cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire
Creators: name: Ostrov, David A.
name: Grant, Barry J.
name: Pompeu, Yuri A.
name: Sidney, John
name: Harndahl, Mikkel
name: Southwood, Scott
name: Oseroff, Carla
name: Lu, Shun
name: Jakoncic, Jean
name: de Oliveira, Cesar Augusto. F.
name: Yang, Lun
name: Mei, Hu
name: Shi, Leming
name: Shabanowitz, Jeffrey
name: English, A. Michelle
name: Wriston, Amanda
name: Lucas, Andrew
name: Phillips, Elizabeth
name: Mallal, Simon
name: Grey, Howard
name: Sette, Alessandro
name: Hunt, Donald F.
name: Buus, Soren
name: Peters, Bjoern
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cell Behavior (q-bio.CB)
subject: FOS: Biological sciences

description: Idiosyncratic adverse drug reactions are unpredictable, dose independent and potentially life threatening; this makes them a major factor contributing to the cost and uncertainty of drug development. Clinical data suggest that many such reactions involve immune mechanisms, and genetic association studies have identified strong linkage between drug hypersensitivity reactions to several drugs and specific HLA alleles. One of the strongest such genetic associations found has been for the antiviral drug abacavir, which causes severe adverse reactions exclusively in patients expressing the HLA molecular variant B*57:01. Abacavir adverse reactions were recently shown to be driven by drug-specific activation of cytokine-producing, cytotoxic CD8+ T cells that required HLA-B*57:01 molecules for their function. However, the mechanism by which abacavir induces this pathologic T cell response remains unclear. Here we show that abacavir can bind within the F-pocket of the peptide-binding groove of HLA-B*57:01 thereby altering its specificity. This supports a novel explanation for HLA-linked idiosyncratic adverse drug reactions; namely that drugs can alter the repertoire of self-peptides presented to T cells thus causing the equivalent of an alloreactive T cell response. Indeed, we identified specific self-peptides that are presented only in the presence of abacavir, and that were recognized by T cells of hypersensitive patients. The assays we have established can be applied to test additional compounds with suspected HLA linked hypersensitivities in vitro. Where successful, these assays could speed up the discovery and mechanistic understanding of HLA linked hypersensitivities as well as guide the development of safer drugs.
Privacy in Immersive Extended Reality: Exploring User Perceptions, Concerns, and Coping Strategies
Creators: name: Hadan, Hilda
name: Wang, Derrick M.
name: Nacke, Lennart E.
name: Zhang-Kennedy, Leah
Publisher: name: arXiv
Year: 2025
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Extended Reality (XR) technology is changing online interactions, but its granular data collection sensors may be more invasive to user privacy than web, mobile, and the Internet of Things technologies. Despite an increased interest in studying developers' concerns about XR device privacy, user perceptions have rarely been addressed. We surveyed 464 XR users to assess their awareness, concerns, and coping strategies around XR data in 18 scenarios. Our findings demonstrate that many factors, such as data types and sensitivity, affect users' perceptions of privacy in XR. However, users' limited awareness of XR sensors' granular data collection capabilities, such as involuntary body signals of emotional responses, restricted the range of privacy-protective strategies they used. Our results highlight a need to enhance users' awareness of data privacy threats in XR, design privacy-choice interfaces tailored to XR environments, and develop transparent XR data practices.
description: 25 pages, 4 figures, 8 tables. the 2024 CHI Conference on Human Factors in Computing Systems (CHI'24)
Frequency dependence of Delta_nu of solar-like oscillators investigated: Influence of HeII ionization zone
Creators: name: Hekker, S.
name: Basu, Sarbani
name: Elsworth, Y.
name: Chaplin, W. J.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Oscillations in solar-like oscillators tend to follow an approximately regular pattern in which oscillation modes of a certain degree and consecutive order appear at regular intervals in frequency, i.e. the so-called large frequency separation. This is true to first order approximation for acoustic modes. However, to a second order approximation it is evident that the large frequency separation changes as a function of frequency. This frequency dependence has been seen in the Sun and in other main-sequence stars. However, from observations of giant stars, this effect seemed to be less pronounced. We investigate the difference in frequency dependence of the large frequency separation between main-sequence and giant stars using YREC evolutionary models.
description: 4 pages, 1 figure, to appear in Astrophysics and Space Science Proceedings series of the 20th Stellar pulsation conference held in Granada (Spain) from 6 to 10 September 2011
Concurrent Dual Band Six Port Receiver
Creators: name: Olopade, Abdullah Oluwatosin
Publisher: name: Graduate Studies
Year: 2014
Subjects: subject: Engineering--Electronics and Electrical
subject: Concurrent Dual-Band Receiver, Direct Conversion Receiver, Six-Port Receiver, Software Defined Radio

