produced by unAA-dependent auxotrophs and the prevention of amber suppressor tRNATyr by the SpCas9-NG system
Retinal vessel segmentation using multi-scale wavelet frame analysis
Creators: name: Lee, Noah
name: Laine, Andrew F.
name: Smith, R. Theodore
name: Busuoic, Mihai
Publisher: name: Columbia University
Year: 2007
Subjects: Biomedical engineering

description: Fundus imaging is a non-invasive technique for in vivo ophthalmoscopic inspection of retinal disorders. Quantitative information about the vascular network can facilitate clinical diagnosis of retinal diseases [1]. Goal: Segmentation of the vascular network in fundus images for further quantification and post processing as a binary classification into object and background. Approach: We perform an over-complete multi-scale wavelet frame expansion with selective channel rejection in the decomposition tree. Remaining channels undergo wavelet shrinkage and enhancement to separate retinal objects from background. Results: Comparison to expert gradings on a pixel by pixel basis show mean sensitivity and specificity of 0.8 and 0.9.
RNA sequencing of PRP19 knockdown and control in Huh7 cell line.
Creators: name: 刘志勇
Publisher: name: CNGB
Year: 2023
Subjects: Genome sequencing and assembly
Other
cell line
Medical

description: To investigate the cooperative function PRP19 in the regulation of liver cancer development, we established PRP19 knockdown Huh7 cell lines by siRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of PRP19 knockdown and control cells.
title: Post-Salvagism. Cultural interventions and cultural evolution in a traumatised community: Dance in the Central West Bank
Creators: name: Rowe, Nicholas
Publisher: name: University of Kent
Year: 2021

description: This thesis examines how 19th Century social dance practices in Palestine have been transformed into 21st Century presentations of dance as a performed art in the Central West Bank An extensive ethnographic history of the local dance culture is collated from various perspectives and (in acknowledging the ongoing collective trauma experienced by the indigenous population during this period) analysed in terms of pre-salvage, salvage and post-salvage phases. This involves an examination of the impact of dominant socio-political paradigms on local dance practices, including European Imperialism, political Zionism, Islamic Reformism, Pan Arabism and Palestinian nationalism. Whilst the experienced community of the Central West Bank is acknowledged as continuously negotiating with various manifestations of an imagined community, this analysis considers how local dance products have not necessarily been limited by such definitions of identity. As the research aims to support (what has been identified here as) post-salvage dance production in the region through cultural interventions, the aesthetic principles and evolutionary processes of post-salvagism are examined and defined here as anti-hegemonic. This examination involves reflections on the author's own approaches to local dance interventions, conducted with dance groups in Ramallah and Al-Bireh from 2000-2006. It also posits a theory of cultural evolution that contrasts with more ethnocentric notions of unilinear progress and development. This proposition includes an algorithm for the evolution of dance that suggests how the processes of learning, creating and evaluating dance can be seen as analogous to the Darwinian evolutionary processes of reproduction, adaptation and selection. In this sense, it considers how post-colonial (and particularly post-development) studies may benefit from applications of Richard Dawkins' (1976) meme theory.
Comparison of metrics obtained with analytic perturbation theory and a numerical code
Creators: name: Cuchí, Javier E.
name: Molina, Alfred
name: Ruiz, Eduardo
Publisher: name: arXiv
Year: 2012
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences
subject: 83C25

description: We compare metrics obtained through analytic perturbation theory with their numerical counterparts. The analytic solutions are computed with the CMMR post-Minkowskian and slow rotation approximation due to Cabezas et al. (2007) for an asymptotically flat stationary spacetime containing a rotating perfect fluid compact source. The same spacetime is studied with the AKM numerical multi-domain spectral code (Ansorg et al., 2002,2003). We then study their differences inside the source, near the infinity and in the matching surface, or equivalently, the global character of the analytic perturbation scheme.
description: 4 pages, 2 figures and 1 table. To appear in the proceedings of the 2011 Spanish Relativity Meeting ERE2011
Image fusion using steerable dyadic wavelet transform
Creators: name: Koren, Iztok
name: Laine, Andrew F.
name: Taylor, Fred
Publisher: name: Columbia University
Year: 1995
Subjects: Biomedical engineering

