cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus
Creators: name: Wang, Xi
name: Xintian You
name: Langer, Julian D.
name: Jingyi Hou
name: Rupprecht, Fiona
name: Vlatkovic, Irena
name: Quedenau, Claudia
name: Schuman, Erin
name: Chen, Wei
Publisher: name: F1000 Research Limited
Year: 2020

description: Background: The structural annotation of genes serves as an important resource in the genomics era. Next-generation sequencing (NGS)-based RNA-seq has been used to reconstruct transcriptomes by assembling short reads; however, coupled alternative RNA processing events occurring over long distances cannot be captured. Although the more recently developed third-generation sequencing (TGS) technologies can generate longer reads, challenges exist in full-length transcriptome (FLT) reconstruction due to their higher sequencing error rate and relatively lower throughput.

Results: Here, to address the above-stated technical challenges and provide practical FLT annotation in rat, we developed a hybrid-sequencing workflow for reconstructing FLT and applied it to rat hippocampus. Our workflow combines high sequencing accuracy from NGS and long read length from TGS, and has two main features: (1) cDNA normalization and size fractionation to facilitate the profiling of diverse transcripts at an affordable throughput; and (2) a computational approach to correct TGS sequencing errors using NGS reads. The error correction substantially improved the read accuracy with respect to gene expression levels. To determine high-confidence FLT, we used independent 5´ and 3´-end profiling data to validate and filter for a final FLT set in rat hippocampus, which contains 28,268 transcripts derived from 6,380 RefSeq gene loci and 849 unannotated loci. Comparing our FLT to RefSeq annotation, we found that our FLT displayed a higher diversity and more than 90% of our FLT isoforms were not annotated in RefSeq. Moreover, we discovered significant co-occurrence of alternative RNA processing events between transcript 5´-ends and 3´-ends, alternative 5´ and 3´ splice sites, and multiple retained intron. Integrating with polysome profiling and ribosome footprinting data, we predicted active or inactive translational status of transcript isoforms, and reconstructed an open reading frame (ORF)-eome in rat hippocampus, which was largely supported by mass spectrometry-based proteomics datasets. Compared to RefSeq-annotated ORFs, only less than one-third of our ORFome were annotated in RefSeq, whereas the majority were ORF variants, and about one-tenth were novel ORFs. Finally, we identify isoforms with specific subcellular localization patterns in neurons.

Conclusions: Altogether, our data expand the current rat gene annotation and provide a rich resource for future functional studies. The developed hybrid-sequencing workflow and downstream analysis can be easily adapted to uncover the complex transcriptome/ORFeome landscapes expressed in other tissues from other organisms.

Full article: PMID: 31676752 PMCID: PMC6825209 DOI: 10.1038/s41467-019-13037-0
Elliptic solutions of isentropic ideal compressible fluid flow in (3+1) dimensions
Creators: name: Conte, R.
name: Grundland, A. M.
name: Huard, B.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 35L40; 76N15

description: A modified version of the conditional symmetry method, together with the classical method, is used to obtain new classes of elliptic solutions of the isentropic ideal compressible fluid flow in (3+1) dimensions. We focus on those types of solutions which are expressed in terms of the Weierstrass P-functions of Riemann invariants. These solutions are of special interest since we show that they remain bounded even when these invariants admit the gradient catastrophe. We describe in detail a procedure for constructing such classes of solutions. Finally, we present several examples of an application of our approach which includes bumps, kinks and multi-wave solutions.
description: 17 pages, 1 figure, 3 tables
Characterization of disease-specific genes and molecular pathways in Alzheimer's disease and Huntington's disease
Creators: name: Afeefa Zainab
name: Obayashi, Takeshi
name: Kinoshita, Kengo
Publisher: name: F1000 Research Limited
Year: 2020

description: Abstract

Neurodegenerative diseases are complex brain diseases and becoming more prevalent around the globe. There is a need to understand the molecular basis of the disease to treat it effectively. Alzheimer’s disease AD is neurodegenerative disease which is progressive in nature with alterations in function, cognition, and behavior. Exact pathways or mechanisms involved in the progression are difficult to understand due to complexity. Huntington’s disease HD is another complex neurodegenerative disease often characterized by neuronal dysfunction in brain regions mainly striatum and cortex. Furthermore, AD and HD share some common symptoms including dementia, depression, and some other cognitive impairments.
 In this study, we have compared expression changes in human prefrontal brain samples in AD patients, HD patients with healthy control samples. Microarray dataset GSE33000 was downloaded from GEO database. The study was aimed at identifying shared genes and pathways in AD and HD. The analysis showed that most of the pathways enriched by the Differentially expressed genes DEGs of AD and HD were similar. This analysis also revealed identification of neurotrophin signaling pathway as strongly enriched pathway which is downregulated in both diseases. Within this pathway, brain derived neurotrphin factor BDNF was observed to be an important regulatory gene as it is responsible for survival of neurons, memory and also plays an important role in HD.
 This study also identified some hub genes, in comparison of AD Vs Healthy samples GNG2, NMU, MCHR2, NMS, GNB5, GNG3, ANXA1, GNG12, HTR5A, GABBR2 were identified as top 10 hub genes. HD Vs healthy C3AR1, C5AR1, FPR1, CXCL1, CXCL2, GNG2, NMU, ADORA3, MCHR2, NMS were found as hub genes. There is still a need to study the molecular pathways in detail by performing research from multiple studies. Further studies including data from other brain regions can further validate our findings.
A Framework for the International Polar Year, 2007-2008
Creators: name: Rapley, Chris
name: Bell, Robin E.
name: Allison, Ian
name: Bindschadler, Robert
name: Casassa, Gino
name: Chown, Steven
name: Duhaime, Gerard
name: Kotlyakov, Vladimir
name: Kuhn, Michael
name: Orheim, Olav
name: Pandey, Prem Chand
name: Petersen, Hanne Kathrine
name: Schalke, Henk
name: Janoschek, Werner
name: Sarukhanian, Eduard
name: Zhang, Zhanhai
Publisher: name: Columbia University
Year: 2004
Subjects: Climatic changes