description: Receiver front-ends have always been a critical component in wireless communication system design. Its performance and characteristics determines the quality and fidelity of the communication systems. Proliferation of communication protocols and standards however, require that the front-ends should become more flexible, multi-standard and reconfigurable. In addition, to enable higher communication throughput, there have been proponents of concurrent dual-band receiver front-ends to receive signals in more than one band simultaneously. Typical architecture for this concurrent multiband operation uses the front-end stack-up technique, which builds parallel receiver paths with each path dedicated to one frequency band. This increases complexity, power requirement, size and cost. The Six-Port receiver (SPR) is a low power and low complexity alternative to conventional homodyne receiver, which is multi-standard, flexible and easily reconfigurable. This thesis proposes the use of the SPR for a concurrent dual-band operation without any component duplication in the frequency down-conversion path.
title: การพัฒนาอาชีพตามหลักเศรษฐกิจพอเพียง บ้านกระออม ตำบลกระออม อำเภอสำโรงทาบ จังหวัดสุรินทร์
Creators: name: สุจิตรา ลีตี
Publisher: name: สถาบันวิชาการเพื่อพัฒนาท้องถิ่น
publisherIdentifierScheme: ROR
Year: 2024
Subjects: อาชีพ
การพัฒนา
เศรษฐกิจพอเพียง

description: วารสารวิชาการพัฒนาท้องถิ่น, 3, 1, 39-48
Reconciling the Classical-Field Method with the Beliaev Broken Symmetry Approach
Creators: name: Wright, Tod M.
name: Davis, Matthew J.
name: Proukakis, Nick P.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We present our views on the issues raised in the chapter by Griffin and Zaremba [A. Griffin and E. Zaremba, in Quantum Gases: Finite Temperature and Non-Equilibrium Dynamics, N. P. Proukakis, S. A. Gardiner, M. J. Davis, and M. H. Szymanska, eds., Imperial College Press, London (in press)]. We review some of the strengths and limitations of the Bose symmetry-breaking assumption, and explain how such an approach precludes the description of many important phenomena in degenerate Bose gases. We discuss the theoretical justification for the classical-field (c-field) methods, their relation to other non-perturbative methods for similar systems, and their utility in the description of beyond-mean-field physics. Although it is true that present implementations of c-field methods cannot accurately describe certain collective oscillations of the partially condensed Bose gas, there is no fundamental reason why these methods cannot be extended to treat such scenarios. By contrast, many regimes of non-equilibrium dynamics that can be described with c-field methods are beyond the reach of generalised mean-field kinetic approaches based on symmetry-breaking, such as the ZNG formalism.
description: 8 pages. Unedited version of chapter to appear in Quantum Gases: Finite Temperature and Non-Equilibrium Dynamics (Vol. 1 Cold Atoms Series). N.P. Proukakis, S.A. Gardiner, M.J. Davis and M.H. Szymanska, eds. Imperial College Press, London (in press). See http://www.icpress.co.uk/physics/p817.html v2: Added arXiv cross-references
On the formation of a tulip flame in closed and semi-open tubes
Creators: name: Liberman, Mikhail A.
name: Qian, Chengeng
name: Wang, Cheng
Publisher: name: arXiv
Year: 2022
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: The paper examines the mechanism of the tulip flame formation for the flames propagating in closed tubes of various aspect ratios and in a half-open tube. The formation of tulip flames in 2D channels is studied using high resolution direct numerical simulations of the reactive Navier Stokes equations coupled with a detailed chemical model for a stoichiometric hydrogen/air flame. It is shown that rarefaction waves generated by the flame during the deceleration stage play a key role in the tulip-shaped flame formation. The interaction of the reverse flow created behind the rarefaction wave with previously produced be accelerating flame flow in the unburned gas, results in the decrease of the flow velocity in the near field zone ahead of the flame and in the increase of the boundary layer thickness. The profile of the axial velocity close ahead of the flame takes the form of an inverted tulip. Therefore, the flame front acquires a tulip shape repeating to a large extent the shape of the of the axial velocity profile in the upstream flow.
description: 44 pages, 23 figures
Marijuana as scapegoat, cannabis as medicine : a cognitive-rhetorical analysis of a Canadian drug-policy problem
Creators: name: Steen, Robin Jonathan
Publisher: name: University of British Columbia
Year: 2010

