gebhart/patrepeval huggingface dataset:
Minimax Rate-optimal Estimation of KL Divergence between Discrete Distributions. (2016)

We refine the general methodology in [1] for the construction and analysis of essentially minimax estimators for a wide class of functionals of finite dimensional parameters, and elaborate on the case of discrete distributions with support size <i>S</i> comparable with the number of observations <i>n</i>. Specifically, we determine the "smooth" and "non-smooth" regimes based on the confidence set and the smoothness of the functional. In the "non-smooth" regime, we apply an unbiased estimator for a "suitable" polynomial approximation of the functional. In the "smooth" regime, we construct a bias corrected version of the Maximum Likelihood Estimator (MLE) based on Taylor expansion. We apply the general methodology to the problem of estimating the KL divergence between two discrete distributions from empirical data. We construct a minimax rate-optimal estimator which is adaptive in the sense that it does not require the knowledge of the support size nor the upper bound on the likelihood ratio. Moreover, the performance of the optimal estimator with <i>n</i> samples is essentially that of the MLE with <i>n</i> ln <i>n</i> samples, i.e., the <i>effective sample size enlargement</i> phenomenon holds.
DNA extraction from benthic Cyanobacteria: comparative assessment and optimization (2016)

These commercial kits allow greater recovery and the elimination of dangerous chemicals for DNA extraction, making them the method of choice for the isolation of DNA from benthic mats. They also facilitate the extraction of DNA from benthic Cyanobacteria, which can help to improve the characterization of Cyanobacteria in environmental studies using qPCRs or population composition analysis using next-generation sequencing.
NeurOS™ and NeuroBlocks™ a neural/cognitive operating system and building blocks (2014)

NeurOS is an open platform for accelerating research, development and hosting execution of intelligent applications. A NeurOS application is a directed “neural graph” of modular components connected by signal paths, similar to biological brain connectivity and functional block diagrams of neural pathways. Built-in reusable modules (NeuroBlocks) provide a wide range of general- and special-purpose capabilities: inputs/senses, outputs/effectors, processing, memory, pattern learning and recognition, visualization/instrumentation, custom module development, integrating external intelligence capabilities, and sub-graph reuse. NeurOS sub-graph assemblies address neural/cognitive functions including perception, pattern learning and recognition, working memory, imagination, prediction, context priming, attention, abstraction, classification, associational thinking and behavior. NeurOS applications are inherently portable, scalable, networkable, extensible and embeddable. NeurOS development tools provide simple intuitive graphical drag and drop application assembly from components without programming, along with testing, debugging, monitoring and visualization. Prototype NeurOS applications have begun to explore a wide range of intelligent functions in diverse areas, including aspects of pattern recognition, vision, music, reading, puzzle solving, reasoning, behavior. Building working intelligent systems using NeurOS and NeuroBlocks lets researchers and developers focus on their core functions and rapidly iterate and instrument working models, fostering both analytical and biological insight as well as usable systems.
The crystallization and morphology of polyethylene and its blends/ (2021)

The techniques of neutron and x-ray scattering have been used to study the morphology and crystallization behavior of polyethylene and blends of polyethylene. Synchrotron radiation was used to study the crystallization behavior of blends of high density polyethylene/ low density polyethylene (HDPE/LDPE) and linear low density/ low density polyethylene (LLDPE/LDPE). Simultaneous real time small and wide angle scattering from blends slowly cooled at (0.5$\\sp\\circ$C/min) seem to indicate that the lamellae are formed in bundles of primarily one component. For blends quickly cooled from the melt (quenched to 60$\\sp\\circ$C) on the other hand, the lamellae are randomly mixed together. HDPE/LDPE and LLDPE/LDPE blends show qualitatively the same crystallization behavior throughout the composition range except for 10%/90% LLDPE/LDPE. At this composition, extensive cocrystallization may be occurring in even slowly cooled samples. Small angle neutron and x-ray scattering was used to determine the location of the short chain branches in selectively deuterated LLDPE. Specially prepared LLDPE with the main chain deuterated was used in these experiments to provide contrast for neutron scattering. Despite density contributions to the neutron scattering from crystalline and amorphous regions, differences between the x-ray and neutron scattering suggest that the concentration of branches may be enhanced at the crystal- amorphous boundary. The extent of this branch-rich region was estimated to be about 30A. Lastly, the chain orientation of ultra high molecular weight PE (UHMWPE) was examined by small angle neutron scattering. A circularly averaging technique was applied in order to avoid sample alignment problems. Between extension ratios of 12 and 60, hot drawn (125$\\sp\\circ$C) gel crystallized UHMWPE does not show appreciable change in the perpendicular radius of gyration. However, changes in the asymptotic behavior of the scattering intensity from I $\\sim$ q$\\sp{-1.56}$ at 12x to I $\\sim$ q$\\sp{-1.2}$ at 60x indicate a change in geometry toward more rod like segments in the higher drawn material.
C/NOFS observations of the equatorial ionospheric electric field response to the 2009 major sudden stratospheric warming event (2011)

