gebhart/patrepeval huggingface dataset:
Regression Models for Haplotype-Based Association Studies (2007)

In this paper, we provide an overview of statistical models for haplotype-based association studies, and summarize their features based on the design matrix. We classify the design matrix into the two types: direct and indirect. For these two kinds of matrices, we present and compare characteristics using a simple hypothetical example, and a real data set. The motivation behind this study was to provide practitioners with an improved understanding, to facilitate the informed selection of the appropriate haplotype-based model and to improve the interpretability of the models.
Understanding Wi-Fi 2.0: from the economical perspective of wireless service providers [Dynamic Spectrum Management] (2010)

Wi-Fi 2.0 refers to Wi-Fi-like Internet access operating on whitespaces in the licensed spectrum using cognitive radio technology. Wi-Fi 2.0 is expected to provide better performance and larger coverage than today's Wi-Fi, thanks to the good propagation characteristics of the legacy spectrum such as TV bands. Wi-Fi 2.0 is modeled as a network consisting of an access point (called CR hotspot) and end-user terminals (CR devices) operated by a CR wireless service provider. In this article we focus on the economical perspective of Wi-Fi 2.0 and discuss various aspects in profit management of Wi-Fi 2.0 WSPs. In particular, we consider profit-maximizing optimal strategies in terms of customer admission/eviction control and inter-WSP market competition. We first show that Wi-Fi 2.0 operates on time-varying spectrum availability due to the ON-OFF channel usage of legacy users, and advocate the necessity of customer eviction control upon appearance of legacy users. We also identify two types of WSP-WSP market competition in leasing the limited spectrum resources from the licensees and in enticing end customers with a competitive price. Then we enumerate the key factors affecting the profit of collocated WSPs, such as channel leasing cost, service tariff, QoS provisioning, and coexistence with legacy services. By examining Wi-Fi 2.0 from an economic point of view, we show its commercial value in developing next-generation CR applications that benefit both legacy and CR users.
Fabrication of Bi-2212/SrSO<sub>4</sub> Composite Superconductors by Melting Powder Mixtures (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Advanced plasma etch for the 10nm node and beyond (2013)

As 14nm node devices begin to permeate into the semiconductor industry, it is becoming increasingly evident that continued pitch scaling is getting more complex throughout the FEOL, MOL and BEOL. The adoption of patterning schemes and pitch splitting techniques such as double exposure/double etch and sidewall image transfer (SIT) are already underway to extend 193nm immersion lithography and enable 3D FinFET / Trigate devices. In addition, BEOL scaling of damascene copper is facing its own challenges, between the patterning and integration of porous ULK materials and the issue of increased resistivity emanating from grain boundary and surface scattering. As such, this paper will present work on novel etch methods envisioned to enable the successful extension of patterning and device integration for the 10nm node and beyond. Work related to the exploration of novel feedgas chemistries to extend etch performance for SiN spacer and oxide etch applications will be reviewed in detail. Specifically, the realization of a silicon nitride etch process which no longer depends on an oxidation mechanism, but rather a polymerization based etch mechanism will be shown. The process exhibits high selectivity to SiO<sub>2</sub>, Si and photoresist and results in reduced SOI loss while simultaneously maintaining all SiN on the gate sidewall and significantly reducing SiN footing. In addition, the feasibility of novel patterning methods such as the introduction of subtractive etching of copper will be reviewed in detail. Subtractive etching of Cu has the potential to overcome current interconnect integration difficulties by enabling blanket Cu film deposition with large grains, and by minimizing plasma damage during ULK etch, respectively. Successful patterning of copper at 25-50nm critical dimension (CD) with smaller than 100nm in pitch is demonstrated using a novel high density plasma based dry etch process.
Selective Amination of Secoiridoid Glycosides to give Monomeric Pyridine, Dimeric Pyridine, and Naphthyridine Alkaloids (2001)

Treatment of the secoiridoids oleuropein (4), ligstroside (5) and methyloleoside (6) by beta-D-glucosidase in the presence of ammonium chloride led exclusively to monomeric pyridine alkaloids 7, 1, and 8. Dimeric 3,4,5-trisubstituted pyridines were obtained from methyloleoside (6) when ammonium chloride was generated in the reaction mixture by successive additions of ammonia and hydrochloric acid. The use of ammonium acetate permitted conversion of secoiridoids 4 and 5 into the naphthyridine alkaloid jasminine (3).
Multitype surface and thin film characterization using light scattering, scanning force microscopy, and white light interferometry (1999)

