gebhart/patrepeval huggingface dataset:
3D-Addressable Redox: Modifying Porous Carbon Electrodes with Ferrocenated 2 nm Gold Nanoparticles (2012)

Nanostructured, high-surface-area carbon electrodes have large electrochemical double-layer capacitances compared to smooth-surfaced electrodes because of their enhanced internal surface areas, e.g., several hundred m2g–1. In the present work, we demonstrate that the electrical capacitance of carbon “nanofoams”, both in commercially available forms and as prepared by the authors, can be significantly enhanced by the insertion into their pores of small Au nanoparticles (∼2 nm diameter core) to whose surfaces are bonded ferrocenyl-hexane thiolate ligands (SC6Fc) (>40 per nanoparticle). The enhanced capacitive behavior of the modified nanoporous carbon (in CH3CN or CH2Cl2 with 1.0 or 2.0 M Bu4NPF6 as the supporting electrolyte) is clearly seen in their cyclic voltammetric responses and is attributed to a combination of the ferrocene redox-capacity and the double-layer capacity of the intercalated nanoparticles. Footprint-normalized, volume-normalized, and gravimetric-normalized integral capacitances of 0.28 F cm–2, 39 F cm–3, and 66 F g–1 are realized over a 1 V potential range. We suggest this approach as a conceptual pathway to improve the science of electrochemically based energy storage systems (e.g., “supercapacitors”).
MCF-10A-NeoST: A New Cell System for Studying Cell-ECM and Cell-Cell Interactions in Breast Cancer (2001)

Purpose: There is a continuing need for genetically matched cell systems to model cellular behaviors that are frequently observed in aggressive breast cancers.Experimental Design: We report here the isolation and initial characterization of a spontaneously arising variant of MCF-10A cells, NeoST, which provides a new model to study cell adhesion and signal transduction in breast cancer.Results: NeoST cells recapitulate important biological and biochemical features of metastatic breast cancer, including anchorage-independent growth, invasiveness in threedimensional reconstituted membranes, loss of E-cadherin expression, and increased tyrosine kinase activity.A comprehensive analysis of tyrosine kinase expression revealed overexpression or functional activation of the Axl, FAK, and EphA2 tyrosine kinases in transformed MCF-10A cells.Conclusions: MCF-10A and these new derivatives provide a genetically matched model to study defects in cell adhesion and signaling that are relevant to cellular behaviors that often typify aggressive breast cancer cells.
Covariation of Mutations in the V3 Loop of HIV-1: An Information Theoretic Analysis (1995)

The V3 loop of the Human Immunodeficiency Virus Type-1 (HIV-1) envelope protein is a highly variable region that is both functionally and immunologically important. We have used an information theoretic quantity called mutual information, a measure of covariation, to quantify dependence between mutations in the loop using available amino acid sequences from the V3 region. Certain pairs of sites, including non-contiguous sites along the sequence, do not have independent mutations, but display considerable, statistically significant, co-varying mutations as measured by mutual information. Such interdependence may have implications for structural or functional relationships between sites; separate experimental evidence indicates functional linkage between some of the pairs of sites with high mutual information. Further specific mutational studies are suggested by our analysis. The methods used are generally applicable to the study of variable proteins.
Interpretability of deep learning models: A survey of results (2017)

Deep neural networks have achieved near-human accuracy levels in various types of classification and prediction tasks including images, text, speech, and video data. However, the networks continue to be treated mostly as black-box function approximators, mapping a given input to a classification output. The next step in this human-machine evolutionary process - incorporating these networks into mission critical processes such as medical diagnosis, planning and control - requires a level of trust association with the machine output. Typically, statistical metrics are used to quantify the uncertainty of an output. However, the notion of trust also depends on the visibility that a human has into the working of the machine. In other words, the neural network should provide human-understandable justifications for its output leading to insights about the inner workings. We call such models as interpretable deep networks. Interpretability is not a monolithic notion. In fact, the subjectivity of an interpretation, due to different levels of human understanding, implies that there must be a multitude of dimensions that together constitute interpretability. In addition, the interpretation itself can be provided either in terms of the low-level network parameters, or in terms of input features used by the model. In this paper, we outline some of the dimensions that are useful for model interpretability, and categorize prior work along those dimensions. In the process, we perform a gap analysis of what needs to be done to improve model interpretability.
Serum-Derived Hepatitis C Virus Infection of Primary Human Hepatocytes Is Tetraspanin CD81 Dependent (2007)