description: The polar regions are integral components of the Earth system. As the heat sinks of the climate system they both respond to and drive changes elsewhere on the planet. Within them lie frontiers of knowledge as well as unique vantage points for science. Yet because of their remoteness and harsh nature, the poles remain insufficiently studied. With recent technological advances providing new scientific possibilities, and humankind‘s need for environmental knowledge and understanding ever increasing, the time is ripe for a coordinated international initiative to achieve a major advance in polar science. For this reason, the International Council for Science (ICSU) decided to take the lead in organizing an International Polar Year (IPY) in 2007-2008. They did so by establishing an IPY Planning Group (PG) charged with developing the IPY 2007-2008 science plan and implementation strategy. This report is the outcome of the PG‘s work. It is based on input from individuals, from over 40 governmental and nongovernmental organizations that have endorsed or expressed support for IPY 2007-2008, and from the 32 IPY National Committees or National Points of Contact established so far. It is also results from discussions and debate at over a dozen international meetings covering the gamut of science disciplines, from a series of "town" meetings, and from two Discussion Forums hosted by ICSU and attended by representatives of the IPY National Committees and a variety of interested polar organizations.
Information for All: Leveraging the Blacklight Search-and-Discovery Layer to Increase International Use of Open Access Collections
Creators: name: Hilliker, Robert J.
name: Baker, Matthew C.
Publisher: name: Columbia University
Year: 2011
Subjects: Library science
Information science

description: In the current environment, even top-tier institutions are feeling the pinch of ever-increasing subscription prices—imagine, then, how much more difficult the situation is in developing countries, where funds are far more limited and very few have access to institutional collections. In response, libraries have supported open access initiatives, establishing open access journals and developing institutional repositories to make faculty and student research available beyond the confines of their campus. Yet even these initiatives cannot bridge the digital divide if collections are not discoverable on the open Web, through popular search engines from Google and Bing to Yandex and Baidu. At Columbia, we recently adopted Blacklight, an open-source search-and-discovery layer, to improve the findability of the resources in our research repository, Academic Commons. Blacklight is fully Unicode-compliant, so content can be displayed in vernacular scripts, further enhancing its discoverability. The results have been better than we imagined: following our relaunch, traffic from Asia and Africa increased 300 and 400%, respectively, and our international users generally spent longer on our site than American users, accessing more content.
Thermal characteristics of the electroslag remelting process
Creators: name: Joshi, Satish V.
Publisher: name: University of British Columbia
Year: 2011

description: The thermal characteristics of the electroslag remelting process have been investigated on a laboratory scale unit. The heat generation and distribution in the slag bed is discussed. The voltage gradients in the slag bed are predicted using a resistance network analogue and tested against experimental results. A self-consistent model for electrode temperature gradients in the electroslag remelting process has been tested against experimental results. An unsteady-state method has been used to determine the electrical resistance and the overall heat transfer coefficient of the interface region, liquid slag/slag skin/copper wall in the electroslag furnace. An accurate heat balance of the process is carried out on laboratory scale ingots. Attention has been devoted to the influence of various melt parameters i.e. polarity, power input, geometry, atmosphere etc. on the melt rate. The power requirements and the melt rate for industrial ingots are predicted and compared with the data collected from the literature. The liquid metal pool volumes in ESR ingots are predicted from the operational data. The pool profiles are computed using a finite difference technique and compared with the experimentally obtained profiles.
Monte Carlo simulations on rare-earth Holmium ultra-thin films
Creators: name: Cinti, Fabio
name: Cuccoli, Alessandro
name: Rettori, Angelo
Publisher: name: arXiv
Year: 2009
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Motivated by recent experimental results in ultra-thin helimagnetic Holmium films, we have performed an extensive classical Monte Carlo simulation of films of different thickness, assuming a Hamiltonian with six inter-layer exchange constants. Both magnetic structure and critical properties have been analyzed. For n>16 (n being the number of spin layers in the film) a correct bulk limit is reached, while for lower n the film properties are clearly affected by the strong competition among the helical pitch and the surface effects, which involve the majority of the spin layers: In the thickness range n=9-16 three different magnetic phases emerge, with the high-temperature, disordered, paramagnetic phase and the low-temperature, long-range ordered one separated by an intriguing intermediate-temperature block phase, where outer ordered layers coexist with some inner, disordered ones. The phase transition of these inner layers displays the signatures of a Kosterlitz-Thouless one. Finally, for n
description: 29 pages, 14 figures
Membrane-Cytoskeleton Connectivity in Alzheimer’s Disease:From Aβ Clearance to TauSpreading by Microglia
Creators: name: Teng, Tao
Publisher: name: University of Illinois at Chicago
Year: 2022
Subjects: Uncategorized

