gebhart/patrepeval huggingface dataset:
Deep Brain Stimulation for Neurological Disorders (2012)

Deep brain stimulation (DBS) involves the delivery of precise electrical signals to specific deep anatomical structures of the central nervous system, with the objective of altering or modulating neural functioning and achieving a reversible, adjustable and therapeutic or clinically beneficial effect. The exact mechanism of action of DBS is still the subject of ongoing investigations. However, based on extensive clinical investigations, it has become an established modality for the surgical treatment of advanced and medication intractable movement disorders such as Parkinson's disease, essential tremor and dystonia. DBS is also being investigated for conditions such as intractable epilepsy, neurobehavioral and psychiatric disorders such as treatment resistant depression, obsessive compulsive disorders, addiction, obesity, Alzheimer's disease and traumatic brain injury. The advantage of DBS over older deep brain lesioning procedures is its reversibility and adjustability. The design of the DBS systems allows for dynamic adjustment of the effects of electrical stimulation by altering the contacts at which electrical pulses are delivered to the brain and changing the stimulation parameters of those pulses. The clinical results from studies on DBS show that it has great potential making it one of most promising fields which could be used to address challenging neurological problems.
Tuning the Composition and Nanostructure of Pt/Ir Films via Anodized Aluminum Oxide Templated Atomic Layer Deposition (2010)

Abstract Nanostructured metal films have been widely studied for their roles in sensing, catalysis, and energy storage. In this work, the synthesis of compositionally controlled and nanostructured Pt/Ir films by atomic layer deposition (ALD) into porous anodized aluminum oxide templates is demonstrated. Templated ALD provides advantages over alternative synthesis techniques, including improved film uniformity and conformality as well as atomic‐scale control over morphology and composition. Nanostructured Pt ALD films are demonstrated with morphological control provided by the Pt precursor exposure time and the number of ALD cycles. With these approaches, Pt films with enhanced surface areas, as characterized by roughness factors as large as 310, are reproducibly synthesized. Additionally, nanostructured PtIr alloy films of controlled composition and morphology are demonstrated by templated ALD, with compositions varying systematically from pure Pt to pure Ir. Lastly, the application of nanostructured Pt films to electrochemical sensing applications is demonstrated by the non‐enzymatic sensing of glucose.
Isothermal titration calorimetry with micelles: Thermodynamics of inhibitor binding to carnitine palmitoyltransferase 2 membrane protein (2013)

Carnitine palmitoyl transferase 2 (CPT-2) is a key enzyme in the mitochondrial fatty acid metabolism. The active site is comprised of a Y-shaped tunnel with distinct binding sites for the substrate acylcarnitine and the cofactor CoA. We investigated the thermodynamics of binding of four inhibitors directed against either the CoA or the acylcarnitine binding sites using isothermal titration calorimetry (ITC). CPT-2 is a monotopic membrane protein and was solubilized by β-octylglucoside (β-OG) above its critical micellar concentration (CMC) to perform inhibitor titrations in solutions containing detergent micelles. The CMC of β-OG in the presence of inhibitors was measured with ITC and small variations were observed. The inhibitors bound to rat CPT-2 (rCPT-2) with 1:1 stoichiometry and the dissociation constants were in the range of K D = 2-20 μM. New X-ray structures and docking models of rCPT-2 in complex with inhibitors enable an analysis of the thermodynamic data in the context of the interaction observed for the individual binding sites of the ligands. For all ligands the binding enthalpy was exothermic, and enthalpy as well as entropy contributed to the binding reaction, with the exception of ST1326 for which binding was solely enthalpy-driven. The substrate analog ST1326 binds to the acylcarnitine binding site and a heat capacity change close to zero suggests a balance of electrostatic and hydrophobic interactions. An excellent correlation of the thermodynamic (ITC) and structural (X-ray crystallography, models) data was observed suggesting that ITC measurements provide valuable information for optimizing inhibitor binding in drug discovery.
Integration of vision and force sensors for grasping (2002)