Hepatitis C virus-positive serum (HCVser, genotypes 1a to 3a) or HCV cell culture (JFH1/HCVcc) infection of primary normal human hepatocytes was assessed by measuring intracellular HCV RNA strands. Anti-CD81 antibodies and siRNA-CD81 silencing markedly inhibited (>90%) HCVser infection irrespective of HCV genotype, viral load, or liver donor, while hCD81-large intracellular loop (LEL) had no effect. However, JFH1/HCVcc infection of hepatocytes was modestly inhibited (40 to 60%) by both hCD81-LEL and anti-CD81 antibodies. In conclusion, CD81 is involved in HCVser infection of human hepatocytes, and comparative studies of HCVser versus JFH1/HCVcc infection of human hepatocytes and Huh-7.5 cells revealed that the cell-virion combination is determinant of the entry process.
The essential Porphyromonas gingivalis type IX secretion system component PorZ delivers anionic-lipopolysaccharide to the PorU sortase for transpeptidase processing of cargos (2020)

Abstract Cargo proteins of the type IX secretion system (T9SS) in human pathogens from phylum Bacteroidetes invariably possess a conserved C-terminal domain (CTD) that functions as a signal for outer membrane (OM) translocation. In Porphyromonas gingivalis , the CTD of selected cargos is cleaved off after translocation, and anionic lipopolysaccharide (A-LPS) is attached. This transpeptidase reaction anchors secreted proteins to the OM. PorZ, a cell surface-associated protein, is an essential component of the T9SS whose function was previously unknown. We recently solved the crystal structure of PorZ, and found that it consists of two β-propeller moieties followed by a CTD. In this study, we performed structure-based modelling suggesting that PorZ is a carbohydrate-binding protein. We found that recombinant PorZ specifically binds A-LPS. Binding was blocked by monoclonal antibodies that specifically react with a phosphorylated branched mannan in the anionic polysaccharide (A-PS) component of the A-LPS, but not with the core oligosaccharide or the lipid A endotoxin. Examination of A-LPS derived from a cohort of mutants producing various truncations of A-PS confirmed that the phosphorylated branched mannan is indeed the PorZ ligand. Moreover, purified recombinant PorZ interacted with the PorU sortase in an A-LPS–dependent manner. This interaction on the cell surface is crucial for the function of the attachment complex composed of PorU, PorZ, and the integral OM β-barrel proteins PorV and PorQ, which is involved in post-translational modification and retention of T9SS cargos on the bacterial surface. Author summary Bacteria have evolved multiple systems to transport effector proteins to their surface or into the surrounding milieu. These proteins have a wide range of functions, including attachment, motility, nutrient acquisition, and toxicity in the host. Porphyromonas gingivalis , the human pathogen responsible for severe gum diseases (periodontitis), uses a recently characterized type IX secretion system (T9SS) to translocate and anchor secreted virulence effectors to the cell surface. Anchorage is facilitated by sortase, an enzyme that covalently attaches T9SS cargo proteins to a unique anionic lipopolysaccharide (A-LPS) moiety of P. gingivalis . Here, we show that the T9SS component PorZ interacts with sortase and specifically binds A-LPS. Binding is mediated by a phosphorylated branched mannan repeat in A-LPS polysaccharide. A-LPS– bound PorZ interacts with sortase with significantly greater affinity, facilitating modification of cargo proteins by the cell-surface attachment complex of the T9SS.
CAN-17-3953 SI tables and figures from Dual Inhibition of DNA and Histone Methyltransferases Increases Viral Mimicry in Ovarian Cancer Cells (2023)

&lt;p&gt;Includes one supplementary table, 13 supplementary figures and figure legends for supplementary figures&lt;/p&gt;
Discovering the RNA Transcription Landscape using Directional Approaches (2013)

