gebhart/patrepeval huggingface dataset:
Time-Varying Radiation Impedance of Microcontroller GPIO Ports and Their Dependence on Software Instructions (2022)

The coupling of short wavelength electromagnetic (EM) interference to critical electronic systems in highly reverberant enclosures is a growing concern in the EM interference/compatibility community. In such highly reverberant cavities, prior research has shown that the induced EM fields, voltages, or currents can be modeled using the wave-chaotic random coupling model (RCM). The RCM partitions the interaction within the cavity into a universally fluctuating part, derived from random matrix theory, and a system-specific part, defined by the radiation impedance of the ports of interest, where the voltages or currents are induced. Earlier researchers have treated the radiation impedance as a time-invariant, frequency-dependent complex quantity. This is true for passive structures but is not true for active semiconductor devices, such as microcontrollers, which can exhibit time-varying radiation properties depending on the instruction cycle being executed at a given instant of time. The estimate of such a time-varying radiation impedance and its correlation with instruction cycles in an elemental microcontroller is the focus of this work. Utilizing clustering algorithms, we observe that the measured radiation impedance, as well as radiative emissions, are correlated to the class of instruction cycles being executed. By clustering the radiation impedance and emissions of the general-purpose input/output ports utilizing the class of instructions being executed, predictive models for microcontroller susceptibility can be derived even when detailed knowledge of the specific instruction cycle being executed is unknown a priori. Such a predictive capability can find multiple applications in the EMI/EMC community.
Short Article Methylation of Histone H3 K4 Mediates Association of the Isw1p ATPase with Chromatin (2003)

Summary active genes (Ng et al., 2003).To understand how K4 H3 methylation regulates tran- Set1p methylates lysine 4 (K4) of histone H3 and regu- scription, we attempted to identify proteins that bind to lates the expression of many genes in yeast. Here methylated K4 H3 specifically. We found that human we use a biochemical approach to identify a protein, hSNF2H and the yeast homolog Isw1p bind to H3 tails Isw1p, which recognizes chromatin preferentially when efficiently only when K4 is di- or trimethylated. We pro- it is di- and trimethylated at K4 H3. We show that on vide in vivo evidence that Set1p and Isw1p act together certain actively transcribed genes, the Isw1p chroma- to regulate transcription. tin remodeling ATPase requires K4 H3 methylation toassociate with chromatin in vivo. Analysis of one suchgene, MET16 , shows that the enzymatic activities of ResultsSet1p and Isw1p are functionally connected: Set1pmethylationandIsw1pATPasegeneratespecificchro- Isw1p Binds to Methylated K4 H3matin changesat the5 endof thegene, arenecessary
Power Output and Durability of Electrospun Fuel Cell Fiber Cathodes with PVDF and Nafion/PVDF Binders (2016)

Membrane-electrode-assemblies (MEAs) with electrospun nanofiber mat electrodes (0.10 mg/cm2 Pt loading) and a Nafion 211 membrane were prepared and tested in a H2/air fuel cell at 100% and 40% relative humidity. The cathode binder was either neat poly(vinylidene fluoride) (PVDF) or a Nafion/PVDF blend (20 to 80 wt% Nafion) and the anode binder was Nafion with poly(acrylic acid). Polarization curves were recorded at 80°C and ambient pressure before, intermittently, and after a carbon corrosion voltage cycling experiment. The Nafion/PVDF cathode MEA with the smallest amount of PVDF (80/20 Nafion/PVDF weight ratio) produced the highest maximum power at beginning-of-life (BoL), 545 mW/cm2 at 100% RH, which was 35% greater than that for a conventional MEA with a neat Nafion binder. Carbon corrosion scaled inversely with cathode PVDF content, with a 33/67 Nafion/PVDF cathode binder MEA producing the highest end-of-life (EoL) power (330 mW/cm2). MEAs with < 50 wt% PVDF in the cathode binder exhibited a power density decline during carbon corrosion, whereas the power increased during/after carbon corrosion for nanofiber cathodes with binders containing > 50 wt% PVDF due to favorable increases in the hydrophilicity of the carbon support and Pt mass activity, coupled with a lower carbon loss.
Reconstruction of Measurement Matrices for Recovering Shape and Motion from Long Image Sequences. (1998)