description: Alzheimer’s disease (AD) is a progressive irreversible neurodegenerative disease affecting about 5.8 million Americans. There’s no cure for AD yet. Amyloid plaques and neurofibrillary tangles are two hallmarks of AD. And their major component, Amyloid-beta (Aβ) and tau protein may be responsible for the cause and progression of AD. Microglia is a type of glial cell important for maintaining brain homeostasis. Cytosolic phospholipase A2 (cPLA2) cleaves phospholipid, the main component of cellular membrane, and release signaling molecules. In this study, we explored the impact of cPLA2 on membrane physical properties such as membrane cytoskeleton connectivity and related signaling pathways in microglia. Effects of cPLA2 on oligomeric Aβ clearance and Tau propagation in AD were also investigated. Our study showed that inhibition of cPLA2 activity increased the membrane cytoskeleton connectivity leading to attenuated oligomeric Aβ uptake by microglia. The results also suggested that inhibition of cPLA2 with arachidonyl trifluoromethyl ketone increased the production of exosomes secreted by microglia fed with Tau. Detailed mechanism on how ATK and cPLA2 affect the production of exosome in microglia and spreading of Tau through exosome will be explored with future experiments. Together, this study provided insight for Aβ clearance and Tau spreading in AD by altering cPLA2 activity in microglia and may be helpful for the development of AD treatments.
Genesis of coexisting itinerant and localized electrons in Iron Pnictides
Creators: name: Medici, Luca de'
name: Hassan, Syed R.
name: Capone, Massimo
Publisher: name: arXiv
Year: 2010
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We show how the general features of the electronic structure of the Fe-based high-Tc superconductors are a natural setting for a selective localization of the conduction electrons to arise. Slave-spin and Dynamical mean-field calculations support this picture and allow for a comparison of the magnetic properties with experiments.
Supporting Humanities Doctoral Student Success: A Collaborative Project between Cornell University Library and Columbia University Libraries
Creators: name: Gessner, Gabriela Castro
name: Jaggars, Damon E.
name: Rutner, Jennifer Anne
name: Tancheva, Kornelia
Publisher: name: Columbia University
Year: 2011
Subjects: Library science

description: In recent years there have been a number of major, large-scale studies in the United States on the high attrition rates for doctoral students in the humanities. The results of these studies reveal a significant gap between the humanities and other disciplines. None of the studies consulted has specifically considered the role of the library in supporting doctoral program completion, even though it is often characterized as the humanist‘s equivalent to the scientific laboratory. This collaborative study includes focus groups and individual interviews with doctoral students in the humanities at both Cornell and Columbia. The study investigates whether the research library might positively impact doctoral student success in the humanities and discusses specific strategies it might employ to do so.
Still Bound for Disappointment? Another Look at Faculty and Library Journal Collections
Creators: name: Rutner, Jennifer Anne
name: Self, Jim
Publisher: name: Columbia University
Year: 2011
Subjects: Library science

description: After the publication of "Bound for Disappointment: Faculty and Journals at Research Institutions" by Jim Self in 2008, academic libraries found new insights into one particularly frustrating piece of data. LibQUAL+ survey results have consistently shown that faculty at institutions with ARL libraries report negative perceptions of library service regarding journal collections. One key finding of Self's study was the strong correlation between satisfaction with journal collections and overall satisfaction with library services for faculty. This study is a continuation of Self's work, and applies the same methodology to recent LibQUAL+ data from ARL libraries and the faculty at Columbia University. Three years later, we hope to understand whether this trend of dissatisfaction has continued at ARL libraries, and particularly at Columbia. Why are faculty at Columbia dissatisfied with journal collections? Have other areas of library service become more important to faculty? As academic libraries continue to invest heavily in journals, particularly electronic journals, how can we continue to understand this issue, and meet faculty needs?
Collecting the Human Rights Web
Creators: name: Graham, Pamela M.
name: Fallon, Tessa A.
name: Thurman, Alexander C.
Publisher: name: Columbia University
Year: 2011
Subjects: Library science