High-throughput complementary DNA sequencing (RNA-Seq) is a powerful technique that allows for sensitive digital quantification of transcript levels. Moreover, RNA-Seq enables the detection of non-canonical transcription start sites and termination sites, alternative splice isoforms and transcript mutation and edition. Standard “next-generation” RNA-sequencing approaches generally require double-stranded cDNA synthesis, which erases RNA strand information. In this approach, the synthesis of randomly primed double-stranded cDNA followed by addition of adaptors for sequencing leads to the loss of information about which strand was present in the original mRNA template. The polarity of the transcript is important for correct annotation of novel genes, identification of antisense transcripts with potential regulatory roles, and for correct determination of gene expression levels in the presence of antisense transcripts. Our objective was to address this need by developing a novel streamlined, low input method for Directional RNA-Sequencing that highly retains strand orientation information while maintaining even coverage of transcript expression. This method is based on second strand labeling and excision after adaptor ligation; allowing differential tagging of the first strand cDNA ends. As a result, we have enabled strand specific mRNA sequencing, as well as whole transcriptome sequencing (Total RNA-Seq) from ribosomal-depleted samples. Total RNA-Seq provides a much broader picture of expression dynamics including discovery of antisense transcripts. This work presents a streamlined, fast solution for complete RNA sequencing, with high quality data that illustrates the complexity and diversity of the RNA transcription landscape.
Retinal Vascular Changes and 20-Year Incidence of Lower Extremity Amputations in a Cohort With Diabetes (2003)

In persons with diabetes, generalized as well as focal retinal arteriolar narrowing may reflect damage to the microvasculature, which manifests itself elsewhere in the body as a need for LEAs.
Semi-deterministic modeling of diffuse scattering component based on propagation graph theory (2014)

Graph theory-based channel modeling is an efficient approach to simulate multipath propagation taking into account the reverberation of electromagnetic waves. In this contribution, without modifying the modeling framework, we proposed a semi-deterministic graph modeling approach by associating the scatterers with realistic environment objects, and by calculating the coefficients of the propagation paths on the base of a proven diffuse scattering theory. An isolated office building scenario is adopted to illustrate the procedure of the proposed method. The performance is thus evaluated by comparing the simulated power-delay-profiles (PDPs) with ray-tracing and real channel measurement data. The results illustrate that the proposed method can accurately predict both the decaying slopes and the diffuse tails of the PDPs.
GSVD based multi-user multi-stream MIMO linear precoding with limited feedback (2012)

We present a generalized singular value decomposition (GSVD) based multi-user (MU) multi-stream multiple-input multiple-output (MIMO) precoding scheme with limited feedback. Our precoding scheme maximizes the signal to leakage and noise ratio (SLNR), so that it does not require any iterations to obtain precoding matrices. However, in MU-MIMO system, the precoding matrix should be computed at transmit side, because the precoding matrix of a user affects those of other users. Accordingly, full channel state information (CSI) for all users is required at the transmitter, which prevents MU-MIMO precoding implementable. To overcome this problem, an efficient limited feedback algorithm optimized to the GSVD based MU-MIMO precoding is proposed. Here, by extracting the parameters to be utilized in GSVD based precoding from the full CSI, the amount of feedback information is reduced. Furthermore, by analyzing their statistical properties, the parameters are efficiently quantized according to their probability densities. Finally, we develop a modified GSVD based precoding considering the channel quantization errors due to the limited feedback.
A materials-science perspective on tackling COVID-19 (2020)

The ongoing SARS-CoV-2 pandemic highlights the importance of materials science in providing tools and technologies for antiviral research and treatment development. In this Review, we discuss previous efforts in materials science in developing imaging systems and microfluidic devices for the in-depth and real-time investigation of viral structures and transmission, as well as material platforms for the detection of viruses and the delivery of antiviral drugs and vaccines. We highlight the contribution of materials science to the manufacturing of personal protective equipment and to the design of simple, accurate and low-cost virus-detection devices. We then investigate future possibilities of materials science in antiviral research and treatment development, examining the role of materials in antiviral-drug design, including the importance of synthetic material platforms for organoids and organs-on-a-chip, in drug delivery and vaccination, and for the production of medical equipment. Materials-science-based technologies not only contribute to the ongoing SARS-CoV-2 research efforts but can also provide platforms and tools for the understanding, protection, detection and treatment of future viral diseases.
Histological Classification of Raman Spectra of Human Coronary Artery Atherosclerosis Using Principal Component Analysis (1999)