description: This thesis examines the remarkable ambivalence towards Cannabis sativa L. in Canada, evidenced in the high-stakes contest between competing public conceptions of, and private interests in, the drug-plant and cash crop. Official policy regarding the enigmatic substance over the first decade of the 21st century has been notably erratic, and during this period a number of dramatic shifts in Canada’s administrative and clinical approaches to cannabis have occurred. This has resulted in changes which stand out significantly in the history of the plant’s medicinal, recreational, and industrial use in this country. Despite the recent surge in acceptance and legitimacy of its medical use in a number of jurisdictions, the definition, classification, regulation, prescription, cultivation, marketing, and consumption of cannabis for therapeutic purposes continue to pose, for many groups and individuals in this country, a medico-legal dilemma—with the boundary between licit and illicit a blurry one in deed, and in word. The many lingering questions about proper ethical and practical conduct within (and parallel to) the framework of the MMAR have made it exceedingly difficult for many participants to arrive at a comfortable fit between the activities pursuant to their roles and the uncertain, unqualifiable, or unappreciated value (or risk) entailed by those roles. I intend not only to improve understanding of the rhetorical, linguistic, and socio-cognitive basis of a particular drug-policy problem, but also to demonstrate, in so doing, the broad analytical reach of rhetorical theory and criticism, and the usefulness of applying rhetorical and cognitive-linguistic methodologies together. Through analysis of suasive elements of key terms and conceptual structures in the discourse, and of differently motivated role-value connections assumed by participants therein, I forward the claim that marijuana has played the part of the scapegoat in medicine and, more broadly, among all drugs.
Tunable phonon-driven magnon-magnon entanglement at room temperature
Creators: name: Liu, Yuefei
name: Bagrov, Andrey
name: Bergman, Anders
name: Delin, Anna
name: Eriksson, Olle
name: Pereiro, Manuel
name: Streib, Simon
name: Thonig, Danny
name: Sjöqvist, Erik
name: Azimi-Mousolou, Vahid
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We report the existence of entangled steady-states in bipartite quantum magnonic systems at elevated temperatures. We consider dissipative dynamics of two magnon modes in a bipartite antiferromagnet, subjected to interaction with a phonon mode and an external rotating magnetic field. To quantify the bipartite magnon-magnon entanglement, we use entanglement negativity and compute its dependence on temperature and magnetic field. We provide evidence that the coupling between magnon and phonon modes is necessary for the entanglement, and that, for any given phonon frequency and magnon-phonon coupling rate, there are always ranges of the magnetic field amplitudes and frequencies for which magnon-magnon entanglement persists at room temperature.
description: 17 pages, 5 figures
Numerical Simulation of Solar Microflares in a Canopy-Type Magnetic Configuration
Creators: name: Jiang, R. -L.
name: Fang, C.
name: Chen, P. -F.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Microflares are small activities in solar low atmosphere, some are in the low corona, and others in the chromosphere. Observations show that some of the microflares are triggered by magnetic reconnection between emerging flux and a pre-existing background magnetic field. We perform 2.5D compressible resistive MHD simulations of magnetic reconnection with gravity considered. The background magnetic field is a canopy-type configuration which is rooted at the boundary of the solar supergranule. By changing the bottom boundary conditions in the simulation, new magnetic flux emerges up at the center of the supergranule and reconnects with the canopy-type magnetic field. We successfully simulate the coronal and chromospheric microflares, whose current sheets are located at the corona and the chromosphere, respectively. The microflare of coronal origin has a bigger size and a higher temperature enhancement than that of chromospheric origin. In the microflares of coronal origin, we also found a hot jet ($\sim$$1.8 \times 10^6$ K), which is probably related to the observational EUV/SXR jets, and a cold jet ($\sim$$10^4$ K), which is similar to the observational H$α$/Ca surges, whereas there is only an H$α$/Ca bright point in the microflares of chromospheric origin. The study of parameter dependence shows that the size and strength of the emerging magnetic flux are the key parameters which determine the height of the reconnection location, and further determine the different observational features of the microflares.
description: 24 pages, 11 figures, accepted by ApJ
Probing Trapped Antihydrogen. In Situ Diagnostics and Observations of Quantum Transitions
Creators: name: Friesen, Timothy Peter
Publisher: name: Graduate Studies
Year: 2014
Subjects: subject: Physics--Atomic
subject: Antimatter
subject: Antihydrogen
subject: Non-neutral Plasmas

description: Antihydrogen, the bound state of a positron and an antiproton, is the simplest pure anti-atomic system and an excellent candidate to test the symmetry between matter and antimatter. This thesis focuses on the magnetic confinement of antihydrogen and the first ever resonant interaction with trapped antihydrogen, as performed by the ALPHA collaboration. The ALPHA apparatus and the techniques that have been developed to form, trap, probe, and detect antihydrogen atoms will be described in detail. The first successful demonstration of trapped antihydrogen will then be described. In the initial demonstrations, 38 trapped antihydrogen atoms were detected after being confined for at least 172 ms. Since then, over 400 antihydrogen atoms have been trapped and confinement times of 1000 s (over 15 minutes) have been demonstrated. Spectroscopy of these trapped antihydrogen atoms is the next major step forward. As an initial proof-of-principle demonstration, ALPHA induced and observed resonant positron spin flip (PSR) transitions between the ground states of antihydrogen. Because of the strong magnetic field dependence of these transition frequencies, the success of this experiment relied heavily on the ability to measure the magnetic field seen by the antihydrogen atoms. A novel method to measure the magnetic field in situ by detecting the cyclotron resonance of a trapped electron plasma is presented. This method allowed ALPHA to measure the magnetic field strength at the minimum of the magnetic antihydrogen trap to within 1.4 parts in 1000. Hardware improvements and further study should allow this resolution to be improved by several orders of magnitude. The cyclotron resonance measurements can also be applied as a rough diagnostic of a microwave field within the ALPHA apparatus. This allowed for important diagnostics of the microwave field used to excite the PSR transitions. Finally, the experimental results demonstrating resonant PSR transitions in antihydrogen are presented. This experiment is the first ever spectroscopic measurement of antihydrogen and an important step towards future precision spectroscopy.
Additional file 1 of Structural brain differences in recovering and weight-recovered adult outpatient women with anorexia nervosa
Creators: name: Brodrick, Brooks B.
name: Adler-Neal, Adrienne L.
name: Palka, Jayme M.
name: Mishra, Virendra
name: Aslan, Sina
name: McAdams, Carrie J.
Publisher: name: figshare
Year: 2021
Subjects: subject: Cell Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1. Cortical Thickness Differences Excluding Low BMI Participants.
Impact of Growth Hormone on Adult Bone Quality in Turner Syndrome - A High Resolution Peripheral Quantitative Computed Tomography Study
Creators: name: Nour, Munier Anwar
Publisher: name: Graduate Studies
Year: 2014
Subjects: subject: Medicine and Surgery
subject: Turner Syndrome
subject: osteoporosis
subject: High Resolution Peripheral Quantitative Computed Tomography
subject: Growth Hormone