This paper describes a set of methods that can be used to integrate real-time external vision sensing with internal force and position sensing to estimate contact forces by the fingers of a hand. Estimating these forces and contacts is essential to performing dextrous manipulation tasks. Most robotic hands are either sensorless or lack the ability to accurately and robustly report position and force information relating to contact. By adding external vision sensing, we can complement any internal sensors to more accurately estimate forces and contact positions. Experiments are described that use real-time visual trackers in conjunction with internal strain gauges and a new tactile sensor to accurately estimate finger contacts and applied forces for a three fingered robotic hand.
Mass production system for RNA-loaded lipid nanoparticles using piling up microfluidic devices (2023)

Microfluidic devices are widely used in lipid nanoparticle (LNP)-based vaccines and nanomedicine research. These devices should be stiff enough to withstand the high flow rate for the mass production of LNPs, and malleable enough to use when fabricating complicated microchannel or micromixer structures, such as staggering herringbone micromixers. Due to the limitations of the available fabrication methods, optimal microfluidic devices have not yet been developed. In this study, we report the development of a glass-based microfluidic device based on the invasive Lipid Nanoparticle Production (iLiNP) device® reported previously. The LNP size controllability of glass-based iLiNP device was similar to that of the poly(dimethylsiloxane) (PDMS)-based iLiNP device, and the glass-iLiNP device was used for mRNA-loaded LNP production with ionizable lipids used for COVID-19 mRNA vaccines. We also demonstrate a piling- and numbering-up strategy based on glass-iLiNP device. The iLiNP unit composed of five-layered microchannels was fabricated by piling-up each glass-iLiNP device followed by parallelization (numbering-up) for the mass production of LNPs. This iLiNP system can produce LNPs with sizes ranging between 20 and 60 nm at a flow rate of 20–50 mL/min, and its performance is comparable to that of the commercially available microfluidic system like NanoAssemblr®.
Human models of breast cancer. (1993)

Experimental systems using human mammary tissue, secretions and tumours may be based on in vitro culture or on growth of tissue or tumour fragments in the nude mouse. In the development of in vitro culture systems, a detailed characterization of the cultured cells within the framework of the epithelial cell lineages found in vivo is crucial. Monoclonal antibodies are useful tools for defining the profile of antigens expressed by the basal and luminal cells in the normal gland and in distinguishing subclasses between these two major groups. When these same reagents are used to characterize breast cancers, the majority are found to show the phenotype of luminal cells, with a small subset showing some evidence of basal markers. Luminal epithelial cells cultured from milk or reduction mammoplasty tissue have a short life span in vitro but can be immortalized using SV40TAg. Demonstrably malignant cells are difficult to culture from primary breast cancer, but ER+ and ER- cell lines showing the luminal phenotypes have been readily developed from metastases: some ER- breast cancer cell lines show a more undifferentiated phenotype, and these may have developed from tumours expressing basal markers. As with in vitro culture, it is difficult to obtain tumour growth in the nude mouse from primary breast cancer specimens, and established cell lines are also difficult to grow in this animal. We have focused our studies on cell lines with the luminal phenotype developed from milk. These non-tumorigenic cell lines differ from breast cancer cell lines (a) in being able to form organized three dimensional structures in the presence of an extracellular matrix and (b) in the correct glycosylation of the polymorphic epithelial mucin, which is expressed and aberrantly glycosylated in cancers. These cell lines are therefore being used to study the mechanisms underlying morphogenesis and the processing of PEM, and also as recipients for oncogenes and proto-oncogenes.
pH-regulated Secretion of a Glyceraldehyde-3-Phosphate Dehydrogenase from Streptococcus gordonii FSS2: Purification, Characterization, and Cloning of the Gene Encoding this Enzyme (2001)

