gebhart/patrepeval huggingface dataset:
Observer-Based Adaptive Robust Control of Friction Stir Welding Axial Force (2010)

Friction stir welding (FSW) is a relatively new and promising joining process that is the subject of much current research. When welding with constant parameters, the axial force can vary significantly due to changes in workpiece temperature and other process variations. These variations produce welds with inconsistent microstructure and tensile strength. Control of the axial weld force is desirable to improve the weld quality. In this paper, an observer-based adaptive robust control (ARC) approach for the axial force of FSW is presented to overcome process disturbances and model errors stemming from the simplistic dynamic models suitable for control. Some correlation is shown between spindle power and axial force, allowing readily available power measurements to be used for feedback. A model of the axial force is developed as a combination of a nonlinear static gain and linear dynamics. An axial force controller is constructed using the ARC approach and estimated state feedback from the adaptive divided difference filter (ADDF). Verification experiments are conducted on a vertical milling machine configured for FSW using an open architecture controller. The combined ARC/ADDF technique is shown to dramatically reduce axial force variations in the presence of significant process disturbances.
ChemInform Abstract: Copper(II) Triflate as a Mild and Efficient Catalyst for Ferrier Glycosylation: Synthesis of 2,3‐Unsaturated O‐Glycosides. (2014)

Abstract 1‐Azabicyclo[2.2.2]octan‐3‐ol fails to react.
Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination (2022)

SARS-CoV-2 Delta and Omicron are globally relevant variants of concern. Although individuals infected with Delta are at risk of developing severe lung disease, infection with Omicron often causes milder symptoms, especially in vaccinated individuals<sup>1,2</sup>. The question arises of whether widespread Omicron infections could lead to future cross-variant protection, accelerating the end of the pandemic. Here we show that without vaccination, infection with Omicron induces a limited humoral immune response in mice and humans. Sera from mice overexpressing the human ACE2 receptor and infected with Omicron neutralize only Omicron, but not other variants of concern, whereas broader cross-variant neutralization was observed after WA1 and Delta infections. Unlike WA1 and Delta, Omicron replicates to low levels in the lungs and brains of infected animals, leading to mild disease with reduced expression of pro-inflammatory cytokines and diminished activation of lung-resident T cells. Sera from individuals who were unvaccinated and infected with Omicron show the same limited neutralization of only Omicron itself. By contrast, Omicron breakthrough infections induce overall higher neutralization titres against all variants of concern. Our results demonstrate that Omicron infection enhances pre-existing immunity elicited by vaccines but, on its own, may not confer broad protection against non-Omicron variants in unvaccinated individuals.
Técnica de Produção do Fungo Entomopatogênico Metarhizium Anisopliae para Uso em Controle Biológico (2013)

Introdução. Desenvolvimento metodológico. Inóculo inicial. Produção do fungo em arroz. Secagem em estufa elétrica. Extração dos conídios secos. Secagem final e armazenamento. Lista de materiais e equipamentos utilizados. Referências.
The Effect of Battery Potential and Charge Rate on the Decomposition Reaction on the Anode Electrode of Lithium Ion Polymer Battery (2014)

The breakdown of the protective solid electrolyte interface (SEI) layer on the anode electrode can initiate further electrolyte decomposition reaction and result in the formation of a non-uniform layer of electronically insulating reaction products on the graphite particles. The results from this study indicated that raising the state of charge (SOC) increased the rate of the electrolyte decomposition side reaction to form a thick deposit layer. The deposit surface layer formed at the electrode/electrolyte interface increased the interfacial charge transfer resistance and rise in the overall batteries impedance. A direct correlation between the capacity fade during cycling and the deposit layer growth was established. Analysis of the anode and the deposit layer showed an increasing amount of lithium in the deposit layer as well as “trapped” lithium in the graphite crystal structure as the batteries were aged at higher SOC.
Semantic Kernels Binarized - A Feature Descriptor for Fast and Robust Matching. (2011)