description: Caused by total or partial X-monosomy, Turner Syndrome (TS) is the most common chromosomal disorder in females. Commonly associated features include short stature, ovarian failure and osteoporosis in adult years. Childhood short-stature in TS is commonly treated with growth hormone (GH). This historic cohort-study using dual x-ray absorptiometry (DXA) and high resolution peripheral quantitative computed tomography (HR-pQCT) was conducted to determine the effect of childhood GH treatment on adult bone quality in TS women. Karyotype confirmed TS women aged 16-45 years were recruited (N=28). GH-treated subjects were 7.4 cm taller than non-GH-treated (p<0.05). Groups were similar in regard to known bone health risk factors. GH-treated subjects had significantly larger bone areas (9-25%, p<0.05) by DXA and HR-pQCT. Bone densities, micro-architecture and estimated fracture thresholds were not different among treatment groups. While no micro-architectural benefits were observed with GH-treatment, the persistent macro-structural differences may provide advantages in future fracture risk.
Transverse in-plane flow: a new probe of symmetry energy in Fermi energy region
Creators: name: Gautam, Sakshi
name: Puri, Rajeev K.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We study the sensitivity of transverse flow towards the different density dependence of symmetry energy in Fermi energy region. Our results show that transverse flow shows sensitivity to different density dependence of symmetry energy. The mechanism for sensitivity towards different density dependence of symmetry energy is also discussed.
description: submitted to DAE Symposium on Nuclear Physics, December 26-30, 2011, Andhra University, Visakhapatnam, A.P., India
title: การมีส่วนร่วมในการจัดการทรัพยากรน้ำของประชาชนในชุมชนบ้านระโยงตำบลท่าสว่าง อำเภอเมือง จังหวัดสุรินทร์
Creators: name: วชิราพร วิมานรัมย์
Publisher: name: สถาบันวิชาการเพื่อพัฒนาท้องถิ่น
publisherIdentifierScheme: ROR
Year: 2024
Subjects: การมีส่วนร่วม
การจัดการทรัพยากรน้ำ
ประชาชน

description: วารสารวิชาการพัฒนาท้องถิ่น, 3, 1, 49-58
Metamodeling methods and their direct methanol fuel cell applications
Creators: name: Yang, Qinwen
Publisher: name: Graduate Studies
Year: 2014
Subjects: subject: Energy
subject: Engineering--Mechanical
subject: Metamodeling
subject: Sampling
subject: Optimization
subject: Direct methanol fuel cells