The characterization of surface and thin film morphologies and roughnesses significantly benefits from appropriately utilizing different measuring techniques. When suitably combining light scattering measurements, scanning force microscopy, and white fight interferometry, comprehensive characterization over a wide range of sample types and roughness scales can be accomplished A concise overview on the characterization techniques is given, followed by examples of combined measurements. The presented results include a variety of samples such as superpolished and microrough substrates, thin film coatings for applications from the visible to the deep ultraviolet region, and rough engineering surfaces.
The ethics of interaction with neurorobotic agents: a case study with BabyX (2021)

Abstract As AI advances, models of simulated humans are becoming increasingly realistic. A new debate has arisen about the ethics of interacting with these realistic agents—and in particular, whether any harms arise from ‘mistreatment’ of such agents. In this paper, we advance this debate by discussing a model we have developed (‘BabyX’), which simulates a human infant. The model produces realistic behaviours—and it does so using a schematic model of certain human brain mechanisms. We first consider harms that may arise due to effects on the user —in particular effects on the user’s behaviour towards real babies. We then consider whether there’s any need to consider harms from the ‘perspective’ of the simulated baby . The first topic raises practical ethical questions, many of which are empirical in nature. We argue the potential for harm is real enough to warrant restrictions on the use of BabyX. The second topic raises a very different set of questions in the philosophy of mind. Here, we argue that BabyX’s biologically inspired model of emotions raises important moral questions, and places BabyX in a different category from avatars whose emotional behaviours are ‘faked’ by simple rules. This argument counters John Danaher’s recently proposed ‘moral behaviourism’. We conclude that the developers of simulated humans have useful contributions to make to debates about moral patiency—and also have certain new responsibilities in relation to the simulations they build.
Unsupervised Domain Adaptation via Regularized Conditional Alignment (2019)

We propose a method for unsupervised domain adaptation that trains a shared embedding to align the joint distributions of inputs (domain) and outputs (classes), making any classifier agnostic to the domain. Joint alignment ensures that not only the marginal distributions of the domains are aligned, but the labels as well. We propose a novel objective function that encourages the class-conditional distributions to have disjoint support in feature space. We further exploit adversarial regularization to improve the performance of the classifier on the domain for which no annotated data is available.
A Naturally Occurring rev1-vpu Fusion Gene Does Not Confer a Fitness Advantage to HIV-1 (2015)

Expression of a rev1-vpu fusion gene does not affect regular Rev and Vpu functions or alter HIV-1 replication in primary target cells. Since there is no evidence for increased replication fitness of rev1-vpu encoding viruses, this polymorphism likely emerged in the context of other mutations within and/or outside the rev1-vpu intergenic region, and may have a neutral phenotype.
An analog parallel array processor for real-time sensor signal processing (2002)

A fully-programmable analog signal processor and its operation in a sensor signal processing system is presented. The analog parallel array processor (APAP) chip is the core of the system. It contains a 20/spl times/20 matrix of computing cells, function-control circuits and interface circuits. The sensor provides the input signals for the APAP chip. The architecture ofthe 400 cells is based on a cellular neural network architecture. The cells have an internal-state node, an input node and an output. The output is the clipped version ofthe state. The cells send two current signals to their nearest neighbors and to itself: one proportional to the input and controlled by the feedforward weights or B-template; the second proportional to the output and controlled by the feedback weights or A-template. In every cell a constant bias source, controlled by the I-template, is also included. The templates are identical for all cells and are the instructions for the APAP. In this implementation the user can program the template weights over a continuous range of values from /spl plusmn/1/4 to /spl plusmn/4. All cells execute the instructions in parallel and in continuous time so that a parallel array processor is obtained with real-time signal processing capabilities. Several 2D global and local feature extraction operations such as edge detection, pixel peeling, hole-filling, connected component detection, and resistive grid filtering can be executed.
Towards a five-minute comprehensive cardiac MR examination using highly accelerated parallel imaging with a 32-element coil array: Feasibility and initial comparative evaluation (2012)

This study demonstrates the technical feasibility and promising image quality of 5-minute comprehensive whole-heart cardiac examinations, with simplified scan prescription and high spatial and temporal resolution enabled by highly parallel imaging technology. The study also highlights technical hurdles that remain to be addressed. Although image quality remained diagnostic for most scan types, the reduced image quality of PERF, CINE, and LGE scans in the Accelerated protocol remain a concern.
Controlling coverage of D‐optimal onion designs and selections (2004)

