cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Fabrication, characterization, and simulation of glass devices with AlN-thin-film-transducers for excitation of ultrasound resonances
Creators: name: Steckel, André G.
name: Bruus, Henrik
name: Muralt, Paul
name: Matloub, Ramin
Publisher: name: arXiv
Year: 2020
Subjects: subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: We present fabrication of 570-um-thick, millimeter-sized soda-lime-silicate float glass blocks with a 1-um-thick AlN-thin-film piezoelectric transducer sandwiched between thin metallic electrodes and deposited on the top surface. The electro-mechanical properties are characterized by electrical impedance measurements in the frequency range from 0.1 to 10 MHz with a peak-to-peak voltage of 0.5 V applied to the electrodes. We measured the electrical impedance spectra of 35 devices, all of width 2 mm, but with 9 different lengths ranging from 2 to 6 mm and with 2-7 copies of each individual geometry. Each impedance spectrum exhibits many resonance peaks, of which we carefully measured the 5 most prominent ones in each spectrum. We compare the resulting 173 experimental resonance frequencies with the simulation result of a finite-element-method model that we have developed. When using material parameters from the manufacturer, we obtain an average relative deviation of the 173 simulated resonance frequencies from the experimental ones of (-4.2 +/-0.04)%. When optimizing the values of the Young's modulus and the Poisson ratio of the float glass in the simulation, this relative deviation decreased to (-0.03 +/- 0.04)%. Our results suggest a method for an accurate in-situ determination of the acoustic parameters at ultrasound frequencies of any elastic solid onto which a thin-film transducer can be attached
description: 9 pages, 5 pdf figures, RevTex
Über psychoanalytische Editionstechnik oder: Wie Geschichte in ein Buch gerät
Creators: name: Métraux, Alexandre
Publisher: name: Österreichische Zeitschrift für Geschichtswissenschaften
Year: 2003

description: Österreichische Zeitschrift für Geschichtswissenschaften, Bd. 14 Nr. 2 (2003): Phsychoanalytisches Wissen
Cosmic variance of weak lensing surveys in the non-Gaussian regime
Creators: name: Semboloni, Elisabetta
name: van Waerbeke, Ludovic
name: Heymans, Catherine
name: Hamana, Takashi
name: Colombi, Stephane
name: White, Martin
name: Mellier, Yannick
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The results from weak gravitational lensing analyses are subject to a cosmic variance error term that has previously been estimated assuming Gaussian statistics. In this letter we address the issue of estimating cosmic variance errors for weak lensing surveys in the non-Gaussian regime. Using standard cold dark matter model ray-tracing simulations characterized by Omega_m=0.3, Omega_Lambda=0.7, h=0.7, sigma_8=1.0 for different survey redshifts z_s, we determine the variance of the two-point shear correlation function measured across 64 independent lines of sight. We compare the measured variance to the variance expected from a random Gaussian field and derive a redshift-dependent non-Gaussian calibration relation. We find that the ratio can be as high as ~30 for a survey with source redshift z_s ~ 0.5 and ~10 for z_s ~ 1. The transition scale theta_c above which the ratio is consistent with unity, is found to be theta_c ~ 20 arcmin for z_s ~ 0.5 and theta_c ~ 10 arcmin for z_s ~ 1. We provide fitting formula to our results permitting the estimation of non-Gaussian cosmic variance errors for any weak lensing analysis, and discuss the impact on current and future surveys. A more extensive set of simulations will however be required to investigate the dependence of our results on cosmology, specifically on the amplitude of clustering.
description: 6 pages, 7 figures. MNRAS Accepted version
Reverse Engineering of RBAC Policy using Access Logs
Creators: name: Datar, Kishorkumar Subhash
Publisher: name: Maryland Shared Open Access Repository
Year: 2009
Subjects: Access Logs
RBAC Policy
Reverse Engineering