description: Direct methanol fuel cells (DMFCs) have emerged in recent years as potential power sources for portable electronic devices due to the high energy density of methanol and low power requirements of the portable electronic devices. Fuel cell system modeling plays an important role in the design of DMFC systems. Despite the progress in modeling of DMFCs, most of these models considered only some of the key operating parameters with overly simplified geometric shapes. In addition, since extensive simulations are usually required in design and control of DMFC systems, advanced modeling tools with high computation quality and efficiency are expected. This research focuses on study of adaptive metamodeling methods and applications of these methods in modeling and design of DMFC systems. A semi-empirical model is developed to build the relationships between all important operating parameters and DMFC performance measures. Coefficients of this semi-empirical model are obtained through experiments and data fitting. The semi-empirical model provides a basis to identify the optimal operating parameters of the DMFC system considering different power requirements. In addition, adaptive metamodeling has been employed to describe the electrochemical relationships in a computational fluid dynamics (CFD) based DMFC model to study influences of both geometric parameters and operating parameters on DMFC performance. The CFD-based DMFC model can be used in optimal design of geometric parameters and optimal control of operating parameters. Metamodeling methods, which were initially developed as “surrogates” of the expensive simulation process, can be used to model the relationship between input and output parameters in DMFC systems. Influences of two factors, noise level and initial sample size, on quality of adaptive metamodeling considering different metamodel schemes and test functions are studied in this work. Guidelines have been developed for selection of the proper adaptive metamodeling methods. In addition, a new sampling method namely weighted sequential sampling (WSS) method is introduced in this research to improve the accuracy of adaptive metamodeling considering influences of sample quality measures in both input and output parameter spaces. Quality of the global optimization can be improved based on the metamodel built using the WSS method.
W-Transformers : A Wavelet-based Transformer Framework for Univariate Time Series Forecasting
Creators: name: Sasal, Lena
name: Chakraborty, Tanujit
name: Hadid, Abdenour
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: Econometrics (econ.EM)
subject: Signal Processing (eess.SP)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences
subject: FOS: Economics and business
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Deep learning utilizing transformers has recently achieved a lot of success in many vital areas such as natural language processing, computer vision, anomaly detection, and recommendation systems, among many others. Among several merits of transformers, the ability to capture long-range temporal dependencies and interactions is desirable for time series forecasting, leading to its progress in various time series applications. In this paper, we build a transformer model for non-stationary time series. The problem is challenging yet crucially important. We present a novel framework for univariate time series representation learning based on the wavelet-based transformer encoder architecture and call it W-Transformer. The proposed W-Transformers utilize a maximal overlap discrete wavelet transformation (MODWT) to the time series data and build local transformers on the decomposed datasets to vividly capture the nonstationarity and long-range nonlinear dependencies in the time series. Evaluating our framework on several publicly available benchmark time series datasets from various domains and with diverse characteristics, we demonstrate that it performs, on average, significantly better than the baseline forecasters for short-term and long-term forecasting, even for datasets that consist of only a few hundred training samples.
Knowledge-based Deep Learning for Modeling Chaotic Systems
Creators: name: Elabid, Zakaria
name: Chakraborty, Tanujit
name: Hadid, Abdenour
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: Computational Physics (physics.comp-ph)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: Deep Learning has received increased attention due to its unbeatable success in many fields, such as computer vision, natural language processing, recommendation systems, and most recently in simulating multiphysics problems and predicting nonlinear dynamical systems. However, modeling and forecasting the dynamics of chaotic systems remains an open research problem since training deep learning models requires big data, which is not always available in many cases. Such deep learners can be trained from additional information obtained from simulated results and by enforcing the physical laws of the chaotic systems. This paper considers extreme events and their dynamics and proposes elegant models based on deep neural networks, called knowledge-based deep learning (KDL). Our proposed KDL can learn the complex patterns governing chaotic systems by jointly training on real and simulated data directly from the dynamics and their differential equations. This knowledge is transferred to model and forecast real-world chaotic events exhibiting extreme behavior. We validate the efficiency of our model by assessing it on three real-world benchmark datasets: El Nino sea surface temperature, San Juan Dengue viral infection, and Bjørnøya daily precipitation, all governed by extreme events' dynamics. Using prior knowledge of extreme events and physics-based loss functions to lead the neural network learning, we ensure physically consistent, generalizable, and accurate forecasting, even in a small data regime.
Correlative light electron microscopy using small gold nanoparticles as single probes
Creators: name: Pope, Iestyn
name: Tanner, Hugh
name: Masia, Francesco
name: Payne, Lukas
name: Arkill, Kenton Paul
name: Mantell, Judith
name: Langbein, Wolfgang
name: Borri, Paola
name: Verkade, Paul
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optics (physics.optics)
subject: Instrumentation and Detectors (physics.ins-det)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: Correlative light electron microscopy (CLEM) requires the availability of robust probes which are visible both in light and electron microscopy. Here we demonstrate a CLEM approach using small gold nanoparticles as a single probe. Individual gold nanoparticles bound to the epidermal growth factor protein were located with nanometric precision background-free in human cancer cells by light microscopy using resonant four-wave-mixing (FWM), and were correlatively mapped with high accuracy to the corresponding transmission electron microscopy images. We used nanoparticles of 10 nm and 5 nm radius, and show a correlation accuracy below 60 nm over an area larger than 10 um size, without the need for additional fiducial markers. Correlation accuracy was improved to below 40 nm by reducing systematic errors, while the localisation precision is below 10 nm. Polarisation-resolved FWM correlates with nanoparticle shapes, promising for multiplexing by shape recognition in future applications. Owing to the photostability of gold nanoparticles and the applicability of FWM microscopy to living cells, FWM-CLEM opens up a powerful alternative to fluorescence-based methods.
Network-Aware Job Placement in Datacenter Environments
Creators: name: Li, Yang
Publisher: name: Graduate Studies
Year: 2014
Subjects: subject: Education--Sciences
subject: Network Guarantee
subject: Datacenter
subject: Job Placement