[1] We present new observations made by the Coupled Ion Neutral Dynamics Investigation (CINDI) Ion Velocity Meter (IVM) instrument onboard the Communication/Navigation Outage Forecasting System (C/NOFS) satellite that show the effects of the January 2009 sudden stratospheric warming (SSW) event on equatorial electric fields. We have used IVM observations to construct composite curves of mean equatorial vertical plasma drifts as a function of local time and longitude sector. These curves show large upward vertical drifts during morning hours and downward drifts during afternoon. Our analysis indicates that this pattern could be observed over the range of longitudes where adequate IVM measurements were available, from approximately 165°E to about 315°E longitude. A clear day-to-day, quasi-deterministic variability in the drifts is also observed, with the transition from upward to downward drifts occurring at increasing local times from 25 to 30 January 2009. The analysis also suggests some level of longitudinal variability in the magnitude of the drifts. These in-situ observations are in good agreement with previous ground-based measurements of the response of equatorial electric fields to SSW events. In particular, we found that IVM drift measurements centered around 285°E depart significantly from climatological values but agree exceptionally well with ground-based measurements of vertical drifts made by the Jicamarca incoherent backscatter radar. Overall, the results agree well with previous studies of SSW events, demonstrate the usefulness of the IVM observations and motivate further studies of the variability of the equatorial ionosphere using C/NOFS.
Fluorosilane-Based Electrolyte Additives to Improve High Temperature Performance of Graphite/LiMn2O4 Li-Ion Cells (2013)

Abstract not Available.
Seminar-Beiträge Cache-Optimierung (1998)

Dieser Bericht enthält die Ausarbeitungen von Vorträgen aus einem Seminar gleichen Namens, das am 29. Januar 1998 am Institut für Programmstrukturen und Datenorganisation unter Leitung von Holger Hopp, Daniela Genius und Michael Philippsen stattfand. Die Ausarbeitungen geben einen Überblick über Techniken und Modelle, um die Zwischenspeicher (Caches), die in praktisch allen heutigen Rechnern eingesetzt werden, effektiv einzusetzen. Dabei stehen insbesondere solche Techniken im Vordergrund, die von Übersetzern ausgeführt werden können wie diverse Schleifentransformationen, Speicherabbildungen, Vorzeitiges Laden von Daten. Außerdem werden Konsistenzmodelle für Parallelrechner untersucht.
Pipelined Delta Sigma Modulator Analog to Digital Converter for SOC Applications (2005)

A two-stage Pipelined Delta Sigma Modulator analog-to-digital converter is presented for broad band, high resolution System-on-a-Chip (SOC) applications. Input bandwidth is 62.5 MHz and the sampling frequency of 1 GHz results in an oversampling ratio of 8, and a 12-bit resolution with a 50 MHz input.
Induced Activation of the Toxoplasma gondiiNucleoside Triphosphate Hydrolase Leads to Depletion of Host Cell ATP Levels and Rapid Exit of Intracellular Parasites from Infected Cells (1998)