description: Role Based Access Control (RBAC) is a flexible and powerful approach to access control which is widely used. We present approaches to finding the functional role hierarchy using access logs. We discuss a method to reconstruct the functional role hierarchy with knowledge of all access rights of all users. New methods of test data generation are introduced. We then present heuristics that work with partial logs to predict an approximate role hierarchy. A method to efficiently use background knowledge is also discussed. We show with empirical evidence that to reconstruct even half the hierarchy correctly with the heuristics; we need significant amount of access logs. We compare the two heuristics in terms of false positives, false negatives and number of correct predictions. The two heuristics are compared w. r. t. parent-child relations as well as ancestor-descendent relations.
Enhancement of ferromagnetism by nickel doping in the 112 cobaltite EuBaCo2O5.50
Creators: name: Raveau, B.
name: Simon, Ch.
name: Caignaert, V.
name: Pralong, V.
name: Lefevre, F. X.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The study of the ordered oxygen deficient perovskite EuBaCo2-xNixO5.50 shows that the doping of cobalt sites by nickel induces a strong ferromagnetic component at low temperature in the antiferromagnetic matrix of EuBaCo2O5.50. This system exhibits indeed phase separation, i.e. consists of ferromagnetic domains embedded in the antiferromagnetic matrix of EuBaCo2O5.50. Besides, a magnetic transition is observed for the first time at 40K in the undoped and nickel doped phases, which can be attributed to the ferromagnetic ordering of the Eu3+ moments below this temperature. Moreover sharp ultra magnetization multisteps are observed below 5K, characteristic of motion of domain walls in a strong pinning system and very different from any metamagnetic transition.
Influence of Functional Groups on Charge Transport in Molecular Junctions
Creators: name: Mowbray, D. J.
name: Jones, G.
name: Thygesen, K. S.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Using density functional theory (DFT), we analyze the influence of five classes of functional groups, as exemplified by NO2, OCH3, CH3, CCl3, and I, on the transport properties of a 1,4-benzenedithiolate (BDT) and 1,4-benzenediamine (BDA) molecular junction with gold electrodes. Our analysis demonstrates how ideas from functional group chemistry may be used to engineer a molecule's transport properties, as was shown experimentally and using a semiempirical model for BDA [Nano Lett. 7, 502 (2007)]. In particular, we show that the qualitative change in conductance due to a given functional group can be predicted from its known electronic effect (whether it is pi/sigma donating/withdrawing). However, the influence of functional groups on a molecule's conductance is very weak, as was also found in the BDA experiments. The calculated DFT conductances for the BDA species are five times larger than the experimental values, but good agreement is obtained after correcting for self-interaction and image charge effects.
description: 6 pages, 3 figures, J. Chem. Phys (in press)
SWISS-MODEL: homology modelling of protein structures and complexes
Creators: name: Tauriello, Gerardo
name: The Developers Of SWISS-MODEL, ProMod3
name: Schwede, Torsten
Publisher: name: F1000 Research Limited
Year: 2019

description: The SWISS-MODEL server (swissmodel.expasy.org) is a state-of-the-art computational protein structure modelling workbench with a user-friendly web interface. By providing high-quality three-dimensional protein structure models, SWISS-MODEL enables structure-guided life science research applications for proteins where experimental structures are not available. In total, it was referenced in 19'642 scientific publications. In the past 12 months, the server generated approximately 1.7 million protein structure models, i.e. 3.2 models per minute have been requested by users through the interactive modelling web interface. The SWISS-MODEL Repository provides weekly updated models for the complete proteomes of 13 selected model organisms.

The fully automated SWISS-MODEL workflow predicts the three-dimensional structures of proteins and complexes in their most likely quaternary structure starting from the respective amino acid sequences. In this talk, we present the workflow to model homo- and hetero-oligomeric protein complexes, the open source modelling engine ProMod3, the model quality estimation method QMEANDisCo, and ModelArchive, a deposition system for persistent archiving of theoretical protein structure models.
Design considerations for simplified sewer network in informal settlements
Creators: name: Reysset, Marie
name: , Bill
Publisher: name: Gates Open Research
Year: 2021

description: This publication is the result of the technical assistance provided by UPM Umwelt-Projekt-Management GmbH (UPM) and its partners, the Centre for Sustainable and Ecological Sanitation (CSES) of the University of Science & Technology Beijing (USTB), and the Lebanese Appropriate Technology Association (LATA) to WASH and Emergency Grantees of the Bill & Melinda Gates Foundation in Lebanon and in Bangladesh.
 The present manual “Simplified Sewer Networks for Informal Tented Settlements” has been elaborated after the implementation of on-site training on “Simplified Sewer Networks” which
 was organized in June 2019 for UNICEF Lebanon and local WASH partners working with Syrian Refugees living in informal settlements and the local communities in the Bekaa Valley in Lebanon. The content was prepared in order to be presented to the WASH community in Cox’s Bazar, Bangladesh but related training had to be canceled due to the COVID-pandemic.
 This training manual is part of a "Methodologies & Application from Documented Experience" series.
The (a,b,s,t)-diameter of graphs: a particular case of conditional diameter
Creators: name: Rodriguez, J. A.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05C50; 05C12; 15A18

description: The conditional diameter of a connected graph $Γ=(V,E)$ is defined as follows: given a property ${\cal P}$ of a pair $(Γ_1, Γ_2)$ of subgraphs of $Γ$, the so-called \emph{conditional diameter} or ${\cal P}$-{\em diameter} measures the maximum distance among subgraphs satisfying ${\cal P}$. That is, \[ D_{\cal P}(Γ):=\max_{Γ_1, Γ_2\subset Γ} \{\partial(Γ_1, Γ_2): Γ_1, Γ_2 \quad {\rm satisfy }\quad {\cal P}\}. \] In this paper we consider the conditional diameter in which ${\cal P}$ requires that $δ(u)\ge α$ for all $ u\in V(Γ_1)$, $δ(v)\ge β$ for all $v\in V(Γ_2)$, $| V(Γ_1)| \ge s$ and $| V(Γ_2)| \ge t$ for some integers $1\le s,t\le |V|$ and $δ\le α, β\le Δ$, where $δ(x)$ denotes the degree of a vertex $x$ of $Γ$, $δ$ denotes the minimum degree and $Δ$ the maximum degree of $Γ$. The conditional diameter obtained is called $(α,β, s,t)$-\emph{diameter}. We obtain upper bounds on the $(α,β, s,t)$-diameter by using the $k$-alternating polynomials on the mesh of eigenvalues of an associated weighted graph. The method provides also bounds for other parameters such as vertex separators.
Generative Design Platform as Social Community
Creators: name: Votintseva, A.
name: Kramer, M.
name: Johnson, R.
Publisher: name: Zenodo
Year: 2021