description: The topic of network-aware job placement in datacenter environments has attracted lots of research attention recently. Since network bandwidth is sometimes a scarce resource in multi-tenant datacenters, several virtualization abstractions have been proposed to avoid oversubscription of datacenter networks, and provide predictable QoS performance for users. In my work, a simulation environment is built to study job placement and scheduling strategies in datacenter networks. In particular, I model the Temporally-Interleaved Virtual Cluster (TIVC) algorithm, and study its sensitivity to different job characteristics and how the configured network capacity affects the system performance. The simulation results indicate that careful management of a delay queue for pending jobs can help achieve high system utilization. Different workload models have a pronounced influence on the system performance. In addition, an anomaly is found under certain datacenter network configurations, wherein increasing the datacenter resources produces "worse" system performance. Further investigation provides an explanation for this counter-intuitive result.
Additional file 1 of Global health classroom: mixed methods evaluation of an interinstitutional model for reciprocal global health learning among Samoan and New Zealand medical students
Creators: name: Bothara, Roshit K.
name: Tafuna’i, Malama
name: Wilkinson, Tim J.
name: Desrosiers, Jen
name: Jack, Susan
name: Pattemore, Philip K.
name: Walls, Tony
name: Sopoaga, Faafetai
name: Murdoch, David R.
name: Miller, Andrew P.
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy

description: Additional file 1. Global Health Classroom Student Guide.
Field Evaluation of an Underfloor Air Distribution System in an Office Building
Creators: name: Baker, Tareq
Publisher: name: Environmental Design
Year: 2014
Subjects: subject: Architecture
subject: FOS: Civil engineering
subject: Engineering--Mechanical
subject: UFAD
subject: Thermal Stratification
subject: Ventilation Effectiveness
subject: Thermal Comfort

description: This thesis presents a field assessment of thermal stratification, ventilation effectiveness and thermal comfort in an office with an underfloor air distribution system. In an earlier study, thermal stratification, ventilation effectiveness and thermal comfort were evaluated with this arrangement, but diffusers were later relocated away from occupants and furniture. The opportunity was taken to investigate and compare the performance of the system before and after relocating the diffusers. Moreover, the underfloor air distribution system investigated in the study building had a unique configuration of ducted horizontal discharge floor diffusers that has been rarely documented in the literature. Even though underfloor air distribution systems with horizontal discharge diffusers are expected to improve ventilation effectiveness compared to those with swirl diffusers and mixing ventilation systems, this study found no difference. The underfloor air distribution system investigated in this research did however create stronger stratification than has been reported in literature for underfloor air distribution systems with swirl diffusers. Thermal comfort conditions in the study building were found to comply with ASHRAE standard 55. This suggested that the underfloor air distribution system with horizontal discharge diffusers could maintain a thermally comfortable environment while increasing the potential for energy savings compared to underfloor air distribution systems with swirl discharge diffusers, due to stronger stratification profiles, and without compromising the ventilation effectiveness seen with other systems.
Immersed boundary parametrizations for full waveform inversion
Creators: name: Bürchner, Tim
name: Kopp, Philipp
name: Kollmannsberger, Stefan
name: Rank, Ernst
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computational Engineering, Finance, and Science (cs.CE)
subject: FOS: Computer and information sciences