Streptococcus gordonii and other viridans streptococci (VS) are primary etiologic agents of infective endocarditis, despite being part of the normal oral microflora. Recently, a surface-bound glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been found on the cells of all tested streptococcal species, where it has been implicated as a virulence factor. In contrast, we observed that a soluble extracellular GAPDH was the major secreted protein from S. gordonii FSS2, an endocarditis strain. The biochemical properties and gene sequence of S. gordonii GAPDH are almost identical to those of other streptococcal GAPDHs. Growth at defined pHs showed that secretion of GAPDH is regulated by environmental pH. GAPDH was primarily surface-associated at growth pH 6.5 and shifted to > 90% secreted at growth pH 7.5. Others have identified S. gordonii promoters that are up-regulated by a pH shift similar to that experienced by organisms entering the blood stream (neutral) from the oral cavity (slightly acid). Analysis of our results suggests that secretion of GAPDH may be a similar adaptation by S. gordonii.
NO-Erkennung durch einen Metallkomplex als Folge der selektiven Dissoziation eines Liganden (2000)

Stickstoffmonoxid reagiert selektiv mit dem O2-stabilen, schwach fluoreszierenden Komplex [Co(DATI-4)] in Dichlormethan unter Dissoziation eines Fluorophor-substituierten Arms des Aminotroponiminatliganden DATI-4. Das dabei gebildete Cobaltdinitrosyladdukt (siehe Bild) fluoresziert hingegen intensiv. Es wird eine Nachweisgrenze für NO von 50–100 μM erreicht.
A hybrid-amplified PON with 75-nm downstream band-width 60 km reach, 1:64 split, and multiple video services (2007)

We demonstrate an upgraded PON providing symmetric 2.488-Gb/s services and three downstream enhancement bands over 60 km to 64 customers. The system uses a SOA-Raman hybrid amplifier and a conventional SOA in an "extender box".
Sparse view Compton scatter tomography with energy resolved data: experimental and simulation results (2017)

X-ray inspection systems play a critical role in many non-destructive testing and security applications, with systems typically measuring attenuation during transmission along straight-line paths connecting sources and detectors. Computed tomography (CT) systems can provide higher-quality images than single- or dual-view systems, but the need to measure many projections through the scene increases system complexity and cost. We seek to maximize the image quality of sparse-view (few-view) systems by combining attenuation data with measurements of Compton-scattered photons, that deflect after scattering and arrive at detectors via broken ray paths that provide additional sampling of the scene. The work below presents experimental validation of a singlescatter forward model for Compton-scatter data measured with energy-resolving detectors, and demonstrates a reconstruction algorithm that combines both attenuation and scatter measurements. The results suggest that including Compton-scattered data in the reconstruction process can improve image quality for few-view systems.
Orientation Zernike Polynomials: a systematic description of polarized imaging using high NA lithography lenses (2008)

We introduce the 'Orientation Zernike Polynomials', a base function representation of retardation and diattenuation which are most relevant for vector imaging. We show that the 'Orientation Zernike Polynomials' provide a complete and systematic description of vector imaging using high NA lithography lenses and, hence, a basis for an in depth understanding of both polarized and unpolarized imaging, and its modeling.
ChemInform Abstract: Reactions of Small Carbon Clusters with Water in Cryogenic Matrices. The FTIR Spectrum of Hydroxyethynylcarbene. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
All normal dispersion nonlinear fiber source for Hyperspectral Stimulated Raman Scattering Microscopy (2019)

We demonstrate the use a low noise all-normal-dispersion nonlinear fiber as a supercontinuum light source for Hyperspectral Stimulated Raman Scattering microscopy.
STATUS OF HIGH ENERGY ELECTRON COOLING IN FNAL’S RECYCLER RING* (2015)