description: This deliverable reports about activities performed in the task T5.2, Generative Design Platform, during the period of M7-M18. The document gives an overview of the technologies of Generative Design, specifies the overall architecture of the platform under development, and describes the current state of the implementation of all components constituting the Generative Design Platform.
Intraband Optical Spectral Weight in the presence of a van Hove singularity: application to Bi$_2$Sr$_2$CaCu$_2$O$_{8+δ}$
Creators: name: Marsiglio, F.
name: Carbone, F.
name: Kuzmenko, A.
name: van der Marel, D.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: The Kubo single band sum rule is used to determine the optical spectral weight of a tight binding band with further than nearest neighbour hopping. We find for a wide range of parameters and doping concentrations that the change due to superconductivity at low temperature can be either negative or positive. In contrast, the kinetic energy change is always negative. We use an ARPES determined tight binding parametrization of Bi$_2$Sr$_2$CaCu$_2$O$_{8+δ}$ to investigate whether this can account for recent observations of a positive change in the spectral weight due to the onset of superconductivity. With this band structure we find that in the relevant doping regime a straightforward BCS calculation of the optical spectral weight cannot account for the experimental observations.
description: 10 page 9 figures
GeneraLight: Improving Environment Generalization of Traffic Signal Control via Meta Reinforcement Learning
Creators: name: Liu, Chang
name: Zhang, Huichu
name: Zhang, Weinan
name: Zheng, Guanjie
name: Yu, Yong
Publisher: name: arXiv
Year: 2020
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: The heavy traffic congestion problem has always been a concern for modern cities. To alleviate traffic congestion, researchers use reinforcement learning (RL) to develop better traffic signal control (TSC) algorithms in recent years. However, most RL models are trained and tested in the same traffic flow environment, which results in a serious overfitting problem. Since the traffic flow environment in the real world keeps varying, these models can hardly be applied due to the lack of generalization ability. Besides, the limited number of accessible traffic flow data brings extra difficulty in testing the generalization ability of the models. In this paper, we design a novel traffic flow generator based on Wasserstein generative adversarial network to generate sufficient diverse and quality traffic flows and use them to build proper training and testing environments. Then we propose a meta-RL TSC framework GeneraLight to improve the generalization ability of TSC models. GeneraLight boosts the generalization performance by combining the idea of flow clustering and model-agnostic meta-learning. We conduct extensive experiments on multiple real-world datasets to show the superior performance of GeneraLight on generalizing to different traffic flows.
description: Proceedings of the 29th ACM International on Conference on Information and Knowledge Management (CIKM). ACM, 2020
Election observation and its role in democracy building : a case study of the Canadian observation mission to the South African election, April 1994
Creators: name: Nelems, Martha
Publisher: name: University of British Columbia
Year: 2009

description: The post-cold war era of the 1980s and 1990s has witnessed a rapid increase in the number of democratically elected regimes in the world. The steady growth of democratically elected regimes in the past five years has brought into focus the role of international observers in legitimizing the outcomes of these elections. This thesis explores the relationship between the practice of international election observation and the growth of democratically elected regimes. In order to achieve this end, this thesis begins with a theoretical discussion of international election observation as understood by international lawyers Thomas Franck and Gregory Fox. After establishing an analytical framework, this thesis proceeds with a case study of the Canadian government's approach to international election observation, as evidenced by the work of Canada's official observation mission to the South African election in April 1994 (CANOMSA). This includes a discussion of Canada's foreign policy framework for this mission. The case study of CANOMSA suggests there is what Franck refers to as 'an emerging right to democratic governance' which is validated by the international community. The Canadian government used its' observation mission to South Africa to support that country's democratic transition; in doing so, it believed that democratic values would be better served in South Africa by a regime that was democratically elected. Implicitly, CANOMSA also served to build the norm that 'only democracy validates governance'. However, the experiences of CANOMSA suggest the practice of election observation is not yet standardized and much can be done to improve its effectiveness. In order to further 'the global entitlement to democracy', Canada should be explicit in its support for this norm. Despite the risks involved in doing so, including a hardening of the division between liberal and non-liberal states, this is a laudable foreign policy goal which Canada should actively pursue through democratic development initiatives such as international election observation. To this end, it is important that one view the work of international election observation on the middle of a continuum which begins with activities such as peacekeeping and ends with what is increasingly referred to as 'peacebuilding'. The reason why Canada engages in all of these activities is the same; the belief that the international community has the moral authority to act because it has a profound stake in building an international order that promotes human security and furthers human dignity.
SMOTE: Scalable Mobile Services Testing and Evaluation Infrastructure
Creators: name: Nandakumar, Vikrant
Publisher: name: Maryland Shared Open Access Repository
Year: 2010