The factorization method for recovering 3D information from image sequences assumes that all feature points selected on the first £rame can be tracked throughout. This assumption is violated, however, if some features disappear or new ones are introduced later. In this paper, based on the factorization method with the paraperspective projection model, we present a method for estimating image coordinates of occluded feature points in order for the estimated locations.to approximate closely their perspective projections. The estimation accuracy is evaluated with synthetic data and some results are presented for 3D information extraction fiom real image sequences. 1
Joint power and bandwidth allocation in cooperative wireless localization networks (2014)

Localization of wireless node is a key feature in many applications. Traditional localization has exploited the signal runtime between “agent” nodes that are to be localized and a set of “anchor” nodes with known position. Recently, cooperative localization that also uses runtime measurement between agent nodes has been shown to provide superior performance. This paper analyzes the optimum power and bandwidth allocation in such systems. We first formulate the general optimization problem and show that it is non-convex. We then develop an approximate algorithm based on Taylor expansion and iterative optimization of power and bandwidth separately to find an approximate solution; simulations show that results are close to the optimum solution (which is NP-hard). We also find that the importance of cooperative localization increases (and agents get assigned more resources) if the anchor deployment is bad in the sense that it provides high geometric dilution of precision and/or suffers from significant blockage between anchors and agents.
TnpI recombinase: identification of sites within Tn5401 required for TnpI binding and site-specific recombination (1995)

The Bacillus thuringiensis class II transposon Tn5401 encodes a recombinase protein, TnpI, that mediates the resolution of cointegrate molecules generated as intermediates during Tn5401 transposition by the TnpA transposase. This recombination event requires a specific target site, or internal resolution site, at which TnpI binds and catalyzes the exchange of DNA strands. Gel mobility shift assays and DNase I footprinting analyses were used to localize the TnpI binding region to the sequence extending from nucleotides 637 to 747 of Tn5401. Deletions within this region blocked TnpI-mediated recombination in vivo. The 12-bp sequence ATGTCC RCTAAY, present in four copies within the TnpI binding region, is proposed to be the recognition sequence for TnpI binding. TnpI also binds to a single copy of this sequence located within the 53-bp terminal inverted repeats of Tn5401. The unique juxtaposition of recombinase and transposase binding sites at the terminal inverted repeats of Tn5401 suggests that TnpI regulates the binding and/or catalytic activity of TnpA transposase.
Linkage disequilibrium of common Gaucher disease mutations with a polymorphic site in the pyruvate kinase PKLR gene (1998)

Gaucher disease (GD), caused by a deficiency of the lysosomal enzyme glucocerebrosidase (GBA), is the most common human glycolipid storage disease. The incidence of the disease is particularly high in the Ashkenazi Jewish population, with a carrier frequency of 0.068. The 1226A→G and 84GG mutations are the two predominant disease-causing alleles. We investigated the association of various mutations in the GBA gene with different alleles of a highly polymorphic site in the adjacent pyruvate kinase (PKLR) gene. Ninety-seven unrelated type I GD patients of various genotypes were studied to determine their genotype for the PKLR gene trinucleotide repeat polymorphism. One hundred out of 104 (96%) alleles carrying the 1226G mutation also carried the A1 allele of the PKLR gene, which is present in only 6.7% of the control population. The calculated linkage disequilibrium between 1226G and the A1 allele of the PKLR gene is 0.957. Mutation 84GG was found to be uniquely associated with the PKLR A6 allele, with a linkage disequilibrium of 1.00. The association of several less frequent GD mutations with PKLR alleles was also studied. These results support the hypothesis that the 1226G and 84GG mutations in the Ashkenazi Jewish population each originated in a single founder. Further studies of the association of the 1226G and 84GG mutations with PKLR alleles in European non-Jewish GD patients could help in the study of the chronological order of these mutations and may shed light on the history of the Ashkenazi Jews in the past two millennia. Am. J. Med. Genet. 78:233–236, 1998. © 1998 Wiley-Liss, Inc.
Prognostic relevance of DNA damage and repair biomarkers in elderly patients with hormone-receptor-positive breast cancer treated with neoadjuvant hormone therapy: evidence from the real-world setting (2019)