Abstract Statistical molecular design (SMD) is a powerful approach for selection of compound sets in medicinal chemistry and quantitative structure–activity relationships (QSARs) as well as other areas. Two techniques often used in SMD are space‐filling and D‐optimal designs. Both on occasions lead to unwanted redundancy and replication. To remedy such shortcomings, a generalization of D‐optimal selection was recently developed. This new method divides the compound candidate set into a number of subsets (‘layers’ or ‘shells’), and a D‐optimal selection is made from each layer. This improves the possibility to select representative molecular structures throughout any property space independently of requested sample size. This is important in complex situations where any given model is unlikely to be valid over the whole investigated domain of experimental conditions. The number of selected molecules can be controlled by varying the number of subsets or by altering the complexity of the model equation in each layer and/or the dependency of previous layers. The new method, called D‐optimal onion design (DOOD), will allow the user to choose the model equation complexity independently of sample size while still avoiding unwarranted redundancy. The focus of the present work is algorithmic improvements of DOOD in comparison with classical D‐optimal design. As illustrations, extended DOODs have been generated for two applications by in‐house programming, including some modifications of the D‐optimal algorithm. The performances of the investigated approaches are expected to differ depending on the number of principal properties of the compounds in the design, sample sizes and the investigated model, i.e. the aim of the design. QSAR models have been generated from the selected compound sets, and root mean squared error of prediction (RMSEP) values have been used as measures of performance of the different designs. Copyright © 2005 John Wiley &amp; Sons, Ltd.
Steady State and Transient Experimentally Validated Analysis of Hybrid Data Centers (2014)

Data centers consume a considerable amount of energy which is estimated to be about 2% of the total electrical energy consumed in the U.S. in the year 2010, and this number continues to increase every year. Thermal management is becoming increasingly important in the effort to improve the energy efficiency and reliability of data centers. The goal is to keep the information technologies (IT) equipment temperature within the allowable range in high power density data centers while reducing the energy used for cooling. In this regard, liquid and hybrid air/water cooling systems are alternatives to traditional air cooling. In particular, these options offer advantages for localized cooling higher power racks which may not be manageable using the room level air cooling system without requiring significantly more energy. In this paper, a hybrid cooling system in data centers is investigated. In addition to traditional raised floor, cold aisle-hot aisle configuration, a liquid–air heat exchanger attached to the back of racks is considered. First of all, the paper presents a review of literature of the study of this heat exchanger strategy in the thermal management of a data center. The discussion focus on rear door heat exchanger (RDHx) performance, both the steady state and transient impact are analyzed. The studies show that under some circumstances, this hybrid approach could be a viable alternative to meet the American Society of Heating, Refrigerating, and Air-Conditioning Engineers (ASHRAE) recommended inlet air temperatures, while at the same time reducing the overall energy consumption in high density data centers. The hybrid design approach can also significantly improve the dynamic performance during rack power increases or computer room air conditioner (CRAC) unit failure. And then, additional parametric steady state and dynamic analyses, are presented in detail for the different scenarios.
Investigation of Forming, SET, and Data Retention of Conductive-Bridge Random-Access Memory for Stack Optimization (2015)

In this paper, we investigate in depth Forming, SET, and Retention of conductive-bridge random-access memory (CBRAM). A kinetic Monte Carlo model of the CBRAM has been developed considering ionic hopping and chemical reaction dynamics. Based on inputs from ab initio calculations and the physical properties of the materials, the model offers the simulation of both the Forming/SET and the Data Retention operations. It aims to create a bond between the physics at atomic level and the device behavior. From the model and experimental results obtained on decananometric devices, we propose an understanding of the physical mechanisms involved in the CBRAM operations. Using the consistent Forming/SET and Data Retention model, we obtained good agreement with the experimental data. Finally, the impact of each layer of the CBRAM on the Forming/SET behavior is decorrelated, allowing an optimization of the performance.
Quality of SOI film after surface smoothing with hydrogen annealing, touch-polishing (2002)

We have conducted an investigation to evaluate the impact of both touch-polish and hydrogen annealing at different temperatures on the roughness, on the SOI film removal, as well as the impact of so processed surface on the integrity of gate oxide thermally grown on it, for SIMOX and BESOI material.
CYCLIC AMP-DEPENDENT PROTEIN KINASE ACTIVITY AND ENDOGENOUS PROTEIN PHOSPHORYLATION IN ISOLATED CORTICAL SEGMENTS OF RABBIT NEPHRON (1982)

Cyclic AMP-dependent protein kinase activity and endogenous protein phosphorylating activity are reported for 6 cortical segments of the rabbit nephron which were microdissected and collected according to their morphology. The 6 cortical nephron segments, namely the glomerulus (Glm), proximal convoluted tubule (PCT), proximal straight tubule (PST), cortical ascending limb of Henle’s loop (CAL), distal convoluted tubule (OCT), and cortical collecting tubule (CCT), showed protein kinase activities which were increased 1.8-4,9 fold by 10-6 M cyclic AMP in the presence of histone MA, histone f2b or histone f3 as a protein substrate. However, all these segments showed little or no cyclic AMP dependent increase of activity with either protamine or α-casein as a protein substrate. Cyclic AMP increased the endogenous protein phosphorylation of Glm (10-6 M cyclic AMP), of CAL (10-7 and 10-8 M cyclic AMP), of DCT (10-6 M cyclic AMP) and of CCT (10-5, 10-7 and 10-6 M cyclic AMP). In contrast. PCT showed decreased endogenous protein phosphorylation in the presence of 10-7,10-5 and 10-4 M cyclic AMP.
The impact of methodological and temporal variation on infarct size quantification in acute myocardial infarction with late enhancement CMR (2015)

