gebhart/patrepeval huggingface dataset:
A Farewell to the Bias-Variance Tradeoff? An Overview of the Theory of Overparameterized Machine Learning (2021)

The rapid recent progress in machine learning (ML) has raised a number of scientific questions that challenge the longstanding dogma of the field. One of the most important riddles is the good empirical generalization of overparameterized models. Overparameterized models are excessively complex with respect to the size of the training dataset, which results in them perfectly fitting (i.e., interpolating) the training data, which is usually noisy. Such interpolation of noisy data is traditionally associated with detrimental overfitting, and yet a wide range of interpolating models -- from simple linear models to deep neural networks -- have recently been observed to generalize extremely well on fresh test data. Indeed, the recently discovered double descent phenomenon has revealed that highly overparameterized models often improve over the best underparameterized model in test performance. Understanding learning in this overparameterized regime requires new theory and foundational empirical studies, even for the simplest case of the linear model. The underpinnings of this understanding have been laid in very recent analyses of overparameterized linear regression and related statistical learning tasks, which resulted in precise analytic characterizations of double descent. This paper provides a succinct overview of this emerging theory of overparameterized ML (henceforth abbreviated as TOPML) that explains these recent findings through a statistical signal processing perspective. We emphasize the unique aspects that define the TOPML research area as a subfield of modern ML theory and outline interesting open questions that remain.
Merging the potential of microbial genetics with biological and chemical diversity: an even brighter future for marine natural product drug discovery (2004)

Marine invertebrates and a growing number of marine bacteria are the sources of novel, bioactive secondary metabolites. Structurally, many of these compounds appear to be biosynthesized by polyketide synthases (PKS) and/or nonribosomal peptide synthetases (NRPS) that have also been found in terrestrial microbes. This review highlights scientific advances from 1999-2003 in the emerging field of molecular genetics of polyketide and nonribosomal peptide natural products isolated from marine organisms. The implications of this research towards the development of marine secondary metabolites as a sustainable source of new drugs are discussed.
Observed structure of addresses in IP traffic (2002)

This paper investigates the structure of addresses contained in IP traffic. Specifically, we analyze the structural characteristics of destination IP addresses seen on Interuet links, considered as a subset of the address space. These characteristics may have implications for algorithms that deal with IP address aggregates, such as routing lookups and aggregatebased congestion control. We find that address structures are well modeled by a multifractal Cantor dust with two parameters. The model may be useful for simulations where realistic IP addresses are preferred. We also develop concise characterizations of address structures, including active aggregate counts and discriminating prefixes. Our structural characterizations are stable over short time scales at a given site, and different sites have visibly different characterizations, so that the characterizations make useful "fingerprints" of the traffic seen at a site. Also, changing traffic conditions, such as worm propagation, significantly alter these "fingerprints".
Discovery of novel peptide hormones using prohormone convertase screening (2009)

Bioactive peptides play critical roles in diverse biological phenomena; the discovery of novel peptides thus has the potential to open entirely new fields of research. The successful sequencing of entire genomes of various organisms has yielded numerous novel candidate precursor genes; however, the identification of novel bioactive peptides from such genomic information has been hampered by their small size. In this study, we attempt to identify novel peptides using a combinatorial screening approach: a predictive algorithm followed by "restriction protease" screening. The algorithm was trained using various properties associated with known peptide precursors. Approximately 150 genes were identified as coding for candidate peptide precursors. In a preliminary screening, 21 genes were chosen from this list and expressed in tagged form in HEK293 cells. Proteolysis using prohormone convertases 1 and 2 and furin was performed in order to confirm cleavage of expressed proteins. Sixteen of 21 precursors were cleaved by one or more convertases; 5 proteins were not cleaved and may represent false bioinformatics hits. In situ hybridization of mouse brain with antisense cDNA from a cleaved precursor indicated limited expression within the mediobasal hypothalamus. These results demonstrate that our bioinformatics/convertase screening approach is a promising method for peptide hormone discovery. (DA05984)
Laparoscopic Partial Nephrectomy Using Holmium Laser in a Porcine Model (2005)

No AccessJournal of UrologyUrological Survey: Urolithiasis, Endourology and Laparoscopy1 Apr 2005Laparoscopic Partial Nephrectomy Using Holmium Laser in a Porcine Model Ralph V. ClaymanM.D. Ralph V. ClaymanRalph V. Clayman More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(05)61046-4AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Laparoscopic Partial Nephrectomy Using Holmium Laser in a Porcine Model." The Journal of Urology, 173(4), pp. 1200–1201 © 2005 by American Urological Association, Inc.FiguresReferencesRelatedDetails Volume 173Issue 4April 2005Page: 1200-1201 Advertisement Copyright & Permissions© 2005 by American Urological Association, Inc.MetricsAuthor Information Ralph V. Clayman More articles by this author Expand All Advertisement PDF downloadLoading ...
Conformal LSMCD deposition of SrBi2(Ta1-xNbx)2O9 (1997)