description: Power point by Fallon, Graham, and Thurman on the Human Rights Web Collection, why it’s important to collect, the selection process between Columbia and Cornell Universities, and the permissions for nominating, processing, and harvesting websites for the program.
Dispersive representation of K -> 3 pi amplitudes and cusps
Creators: name: Kampf, Karol
name: Knecht, Marc
name: Novotny, Jiri
name: Zdrahal, Martin
Publisher: name: arXiv
Year: 2008
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The NA48/2 collaboration has shown clear experimental evidence for a cusp in the data for K -> pi pi^0 pi^0. This effect can be used to extract information on the pi-pi scattering lengths. We address this issue using a two-loop dispersive construction of pi pi -> pi pi and K -> pi pi pi amplitudes in the presence of isospin breaking.
description: 4 pages, 1 figure, to appear in Proceedings of the conference QCD 08, Montpellier, 7-12 July 2008
The feasibility of using computer-based treatment for specific phobia ; A controlled comparison of computer-based vicarious exposure versus live exposure in the treatment of spider phobia
Creators: name: Gilroy, LJ
Publisher: name: University Of Tasmania
Year: 2023

description: Literature review An important goal in clinical psychology is the development of safe, cost effective, widely available treatment strategies. This review targets a particular problem, specific phobia, as a reference point in exploring the feasibility of using computers in delivering behavioural treatment for anxiety disorders. This review summaries conventional treatment methods, and evaluates their efficacy and availability. It addresses the advantages as well as the ethical and technical limitations of the use of computers in delivering psychological treatments and reviews current developments and outcome studies. It is concluded that although computer-based treatments are still in their infancy, significant advances have been made in establishing such strategies as an effective, safe and efficient treatment for phobias. Further research to establish computer-based behavioural treatment as a comparable alternative to therapist-directed live exposure for phobias, will allow the efficacy of computer-based treatment to be accurately weighed against the ethical issues. Empirical study The purpose of this study was to examine the efficacy of a computer-based vicarious exposure treatment for spider phobia compared to the standard treatment, therapist-directed live exposure. A total of 45 participants diagnosed with specific phobia (spiders) were included in the study following assessment. Participants were randomly assigned to one of three treatment conditions: computer-based treatment, therapist-directed live exposure treatment or a relaxation placebo treatment. Each treatment group received three 45 minute sessions. Phobic symptomatology was measured at pre treatment and post treatment and at a three month follow-up by the Spider Questionnaire, Fear Questionnaire, Phobic Targets and Work Adjustment Scale and a Behavioural Assessment Test. The results showed that the computer-based treatment was an effective treatment for spider phobia and comparable to therapist-directed live exposure, in producing a significant improvement on all relevant measures of phobic symptomatology. Both the computer-based and live exposure treatments were more effective than the relaxation placebo treatment. The computer-based treatment required substantially less therapist time than that of the live exposure treatment and was rated by participants as a helpful and acceptable treatment. These finding warrant the further development of the computer-based techniques in treating phobic disorders.
Gate-controlled non-volatile graphene-ferroelectric memory
Creators: name: Zheng, Yi
name: Ni, Guang-Xin
name: Toh, Chee-Tat
name: Zeng, Ming-Gang
name: Chen, Shu-Ting
name: Yao, Kui
name: Ozyilmaz, Barbaros
Publisher: name: arXiv
Year: 2009
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: In this letter, we demonstrate a non-volatile memory device in a graphene FET structure using ferroelectric gating. The binary information, i.e. "1" and "0", is represented by the high and low resistance states of the graphene working channels and is switched by controlling the polarization of the ferroelectric thin film using gate voltage sweep. A non-volatile resistance change exceeding 200% is achieved in our graphene-ferroelectric hybrid devices. The experimental observations are explained by the electrostatic doping of graphene by electric dipoles at the ferroelectric/graphene interface.
description: 4 papes, 4 figures
Harnessing the Semantic Web for Scholarship
Creators: name: (:Unav)
Publisher: name: Columbia University
Year: 2011
Subjects: Information science
Internet

description: The Semantic Web links data to other data via machine-readable information. Scholars from a wide variety of fields are applying semantic technologies to their research. At this event, panelists cover examples of the scholarly use of linked data and its creation. The panel also consider how linked data is changing the process and outcomes of research.
The Role of School Practices in the Racial Socialization of Black Youth: A Case Study of the WCS
Creators: name: Milam-Brooks, K.
Publisher: name: University of Illinois at Chicago
Year: 2022
Subjects: Uncategorized

description: The purpose of this study was to explore how World Citizen School attend to the racial socialization of their predominantly Black student body and the extent to which procultural racial socialization as described by Winkler (2012) can be found at WCS through it practices. Findings indicate that schools, teachers and parents all contribute to students’ racial understanding in different ways, and they each inform how the students make meaning of their experiences as Black youth. ​
Additional file 1 of Determining the impact of the Zika pandemic on primary care providers’ contraceptive counseling of non-pregnant patients in the US: a mixed methods study
Creators: name: Kaiser, Jennifer E.
name: Galindo, Eduardo
name: Sanders, Jessica N.
name: Simmons, Rebecca G.
name: Gawron, Lori M.
name: Herrick, Jennifer S.
name: Brintz, Benjamin
name: Turok, David K.
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: Computational Biology