This paper presents a new approach for feature description used in image processing and robust image recognition algorithms such as 3D camera tracking, view reconstruction or 3D scene analysis. State of the art feature detectors distinguish interest point detection and description. The former is commonly performed in scale space, while the latter is used to describe a normalized support region using histograms of gradients or similar derivatives of the grayscale image patch. This approach has proven to be very successful. However, the descriptors are usually of high dimensionality in order to achieve a high descriptiveness. Against this background, we propose a binarized descriptor which has a low memory usage and good matching performance. The descriptor is composed of binarized responses resulting from a set of folding operations applied to the normalized support region. We demonstrate the real-time capabilities of the feature descriptor in a stereo matching environment.
A glycosaminoglycan inhibitor of thrombin: A new mechanism for abnormal hemostatic assays in cancer (1991)

The isolation and partial characterization of a novel anticoagulant from the plasma of a patient with metastatic prostate cancer is described. The patient had a prolonged activated partial thromboplastic time, prothrombin time and thrombin time which did not correct by mixing with normal plasma. The reptilase time was normal and the prolonged thrombin time was corrected with protamine sulfate suggesting a heparin-like anticoagulant. A glycosaminoglycan anticoagulant (GAC) was isolated from the patient's plasma. The inhibitory activity of the GAC was destroyed by treatment with chondroitinase ABC. The GAC migrated on agarose gel electrophoresis between keratin sulfate and heparan sulfate. Purified GAC possessed only 2% (W/W) of the antithrombin III cofactor activity of porcine heparin. In assays using purified fibrinogen, the GAC was shown to directly inhibit fibrinogen proteolysis by thrombin. It is concluded that this glycosaminoglycan anticoagulant directly inhibits thrombin clotting of fibrinogen and is a new mechanism for abnormal hemostatic assays in cancer.
Long-read, whole-genome shotgun sequence data for five model organisms (2014)

Abstract Single molecule, real-time (SMRT) sequencing from Pacific Biosciences is increasingly used in many areas of biological research including de novo genome assembly, structural-variant identification, haplotype phasing, mRNA isoform discovery, and base-modification analyses. High-quality, public datasets of SMRT sequences can spur development of analytic tools that can accommodate unique characteristics of SMRT data (long read lengths, lack of GC or amplification bias, and a random error profile leading to high consensus accuracy). In this paper, we describe eight high-coverage SMRT sequence datasets from five organisms (Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, and Drosophila melanogaster) that have been publicly released to the general scientific community (NCBI Sequence Read Archive ID SRP040522). Data were generated using two sequencing chemistries (P4C2 and P5C3) on the PacBio RS II instrument. The datasets reported here can be used without restriction by the research community to generate whole-genome assemblies, test new algorithms, investigate genome structure and evolution, and identify base modifications in some of the most widely-studied model systems in biological research.
Evaluation of RNA-sequencing (RNA-seq) signatures with pembrolizumab (pembro) in patients (pts) with renal cell carcinoma (RCC) from KEYNOTE-427 cohort A. (2020)

729 Background: We evaluated the association (assoc) of baseline RNA-seq–based signatures with response/resistance to pembro from the phase 2 KEYNOTE-427 study (NCT02853344) in pts with advanced clear cell RCC enrolled in cohort A (n = 110). Methods: In pembro-treated pts with RNA-seq and clinical data (N = 78), we analyzed the assoc of signatures (18-gene tumor T-cell–inflamed GEP; 10 non–T-cell–inflamed GEP canonical signatures [angiogenesis, gMDSC, glycolysis, hypoxia, mMDSC, MYC, proliferation, RAS, stromal/EMT/TGFβ, WNT]) quantifying the TME with clinical outcomes. Canonical signatures were derived from 2 databases (TCGA, Moffit) using an algorithm that included genes based on their correlation to reference signatures in the literature. Signature definitions were finalized before linking to the clinical data, and significance was prespecified at 0.10 given the potential for limited power. Canonical signatures were also analyzed through regression testing of response and the residuals of consensus signatures after adjusting for T-cell–inflamed GEP and IMDC scores in the model. P values were adjusted for multiplicity. Database cutoff date for clinical data: March 12, 2019. Results: Pt characteristics for this analysis were similar to those of the overall cohort A population. T-cell–inflamed GEP was statistically significantly assoc with ORR ( P = 0.021) but not PFS ( P = 0.116). When adjusting for PD-L1 expression (CPS by IHC) and IMDC scores, T-cell–inflamed GEP remained statistically significantly assoc with ORR ( P = 0.059). The angiogenesis signature was not assoc with response. PD-L2 RNA-seq expression was not assoc with response with multiplicity-adjusted P values. Like PD-L1 IHC, PD-L2 RNA-seq expression moderately correlated with T-cell–inflamed GEP and did not show independent predictive value when adjusted for T-cell–inflamed GEP and IMDC scores. Conclusions: RNA-seq–based, T-cell–inflamed GEP was assoc with ORR in pts with clear cell RCC receiving first-line pembro monotherapy; no canonical signatures showed statistical significance. Future directions for these data include whole exome sequencing analysis. Clinical trial information: NCT02853344.
C2‐Symmetric Bissulfoximines as Ligands in Copper‐Catalyzed Enantioselective Diels—Alder Reactions. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
A multi-tag access scheme for indoor UWB localization systems used in medical environments (2011)