We present a nonparametric method of analysis of Raman spectra of coronary artery tissue to classify atherosclerotic lesions. The method correlates the principal component scores of the Raman spectra with the tissue pathology. A data set composed of 97 samples of human coronary artery was used to develop the diagnostic algorithm, and a second data set composed of 68 samples was then used to test this algorithm prospectively. The results show that the algorithm can accurately classify coronary artery tissue into three classes: nonatherosclerotic, noncalcified plaque, and calcified plaque. The accuracy of this classification scheme is comparable to that previously achieved by means of a biochemical analysis of the Raman spectra using the same data.
Silver(I) Complexation with Glutathione in the Presence of Tetramethylthiourea (2009)

Preparation of five silver(I) complexes of glutathione (Glut) [Ag(Glut) 1 , [Ag(Glut) 2 ] − , [(Metu) 2 Ag(Glut)], [(Tmtu) 1 Ag(Glut)] and [(Tmtu) 2 Ag(Glut)] (where, Metu = N-methylthiourea and Tmtu = N,N,N′,N′-tetramethylthiourea) has been attempted and the products were characterized by elemental analysis, IR spectroscopy and thermal analysis. The results reveal that in all the reactions, thiourea ligands are replaced on addition of glutathione, and the same product ([Ag(Glut) 1 ]) is formed. The replacement of thione ligands is explained on the basis of assumption that glutathione is able to occupy all the coordination sites around Ag(I), and as result a more stable complex is formed.
Developing an Electronic Record Tool Representative of Primary Health Care in the Public Health Care System of Buenos Aires City (2019)

The Primary Health Care strategy is based on organization of interdisciplinary teams and comprehensive approach to health, disease and health care processes. To strengthen information systems so that they represent primary health care complexities, participatory meetings were held with primary care practitioners from the public health care system of Buenos Aires City. Terms for the record tool and its components were chosen using consensus methodologies. This process involved 300 practitioners from 49 centers, and submission of 21 proposals. It was decided to change the term "Electronic Medical Record" with "Comprehensive Health Record." It was also agreed that, apart from "Reason for Consultation," the field "Problem Situation" would be added, that "Care Service" would be replaced with "Care Act," and that a new module "Health Team Management and Education Activities" would be included to document practitioners team activities.
Advancements in pancreatic neuroendocrine tumors (2013)

Pancreatic neuroendocrine tumors (PanNETs) have increased in incidence in the USA over the last 20 years. Although PanNETs are often misconceived as being indolent tumors as they have a far more favorable prognosis over pancreatic adenocarcinoma, roughly 60-70% of patients have metastatic disease at the time of diagnosis due to presentation late in the disease process. While improvements in imaging modalities allow for early detection and better tumor localization, recent advancements in basic science, as well as surgical and medical management of PanNETs have further improved the prognosis. The mainstay of therapy for localized PanNETs is surgical intervention, which has become safer and is slowly shifting towards a more minimally invasive approach. However, the prognosis still remains relatively bleak for patients with unresectable disease. Fortunately, novel molecular targeted therapies, such as everolimus and sunitinib, have recently come into the limelight and have shown significant promise for the treatment of locally advanced and metastatic disease.
Concepts and Implementation of a Semantic Web Archiving and Simulation System for RF Propagation Measurements (2011)

In this paper, we present an Open-Source web-based archiving system to organize and share wireless RF propagation measurement data, models, and simulation software in a centralized, standardized archive. This archiving system is based on Semantic Web ideas that will enable the wireless research community to easily share and access measured data and simulators provided by researchers across the globe. To begin development of the web-based archiving environment, we use a previously developed RF propagation simulator, SIRCIM, to represent the range of values, types of measurements, and file format types that would be needed to properly archive measurements from the research community at large. This paper also explores development issues and considerations required to build a Semantic Web on-line propagation channel measurement and modeling archiving system for global use.
Structuration par nanoimpression de couches sol-gel hybrides pour l'extraction de lumière (2010)

International audience
ECG-free 2D cardiac cine MRI with data-driven clustering (2023)