description: Additional file 1.
Rashba-induced transverse pure spin currents in a four-terminal quantum dot ring
Creators: name: Gong, Weijiang
name: Han, Yu
name: Wei, Guozhu
name: Zheng, Yisong
Publisher: name: arXiv
Year: 2009
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: By applying a local Rashba spin-orbit interaction on an individual quantum dot of a four-terminal four-quantum-dot ring and introducing a finite bias between the longitudinal terminals, we theoretically investigate the charge and spin currents in the transverse terminals. It is found that when the quantum dot levels are separate from the chemical potentials of the transverse terminals, notable pure spin currents appear in the transverse terminals with the same amplitude and opposite polarization directions. Besides, the polarization directions of such pure spin currents can be inverted by altering structure parameters, i.e., the magnetic flux, the bias voltage, and the values of quantum dot levels with respect to the chemical potentials of the transverse terminals.
description: 4 pages, 3 figures, Submitted to nanotechnology
Integrated Reconnaissance of the Physical and Biogeochemical Characteristics of Jamaica Bay
Creators: name: Gordon, Arnold L.
name: Bell, Robin E.
name: Carbotte, Suzanne M.
name: Flood, Roger D.
name: Hartig, Ellen K.
name: Kolker, Alexander S.
name: Gornitz, Vivien
name: Peteet, Dorothy M.
name: Lieberman, Louisa
name: Houghton, Robert W.
name: Huber, Bruce A.
name: Rubenstone, James L.
name: Takesue, Renee
name: Van Geen, Alexander
name: Langdon, Christopher
name: Sambrotto, Raymond N.
Publisher: name: Columbia University
Year: 2001
Subjects: subject: Marine biology
subject: Marine ecology
subject: Chemical oceanography
subject: Oceanography
subject: FOS: Earth and related environmental sciences

description: Researchers at The Earth Institute of Columbia University have carried out an integrated, coordinated pilot reconnaissance of the physical, chemical, geological, and biological systems within Jamaica Bay, entitled "Integrated Reconnaissance of the Physical and Biogeochemical Characteristics of Jamaica Bay." We believe that such an integrated approach is necessary to fully understand the complex inter-relationship of the wetland ecosystem. The program focused on obtaining a synergistic view of the varied elements of Jamaica Bay by carrying out coordinated research in four areas: submarine sediment morphology, sediment and soil sampling, circulation and mixing, and chemical analysis of the Bay waters.
Correction of Field Rotator-Induced Flat-Field Systematics - A Case Study Using Archived VLT-FORS Data
Creators: name: Moehler, S.
name: Freudling, W.
name: Moller, P.
name: Patat, F.
name: Rupprecht, G.
name: O'Brien, K.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: ESO's two FOcal Reducer and low dispersion Spectrographs (FORS) are the primary optical imaging instruments for the VLT. They are not direct-imaging instruments, as there are several optical elements in the light path. In particular, both instruments are attached to a field rotator. Obtaining truly photometric data with such instruments present a significant challenge. In this paper, we investigate in detail twilight flats taken with the FORS instruments. We find that a large fraction of the structure seen in these flatfields rotates with the field rotator. We discuss in detail the methods we use to determine the cause of this effect. The effect was tracked down to be caused by the Linear Atmospheric Dispersion Corrector (LADC). The results are thus of special interest for designers of instruments with LADCs and developers of calibration plans and pipelines for such instruments. The methods described here to find and correct it, however, are of interest also for other instruments using a field rotator. If not properly corrected, this structure in the flatfield may degrade the photometric accuracy of imaging observations taken with the FORS instruments by adding a systematic error of up to 4% for broad band filters. We discuss several strategies to obtain photometric images in the presence of rotating flatfield pattern.
description: resolution of some figures reduced
Bridging the Poles: Education Linked with Research: A Report on the Workshop: 23-25 June 2004, Washington, D.C.
Creators: name: Pfirman, Stephanie L.
name: Bell, Robin E.
name: Turrin, Margaret J.
name: Maru, Poonam
Publisher: name: Columbia University
Year: 2004
Subjects: Climatic changes
Science--Study and teaching