Ultra wideband (UWB) wireless systems have many advantages in indoor environments with dense multipath. UWB positioning systems are increasingly used in indoor environments to track and locate important assets. Many applications exist in medicine for UWB positioning which includes tracking personnel, assets, and even surgical navigation. We have designed a UWB positioning system with millimeter range accuracy with potential use in surgical navigation. This paper outlines a multi-tag access scheme for our UWB positioning system which integrates a 2.4 GHz physical layer to allow simultaneous tracking of up to 30 UWB tags. A static experiment was performed with two UWB tags while switching between the tags at 20 Hz. Millimeter accuracy was achieved even when tracking two tags. A 10% system latency was experienced when adding the multi-tag overhead, although a 744 Hz system update rate was still achieved. Asynchronous communication between the FPGA and microcontroller at the main control station ensured correct synchronization of the 3-D positioning data and corresponding tag ID. Future work includes a full dynamic experiment with simultaneous tracking of 5-10 tags.
Table S2 from Growth of Triple-Negative Breast Cancer Cells Relies upon Coordinate Autocrine Expression of the Proinflammatory Cytokines IL-6 and IL-8 (2023)

&lt;p&gt;Table S2 - XLSX file 77K, Verification of lentiviral shRNA knock-down in SUM159 cells by quantitative RT-PCR&lt;/p&gt;
Un-Trusted-HB: Security Vulnerabilities of Trusted-HB. (2009)

With increased use of passive RFID tags, the need for secure lightweight identification protocols arose. HB+ is one such protocol, which was proven secure in the detection-based model, but shown breakable by man-in-the-middle attacks. Trusted-HB is a variant of HB+, specifically designed to resist man-in-the-middle attacks. In this paper, we discuss several weaknesses of Trusted-HB, show that the formal security proof provided by its designers is incorrect, and demonstrate how to break it in realistic scenarios.
A Genetic and Sequencing Study of IS1 and Tn9 Insertions in the Escherichia coli lac Operon (1979)

The quintessential feature of transposable elements is their ability to translocate to different positions on the chromosome or to another replicon in the cell, without regard to extensive sequence homology (for reviews, see Cohen 1976; Starlinger and Saedler 1976; Bukhari et al. 1977; Kleckner 1977; Nevers and Saedler 1977). The molecular mechanism of transposition is not understood. What happens to the DNA of such elements and their target sites during translocation? To investigate this question, we have combined genetic and sequencing studies of insertions of the transposable elements IS1 and Tn9 in the lac operon of Escherichia coli. IS1 is a transposable sequence of 768 bp (Ohtsubo and Ohtsubo 1978; L. Johnsrud, in prep.) present at about 10 copies/cell (Saedler and Heiss 1973; Chow 1977). It has strong polar effects when inserted within an operon (Jordan et al. 1967; Saedler and Starlinger 1967a,b; Adhya and Shapiro 1969; Shapiro and Adhya...
The streaming of the submandibular gland II: parenchyma and stroma advance at the same velocity (1989)