Background: The logic behind the outcome of endocrine therapy in breast cancer has long remained poorly understood. The prognostic role of DNA damage and repair biomarkers (DDR) was explored in postmenopausal, hormone-receptor-positive breast cancer patients treated with neoadjuvant hormone therapy (NAHT). Methods: Data on 55 patients were included. The phosphorylated ataxia-teleangectasia and Rad3-related protein (pATR), phosphorylated ataxia-telangiectasia mutated (ATM) kinase, and phosphorylated H2A Histone Family Member X (γ-H2AX) were evaluated by immunohistochemistry in paired tissues collected at baseline and following NAHT. Biomarkers were considered both singularly and within signatures. Ki-67 percentage change was the primary biomarker endpoint. Classical endpoints were also considered. Results: The most favorable Ki-67 outcome was associated with the γ-H2AX/pATM signature ( p = 0.011). In models of Ki-67 reduction, ‘luminal B’ subtype, higher grade of anaplasia, and the γ-H2AX/pATM signature tested as significant ( p &lt; 0.05 for all). Results were confirmed in multivariate analysis. No association was observed with pathologic response. An increase of ∆γ-H2AX in paired breast tissues was associated with longer event-free survival ( p = 0.027) and overall survival ( p = 0.042). In Cox models, both survival outcomes were solely affected by grade of anaplasia, with less favorable prognosis in the highest grades ( p &lt; 0.05 for both). Conclusions: We report novel evidence of the prognostic role of DDR biomarkers on important patient outcomes in postmenopausal hormone-receptor-positive breast cancer patients treated with NAHT. If confirmed in future and adequately sized trials, our results may help inform therapeutic decisions and clarify underlying biological mechanisms.
Prediction of poor outcome using detector of epileptiform EEG in ICU patients resuscitated after cardiac arrest (2007)

Assessing the brain status of patients admitted to intensive care unit (ICU) after out-of-hospital cardiac arrest is challenging. We had earlier found wavelet subband entropy (WSE) to be a useful tool for quantifying the epileptiform content of EEG during anesthesia. In this paper, WSE was applied for EEG of ICU patients to study its prognostic value. During their stay in ICU, EEG was recorded from 20 patients resuscitated after out-of-hospital cardiac arrest. For the analysis, the patients were divided into subgroups of poor outcome (persistent vegetative state, N=4) and good outcome (regain of consciousness, N=16). WSE for each 5-sec segment of EEG was calculated and also the average of WSE for each hour. Also, similar results were calculated for EEG powers in the bands 16-32 Hz and 1-60 Hz to be used as references. The statistical analysis was made by comparing the medians of the distributions of average WSE of each hour between poor and good outcome groups. The median of WSE of poor outcome group was significantly lower than that of good outcome group. The reference indicators did not show significant differences between the groups. The results suggest that WSE can be a valuable prognostic indicator for detecting the patients with poor outcome.
One for All: Towards Language Independent Named Entity Linking (2016)

Entity linking (EL) is the task of disambiguating mentions in text by associating them with entries in a predefined database of mentions (persons, organizations, etc). Most previous EL research has focused mainly on one language, English, with less attention being paid to other languages, such as Spanish or Chinese. In this paper, we introduce LIEL, a Language Independent Entity Linking system, which provides an EL framework which, once trained on one language, works remarkably well on a number of different languages without change. LIEL makes a joint global prediction over the entire document, employing a discriminative reranking framework with many domain and language-independent feature functions. Experiments on numerous benchmark datasets, show that the proposed system, once trained on one language, English, outperforms several state-of-the-art systems in English (by 4 points) and the trained model also works very well on Spanish (14 points better than a competitor system), demonstrating the viability of the approach.
Dysregulation of genome-wide gene expression and DNA methylation in abnormal cloned piglets (2014)