description: The goals of the "Bridging the Poles" workshop of June 23-25, 2004 were to define strategies to engage the next generation of polar scientists, engineers and leaders, and inspire and educate the general public. The timeframe considered was the next five years, including maximizing the educational impact of the International Polar Year (IPY) in 2007-2009 (see inset below). The ca. 65 participants included K-12 educators, undergraduate professors, Arctic and Antarctic research scientists, Alaskan natives and residents, museum curators, representatives from agencies, the media and international programs. The workshop focused on four major themes: Reaching different levels; Engaging diverse communities; Possibilities for thematic areas; and Programs to feature nationally and internationally. The 22 roundtable discussions on these topics resulted in numerous recommendations to engage both future scientists and the general public. This report synthesizes opportunities for polar education and outreach identified at the workshop, recommends ways to maximize the impact of the IPY, and proposes "Next Steps" to develop polar education and outreach over the next five years.
Observation of a multiferroic critical end point
Creators: name: Kim, Jae Wook
name: Haam, S. Y.
name: Oh, Y. S.
name: Park, S.
name: Cheong, S. -W.
name: Sharma, P. A.
name: Jaime, M.
name: Harrison, N.
name: Han, Jung Hoon
name: Jeon, Gun-Sang
name: Coleman, P.
name: Kim, Kee Hoon
Publisher: name: arXiv
Year: 2008
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The study of abrupt increases in magnetization with magnetic field known as metamagnetic transitions has opened a rich vein of new physics in itinerant electron systems, including the discovery of quantum critical end points with a marked propensity to develop new kinds of order. However, the electric analogue of the metamagnetic critical end point, a "metaelectric" critical end point has not yet been realized. Multiferroic materials wherein magnetism and ferroelectricity are cross-coupled are ideal candidates for the exploration of this novel possibility using magnetic-field (\emph{H}) as a tuning parameter. Herein, we report the discovery of a magnetic-field-induced metaelectric transition in multiferroic BiMn$_{2}$O$_{5}$ in which the electric polarization (\emph{P}) switches polarity along with a concomitant Mn spin-flop transition at a critical magnetic field \emph{H}$_{\rm c}$. The simultaneous metaelectric and spin-flop transitions become sharper upon cooling, but remain a continuous crossover even down to 0.5 K. Near the \emph{P}=0 line realized at $μ_{0}$\emph{H}$_{\rm c}$$\approx$18 T below 20 K, the dielectric constant ($\varepsilon$) increases significantly over wide field- and temperature (\emph{T})-ranges. Furthermore, a characteristic power-law behavior is found in the \emph{P}(\emph{H}) and $\varepsilon$(\emph{H}) curves at \emph{T}=0.66 K. These findings indicate that a magnetic-field-induced metaelectric critical end point is realized in BiMn$_2$O$_5$ near zero temperature.
description: 6 pages, 3 figures
Additional file 4 of Auto-HMM-LMF: feature selection based method for prediction of drug response via autoencoder and hidden Markov model
Creators: name: Emdadi, Akram
name: Eslahchi, Changiz
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 4. The scatter plots of observed and predicted drug responses by the Auto-HMM-LMF model of 20 drugs in the CCLE dataset.
Derived categories and functors
Creators: name: Loo, Donald Doo Fuey
Publisher: name: University of British Columbia
Year: 2011

description: For each abelian category A, there is a category D(A), called the derived category of A, whose objects are complexes of objects of A, and whose morphisms are formal fractions of homotopy classes of complex morphisms having as denominators homotopy classes inducing isomorphisms in cohomology. If F : A →B is an additive functor between abelian categories, then under suitable conditions on A, there is a functor RF : D(A) → D(B) with the property that if objects X of A are considered as complexes concentrated at degree 0, then there are isomorphisms [formula omitted] for all n, where [formula omitted] is the ordinary [formula omitted] right derived functor of F. RF is called the derived functor of F, and one may look upon it as a kind of extension of F.
Nan Chauncy's Comfort me with applies : a diplomatic transcription
Creators: name: Eastman, B
Publisher: name: University Of Tasmania
Year: 2023

description: This thesis presents two parts: a transcription of Nan Chauncy's only unpublished adult novel Comfort me: With Apples and a short introduction to that text. The transcription is presented as a diplomatic edition of the typescript of the novel held in Nan Chauncy's papers in the Tasmanian State Archives. This edition is collated with a second typescript of the novel previously owned by the author's brother and which is now called the Reedwind text. The Reedwind text is now in the possession of the candidate. The transcribing of Comfort Me With Apples has been made in accordance with the principles of textual editing outlined by D.C. Greetham in Textual Scholarship: An Introduction (New York: Garland, 1994). This edition of the text has been produced for research purposes and is the only edition available outside the TSA. The Introduction consists in a description of text and provenance; a summary of the novel's parts; an analysis of genre and literary evaluation; a biography of author and chronology of works. Notes include a family tree and maps of relevant geographical locations.
The cellular mechanism underlying neuronal changes in Alzheimer's disease
Creators: name: Dickson, Tracey
Publisher: name: University Of Tasmania
Year: 2023