description: Full Waveform Inversion (FWI) is a successful and well-established inverse method for reconstructing material models from measured wave signals. In the field of seismic exploration, FWI has proven particularly successful in the reconstruction of smoothly varying material deviations. In contrast, non-destructive testing (NDT) often requires the detection and specification of sharp defects in a specimen. If the contrast between materials is low, FWI can be successfully applied to these problems as well. However, so far the method is not fully suitable to image defects such as voids, which are characterized by a high contrast in the material parameters. In this paper, we introduce a dimensionless scaling function $γ$ to model voids in the forward and inverse scalar wave equation problem. Depending on which material parameters this function $γ$ scales, different modeling approaches are presented, leading to three formulations of mono-parameter FWI and one formulation of two-parameter FWI. The resulting problems are solved by first-order optimization, where the gradient is computed by an ajdoint state method. The corresponding Fréchet kernels are derived for each approach and the associated minimization is performed using an L-BFGS algorithm. A comparison between the different approaches shows that scaling the density with $γ$ is most promising for parameterizing voids in the forward and inverse problem. Finally, in order to consider arbitrary complex geometries known a priori, this approach is combined with an immersed boundary method, the finite cell method (FCM).
description: 23 pages, 21 figures
The Millimeter Astronomy Legacy Team 90 GHz (MALT90) Pilot Survey
Creators: name: Foster, Jonathan B.
name: Jackson, James M.
name: Barris, Elizabeth
name: Brooks, Kate
name: Cunningham, Maria
name: Finn, Susanna C.
name: Fuller, Gary A.
name: Longmore, Steve N.
name: Mascoop, Joshua L.
name: Peretto, Nicholas
name: Rathborne, Jill
name: Sanhueza, Patricio
name: Schuller, Frédéric
name: Wyrowski, Friedrich
Publisher: name: arXiv
Year: 2011
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We describe a pilot survey conducted with the Mopra 22-m radio telescope in preparation for the Millimeter Astronomy Legacy Team Survey at 90 GHz (MALT90). We identified 182 candidate dense molecular clumps using six different selection criteria and mapped each source simultaneously in 16 different lines near 90 GHz. We present a summary of the data and describe how the results of the pilot survey shaped the design of the larger MALT90 survey. We motivate our selection of target sources for the main survey based on the pilot detection rates and demonstrate the value of mapping in multiple lines simultaneously at high spectral resolution.
description: Accepted to ApJS. 23 pages and 16 figures. Full resolution version with an appendix showing all the data (12.1 MB) is available at http://malt90.bu.edu/publications/Foster_2011_Malt90Pilot.pdf
Banding, Excitability and Chaos in Active Nematic Suspensions
Creators: name: Giomi, L.
name: Mahadevan, L.
name: Chakraborty, B.
name: Hagan, M. F.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Motivated by the observation of highly unstable flowing states in suspensions of microtubules and kinesin, we analyze a model of mutually-propelled filaments suspended in a solvent. The system undergoes a mean-field isotropic-nematic transition for large enough filament concentrations when the nematic order parameter is allowed to vary in space and time. We analyze the model in two contexts: a quasi-one-dimensional channel with no-slip walls and a two-dimensional box with periodic boundaries. Using stability analysis and numerical calculations we show that the interplay between non-uniform nematic order, activity, and flow results in a variety of complex scenarios that include spontaneous banded laminar flow, relaxation oscillations, and chaos.
description: 15 pages, 15 figures
The Salmon Project: Improving RNA-seq Quantification & Building an Inclusive Community
Creators: name: Kingsford
name: Patro
name: Marçais
Publisher: name: Zenodo
Year: 2020
Subjects: gene expression, open source, single-cell, RNA-seq

description: A description of the Salmon Project (including the salmon, alevin, and alevin-fry tools) and its ecosystem for gene expression quantification from bulk and single-cell RNA-seq, along with a discussion of the goals for the current CZI grant.
Augmenting Interpretable Models with LLMs during Training
Creators: name: Singh, Chandan
name: Askari, Armin
name: Caruana, Rich
name: Gao, Jianfeng
Publisher: name: arXiv
Year: 2022
Subjects: subject: Artificial Intelligence (cs.AI)
subject: Computation and Language (cs.CL)
subject: Machine Learning (cs.LG)
subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: Recent large language models (LLMs) have demonstrated remarkable prediction performance for a growing array of tasks. However, their proliferation into high-stakes domains (e.g. medicine) and compute-limited settings has created a burgeoning need for interpretability and efficiency. We address this need by proposing Augmented Interpretable Models (Aug-imodels), a framework for leveraging the knowledge learned by LLMs to build extremely efficient and interpretable models. Aug-imodels use LLMs during fitting but not during inference, allowing complete transparency and often a speed/memory improvement of greater than 1,000x for inference compared to LLMs. We explore two instantiations of Aug-imodels in natural-language processing: (i) Aug-GAM, which augments a generalized additive model with decoupled embeddings from an LLM and (ii) Aug-Tree, which augments a decision tree with LLM feature expansions. Across a variety of text-classification datasets, both outperform their non-augmented counterparts. Aug-GAM can even outperform much larger models (e.g. a 6-billion parameter GPT-J model), despite having 10,000x fewer parameters and being fully transparent. We further explore Aug-imodels in a natural-language fMRI study, where they generate interesting interpretations from scientific data. All code for using Aug-imodels and reproducing results is made available on Github.
Gene Expression Study Of Mycobacterium avium subspecies paratuberculosis Infected Cows – “A road to identify transcripts that could serve as biomarkers for early diagnosis of Johne’s disease”
Creators: name: David, Joel
Publisher: name: Graduate Studies
Year: 2014
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Biology--Molecular
subject: Johne’s disease
subject: Mycobacterium avium subspecies paratuberculosis
subject: Transcriptomic
subject: Biomarkers

description: Current diagnostic tools lack sensitivity to detect JD early after infection. Hence, this study aimed to find biomarkers for early diagnosis of JD. An infection trial was set up with a high dose (n=5) and low dose (n=5) oral challenge with Mycobacterium avium subsp. paratuberculosis at 2 weeks of age and 5 non-infected control animals. Whole blood was collected at a 3-month interval (3, 6, 9, 12 and 15 months) for gene expression analysis using Affymetrix® GeneChip® Bovine Genome Array on samples obtained at 3, 6 and 9 months after infection. Microarray findings were confirmed using qPCR and longitudinal assays profiling transcripts over 15-month period was carried out. This study found differential gene expression at each sampled time point and found transcripts for potential biomarker use. CD46 was upregulated and BOLA and BNBD9-like genes were downregulated over the entire 15-months. Overall immune response was inhibited in MAP-challenged animals.
Additional file 2 of Global health classroom: mixed methods evaluation of an interinstitutional model for reciprocal global health learning among Samoan and New Zealand medical students
Creators: name: Bothara, Roshit K.
name: Tafuna’i, Malama
name: Wilkinson, Tim J.
name: Desrosiers, Jen
name: Jack, Susan
name: Pattemore, Philip K.
name: Walls, Tony
name: Sopoaga, Faafetai
name: Murdoch, David R.
name: Miller, Andrew P.
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy

description: Additional file 2. Summary of the Student Presentation Template.
Ensemble Machine Learning Model Trained on a New Synthesized Dataset Generalizes Well for Stress Prediction Using Wearable Devices
Creators: name: Vos, Gideon
name: Trinh, Kelly
name: Sarnyai, Zoltan
name: Azghadi, Mostafa Rahimi
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: Signal Processing (eess.SP)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: I.2.0

description: Introduction. We investigate the generalization ability of models built on datasets containing a small number of subjects, recorded in single study protocols. Next, we propose and evaluate methods combining these datasets into a single, large dataset. Finally, we propose and evaluate the use of ensemble techniques by combining gradient boosting with an artificial neural network to measure predictive power on new, unseen data. Methods. Sensor biomarker data from six public datasets were utilized in this study. To test model generalization, we developed a gradient boosting model trained on one dataset (SWELL), and tested its predictive power on two datasets previously used in other studies (WESAD, NEURO). Next, we merged four small datasets, i.e. (SWELL, NEURO, WESAD, UBFC-Phys), to provide a combined total of 99 subjects,. In addition, we utilized random sampling combined with another dataset (EXAM) to build a larger training dataset consisting of 200 synthesized subjects,. Finally, we developed an ensemble model that combines our gradient boosting model with an artificial neural network, and tested it on two additional, unseen publicly available stress datasets (WESAD and Toadstool). Results. Our method delivers a robust stress measurement system capable of achieving 85% predictive accuracy on new, unseen validation data, achieving a 25% performance improvement over single models trained on small datasets. Conclusion. Models trained on small, single study protocol datasets do not generalize well for use on new, unseen data and lack statistical power. Ma-chine learning models trained on a dataset containing a larger number of varied study subjects capture physiological variance better, resulting in more robust stress detection.
description: 37 pages, 11 figures
Comments on Holographic Entanglement Entropy and RG Flows
Creators: name: Myers, Robert C.
name: Singh, Ajay
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Using holographic entanglement entropy for strip geometry, we construct a candidate for a c-function in arbitrary dimensions. For holographic theories dual to Einstein gravity, this c-function is shown to decrease monotonically along RG flows. A sufficient condition required for this monotonic flow is that the stress tensor of the matter fields driving the holographic RG flow must satisfy the null energy condition over the holographic surface used to calculate the entanglement entropy. In the case where the bulk theory is described by Gauss-Bonnet gravity, the latter condition alone is not sufficient to establish the monotonic flow of the c-function. We also observe that for certain holographic RG flows, the entanglement entropy undergoes a 'phase transition' as the size of the system grows and as a result, evolution of the c-function may exhibit a discontinuous drop.
description: References added
PsychoPy ecosystem for open source experiments in Psychology
Creators: name: Peirce, J W
Publisher: name: Zenodo
Year: 2020
Subjects: PsychoPy
Python
Open source
psychology
experiments
online studies

description: Summary slides from our demo at the Chan Zuckerberg Initiative second meeting for the Essential Open Source Software initiative. The actual talk was mostly a demonstration of the features of PsychoPy but there were a few slides with summary information.
Temporal and spectral evolution in X- and gamma-rays of magnetar 1E 1547.0-5408 since its October 2008 outburst: the discovery of a transient hard pulsed component after its January 2009 outburst
Creators: name: Kuiper, L.
name: Hermsen, W.
name: Hartog, P. R. den
name: Urama, J. O.
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The magnetar 1E 1547.0-5408 exhibited outbursts in October 2008 and January 2009. In this paper we present in great detail the evolution of the temporal and spectral characteristics of the persistent total and pulsed emission of 1E 1547.0-5408 between ~1 and 300 keV starting in October 3, 2008, and ending in January 2011. We analyzed data collected with the Rossi X-ray Timing Explorer, the International Gamma-Ray Astrophysics Laboratory and the Swift satellite.
description: 33 pages, 14 figures of which 3 in color, accepted by ApJ on Jan 26, 2012
Additional file 3 of Global health classroom: mixed methods evaluation of an interinstitutional model for reciprocal global health learning among Samoan and New Zealand medical students
Creators: name: Bothara, Roshit K.
name: Tafuna’i, Malama
name: Wilkinson, Tim J.
name: Desrosiers, Jen
name: Jack, Susan
name: Pattemore, Philip K.
name: Walls, Tony
name: Sopoaga, Faafetai
name: Murdoch, David R.
name: Miller, Andrew P.
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy

description: Additional file 3. Summary of the GHCR Case Presentation Topics.