description: In today's world, people's reliance on smart phones and mobile devices has been growing at a phenomenal rate. In addition, it is a fair prediction that the future mobile devices are going to be more sophisticated with constantly increasing data and bandwidth demands. Even with the proliferation of 3G/4G wireless networks, these demands need to be handled more efficiently. It is important for a mobile service provider to maintain a good Quality of Experience (QoE) and a superior Quality of Service (QoS) to their users at all times. One way to achieve a superior QoS, is for the network to have usage information from each device and to take pro-active decisions that match the demands from the users. This research aims at identifying and monitoring the key performance indicators affecting QoE and QoS for the mobile network. For the core mobile network, a better understanding of its user's usage pattern is the key to predict perceived future activity with a greater accuracy. This thesis presents a Scalable Mobile Services Testing and Evaluation Infrastructure (SMOTE) which allows developers and network providers to perform experiments and collect performance data. A novel system architecture is proposed, designed, implemented and evaluated as a part of this research. SMOTE could discover a cloud of mobile devices, control them remotely, simulate user actions and collect results from the simulation runs. Experiments are performed using the system to test its scalability, correctness, consistency and the results are documented.
Gluon mass generation and infrared Abelian dominance in Yang-Mills theory
Creators: name: Shibata, A.
name: Ito, S.
name: Kato, S.
name: Kondo, K. -I.
name: Murakami, T.
name: Shinohara, T.
Publisher: name: arXiv
Year: 2006
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: The dual superconductivity is believed to be a promising mechanism for quark confinement. Indeed, what this picture is true has been confirmed in the maximal Abelian (MA) gauge. However, it is not yet confirmed in any other gauge and the MA gauge explicitly breaks color symmetry. To remedy this defect, we propose to use our compact formulation of a non-linear change of variables on a lattice. This formulation has succeeded to extract the magnetic monopole with integer-valued magnetic charge in the gauge-invariant way. In this talk, we present measurements of various correlation functions for the operators constructed from the CFN variables in SU(2) Yang-Mills theory. Some of our results reproduce previous results obtained in MA gauge, e.g., DeGrant-Toussaint monopole, infrared Abelian dominance and off-diagonal gluon mass generation. These studies preserve color symmetry, in sharp contrast to the conventional MA gauge. We argue the gauge fixing independence of these results and the implications to quark confinement
description: 7 pages, 4 figures, talk presented at Lattice 2006 (Confinement and Topology)
Anaerobic baffled reactor (ABR) design considerations for faecal sludge
Creators: name: Reysset, Marie
name: , Bill
Publisher: name: Gates Open Research
Year: 2021

description: This publication is the result of the technical assistance provided by UPM Umwelt-Projekt- Management GmbH (UPM) and its partners, the Centre for Sustainable and Ecological Sanitation (CSES) of the University of Science & Technology Beijing (USTB), and the Bureau of Socioeconomic Research and Training (BSERT) of the Bangladesh University of Agriculture (BAU) to the United Nations High Commissioner for Refugees (UNHCR), the Department of Public Health Engineering (DPHE) and the local WASH sector in Cox’s Bazar, Bangladesh, in cooperation with the Bill & Melinda Gates Foundation.
 The goal of this technical assistance assignment was to provide support to the emergency WASH sector and local administration, regarding sanitation and faecal sludge management, with a focus on value—recovery in emergency settings, in order to sustainably improve the living conditions of displaced populations a reasonable ability to plan, design and monitor a project as an output d their hosting communities.

 The present manual “Anaerobic Baffled Reactor (ABR) Design Considerations for Faecal Sludge” was elaborated in the context of a series of training workshops organised by UPM and its partners in Cox’s Bazar based on a Training Needs Assessment implemented among the local WASH community.
 The content of this manual was presented as part of the Training “Anaerobic Baffled Reactor and Anaerobic Filters” organized in Cox’s Bazar in September 2019. The objectives of the training were to support trainees to gain reasonable ability to plan, design and monitor related project.