The abnormal cloned piglets showed substantial changes both in the DNAm and the gene expression. Our data may provide new insights into understanding the molecular mechanisms of the reprogramming of genetic information in cloned animals.
Solution Self-Assembly and Photophysics of Platinum Complexes Containing Amphiphilic Triblock Random Copolymers Prepared by ROMP (2009)

Ring-opening metathesis polymerization was used to synthesize amphiphilic, phosphorescent block copolymers that self-assemble into nanometer-scaled aggregates when dissolved in a selective solvent. The triblock random copolymer architecture is built up by using an oligoglycol-substituted norbornene derivative for the hydrophilic part, 2,3-norbornenedicarboxylic acid dimethyl ester, as the first segment of the hydrophobic part and a statistical segment made using norbornene-functionalized dyes as the second segment of the hydrophobic part. The dyes comprise a blue fluorescent carbazole derivative serving as the host and a red phosphorescent platinum complex serving as the guest material. Emission properties of the amphiphilic triblock random copolymer dissolved in a nonselective solvent are exclusively determined by the host material. Only blue emission of the carbazole-derivative can be observed. When the polymer is dissolved in a selective solvent, polymer aggregates are formed and energy transfer occurs. In this case, deep red phosphorescence stemming from the platinum complex used as guest component can be observed. The amphiphilic triblock random copolymer architecture allows for the dispersion of the platinum chromophore in a solvent in which the parent chromophore is insoluble, the realization of a large Stokes shift of about 260 nm and significant suppression of platinum complex self-quenching, resulting in considerable phosphorescent quantum yields. Absorbance, luminescence, quantum yield, and lifetime measurements of this polymer and several model polymers in selective and unselective solvents as well as in the solid state have been performed to understand the energy transfer from the host to the guest dye in this particular system.
RaTTy: Mouse cum Pen (2016)

The name "RaTTy" comes from the word "Rat" which means "Mouse" and the reason that it has been named as RaTTy is, the proposed technology is an enhancement of existing optical mouse and pen technology. RaTTy is an accurate combination of optical mouse and pen as the mouse structure has been reshaped and then a pen mechanism has been added up to make it similar to a "Mouse cum Pen".
Optical Technology for NFV Converged Networks (2021)

5G and its evolution towards 6G is unlocking new use cases that will require the reconsideration of the existing network architectures and its operation. As the network will be required to support new service types and radio protocol splits, the traditional physical point to point connections will need to be replaced with a transport network up to the antenna site to guarantee low latency services and high bandwidth. Optical based transport is a key enabler to realize such a convergent network, where the traditional fixed infrastructure in use for mobile services and mobile infrastructure should also support enterprises services. The Software Defined Network (SDN) and Network Function Virtualization (NFV) technology plays a key role to evolve towards digitalization. It allows to simplify the creation of new services and to implement a real decoupling between the infrastructure and the network functions that run virtually, on generic processing units located everywhere in the network. Supporting automation is a key requirement that traditional optical technology is not able to meet. In this paper the reference scenarios for the access network are presented with the analysis of their requirements and the enabling optical solutions based on integrated silicon photonics.
Interfaces in organic devices studied with resonant soft x-ray reflectivity (2011)

Interfaces between donor and acceptor semiconducting polymers are critical to the performance of polymer light-emitting diodes and organic solar cells. Similarly, interfaces between a conjugated polymer and a dielectric play a critical role in organic thin-film transistors. Often, these interfaces are difficult to characterize with conventional methods. Resonant soft x-ray reflectivity (R-SoXR) is a unique and relatively simple method to investigate such interfaces. R-SoXR capabilities are exemplified by presenting or discussing results from systems spanning all three device categories. We also demonstrate that the interfacial widths between active layers can be controlled by annealing at elevated temperature, pre-annealing of the bottom layer, or casting from different solvent mixtures. The extension of R-SoXR to the fluorine K absorption edge near 698 eV is also demonstrated.
AN INDUSTRIAL EMBEDDED CONTROL SYSTEM DESIGN PROCESS (2011)