description: An image fusion algorithm based on multiscale analysis along arbitrary orientations is presented. After a steerable dyadic wavelet transform decomposition of multi-sensor images  is carried out, the maximum local oriented energy is determined at each level of scale and spatial position. Maximum local oriented energy and local dominant orientation are used to combine transform coefficients obtained from the analysis of each input image. Reconstruction is accomplished from the modified coefficients, resulting in a fused image. Examples of multi-sensor fusion and fusion using different settings of a single sensor are demonstrated.
Edge detection in echocardiographic image sequences by 3-D multiscale analysis
Creators: name: Koren, Iztok
name: Laine, Andrew F.
name: Fan, Jian
name: Taylor, Fred
Publisher: name: Columbia University
Year: 1994
Subjects: Biomedical engineering

description: Robust and reliable edge detection is an important step for accomplishing automatic detection of heart wall boundaries in echocardiograms. We present an edge detection algorithm that makes use of both spatial and temporal information. Our algorithm is comprised of (1) a 3-D discrete dyadic wavelet transform carried out on a sequence of images, (2) edge detection that is carried out by maxima detection and a search strategy for maxima curves within the transform space. Using detected edges and "a priori" knowledge of cardiographic features we demonstrate the performance of fully automatic detection of epicardial and endocardial boundaries along the posterior and anterior walls in 2-D short-axis echocardiographic image sequences.
Shedding light on Portugal’s first major forensic case: elemental analysis of biological samples 132 years later
Creators: name: Silva-Bessa, Â.
name: Azevedo, R.
name: Almeida, A.
name: Dinis-Oliveira, R. J.
Publisher: name: Scientific Letters
Year: 2023

description: Background: In the late 19th century, Vicente Urbino de Freitas was accused of the death of his nephew, Mário Guilherme Augusto de Sampaio, and his brother-in-law, José António de Sampaio Junior [1-3]. Despite the controversy at the time surrounding the testimonies, autopsy reports and toxicological analyses carried out, Urbino de Freitas was found guilty. After an extensive research and consolidation of all historical records, Sampaio Junior’s body was found buried at the Cemetery of Agramonte, Porto, in 2020. Permission for a new autopsy was granted, and biological samples were collected for further analysis. Objective: The main objective of this study was to perform an elemental analysis of the deceased’s biological samples aiming to find additional relevant information regarding the possible cause-of-death, 132 years later. Methods: A total of thirteen freeze-dried soft and hard tissues (0.4-0.5 g) were mineralized using a microwave-assisted acid digestion procedure. The concentration of twenty-seven trace elements was determined by Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) using a Thermo Fisher Scientific iCAP™Q instrument (Waltham, MA, USA). Data analysis was performed using the R programming language. Here we present and discuss the results for Li, Fe, Co, Ni, Cu, Zn, Hg, and Pb. Results: Overall, the concentration of elements differed considerably according to the analysed specimen. Fe and Pb concentrations varied from 0.20 to 1.02 mg/g (mean=0.50; SD=0.29) and from 0.63 to 52.6 mg/g (mean=8.7; SD=14.3), respectively. Conclusions: This study provides important information on the levels of various metals in the cadaveric remains of a famous and old forensic case. However, this work has some limitations associated with the degradation of the biological materials and their possible postmortem contamination, mainly due to prolonged exposure to the coffin. Further analyses are needed and will be conducted on teeth due to their lower susceptibility to postmortem exchanges with the surrounding environment.
description: Scientific Letters, Vol. 1 No. Sup 1 (2023)
Optimizing the catching of atoms or molecules in two-dimensional traps
Creators: name: Singh, V. P.
name: Ruschhaupt, A.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Physics (quant-ph)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Single-photon cooling is a recently introduced method to cool atoms and molecules for which standard methods might not be applicable. We numerically examine this method in a two-dimensional wedge trap as well as in a two-dimensional harmonic trap. An element of the method is an optical dipole box trapping atoms irreversibly. We show that the cooling efficiency of the single-photon method can be improved by optimizing the trajectory of this optical dipole box.
description: 8 pages, 11 figures, improved version with corrected typos etc