Funding This project was funded by a grant from the MRC(UK).
Functional Analysis of Porphyromonas gingivalis W83 CRISPR-Cas Systems (2015)

The CRISPR-Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) system is a unique system that provides prokaryotic cells with an adaptive and heritable immunity. In this report, we show that the CRISPR-Cas system of P. gingivalis, an important human pathogen associated with periodontitis and possibly also other conditions, such as rheumatoid arthritis and cardiovascular disease, is active and provides protection from foreign genetic elements. Importantly, the data presented here may be useful for better understanding the communication between cells in larger bacterial communities and, consequently, the process of disease development and progression.
High-Frequency TaO<sub><italic>x</italic></sub>-Based Compact Oscillators (2015)

In this paper, we demonstrate three key features of oxide-based nano-oscillators: 1) the observation of threshold switching and filamentary oscillations in TaO x ; 2) the highest frequency achieved by oxide-based oscillators; and 3) a study with linear (resistor) and nonlinear (transistor) ballasts to clearly understand the role of filament dynamics in scaling. These oscillators show frequency tunability over the range of 20 kHz–250 MHz, with 250 MHz being the highest reported frequency for this class of oscillators. Different types of ballasts show frequency tunability using two distinct methods: 1) by tuning the channel resistance of the transistor and 2) by increasing the rail voltage across the ballast–device pair. This sheds new light on the oscillator dynamics for dense oscillator arrays aimed at oscillatory neural networks and other applications.
OS0116 Electrode Potential Measurement of Cu under Laminar Pure Water Flow in a Microfluidic Channel (2016)

Cleaning using water is performed repeatedly to the wafers having bare copper interconnects in the fabrication process of integrated circuits. Even nm scale copper corrosion during the cleaning processes causes defects in the products. To understand the fundamental behavior of copper corrosion with water, copper surface was optically observed under laminar water flow using a microfluidic device, and it was found that dissolved oxygen has large effect on the copper corrosion. In this study, electrode potential was simultaneously observed with optical surface. Some observational results suggested drop of copper surface brightness below a certain electrode potential.
On road network utility based on risk-aware link choice (2013)

We have previously shown how it is possible to lower accident risk levels while at the same time increasing traffic flows with the aid of vehicular ad-hoc networks. In this paper, we extend the online traffic accident risk mitigation system to include link choice. We develop an algorithm that allows vehicles to choose road links that provide the current maximal utility, based on information received over a vehicular network, whilst remaining below acceptable risk levels. Additionally, we investigate how to improve the performance of this algorithm by considering the effect a vehicle's link choice has on the utility of other vehicles. We introduce a social penalty for reducing other vehicles' utility and investigate the effects of including this as a factor in vehicles' link choices. The resulting system sheds new light on the problem of effective link choice by route selection algorithms and highlights the potential that exists in VANET-based traffic management.
Adaptive measurement and correction of polarization aberrations (2019)

We present the concept of adaptive polarization optics and validate it using a system that contains full polarization control and measurement at pixel level. Polarization control is implemented based on double pass spatial light modulator (SLM) system while the measurement is realized via an imaging Stokes polarimeter. Our design is able to extract the variation in polarization state across a beam and from this extracted information about a birefringent sample that introduces a polarization disturbance into the system. This information is used to control the SLM-based polarization state generator in order to restore the light to the desired state after passing through the sample. The method is demonstrated using a vortex half-wave retarder as the birefringent sample.
ChemInform Abstract: A New Synthesis of α,β‐Unsaturated Aldehydes. (1990)

Abstract Coupling of chloroacetyl chloride (I) with O,N‐dimethylhydroxylamine hydrochloride (II) gives the hydroxamate (III) which is treated with triethyl phosphite (IV), forming N‐methoxy‐N‐methyldiethoxyphosphorylacetamide (V).
Holy smartphones and tablets, Batman! (2013)

It is becoming increasingly more common for people to own botha smartphone and a tablet, providing a design opportunity to leverage the combination of these two formfactors. Our work aims to explore this by: a) defining the design space of distributed input and output solutions that rely on and benefit from phone--tablet collaboration, both physically and digitally; andb) reveal the idiosyncrasies of each particular device combination via interactive prototypes. Our research provides actionable insight in this emerging area by defining a design space, suggesting a developer's framework and implementing prototypical applicationsin such areas as distributed information display, distributed control and various configurations of these. For each of these, we present several example techniques and demonstrate an application that combinessuch techniques.