Conventional 2D cardiac cine imaging relies on ECG-gating whereas self-gated approaches mitigate ECG-dependency by assuming that cardiac motion is periodic with well-defined frequencies. This assumption breaks down when patients have irregular cardiac rhythm. We propose a segmented Cartesian golden step balanced steady-state free precession sequence (bSSFP) with motion navigators and a clustering algorithm to alleviate the dependency on regular motion assumptions and to emphasize the intrinsic similarity of mechanical motion. Compared to standard ECG-gated 2D bSSFP cine performed in normal sinus rhythm, initial validation using our approach achieved similar image quality and quantitative metrics for cardiac function.
Infinite dilution viscoelastic properties of poly(γ‐benzyl‐L‐glutamate) in m‐cresol (1976)

Abstract The real and imaginary parts of complex viscosity, η′ and η″, are measured for dilute solutions of poly(γ‐benzyl‐ L ‐glutamate) in m‐cresol, a helicogenic solvent. The frequency range is 2.2–525 kHz; the concentration range 0.2–5 g/dl; the temperature 30°C, and the molecular weights M r are 6.4 × 10 4 –17 × 10 4 . The dispersion curve of extrapolated intrinsic dynamic viscosity [η′] of samples with M r &gt; 10 5 is interpreted in terms of three mechanisms appearing from low to high frequencies: end‐over‐end rotation, flexural deformation, and side‐chain motion. For a sample with M r &lt; 10 5 , the flexural relaxation disappears and a plateau of [η′] is distinctly observed between rotational and side‐chain relaxations. Rotational relaxation times of all the samples obey the Kirkwood–Auer theory. The strong concentration dependence of rotational relaxation time is explained by collisions of molecules rather than association. Flexural relaxation times calculated from a theory by assuming the persistence length as 1200 Å are consistent with observed dispersion curves of [η′].
Scenarios and business models for mobile network operators utilizing the hybrid use concept of the UHF broadcasting spectrum (2016)

This paper explores and presents scenarios and business models for mobile network operators (MNOs) in the novel hybrid use spectrum sharing concept of the Ultra High Frequency broadcasting spectrum (470-790 MHz) used for Digital Terrestrial TV (DTT) and Mobile Broadband (MBB). More flexible use of t
Extraction and Chemical Characterization of Humic Acid from Nitric Acid Treated Lignite and Bituminous Coal Samples (2021)

Currently, conversion of coal into alternative fuel and non-fuel valuable products is in demand and growing interest. In the present study, humic acid was extracted from two different ranks of coal, i.e., low rank and high rank (lignite and bituminous), through chemical pretreatment by nitric acid. Samples of lignite and bituminous coal were subjected to nitric acid oxidation followed by extraction using KOH and NaOH gravimetric techniques. The chemical pretreatment of both types of coal led to enhanced yields of humic acid from 21.15% to 57.8% for lignite low-rank coal and 11.6% to 49.6% bituminous high rank coal. The derived humic acid from native coal and nitric acid treated coal was analyzed using elemental analysis, E4/E6 ratio of absorbance at 465 nm and 665 nm using UV-Visible spectrophotometry and Fourier transformed infrared spectroscopy FTIR. The chemical characteristics of coal treated with nitric acid have shown increased molecular weight and improved aromaticity with more oxygen and nitrogen and lower C, H, and sulphur content. The E4/E6 ratio of nitric acid-treated low and high ranks of coal was high. The FTIR spectroscopic data of nitric acid-treated lignite coal indicates an intensive peak of carboxyl group at 2981.84 cm−1, while bituminous coal was shown in cooperation with the N-H group at 2923.04 cm−1. SEM was performed to detect the morphological changes that happen after producing humic acid from HNO3 treatment and native coal. The humic acid produced from HNO3 treated coal had shown clear morphological changes and some deformations on the surface. SEM-EDS detected the major elements, such as nitrogen, in treated humic acid that were absent in raw coal humic acid. Hence, the produced humic acid through HNO3 oxidation showed a more significant number of humic materials with improved efficiency as compared to native coal. This obtained humic acid can be made bioactive for agriculture purposes, i.e., for soil enrichment and improvement in growth conditions of plants and development of green energy solutions.