 This training manual is part of a "Methodologies & Application from Documented Experience" series.
Situation Aware Intrusion Detection Model
Creators: name: More, Sumit Surendra
Publisher: name: Maryland Shared Open Access Repository
Year: 2012
Subjects: Information Extraction
Intrusion Detection
Ontology
Semantic Web

description: Today, information technology and cyber-services have become the foundation pillars of every business and manufacturing industry. The importance of cyber-services and their extensive use by every section of the society has paved the way for cyber-crimes like espionage, politically motivated attacks, credit card frauds, unauthorized infrastructure access, denial-of-service attacks, and stealing of valuable data. Intrusion Detection Systems (IDS) are applications which monitor cyber-systems to identify any malicious activities, generate an alert when such an activity is detected, and redress the problem if possible. Most of the intrusion detection/prevention systems available today are based on rule-based or signature based activity monitoring which detect threats and vulnerabilities by cross-referencing the threat or vulnerability signatures in their databases. These Intrusion Detection Systems (IDS) face limitations in detecting newly published attacks or variants of existing attacks. They are also point solutions that focus on a single system/component. We argue that integrating information coming from multiple data channels  can lead to a better threat detection model. Data source of web including blogs, chat-rooms, forums etc. can be a good source of information for upcoming attacks or attacks whose signatures have not yet been tracked for the intrusion detection systems to catch. Semantic integration of the data sources from web, information from IDS/IPS modules at the network and host level, and the expert knowledge can be used to create a `Situation Aware Intrusion Detection Model' which can lead to better intrusion detection and prevention results. In this work, we present such a system which makes use of semantic web technologies to find relationships between the information gathered from the web, sensor data coming from IDS/IPS modules and network activity monitors, and reasons over this data and expert provided rules in-order to detect possibility of a cyber attack.
Ages and metallicities of circumnuclear star formation regions from Gemini IFU observations
Creators: name: Dors, O. L.
name: Storchi-Bergmann, T.
name: Riffel, Rogemar A.
name: Schimdt, A. A
Publisher: name: arXiv
Year: 2008
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Aims: We derive the age and metallicity of circumnuclear star formation regions (CNSFRs) located in the spiral galaxies NGC6951 and NGC1097, and investigate the cause of the very low equivalent widths of emission lines found for these regions. Methods: We used optical two-dimensional spectroscopic data obtained with Gemini GMOS-IFUs and a grid of photoionization models to derive the the metallicities and ages of CNSFRs. Results: We find star formation rates in the range 0.002-0.14 Msun/yr and oxygen abundance of 12+log(O/H)~8.8 dex, similar to those of most metal-rich nebulae located in the inner region of galactic disks. Conclusions: We conclude that the very low emission-line equivalent widths observed in CNSFRs are caused by the ``contamination'' of the continuum by (1) contribution of the underlying bulge continuum combined with (2) contribution from previous episodes of star formation at the CNSFRs.
description: Accepted for publication in Astronomy and Astrophysics
Reconstruction of the Escherichia coli LEE pathogenicity island network
Creators: name: Luna, Sara Berenice Martínez
name: Yalbi Itzel Balderas Martínez
name: Romero, Laura Gomez
name: García, José Luis Puente
name: Vides, Julio Collado
name: Castro, Socorro Gama
Publisher: name: F1000 Research Limited
Year: 2021

description: Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic Escherichia coli (EHEC) are pathogens of humans containing the locus of enterocyte effacement (LEE) pathogenic island which contains the virulence genes that confer the ability to produce the Attaching and Effacing (A/E) lesion in humans causing acute diarrhea. Albeit it is of medical importance, there are few efforts to build the regulatory network of the genes related to this island. At this moment, it has not been integrated all the information due to the complexity of the global and local regulation, and because the manual extraction of the data accumulated in the literature can take a lot of time and effort. Semi-automatic biocuration systems are tools that help to obtain, in a reasonable time, the complete regulatory interactions. Once all the available information is recovered, it is possible to detect mechanisms that have not been described together, such as feedback loops, and to generate new predictions. Here, we show a semi-automatic curation workflow to obtain the LEE pathogenicity island regulatory network from scientific articles, through the extraction of regulatory interactions and their properties. This regulatory network contains the genes belonging to the LEE island and genes non-encoded in this island but that they are regulated by LEE regulators in EPEC and EHEC strains. Our network is composed of 239 regulatory interactions obtained from 250 papers, which include 43 transcription factors and 84 target genes. The interactions from this network are classified as either direct or indirect relationships and as interactions with weak or strong evidence based on the experimental methods used to obtain them. The network integration allowed us to find new feedback loops that have not been previously integrated and we conclude that our network contains 85 regulatory interactions of which the representative and dual nodes are Ler (LEE1) and GrlR-A (LEE7) the master regulators of the pathogenicity island.
A molecular taxonomy of tumors independent of tissue-of-origin
Creators: name: Nguyen, Peter Tuan
name: Coetzee, Simon G
name: Lakeland, Daniel L
name: Hazelett, Dennis J
Publisher: name: F1000 Research Limited
Year: 2021