Abstract This paper presents new results of Liquid Source Misted Chemical Deposition (LSMCD) of SrBi2(Ta1-xNbx)2O9 thin films showing good step coverage of 150 nm thick films into square openings approximately 1 μm deep by 0.6 μm wide. A SAMCO model HDF-6000 LSMCD machine was used for the ferroelectric deposition. Prior to the deposition of the ferroelectric film, a Pt bottom electrode of approximately 200 nm thickness was sputtered into an initial opening 1μm deep by 1μm wide. The LSMCD and new chemistry methodologies by which these results were obtained will be described in this paper. The electrical characteristics of the LSMCD films will also be reported. LSMCD films resulted in higher switched charge (2Pr) than the spin-on films. The coercive fields (2Ec) and maximum leakage currents were comparable for the two deposition methods. These results show that conformal LSMCD thin films can be used for sub-micron circuits containing ferroelectric memory.
ChemInform Abstract: Design and Synthesis of Novel Conformationally Restricted HIV Protease Inhibitors. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Quantitative comparison of hardware transactional memory for Blue Gene/Q, zEnterprise EC12, Intel Core, and POWER8 (2015)

Transactional Memory (TM) is a new programming paradigm for both simple concurrent programming and high concurrent performance. Hardware Transactional Memory (HTM) is hardware support for TM-based programming. It has lower overhead than software transactional memory (STM), which is a software-based implementation of TM. There are now four commercial systems, IBM Blue Gene/Q, IBM zEnterprise EC12, Intel Core, and IBM POWER8, offering HTM. Our work is the first to compare the performance of these four HTM systems. We measured the STAMP benchmarks, the most widely used TM benchmarks. We also evaluated the specific features of each HTM system. Our experimental results show that: (1) there is no single HTM system that is more scalable than the others in all of the benchmarks, (2) there are measurable performance differences among the HTM systems in some benchmarks, and (3) each HTM system has its own implementation characteristics that limit its scalability.
Optical scintillation measurements in a desert environment I: direct link ranges of 2 to 24 km (2011)

Experiments have been carried out over a series of ranges at China Lake in which the irradiance fluctuations, angle-of-arrival variance and images of the scintillation patterns were recorded, together with meteorological parameters. The decrease in scintillation index associated with the lower turbulence conditions at sunset was observed for the shorter ranges but not for the longer ranges of 19 and 24km where the propagation was in the saturated regime.
Optimization of pillar electrodes in subretinal prosthesis for enhanced proximity to target neurons (2018)

3D electrodes in subretinal prostheses help reduce electrode-tissue separation and decrease stimulation thresholds to enable smaller pixels, and thereby improve visual acuity of prosthetic vision.
A Sectional Model for Investigating Microcontamination in a Rotating Disk CVD Reactor (2004)

A sectional model is employed to study the aerosol dynamics in a rotating disk CVD reactor. The aerosol model is implemented into a numerical code that employs detailed chemistry and transport and a one-dimensional similarity transform to simulate this system. The numerical results are compared to experimental data where conditions are such that particles are formed from gas-phase reactions. A thin particle layer is reproduced and the thickness is accurately determined. The location of the layer is predicted within 5%. The thin layer is a consequence of the particle stagnation region that develops due to convection towards the disk being opposed by a particle thermophoretic velocity away from the disk. The effect of sticking coefficient is examined, and it is shown that with a small sticking coefficient a smaller mean particle size and broader particle layer is obtained. It is also found that particle layers are driven farther away from the disk when the temperature of the disk is higher or the chamber pressure is lower, both of which result in higher thermophoretic velocities for the particles. The thickness of the particle layer is found to be insensitive to pressure. The sectional model also reveals that the particle size distributions are bimodal throughout most of the particle layer. This is a result of the broad regions for nucleation and surface growth as well as the opposing convective and thermophoretic velocities.
Retinoic acid is a negative regulator of the Epstein-Barr virus protein (BZLF1) that mediates disruption of latent infection. (1993)