The nucleoside triphosphate hydrolase of Toxoplasma gondii is a potent apyrase. The protein is synthesized in large amounts and transported through the secretory pathway of the parasite and into the vacuolar space in an oxidized and thereby enzymatically inactive form. Complete activation of the purified enzyme is known to require dithiols (e.g. DTT); subcellular fractionation demonstrates that little if any (<5%) of the enzyme in the vacuolar space is active in the absence of DTT. Both native and epitope-tagged nucleoside triphosphate hydrolase (NTPase) were partially activated during immunoprecipitation, precluding precise assessment of enzyme activity in the vacuolar space but suggesting that protein-protein interactions may trigger activation. When infected cells were treated with DTT, the NTPase was activated in a dose-response fashion, as assessed by migration on SDS-polyacrylamide gel electrophoresis and by an increase in enzymatic activity. After activation, enzyme activity decreased with time in the presence of DTT; this inactivation was slowed by the presence of excess ATP. A rapid fall in host cell ATP was accompanied by an abrupt exit of parasites from cells. These results demonstrate that the oxidation/reduction status of the NTPase, the only parasite dense granule protein that contains disulfide bonds, is tightly controlled within the vacuolar space and may influence parasite exit from cells.
Crystal structure of 4-amino-1-arsenoso-benzene dihydrate, H2NC6H4As(OH)2(H2O) (1995)

Article Crystal structure of 4-amino-1-arsenoso-benzene dihydrate, H2NC6H4As(OH)2(H2O) was published on August 1, 1995 in the journal Zeitschrift für Kristallographie - Crystalline Materials (volume 210, issue 8).
Molecular basis of a novel rhino (hrrhChr) phenotype: a nonsense mutation in the mouse hairless gene (1998)

The hairless and rhino mutations are autosomal recessive allelic mutations that map to mouse Chromosome 14. In general, the rhino phenotype is a more severe manifestation of the hairless phenotype. In both hairless and rhino mice, the hair begins shedding in a cephalocaudal pattern within 7 days after birth, and never regrows due to a series of irreversible cellular events. The hairless mutation closely resembles the human disease known as papular atrichia (MIM 209500). Recently, this disease was linked to Chromosome 8p12, the human homolog of hairless was cloned and mapped to the same locus, and mutations have been identified in several different families. In order to gain insight into the pathophysiology of disease in papular atrichia, we sought to utilize mouse mutations as in vivo model systems. In this study, we report the identification of a homozygous nonsense mutation in the coding region of the hr gene in a hairless mouse captured on a chicken farm in the Midwestern United States. To reflect the place of identification of this new mutation at the hr locus, we have designated this allele hr(rhChr) using the laboratory code Chr (Christiano).
DeepSigns: A Generic Watermarking Framework for IP Protection of Deep Learning Models (2018)

Deep Learning (DL) models have caused a paradigm shift in our ability to comprehend raw data in various important fields, ranging from intelligence warfare and healthcare to autonomous transportation and automated manufacturing. A practical concern, in the rush to adopt DL models as a service, is protecting the models against Intellectual Property (IP) infringement. The DL models are commonly built by allocating significant computational resources that process vast amounts of proprietary training data. The resulting models are therefore considered to be the IP of the model builder and need to be protected to preserve the owner's competitive advantage. This paper proposes DeepSigns, a novel end-to-end IP protection framework that enables insertion of coherent digital watermarks in contemporary DL models. DeepSigns, for the first time, introduces a generic watermarking methodology that can be used for protecting DL owner's IP rights in both white-box and black-box settings, where the adversary may or may not have the knowledge of the model internals. The suggested methodology is based on embedding the owner's signature (watermark) in the probability density function (pdf) of the data abstraction obtained in different layers of a DL model. DeepSigns can demonstrably withstand various removal and transformation attacks, including model compression, model fine-tuning, and watermark overwriting. Proof-of-concept evaluations on MNIST, and CIFAR10 datasets, as well as a wide variety of neural network architectures including Wide Residual Networks, Convolution Neural Networks, and Multi-Layer Perceptrons corroborate DeepSigns' effectiveness and applicability.
Saturation of 1.064 μm absorption in Cr,Ca:Y3Al5O12 crystals (1992)