description: The cause of the degeneration of nerve cells, and the loss of specific synaptic connections, that underlies the emergence and progressive development of dementia in sufferers of Alzheimer's disease remains elusive. Furthermore, although individually the B-amyloid plaque, neurofibrillary tangle and dystrophic neurite, pathological hallmarks of the disease, have been extensively investigated, the mechanism that links these structures also remains to be defined. This thesis, therefore, sought to address three aims that were principally associated with the relationship between the pathological structures and the mechanism underlying Alzheimer's disease. Firstly, to determine the neurochemical and morphological diversity of abnormal neurites associated with B-amyloid plaque formation in the early and late stages of Alzheimer's disease. Secondly, to examine the relationship between apolipoprotein E immunolabelling and 13-amyloid deposition, neuritic plaques and neurofibrillary tangles using immunofluorescent double labeling techniques. Finally, to develop an in vitro experimental model that mimics the effects of B-amyloid plaques on surrounding neuronal processes. The major conclusions from these investigations were that the dystrophic neurites associated with subsets of B-amyloid plaques develop through a distinct morphological and neurochemical sequence. This sequence of change is intimately linked to various components of the neuronal cytoskeleton, including neurofilaments. The similarity between these changes and those present within axons undergoing a response to physical damage lead to the development of a new hypothesis that B-amyloid plaque deposition causes physical damage to surrounding neurites which results in the formation of dystrophic neurites. This hypothesis was further supported by results obtained from an in vitro model of physical damage. In summary, this study further clarified the relationship between 13- amyloid plaques and dystrophic neurites, particularly with regard to determining the role of specific cytoskeletal changes. Identification of the earliest pathological changes that occur in Alzheimer's disease is necessary for the development of effective therapeutic strategies aimed at preventing or slowing the ongoing neuronal changes that ultimately lead to cell death and dementia.
Additional file 1 of Cross-level analysis of molecular and neurobehavioral function in a prospective series of patients with germline heterozygous PTEN mutations with and without autism
Creators: name: Frazier, Thomas W.
name: Jaini, Ritika
name: Busch, Robyn M.
name: Wolf, Matthew
name: Sadler, Tammy
name: Klaas, Patricia
name: Hardan, Antonio Y.
name: Martinez-Agosto, Julian A.
name: Sahin, Mustafa
name: Eng, Charis
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1.
Interacting antiferromagnetic and ferroelectric domain structures
Creators: name: Gareeva, Z. V.
name: Zvezdin, A. K.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The correlation between antiferromagnetic and ferroelectric domain structures in multiferroics has been studied. The role of magnetoelectric interactions in a formation of antiferromagnetic domain structure has been analysed. It has been shown the major physical mechanism binding antiferromagnetic domains to ferroelectrics ones is inhomogeneous flexomagnetoelectric interaction of the Pz((lgrad)lz-lz(divl)) type. The dependences illustrating rearrangement of antiferromagnetic domain pattern together with change of ferroelectric domains thickness has been performed.
description: 4 pages, 4 figures
Security bound of continuous-variable quantum key distribution with noisy coherent states and channel
Creators: name: Shen, Yong
name: Yang, Jian
name: Guo, Hong
Publisher: name: arXiv
Year: 2009
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Security of a continuous-variable quantum key distribution protocol based on noisy coherent states and channel is analyzed. Assuming the noise of coherent states is induced by Fred, a neutral party relative to others, we prove that the prepare and measurement scheme and entanglement-based scheme are equivalent. Then, we show that this protocol is secure against Gaussian collective attacks even if the channel is lossy and noisy, and further, a lower bound to the secure key rate is derived.
description: 4 pages and 3 figures; Two references (ref. [1] and [2] in this new version) are added;
On asymptotically flat algebraically special spacetimes in higher dimensions
Creators: name: Ortaggio, Marcello
name: Pravda, Vojtech
name: Pravdova, Alena
Publisher: name: arXiv
Year: 2009
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We analyze asymptotic properties of higher-dimensional vacuum spacetimes admitting a "non-degenerate" geodetic multiple WAND. After imposing a fall-off condition necessary for asymptotic flatness, we determine the behaviour of the Weyl tensor as null infinity is approached along the WAND. This demonstrates that these spacetimes do not "peel-off" and do not contain gravitational radiation (in contrast to their four-dimensional counterparts). In the non-twisting case, the uniqueness of the Schwarzschild-Tangherlini metric is also proven.
description: 6 pages, references added
Additional file 1 of Mechanical power normalized to predicted body weight is associated with mortality in critically ill patients: a cohort study
Creators: name: Zhu, Yanhong
name: Peng, Wenyong
name: Zhen, Shuai
name: Jiang, Xiaofeng
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 1: eTable 1. Comparisons of PEEP between different PIP level.
Data Management and Federal Funding: What Researchers Need to Know
Creators: name: (:Unav)
Publisher: name: Columbia University
Year: 2011
Subjects: Information science

description: New requirements from the National Science Foundation and other federal agencies have brought data management and sharing into the spotlight. This trend will continue as more research sponsors, and the general public, demand increased access to federally-funded research data. This event examines the goals of these requirements and explore the technical, scientific, and professional challenges resulting from efforts to preserve and share data.
Quantitative comparison of within-sample heterogeneity scores for DNA methylation data
Creators: name: Scherer, Michael
name: Nebel, Almut
name: Franke, Andre
name: Joern Walter
name: Lengauer, Thomas
name: Bock, Christoph
name: Mueller, Fabian
name: List, Markus
Publisher: name: F1000 Research Limited
Year: 2020