Embedded software provides a flexible and powerful means to differentiate products and achieve competitive advantage. However, the design of embedded software tends to be difficult to manage. This paper describes the use of model-based design to help manage the design of embedded control systems. It presents typical design configurations, such as rapid prototyping, software-in-the-loop, processor-in-the-loop, and hardware-in-the-loop, and discusses their differences and usages. Finally, an overview of some of the aspects typical in developing embedded control systems using model-based design is given.
The role of ZBED6 in transcriptional regulation studied by transcriptome analysis after RNAi in mouse myoblasts (2012)

ZBED6 is a recently discovered transcription factor that has evolved from a domesticated DNA transposon and is unique to placental mammals. Here we further characterize the functional significance ...
Phylogenetic Analysis of Anaerobic Co-Digestion of Animal Manure and Corn Stover Reveals Linkages between Bacterial Communities and Digestion Performance (2016)

Over 3 million tons of manures are produced annually in the United States and pose environmental and health risks if not remediated. Anaerobic digestion is an effective method in treating organic wastes to reduce environmental impacts and produce methane as an alternative energy. Previous studies suggested that optimization of feed composition, hydraulic retention time, and other operational conditions can greatly improve total solids removal and increase methane productivity. These environmental factors improve functionality by altering the microbial community structure but explicit details of how the bacterial community shifts are poorly understood. Our investigations were conducted to investigate the relationship between environmental factors, microbial community structure and bioreactor efficiency by using metagenomic analysis of the microbial communities. Our results indicated that the bioreactor with the greatest methane production, digestion efficiency and reduced levels of E. coli/Shigella had a distinctive community structure at the genus level with unique and abundant uncultivated strains of Bacteroidetes. Moreover the same bioreactor was enriched in Aminomonas paucivorans and Clostridia populations that can utilize secondary metabolites produced during cellulose/hemicellulose degradation to generate hydrogen and acetate. Hence specific digestion conditions that enrich for these populations may provide a route to the optimization of co-digestion systems and control the variability in reactor performance.
The Role of Ultrasound-Driven Microbubble Dynamics in Drug Delivery: From Microbubble Fundamentals to Clinical Translation (2019)

In the last couple of decades, ultrasound-driven microbubbles have proven excellent candidates for local drug delivery applications. Besides being useful drug carriers, microbubbles have demonstrated the ability to enhance cell and tissue permeability and, as a consequence, drug uptake herein. Notwithstanding the large amount of evidence for their therapeutic efficacy, open issues remain. Because of the vast number of ultrasound- and microbubble-related parameters that can be altered and the variability in different models, the translation from basic research to (pre)clinical studies has been hindered. This review aims at connecting the knowledge gained from fundamental microbubble studies to the therapeutic efficacy seen in in vitro and in vivo studies, with an emphasis on a better understanding of the response of a microbubble upon exposure to ultrasound and its interaction with cells and tissues. More specifically, we address the acoustic settings and microbubble-related parameters (i.e., bubble size and physicochemistry of the bubble shell) that play a key role in microbubble-cell interactions and in the associated therapeutic outcome. Additionally, new techniques that may provide additional control over the treatment, such as monodisperse microbubble formulations, tunable ultrasound scanners, and cavitation detection techniques, are discussed. An in-depth understanding of the aspects presented in this work could eventually lead the way to more efficient and tailored microbubble-assisted ultrasound therapy in the future.
An O(n) algorithm for transistor stacking with performance constraints (1996)

We describe a new constraint-driven stacking algorithm for diffusion area minimization of CMOS circuits. It employs an Eulerian trail finding algorithm that can satisfy analog-specific performance constraints. Our technique is superior to other published approaches both ill terms of its time complexity and in the optimality of the stacks it produces. For a circuit with n transistors. The time complexity is O(n). All performance constraints are satisfied and, for a certain class of circuits, optimum stacking is guaranteed.