Saturation absorption experiments are conducted on the title compound at 1.064 μm with laser light propagating along both the [001] and [111] crystallographic axes. Rotation of the crystals about these axes during the experiments reveals that the transmission of the polarized 1.064 μm radiation is highly anisotropic in the saturation regime. The details of the anisotropy and saturation curves are explained using a simple model of subsets of optical centers along with a relevant set of rate equations. The ground and excited-state absorption cross sections at 1.064 μm are calculated to be σgs=5.7(±2)×10−18 cm2 and σes=8(±2)×10−19 cm2, respectively, and the optimum crystallographic orientation for utilization in optical devices is discussed.
Oyster Reefs as Natural Breakwaters Mitigate Shoreline Loss and Facilitate Fisheries (2011)

Shorelines at the interface of marine, estuarine and terrestrial biomes are among the most degraded and threatened habitats in the coastal zone because of their sensitivity to sea level rise, storms and increased human utilization. Previous efforts to protect shorelines have largely involved constructing bulkheads and seawalls which can detrimentally affect nearshore habitats. Recently, efforts have shifted towards "living shoreline" approaches that include biogenic breakwater reefs. Our study experimentally tested the efficacy of breakwater reefs constructed of oyster shell for protecting eroding coastal shorelines and their effect on nearshore fish and shellfish communities. Along two different stretches of eroding shoreline, we created replicated pairs of subtidal breakwater reefs and established unaltered reference areas as controls. At both sites we measured shoreline and bathymetric change and quantified oyster recruitment, fish and mobile macro-invertebrate abundances. Breakwater reef treatments mitigated shoreline retreat by more than 40% at one site, but overall vegetation retreat and erosion rates were high across all treatments and at both sites. Oyster settlement and subsequent survival were observed at both sites, with mean adult densities reaching more than eighty oysters m(-2) at one site. We found the corridor between intertidal marsh and oyster reef breakwaters supported higher abundances and different communities of fishes than control plots without oyster reef habitat. Among the fishes and mobile invertebrates that appeared to be strongly enhanced were several economically-important species. Blue crabs (Callinectes sapidus) were the most clearly enhanced (+297%) by the presence of breakwater reefs, while red drum (Sciaenops ocellatus) (+108%), spotted seatrout (Cynoscion nebulosus) (+88%) and flounder (Paralichthys sp.) (+79%) also benefited. Although the vertical relief of the breakwater reefs was reduced over the course of our study and this compromised the shoreline protection capacity, the observed habitat value demonstrates ecological justification for future, more robust shoreline protection projects.
Risk Factors and Clinical Outcome for Herpes Simplex Virus Reactivation in Patients after Allogeneic Hematopoietic Stem Cell Transplantation (2015)

Immune reconstitution is often impaired for months to years in patients after allogeneic hematopoietic stem cell transplantation (HSCT) which predisposes them to a wide collection of clinical infections.
Highly Stable, Amide‐Bridged Autoinducing Peptide Analogues that Strongly Inhibit the AgrC Quorum Sensing Receptor in Staphylococcus aureus (2016)

Blocking quorum sensing (QS) pathways has attracted considerable interest as an approach to suppress virulence in bacterial pathogens. Toward this goal, we recently developed analogues of a native autoinducing peptide (AIP-III) signal that can inhibit AgrC-type QS receptors and attenuate virulence phenotypes in Staphylococcus aureus. Application of these compounds is limited, however, as they contain hydrolytically unstable thioester linkages and have only low aqueous solubilities. Herein, we report amide-linked AIP analogues with greatly enhanced hydrolytic stabilities and solubilities relative to our prior analogues, whilst maintaining strong potencies as AgrC receptor inhibitors in S. aureus. These compounds represent powerful tools for the study of QS.
Effect of Psychotropic Drugs on Development of Diabetes Mellitus in Patients With Alzheimer's Disease (2015)