Thirty young male rats aged 7 weeks, weighing 200 g, were injected with 18.5 kBq g-1 (0.5 microCi g-1) body weight tritiated thymidine [3H]TdR (specific activity 185 GBq). The rats were then killed in groups of five, at the following times: 1 hour, and 14, 30, 60, 90, and 120 days. Autoradiograms of sections through the submandibular gland were prepared, and the location of labelled cells in tubular and acinar cross sections was recorded. The nuclear content of each cross section was defined as its 'class'. In this numbering system, narrow tubuli, e.g. intercalated ducts are of low class, and wider tubuli, e.g. striated ducts, of high class. One hour after labelling most labelled tubular cells were found in low class cross sections, i.e. intercalated ducts and narrow granular ducts. Striated ducts were not labelled. From then onward labelled cells entered wider tubuli, e.g. striated ducts. The advancing labelled epithelium was accompanied by labelled stroma. Both cell types traversed 0.089 classes per day. In acini, labelled cells advanced in the opposite direction, starting from acinar cross sections of high class and ending in class-1 cross sections.
A three dimensional children head database for acoustical research and development (2013)

Most computational-acoustic work within spatial hearing relies on head-related transfer functions from databases of measurements taken on adult humans or dummy heads. We aim to provide a set of 3D digital heads including children, from which head-related transfer functions can be computed instead of measured. However, current volumetric scanning techniques do not have sufficient resolution for accurately scanning the external ear, and computed tomography also involves radiation. In this paper we propose a framework for scanning, stitching and meshing complete human heads. The process starts by acquisition of multiple 3D surface scans of the same subject using a high-resolution photogrammetric scanner. Secondly, the scans are semi-automatically aligned and noise and incoherence is removed. This is followed by an iterative process where a volumetric implicit representation of the head is optimized. The process consists of a regularized surfacereconstruction step followed by an alignment step. Finally, a surface representation of the entire head is extracted using a triangulation of the zero-level iso-surface of the implicit volume. The process has been used to reconstruct the heads of children aged 10 months to 9 years. The data and the associated reconstruction algorithms will be made publicly available for use in acoustical research and development.
ChemInform Abstract: A NOVEL DIASTEREOSELECTIVE SYNTHESIS OF THE LACTONE MOIETY OF COMPACTIN (1984)

Abstract Phloroglucin (I) wird über Ra‐Ni zu (IIIa) reduziert, selektiv zu (IIIb) silyliert und dann zum Keton (IV) oxidiert, das nach Baeyer‐Villiger zum Lacton (V) oxidiert wird.
Thermodynamic Limit of Interacting Particle Systems over Time-varying Sparse Random Networks (2017)

We establish a functional weak law of large numbers for observable macroscopic state variables of interacting particle systems (e.g., voter and contact processes) over fast time-varying sparse random networks of interactions. We show that, as the number of agents $N$ grows large, the proportion of agents $\left(\overline{Y}_{k}^{N}(t)\right)$ at a certain state $k$ converges in distribution -- or, more precisely, weakly with respect to the uniform topology on the space of \emph{càdlàg} sample paths -- to the solution of an ordinary differential equation over any compact interval $\left[0,T\right]$. Although the limiting process is Markov, the prelimit processes, i.e., the normalized macrostate vector processes $\left(\mathbf{\overline{Y}}^{N}(t)\right)=\left(\overline{Y}_{1}^{N}(t),\ldots,\overline{Y}_{K}^{N}(t)\right)$, are non-Markov as they are tied to the \emph{high-dimensional} microscopic state of the system, which precludes the direct application of standard arguments for establishing weak convergence. The techniques developed in the paper for establishing weak convergence might be of independent interest.
O5‐10‐05: NOVEL INSIGHTS OF TAU RNA‐PROTEIN BIOLOGY IN THE PRECIPITATING ROLE OF CHRONIC STRESS ON ALZHEIMER'S DISEASE BRAIN PATHOLOGY (2019)