description: Cancer is an organism-level disease, impacting processes from cellular metabolism and the microenvironment to systemic immune response. Nevertheless, efforts to distinguish overarching mutational processes from interactions with the cell of origin for a tumor have seen limited success, presenting a barrier to individualized medicine. Here we present a novel, pathway-centric approach, extracting somatic mutational profiles within and between tissues, largely orthogonal to cell of origin, mutational burden, or stage. Known predisposition variants are equally distributed among clusters, and largely independent of molecular subtype. Prognosis and risk of death vary jointly by cancer type and cluster. Analysis of metastatic tumors reveals that differences are largely cluster-specific and complementary, implicating convergent mechanisms that combine familiar driver genes with diverse low-frequency lesions in tumor-promoting pathways, ultimately producing distinct molecular phenotypes. The results shed new light on the interplay between organism-level dysfunction and tissue-specific lesions.
Semiconductor laser dynamics with opto-electronic feedback
Creators: name: Shahine, Mohamad Haidar
Publisher: name: Maryland Shared Open Access Repository
Year: 2012
Subjects: analog to digital conversion
control
feedback
linewidth
photonic samling
semiconductor laser

description: Semiconductor lasers have been one of the major building blocks of fiber-optics based communication systems. For the past two decades, specifications of these lasers have been tailored to particular applications by defining certain performance parameters that do not necessarily overlap from one application to another. In order to commoditize laser sources by increasing volume and reducing cost, the laser performance parameters needed to be generic and not customized. In this simulation work, we modify and enhance essential performance parameters of a simple, low-cost laser with generic specifications and tailor it to specific applications that normally require advanced and complicated laser structures, by using electronic feedback for instantaneous impairment correction, while at the same time maintain a compact size for the laser and the supporting circuitry around it. We essentially use the same laser chip to cover the three distinct applications being analyzed. Maintaining generic laser chip specifications while only modifying the feedback loop circuit design parameters can facilitate photonic hybrid integration. Specific applications targeted are, linear optical-analog transmission for wireless backhauling by reducing the laser relative intensity noise while maintaining and enhancing transmitter linearity, improving laser modulation response and increasing the laser relaxation-oscillation frequency, another application covers laser linewidth reduction to target long haul transmission and coherent detection and finally an application that requires producing a self-pulsating laser for analog to digital conversion sampling application. The performance for all these application is analyzed in both the time and frequency domains. For the analog-signal laser, a laser RIN reduction of 15 dB was realized in the simulation and experiment. For the linewidth-reduction application, the simulation also shows a reduction of linewidth from 2.4 MHz to 24 Hz can be achieved along with simultaneous reduction of 1/f noise at low frequencies, and carrier effect noise at high frequencies to flatten the laser FM response. As for the pulse-generation application, an analysis on controlling the self-pulsation characteristics of semiconductor DFB laser was performed. A detailed analysis of the noise effects on the jitter performance of this system is also carried out. This work also establishes methods to optimize and control a pulsing DFB-laser system for photonic analog-to-digital conversion application by tuning the laser drive current with the potential to replace mode-locked fiber lasers in many applications from RF photonics to chaos communication and optical signal processing.
Possible periodic activity in the short bursts of SGR 1806-20: connection to fast radio bursts
Creators: name: Zhang, G. Q.
name: Tu, Zuo-Lin
name: Wang, F. Y.
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Magnetars are highly magnetized neutron stars that are characterized by recurrent emission of short-duration bursts in soft gamma-rays/hard X-rays. Recently, FRB 200428 were found to be associated with an X-ray burst from a Galactic magnetar. Two fast radio bursts (FRBs) show mysterious periodic activity. However, whether magnetar X-ray bursts are periodic phenomena is unclear. In this paper, we investigate the period of SGR 1806-20 activity. More than 3000 short bursts observed by different telescopes are collected, including the observation of RXTE, HETE-2, ICE and Konus. We consider the observation windows and divide the data into two sub-samples to alleviate the effect of unevenly sample. The epoch folding and Lomb-Scargle methods are used to derive the period of short bursts. We find a possible period about $ 398.20 \pm 25.45 $ days. While other peaks exist in the periodograms. If the period is real, the connection between short bursts of magnetars and FRBs should be extensively investigated.
description: 14 pages, 4 figures, accepted for publication in ApJ
Semantic Light: Building Blocks
Creators: name: Lohr, Charles Nicholas
Publisher: name: Maryland Shared Open Access Repository
Year: 2011
Subjects: Augmented Reality, Fiducial, Lighting, Projection, Semantic Light

description: The concept of Semantic Light is simply that lighting systems can be aware of  what they are lighting. This offers a number of potential advantages over conventional lighting in quality and efficiency.  Semantic Light requires fine grained control  of the output of many lights and requires sensors to take in information about what  is being lit.  It uses this information to control the output lighting in great detail.   By running various algorithms, Semantic Light can provide information to the user  and has a number of applications including augmented reality. Traditional lighting that is currently in wide use has limited control of quality  and quantity of the light produced.  Few lights for large-scale use are intended to  control their output in any kind of detailed manner.  Most area lighting only has a  switch that must be manually turned on or off.  While there are many commercial  systems that allow for more fine grained control, they are typically limited to remote  control, motion control and extra manual controls.  These systems can be wasteful,  or they may provide inappropriate amounts of light, or they may be on when no  one is using them. It is important to think of the many concepts covered as primary building  blocks, rather than a complete commercial system.  A number of refinements and  extensions will be needed to produce a commercial viable product.  We demonstrate  all of the needed building blocks in a concise, prototyped system.
description: C++ program files and latex files available from Special Collections on request.
Selective Knowledge Transfer for Machine Learning
Creators: name: Eaton, Eric
Publisher: name: Maryland Shared Open Access Repository
Year: 2009
Subjects: boosting
knowledge transfer
machine learning
spectral graph theory
transfer learning