We aimed to examine risk of diabetes mellitus (DM) among older adults with Alzheimer's disease receiving 3 types of psychotropic drugs, that is, antipsychotics, antidepressants, and sedative anxiolytics. We retrospectively analyzed data from a hospital-based Clinical Research Center for Dementia of South Korea (CREDOS) study conducted between January 1, 2008 and December 31, 2012. Participants (n = 3042) with Alzheimer's disease were aged 65 or older and had no preexisting history of DM. Development of DM was identified using claims for initiating at least 1 prescription of antidiabetic medications or a diagnosis of DM during the follow-up period. Cox proportional hazards regression was used to demonstrate the Hazard ratio of DM in use of each psychotropic drug. Among the 3042 participants, 426 patients (14.0%) developed DM, representing an incidence rate of 5.2/100 person-years during an average 2.9 years of follow-up period. Among the 3 types of psychotropic drugs, antipsychotic users had a significantly higher risk of DM (hazard ratio = 1.74, 95% confidence interval = 1.10, 2.76) than nonusers, after adjusting covariates. Antidepressants and sedative anxiolytics did not achieve statistical significance. These results suggested that the diabetes risk was elevated in Alzheimer patients on antipsychotic treatment. Therefore, patients with Alzheimer's disease receiving antipsychotic treatment should be carefully monitored for the development of DM.
An EV on-board battery charger (2002)

A battery charger for electric vehicles (EV) is described. This charger is designed to provide the minimum recharge time by completely utilizing the available power sources. Charging rates up to 10 kW are supported. The required external infrastructure is also minimized so that charging may safely occur without specialized equipment. The power sources utilized are as flexible as possible to permit charging at as many places as possible. Additionally a DC power source, such as another EV, can be used as the power source permitting safe energy transfer between vehicles. The charging circuitry is lightweight and small, 37 pounds and 720 cubic inches, since the charger is on board the vehicle. Efficiency has been optimized, to reduce the need for heavy heat sinks and to maximize the energy available for charging. A microprocessor controls the charging process and tracks state of charge for several battery electrochemistries.
Abstract BL2: Lessons learned from an expedition exploring the world of HER2 positive breast cancer (2016)

Abstract HER2 positive breast cancer (BC) is often cited as a model of “treatment individualization”. This presentation will attempt to review the biomarker research efforts for this disease, with a special focus on the work coordinated by the Institut Jules Bordet in the advanced setting and the work of the Breast International Group (BIG) in the adjuvant setting. Biomarker (BM) exploration in the context of the CLEOPATRA and EMILIA trials has highlighted the poor prognosis associated with PiK3CA mutations, but has failed to identify any predictive BM beyond HER2. Our group, in collaboration with Dutch cancer centers, has prospectively “imaged” 57 patients under T-DM1 treatment using both “target imaging” (trastuzumab-zirconium PET) and FDG-PET: 4 imaging patterns have emerged, providing a striking illustration of advanced disease heterogeneity. Ongoing work will confirm whether these molecular imaging patterns can help to refine the selection of anti-HER2 therapies and, more specifically, support early discontinuation of expensive drug treatment that is unlikely to benefit patients. The translational research programs of BIG in the context of its (neo)adjuvant trials for HER2-positive BC will be reviewed and put into the context of findings by other researchers as well as the real needs of patients, which include the following: Can aggressive chemotherapy be avoided ? Can duration of treatment be shortened? Who does not need treatment “escalation”? Citation Format: Piccart M. Lessons learned from an expedition exploring the world of HER2 positive breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr BL2.
Contributions of White Matter Connectivity and BOLD Modulation to Cognitive Aging: A Lifespan Structure-Function Association Study (2019)

The ability to flexibly modulate brain activation to increasing cognitive challenge decreases with aging. This age-related decrease in dynamic range of function of regional gray matter may be, in part, due to age-related degradation of regional white matter tracts. Here, a lifespan sample of 171 healthy adults (aged 20-94) underwent magnetic resonance imaging (MRI) scanning including diffusion-weighted imaging (for tractography) and functional imaging (a digit n-back task). We utilized structural equation modeling to test the hypothesis that age-related decrements in white matter microstructure are associated with altered blood-oxygen-level-dependent (BOLD) modulation, and both in turn, are associated with scanner-task accuracy and executive function performance. Specified structural equation model evidenced good fit, demonstrating that increased age negatively affects n-back task accuracy and executive function performance in part due to both degraded white matter tract microstructure and reduced task-difficulty-related BOLD modulation. We further demonstrated that poorer white matter microstructure integrity was associated with weakened BOLD modulation, particularly in regions showing positive modulation effects, as opposed to negative modulation effects. This structure-function association study provides further evidence that structural connectivity influences functional activation, and the two mechanisms in tandem are predictive of cognitive performance, both during the task, and for cognition measured outside the scanner environment.