Electron cooling of 8 GeV antiprotons at Fermilab&amp;apos;s Recycler storage ring is now routinely used in the collider operation. It requires a 0.1-0.5 A, 4.3 MeV DC electron beam to increase the longitudinal phase-space density of the circulating antiproton beam. This paper discusses the latest status of the electron cooler and its mode of operation within the context of Fermilab&amp;apos;s accelerator complex. In addition, we will show preliminary results that demonstrate electron cooling of the transverse phase-space of the antiproton beam.
Piriformis Syndrome With Variant Sciatic Nerve Anatomy: A Case Report (2015)

A 68-year-old male long distance runner presented with low back and left buttock pain, which eventually progressed to severe and debilitating pain, intermittently radiating to the posterior thigh and foot. A comprehensive workup ruled out possible spine or hip causes of his symptoms. A pelvic magnetic resonance imaging neurogram with complex oblique planes through the piriformis demonstrated variant anatomy of the left sciatic nerve consistent with the clinical diagnosis of piriformis syndrome. The patient ultimately underwent neurolysis with release of the sciatic nerve and partial resection of the piriformis muscle. After surgery the patient reported significant pain reduction and resumed running 3 months later. Piriformis syndrome is uncommon but should be considered in the differential diagnosis for buttock pain. Advanced imaging was essential to guide management.
Genital Paget's Disease: Report of a Case Which Developed after Prostatic Carcinoma and was Followed by Hepatocellular Carcinoma. (1996)

65歳の男性。前立腺癌術後4年目に外陰部Paget病を, さらにその1年後に肝細胞癌を生じた1例を報告した。三重複癌であるとの観点から前立腺癌の治療に用いられたリン酸エストラムスチンナトリウムにより後二者の癌が誘発された可能性について考察を加えた。
Quality Assessment of Tympanoplasty by Means of Endoscopic Optical Coherence Tomography (2019)

The endoscopic optical coherence tomography (eOCT) allows the direct, contactless representation and evaluation of the morphology and oscillation behaviour of the tympanic membrane and adjoining tympanic cavity content. After further development of the measuring technology, the eOCT will be able to be used in vivo for the assessment of tympanoplasty results.
Metal Ion Enhanced Charge Transfer in a Terpyridine-bis-Pyrene System (2009)

The synthesis, electrochemical and photophysical properties of a branched molecule 3,5-bis(pyrene-1-yl)-4'-phenyl-2,2':6',2″-terpyridine are reported. Spectroscopy in different solvents reveals that an optical electron transfer from the pyrene donor to the terpyridyl electron acceptor can occur in polar media, as the system displays both charge transfer (CT) absorption and CT emission. Furthermore, the study of the zinc complex as well as the bis-protonated form shows an enhancement of the electron transfer character of the system, by an increase of the acceptor strength. This is accompanied by a large increase of the non-radiative processes. With sub-nanosecond transient absorption spectroscopy, the CT state, consisting of the pyrene radical cation and the terpyridine radical anion, has been detected. At room temperature, the study of the nanosecond transient absorption spectra reveals the formation of a low-lying triplet excited state that we attribute to the pyrene moiety through which the CT state decays. At 77K, the absence of the terpyridine triplet emission also suggests the population of a low-lying triplet state of the pyrene unit.
FIRE BEHAVIOR OF CABLE SHEATHING AT REDUCED SCALE (2019)

International audience
Radar detection for non-stationary Doppler signal in one burst based on information geometry distance between paths (2015)

Classical Radar processing for non-stationary signal, corresponding to fast time variation of Doppler Spectrum in one burst, is no longer optimal. This phenomenon could be observed for high speed or abrupt Doppler variations of clutter or target signal but also in case of target migration during the burst duration due to high range resolution. We propose new Radar Doppler processing assuming that each non-stationary signal in one burst can be split into several short signals with less Doppler resolution but locally stationary, represented by time series of Toeplitz covariance matrices. In Information Geometry (IG) framework, these time series could be defined as a geodesic path (or geodesic polygon in discrete case) on covariance Toeplitz Hermitian Positive Definite matrix manifold. For this micro-Doppler analysis, we generalize the Fréchet distance between two curves in the plane to geodesic paths in abstract IG metric spaces of covariance matrix manifold. This approach is used for robust detection of target in case of non-stationary Time-Doppler spectrum (NS-OS-HDR-CFAR).
Comments on comments (2022)