description: Knowledge transfer from previously learned tasks to a new task is a fundamental com-ponent of human learning. Recent work has shown that knowledge transfer can also im-prove machine learning, enabling more rapid learning or higher levels of performance. Transfer allows learning algorithms to reuse knowledge from a set of previously learned source tasks to improve learning on new target tasks. Proper selection of the source knowledge to transfer to a given target task is critical to the success of knowledge trans-fer. Poorly chosen source knowledge may reduce the effectiveness of transfer, or hinder learning through a phenomenon known as negative transfer. This dissertation proposes several methods for source knowledge selection that are based on the transferability between learning tasks. Transferability is introduced as the change in performance on a target task between learning with and without transfer. These methods show that transferability can be used to select source knowledge for two major types of transfer: instance- based transfer, which reuses individual data instances from the source tasks, and model- based transfer, which transfers components of previously learned source models. For selective instance- based transfer, the proposed TransferBoost algorithm uses a novel form of set- based boosting to determine the individual source instances to transfer in learning the target task. TransferBoost reweights instances from each source task based on their collective transferability to the target task, and then performs regular boosting to adjust individual instance weights. For model- based transfer, the learning tasks are organized into a directed network based on their transfer relationships to each other. Tasks that are close in this network have high transferability, and tasks that are far apart have low transferability. Model- based transfer is equivalent to learning a labeling function on this network. This dissertation proposes the novel Spectral Graph Labeling algorithm that constrains the smoothness of the learned function using the graph’s Laplacian eigenvalues. This method is then applied to the task transferability network to learn a transfer function that automatically determines the model parameter values to transfer to a target task. Experiments validate the success of these methods for selective knowledge transfer, demonstrating significantly improved performance over existing methods.
Aplicação do Movimento Browniano Geométrico para Simulação de Preços de Ações do Índice Brasileiro de Small Caps
Creators: name: Araújo, Marcos Vinícius dos Santos
Publisher: name: arXiv
Year: 2020
Subjects: subject: Statistical Finance (q-fin.ST)
subject: FOS: Economics and business

description: This work addressed the use of the geometric Brownian motion to simulate the prices of shares listed in the Small Caps index of the Brazilian stock exchange B3 (Brazil, Bolsa, Balcão). The data used refer to the price history from January 2016 to December 2018. The price history of 2019 was used to be compared with the simulated prices. The data was imported from the Yahoo Finance database using the Python programming language, and the simulations were performed for each stock individually, and for portfolios formed based on expected returns, risk and the Sharpe Index. The results were better for portfolios with higher returns, lower risks and higher Sharpe Indexes.
description: in Portuguese
Security Innovations in the Punchscan Voting System
Creators: name: Carback III, Richard Thomas
Publisher: name: Maryland Shared Open Access Repository
Year: 2008
Subjects: Computer Science (0984)
Punchscan
voting system security
optical scan
end-to-end cryptographic audit trail

description: Punchscan is a so-called end-to-end (E2E)
Symmetries and Phase Structure of the Layered Sine-Gordon Model
Creators: name: Nandori, I.
Publisher: name: arXiv
Year: 2006
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The phase structure of the layered sine-Gordon (LSG) model is investigated in terms of symmetry considerations by means of a differential renormalization group (RG) method, within the local potential approximation. The RG analysis of the general N-layer model provides us with the possibility to consider the dependence of the vortex dynamics on the number of layers. The Lagrangians are distinguished according to the number of zero eigenvalues of their mass matrices. The number of layers is found to be decisive with respect to the phase structure of the N-layer models, with neighbouring layers being coupled by terms quadratic in the field variables. It is shown that the LSG model with N layers undergoes a Kosterlitz--Thouless type phase transition at the critical value of the parameter β^2_{c} = 8 N π. In the limit of infinitely many layers the LSG model can be considered as the discretized version of the three-dimensional sine-Gordon model which has been shown to have a single phase within the local potential approximation. The infinite critical value of the parameter β_c^2 for the LSG model in the continuum limit (N -> \infty) is consistent with the latter observation.
description: 14 pages, 2 figures
A multi-epitope vaccine against the highly pathogenic SARS-CoV-2
Creators: name: Marchan, Jose
Publisher: name: F1000 Research Limited
Year: 2021