description: Background: DNA methylation is an epigenetic mark with important regulatory roles in cellular identity and can be quantified at base resolution using bisulfite sequencing. Most studies are limited to the average DNA methylation levels of individual CpGs and thus neglect heterogeneity within the profiled cell populations. To assess this within-sample heterogeneity (WSH) several window-based scores that quantify variability in DNA methylation in bisulfite sequencing reads have been proposed.
Results: We performed the first systematic comparison of four published WSH scores based on simulated and publicly available datasets. Moreover, we propose two new scores and provide guidelines for selecting appropriate scores to address cell-type heterogeneity, cellular contamination and allele-specific methylation. Most of the measures were sensitive in detecting DNA methylation heterogeneity in these scenarios, while we detected differences in susceptibility to technical bias. Using recently published DNA methylation profiles of Ewing sarcoma samples, we show that DNA methylation heterogeneity provides information complementary to the DNA methylation level.
Conclusions: WSH scores are powerful tools for estimating variance in DNA methylation patterns and have the potential for detecting novel disease-associated genomic loci not captured by established statistics. We provide an R-package (github.com/MPIIComputationalEpigenetics/WSHPackage) implementing the WSH scores for integration into analysis workflows.
Variant annotation of ADME genes using SWAAT: a structural bioinformatics approach
Creators: name: Houcemeddine Othman
name: Rocha, Jorge Da
name: Hazelhurst, Scott
Publisher: name: F1000 Research Limited
Year: 2020

description: ADME (Absorption, Distribution, Metabolism, and Excretion) genes are key players to determine the pharmacokinetics and pharmacodynamics properties of a drug and in defining the drug-host response. The impact of variants on putative protein-drug interaction is critical for functional predictions in pharmacogenomic analysis. Therefore, sequence-based annotation only offers a narrow perspective for interpreting the ADME variants. We describe the design of SWAAT workflow (Structural Workflow for the Annotation of ADME Targets) for the characterization of ADME variants from high throughput sequencing data. The tool integrates in-house Python and R scripts in Nextflow to process the variants from a VCF file and maps them on 26 structures from different genes. SWAAT was designed to account for the low scale and large scale conformational structural events and provides a machine learning model for binary classification of the impact of the variants. It allows predicting the impact of variants on the protein structure integrity and the conformational landscape of the ADME proteins. Moreover, SWAAT extends the analysis to map the effect on putative drug-ADME protein interaction hotspots. We plan to include the extended ADME genes for further improvement. The workflow is intended for an application on a novel high-coverage data set of African WGS.
Transverse hydrodynamics in relativistic heavy-ion collisions
Creators: name: Ryblewski, Radoslaw
Publisher: name: arXiv
Year: 2009
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: General features of the formalism describing hydrodynamic evolution of transversally thermalized matter possibly produced at the very early stages of ultra-relativistic heavy-ion collisions are presented. Thermodynamical consistency of the model is emphasized. The covariant formulas for the moments of the phase-space distribution function are derived. The simple model for the transition from purely transverse to standard perfect-fluid hydrodynamics is proposed.
description: Talk presented at the 2009 Cracow Epiphany Conference, 10 pages, 1 figure
Tri-bimaximal and bimaximal neutrino mixing from discrete symmetries
Creators: name: Merlo, Luca
Publisher: name: arXiv
Year: 2009
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The neutrino oscillation data are well explained by the tri-bimaximal pattern. Recently it has been shown that also the bimaximal pattern could be a very good starting point in order to describe the lepton mixing. In this paper I review both the flavour structures and then I present an explicit example.
description: 4 pages; Talk given at IFAE 2009: Incontri di Fisica delle Alte Energie, Bari, Italy, 15-17 April 2009
Zero temperature phases of the frustrated J1-J2 antiferromagnetic spin-1/2 Heisenberg model on a simple cubic lattice
Creators: name: Majumdar, Kingshuk
name: Datta, Trinanjan
Publisher: name: arXiv
Year: 2009
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: At zero temperature magnetic phases of the quantum spin-1/2 Heisenberg antiferromagnet on a simple cubic lattice with competing first and second neighbor exchanges (J1 and J2) is investigated using the non-linear spin wave theory. We find existence of two phases: a two sublattice Neel phase for small J2 (AF), and a collinear antiferromagnetic phase at large J2 (CAF). We obtain the sublattice magnetizations and ground state energies for the two phases and find that there exists a first order phase transition from the AF-phase to the CAF-phase at the critical transition point, pc = 0.28. Our results for the value of pc are in excellent agreement with results from Monte-Carlo simulations and variational spin wave theory. We also show that the quartic 1/S corrections due spin-wave interactions enhance the sublattice magnetization in both the phases which causes the intermediate paramagnetic phase predicted from linear spin wave theory to disappear.
description: 19 pages, 4 figures, Fig. 1b modified, Appendix B text modified