A central function of code review is to increase understanding; helping reviewers understand a code change aids in knowledge transfer and finding bugs. Comments in code largely serve a similar purpose, helping future readers understand the program. It is thus natural to study what happens when these two forms of understanding collide. We ask: what documentation-related comments do reviewers make and how do they affect understanding of the contribution? We analyze ca. 700K review comments on 2,000 (Java and Python) GitHub projects, and propose several filters to identify which comments are likely to be either in response to a change in documentation and/or call for such a change. We identify 65K such cases. We next develop a taxonomy of the reviewer intents behind such "comments on comments". We find that achieving a shared understanding of the code is key: reviewer comments most often focused on clarification, followed by pointing out issues to fix, such as typos and outdated comments. Curiously, clarifying comments were frequently suggested (often verbatim) by the reviewer, indicating a desire to persist their understanding acquired during code review. We conclude with a discussion of implications of our comments-on-comments dataset for research on improving code review, including the potential benefits for automating code review.
ChemInform Abstract: Synthesis of Betulin Derivatives with Solid Supported Reagents. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Perception of sexuality and fertility in women living with HIV: a questionnaire study from two Nordic countries (2015)

In conclusion, the majority of WLWH in industrialized settings in Denmark and Finland have few HIV-related symptoms, are sexually active and have a strong desire for children.
Comparative Study of 125I- and [3H]Acetate-Labeled Antibodies in Detecting Iridescent Viruses (1974)

Radioimmunoassays for detecting cell-associated or released virus are described using either 125I- or [3H]acetate-labeled antibodies. In the first assay system, antigen-antibody complexes were separated from free antibody by centrifugation. Sensitivities of 0.1 μg of iridescent virus could be achieved with either 125I- or [3H]acetate-labeled antibody. In the second assay, the antigen was fixed to cover-slip cell cultures, and then reacted with labeled antibody, unbound radioactivity being removed by repeated washing. Nonspecific binding with this method was 0.5 to 1% of the total radioactivity added and sensitivities of 0.1 or 10 μg were achieved with 125I and [3H]acetate, respectively. Immunoglobulins were labeled at the rate of 1 in 300 for 125I and 1 in 200 with [3H]acetate although there was a 400-fold greater isotopic abundance of 125I relative to 3H. The possibility of preparing labeled protein of high specific activity using carrier-free [2-3H]iodoacetic acid is discussed.
Preclinical evaluation of multi antigenic HCV DNA vaccine for the prevention of Hepatitis C virus infection (2017)

Direct-acting antiviral treatment for hepatitis C virus (HCV) infection is costly and does not protect from re-infection. For human and chimpanzees, recovery from acute HCV infection correlates with host CD4+ and CD8+ T cell responses. DNA plasmids targeting the HCV non-structural antigens NS3, NS4, and NS5, were previously reported to induce robust and sustained T cell responses in mice and primates. These plasmids were combined with a plasmid encoding cytokine IL-28B, together named as VGX-6150. The dose-dependent T cell response and safety of VGX-6150 administered intramuscularly and followed by electroporation was assessed in mice. Immune responses plateaued at 20 μg/dose with IL-28B demonstrating significant immunoadjuvant activity. Mice administered VGX-6150 at 40, 400, and 800 μg given either as a single injection or as 14 injections given bi-weekly over 26 weeks showed no vaccine related changes in any clinical parameter compared to placebo recipients. There was no evidence of VGX-6150 accumulation at the injection site or in any organ 1 month following the 14<sup>th</sup> vaccination. Based on these studies, the approximate lethal dose (ALD) exceeds 800 μg/dose and the NOAEL was 800 μg/dose in mouse. In conclusion, VGX-6150 appears safe and a promising preventive vaccine candidate for HCV infection.