Imbalance of neuronal proteostasis associated with misfolding and aggregation of Tau protein is a common neurodegenerative feature in Alzheimer's disease (AD) and other Tauopathies. Consistent with suggestions that lifetime stress maybe an important AD precipitating factor, we previously reported that environmental stress and high glucocorticoid (GC) levels induce accumulation of aggregated Tau; however, the underlying molecular mechanisms for such process remain poorly understood Hereby, we monitor a novel interplay between stress granules (SGs), an RNA-protein granule mechanism, and autophagic machinery in the underlying mechanisms through which chronic stress and high GC levels impact on Tau proteostasis precipitating Tau aggregation by using molecular, pharmacological, cellular and behavioral analysis. We demonstrate that prolong environmental stress and high GC trigger an mTOR-dependent inhibition of autophagy, leading to the accumulation of Tau aggregates and cell death in P301L-Tau expressing mice and cells. In parallel, we found that chronic stress and GC exposure disturb cellular homeostasis of various RNA-binding proteins, such as TIA-1, G3BP1 and FUS, stimulating the induction of SG, recently shown to promote Tau aggregation and neurotoxicity. Interestingly, an mTOR-driven pharmacological stimulation of autophagy attenuates the GC-driven accumulation of Tau and SGs as well as cell death, indicating a critical interface between autophagy and the SG response in the neurodegenerative potential of chronic stress and GC. These studies provide novel insights into the RNA-protein intracellular signaling regulating the precipitating role of environmental stress and GC on Tau-driven brain pathology.
Ultrasound Despeckling Using an Adaptive Window Stochastic Approach (2006)

A novel stochastically driven filtering method to despeckle B mode ultrasound images is presented. This method is motivated by viewing the pixel values as a stochastic process and removing outliers, where outliers are defined by local extrema. These outliers are removed by local averaging. This produces another image with new outliers (local extrema) and the process is iterated. With each iteration homogeneous regions become smoother while edges that defined these regions are preserved. By allowing a dynamically varying window to determine the local mean, we achieve equivalent results with fewer iterations.
Overexpression of the p53 Tumor Suppressor Gene Product in Primary Lung Adenocarcinomas Is Associated with Cigarette Smoking (1993)

Mutations in the p53 tumor suppressor gene are frequently observed in primary lung adenocarcinomas, suggesting that these mutations are critical events in the malignant transformation of airway cells. These mutations are often associated with stabilization of the p53 gene product, resulting in the accumulation of p53 protein. In this study, 70 formalin-fixed, paraffin-embedded primary lung adenocarcinomas resected for potential cure were examined for p53 overexpression. These 70 lung adenocarcinomas were obtained from a series of patients with well-documented clinical histories, and all 70 carcinomas had been previously evaluated for point mutations in codon 12 of the K-ras oncogene. Overexpression of the p53 protein was detected using an antigen retrieval system (Target Unmasking Fluid) and the anti-p53 antibody CM-1. CM-1 is a polyclonal antibody directed against the wild-type p53 protein. Overexpression of the p53 protein was found in 23 (33%) of the 70 lung adenocarcinomas. In all 23 cases, overexpression was confined to neoplastic cells. Overexpression of the p53 protein correlated with cigarette smoking: 10 (56%) of the 18 adenocarcinomas from patients who were current smokers overexpressed p53 compared with 13 (33%) of the 40 adenocarcinomas from patients who had quit smoking and 0 (0%) of the 12 adenocarcinomas from patients who had never smoked (p = 0.002, trend test). Overexpression of the p53 protein was also related to the degree of histologic differentiation: 48% of the p53 negative carcinomas were well differentiated, whereas only 13% (p = 0.003) of the carcinomas in which p53 was overexpressed were well differentiated. Overexpression of the p53 protein did not correlate with point mutations in codon 12 of the K-ras oncogene, nor did it correlate with tumor stage or patient survival. These findings indicate that p53 protein is frequently overexpressed in primary lung adenocarcinomas. Furthermore, the association of tobacco smoking with this overexpression suggests that the p53 gene is a target of specific mutagens in tobacco smoke.