Disruption of latent Epstein-Barr virus (EBV) infection is induced by the key immediate-early protein BZLF1 (or Z, a member of the basic leucine-zipper family), which transactivates the viral early promoters. Viral reactivation is marked by renewed synthesis of early gene products such as EBV early antigen-diffuse (EA-D). Retinoic acid has been previously shown to inhibit reactivation of EBV infection. Retinoic acid responsive receptors are known to act as positively regulating transcription factors but can also negatively regulate AP-1 responsive genes. Here we demonstrate that the retinoic acid receptor alpha (RAR alpha) and retinoid X receptor alpha (RXR alpha) inhibit the ability of the Z protein to transactivate the viral early promoter BMRF1, which directs transcription of EA-D. Z can also reciprocally inhibit RAR alpha- and RXR alpha-induced activation of an autoregulated cellular promoter for the RAR beta gene (BRE) through a non-DNA binding mechanism. RXR alpha inhibits Z from binding to the AP-1 motif in the BMRF1 promoter and, reciprocally, Z inhibits RAR alpha from binding to its retinoic acid response element in the BRE promoter. Furthermore, a glutathione-S-transferase-RXR alpha fusion protein can interact directly with the Z protein. These results suggest that a direct protein-protein interaction between Z (the viral protein) and RAR alpha and RXR alpha (cellular proteins) can modulate the reactivation of latent EBV infection.
MIT virtual source GaNFET‐high voltage (MVSG‐HV) model: A physics based compact model for HV‐GaN HEMTs (2014)

Abstract A new physics based transport and charge model for long channel GaN HEMTs is proposed. The model is based on the concept of virtual source (VS) carrier transport (A. Khakifirooz et al., IEEE‐TED 56 (8), 1674 (2009) [1]) and is extended to drift diffusion regime. The model is fully scalable from non‐velocity saturation to velocity saturation regime. In addition, non‐linear access regions are modeled as implicit‐gated transistors. Self‐heating effects and self‐consistent charge models are included. The model is validated against state of the art industry devices. (© 2014 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Self‐Assemblage and Patterning of Thin‐Film Ferroic Nanostructures (2016)

Numerous studies have been conducted to develop non-invasive techniques to avoid damage, either by doing the patterning step prior to the final crystallization or by using other bottom-up approaches, where patterning is obtained by free and site-induced self-assembly (SA) methods. Among the chemical methods, chemical solution deposition (CSD) offers a number of advantages, such as high flexibility with regard to composition and coating technique. Compared to gas-phase methods it is cheap regarding operation and technical equipment and therefore ideally suited for research and development as well as applications where no conformal step coverage of ultra-small trenched structures is required. This chapter discusses predominantly wet chemical preparation methods with a focus on the various non-invasive procedures often combined with true bottom-up steps. The reported approaches are limited to those that yield ferroic nanostructures on suitable substrates. Sometimes wet chemical techniques combined with vapor-based deposition techniques are the method of choice.
Geotracker (2003)

geoTracker is an application that provides a visitor-based snapshot of the global weather in near-real time.As each visitor enters the application they start on a world map at their location, and their current weather is displayed. Then, they can travel around the world looking at information for other cities in other countries. Most importantly, all user's paths are visible to everyone else.
Design of a portable microprocessor-based stimulator for the recreation of impaired gastrointestinal motility (2002)

With the development and the miniaturization of microprocessors, the possibility of designing implantable real-time electronic devices for recreation of impaired gastrointestinal motility looks more realistic than ever. In this paper, a solution for the design of portable microprocessor-based stimulator is proposed, which can be regarded as a preliminary version of an implantable stimulator.
Preface/Front Matter (1993)

It was in 1970 that back-to-back reports in the journal Nature by Baltimore ( Nature 226: 1209–1211, 1970) and by Temin and Mizutani ( Nature 226: 1211–1213, 1970) provided the first evidence for the existence of an RNA-dependent DNA polymerase in retroviral particles. The editorial commentary that accompanied the reports promised that this discovery would “have important implications, not only for carcinogenesis by RNA viruses, but also for the general understanding of genetic transcription.” Indeed, this new enzyme, reverse transcriptase, was to play a central role in molecular biology in the ensuing years for these and other reasons as well. The first impact of the discovery of reverse transcriptase was to refute the strict interpretation of the “Central Dogma” of molecular biology that information transfer was always unidirectional from DNA to RNA to protein. In revising dogma, a new generation of scientists was reinstructed in an essential element of good science: the challenging of “established” concepts. Second, reverse transcriptase was important to our understanding of cancer: Its presence explained how an RNA virus could induce genetic changes in a cell, ultimately leading to our present concept of the genetic basis of the disease. Third, the enzyme has played an important role in the development of our understanding of recombination and transduction in eukaryotic cells. Most of our younger generation of molecular biologists have been introduced to reverse transcriptase as a tool for the synthesis and cloning of cDNAs. In the last several years, reverse transcriptase has also become important as
Performance of the Massive MIMO Uplink With OFDM and Phase Noise (2016)