description: Immunoinformatics may aid to predict prominent immunogenic regions from critical SARS-CoV-2 proteins for their use in prophylactic interventions. This work aimed to design a vaccine against SARS-CoV-2 using an integrated in silico approach. The S glycoprotein was selected as target. The best T- and B-cell epitopes showed high viral antigenicity and suitable interactions with Human Leukocyte Antigen molecules. Remarkably, SARS-CoV-2 receptor-binding domain harbour potential epitopes. The data indicate that the vaccine has an appropriate conformation and stability. An efficient binding Toll-Like Receptor 4/vaccine was observed. Interestingly, the vaccine could be used worldwide. The results also suggest that the vaccine model has a robust potential to evoke/maximize immune effector responses and immunological memory to SARS-CoV-2. Further research is needed prior to clinical trials.
$L$-functions for families of generalized Kloosterman sums and $p$-adic differential equations
Creators: name: Wang, Chunlin
name: Yang, Liping
Publisher: name: arXiv
Year: 2020
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: Primary 11L05, 11S40, 14F30, 14G15

description: In this paper, we focus on a family of generalized Kloosterman sums over the torus. With a few changes to Haessig and Sperber's construction, we derive some relative $p$-adic cohomologies corresponding to the $L$-functions. We present explicit forms of bases of top dimensional cohomology spaces, so to obtain a concrete method to compute lower bounds of Newton polygons of the $L$-functions. Using the theory of GKZ system, we derive the Dwork's deformation equation for our family. Furthermore, with the help of Dwork's dual theory and deformation theory, the strong Frobenius structure of this equation is established. Our work adds some new evidences for Dwork's conjecture.
description: 25 pages
Metadata Automation: A TF-IDF and Nearest Neighbors Approach
Creators: name: Hartley, Emily
name: Roopal Bhatnagar
name: Michels, Kurt
Publisher: name: F1000 Research Limited
Year: 2021

description: The goal of the Metadata Automation DREAM Challenge was to develop a tool to automate the annotation of metadata fields and values in structured biomedical data files with the best candidate Common Data Element (CDE) matches from the Cancer Data Standards Registry and Repository (caDSR). We chose to implement our model in Python 3.6 and approached this challenge from the perspective that it was essentially a fuzzy matching problem. Our approach utilizes Scikit-Learn’s TfidfVectorizer class along with a custom n-gram function to vectorize the data. These term frequency - inverse document frequency (TF-IDF) vectors are passed to Scikit-Learn’s Nearest Neighbor class which returns the k nearest CDE neighbors and their associated distance scores for each column header in the biomedical data file. For the returned CDEs with enumerated values, the Levenshtein distances from the observed values in the data to the CDE’s permissible values are computed using Python’s FuzzyWuzzy library. We then use a decision tree approach based on the TF-IDF distance scores and the observed values’ average Levenshtein distance scores to select and rank the top three CDE matches from the set of nearest neighbors for each column header. In this final ranking step, we apply cutoff values to the distance scores to determine when to include ‘NOMATCH’ as one of the three results. Throughout the challenge we experimented with many aspects of the algorithm including modifying the n-gram function, the selection of caDSR fields to include in the TF-IDF vectorization and applying different cutoff values. The final version of our model was arrived at by selecting the features and parameters that maximized the overall score across all the provided test datasets.
Ledidi: Designing genomic edits that induce functional activity
Creators: name: Schreiber, Jacob
name: Lu, Yang
name: Noble, William
Publisher: name: F1000 Research Limited
Year: 2021

description: Ledidi is a method for turning any pre-trained machine learning model into a sequence editor. In this presentation we go over the method behind how it works, and show examples of editing CTCF binding and cell type-specific JUND binding.
Unconventional spin density wave in Bechgaard salt (TMTSF)2NO3
Creators: name: Basletic, Mario
name: Korin-Hamzic, Bojana
name: Maki, Kazumi
name: Tomic, Silvija
Publisher: name: arXiv
Year: 2006
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Among many Bechgaard salts, TMTSF2NO3 exhibits very anomalous low temperature properties. Unlike conventional spin density wave (SDW), TMTSF2NO3 undergoes the SDW transition at $\T_SDW\approx 9.5$ K and the low temperature quasiparticle excitations are gapless. Also, it is known that TMTSF2NO3 does not exhibit superconductivity even under pressure, while FISDW is found in TMTSF2NO3 only for P=8.5 kbar and B>20 T. Here we shall show that both the angle dependent magnetoresistance data and the nonlinear Hall resistance of TMTSF2NO3 at ambient pressure are interpreted satisfactory in terms of unconventional spin density wave (USDW). Based on these facts, we propose a new phase diagram for Bechgaards salts.
description: 4 pages, 4 figs, RevTeX
Canoe Race Participant Notes
Creators: name: Springs Historical Society/Library
Publisher: name: Unknown
Year: 0
Subjects: Springs
East Hampton
Rowing races
Canoes
Boats
Regattas

description: This document shows handwritten notes that describe the details of one of the annual Canoe Races held by the Springs Historical Society.
description: This material was lent to the Long Island Collection by the Springs Historical Society Library for digitization purposes.