The performance of multi-user massive multiple-input multiple-output orthogonal frequency division multiplexing uplink systems in the presence of base station (BS) phase noise impairments is investigated. Closed-form achievable rate expressions are rigorously derived under two different operations, namely, the case of a common oscillator (synchronous operation) at the BS and the case of independent oscillators at each BS antenna (non-synchronous operation). It is observed that the non-synchronous operation exhibits superior performance due to the averaging of a portion of the intercarrier interference. Furthermore, radiated power scaling laws are derived, which are identical to the phase-noise-free case.
A Bayesian model selection criterion for HMM topology optimization (2002)

This paper addresses the problem of estimating the optimal Hidden Markov Model (HMM) topology. The optimal topology is defined as the one that gives the smallest error-rate with the minimal number of parameters. The paper introduces a Bayesian model selection criterion that is suitable for Continuous Hidden Markov Models topology optimization. The criterion is derived from the Laplacian approximation of the posterior of a model structure, and shares the algorithmic simplicity of conventional Bayesian selection criteria, such as Schwarz's Bayesian Information Criterion (BIC). Unlike, BIC, which uses a multivariate Normal distribution assumption for the prior of all parameters of the model, the proposed HMM-oriented Bayesian Information Criterion (HBIC), models each parameter by a different distribution, one more appropriate for that parameter The results on an handwriting recognition task shows that the HBIC realizes a much smaller and efficient system than a system generated through the BIC.
Minimum Probability Flow Learning (2009)

Fitting probabilistic models to data is often difficult, due to the general intractability of the partition function and its derivatives. Here we propose a new parameter estimation technique that does not require computing an intractable normalization factor or sampling from the equilibrium distribution of the model. This is achieved by establishing dynamics that would transform the observed data distribution into the model distribution, and then setting as the objective the minimization of the KL divergence between the data distribution and the distribution produced by running the dynamics for an infinitesimal time. Score matching, minimum velocity learning, and certain forms of contrastive divergence are shown to be special cases of this learning technique. We demonstrate parameter estimation in Ising models, deep belief networks and an independent component analysis model of natural scenes. In the Ising model case, current state of the art techniques are outperformed by at least an order of magnitude in learning time, with lower error in recovered coupling parameters.
2SJ-01 Analysis of Protein-Protein Interaction and Electron Transfer Processes Based on the Protein Electron-Transfer Complex Structures(2SJ New developments in protein complex research: From molecules to supramolecules and aggregates,The 49th Annual Meeting of the Biophysical Society of Japan) (2011)

IncorporatedAssociationresults indicated involvement of actomyosin systcm in the gliding movement.
Serendipita indica changes host sugar and defense status in Arabidopsis thaliana: cooperation or exploitation? (2021)

Manipulation of sugar metabolism upon S. indica root colonization triggers changes in sugar pools and defense responses in A. thaliana. Serendipita indica is an endophytic fungus that establishes mutualistic relationships with many different plants including important crops as well as the model plant A. thaliana. Successful root colonization typically results in growth promotion and enhanced tolerance against various biotic and abiotic stresses. The fungus delivers phosphorus to the host and receives in exchange carbohydrates. There are hints that S. indica prefers hexoses, glucose, and fructose, products of saccharose cleavage driven by invertases (INVs) and sucrose synthases (SUSs). Carbohydrate metabolism in this interaction, however, remains still widely unexplored. Therefore, in this work, the sugar pools as well as the expression of SUSs and cytosolic INVs in plants colonized by S. indica were analyzed. Using sus1/2/3/4 and cinv1/2 mutants the importance of these genes for the induction of growth promotion and proper root colonization was demonstrated. Furthermore, the expression of several defense-related marker genes in both multiple mutants in comparison to the wild-type plants was determined. Our results show that in colonized A. thaliana plants S. indica manipulates the sugar metabolism by altering the expression of host's INV and SUS and modulates both the sugar pools and plant defense in its favor. We conclude that the interaction A. thaliana-S. indica is a balancing act between cooperation and exploitation, in which sugar metabolism plays a crucial role. Small changes in this mechanism can lead to severe disruption resulting in the lack of growth promotion or altered colonization rate.
Light alkane oxidation using catalysts prepared by chemical vapour impregnation: tuning alcohol selectivity through catalyst pre-treatment (2014)

Heat treating Fe/ZSM-5 under hydrogen leads to high dispersion of Fe species and higher alcohol selectivity in the oxidation of alkanes, as compared to oxygen treated catalysts.
A multilevel approach toward quadrupling the density of flash memory (1998)

A multilevel scheme is presented that explores the possibility of quadrupling flash EEPROM storage density. Sixteen levels (4 bits/cell) of charge are stored in existing NOR stacked gate devices. A distinction is made between logical threshold voltages (as seen by the sense amplifier) and transistor threshold voltages (as defined by the gate characteristics), and precise programming gives distinct logical threshold voltage distributions, whereas transistor threshold voltage distributions are contained in a small 2.5 V range and kept low so that logical distributions survive a ten-year equivalent data retention bake.