gebhart/patrepeval huggingface dataset:
Capture and elongation of single chromosomal DNA molecules using optically driven microchopsticks (2020)

DNA analysis based on the observation of single DNA molecules has been a key technology in molecular biology. Several techniques for manipulating single DNA molecules have been proposed for this purpose; however, these techniques have limits on the manipulatable DNA. To overcome this, we demonstrate a method of DNA manipulation using microstructures captured by optical tweezers that allow the manipulation of a chromosomal DNA molecule. For proper DNA handling, we developed microstructures analogous to chopsticks to capture and elongate single DNA molecules under an optical microscope. Two microstructures (i.e., microchopsticks) were captured by two focused laser beams to pinch a single yeast chromosomal DNA molecule between them and thereby manipulate it. The experiments demonstrated successful DNA manipulation and revealed that the size and geometry of the microchopsticks are important factors for effective DNA handling. This technique allows a high degree of freedom in handling single DNA molecules, potentially leading to applications in the study of chromosomal DNA.
A generative-oriented model-driven design environment for customizable video surveillance systems (2012)

To tackle the growing complexity and huge demand for tailored domestic video surveillance systems along with a high demanding time-to-market expectation, engineers at IVV Automação, LDAa are exploiting video surveillance domain as families of systems that can be developed following a pay-as-you-go fashion rather than developing an ex-nihilo new product. Several and different new functionalities are required for each new product’s hardware platforms (e.g., ranging from mobile phone, PDA to desktop PC) and operating systems (e.g., flavors of Linux, Windows and MAC OS X). Some of these functionalities have special economical constraints of development time and memory footprint. To better accommodate all the above listing requirements, a model-driven generative software development paradigm supported by mainstream tools is proposed to offer a significant leverage in hiding commonalities and configuring variabilities across families of video surveillance products while maintaining the new product quality.
Polarization analysis for small-angle neutron scattering with a <sup>3</sup>He spin filter at a pulsed neutron source (2021)

Neutron polarization analysis (NPA) for small-angle neutron scattering (SANS) experiments using a pulsed neutron source was successfully achieved by applying a 3 He spin filter as a spin analyzer for the neutrons scattered from the sample. The cell of the 3 He spin filter gives a weak small-angle scattering intensity (background) and covers a sufficient solid angle for performing SANS experiments. The relaxation time of the 3 He polarization is sufficient for continuous use for approximately 2 days, thus reaching the typical duration required for a complete set of SANS experiments. Although accurate evaluation of the incoherent neutron scattering, which is predominantly attributable to the extremely large incoherent scattering cross section of hydrogen atoms in samples, is difficult using calculations based on the sample elemental composition, the developed NPA approach with consideration of the influence of multiple neutron scattering enabled reliable decomposition of the SANS intensity distribution into the coherent and incoherent scattering components. To date, NPA has not been well established as a standard technique for SANS experiments at pulsed neutron sources such as the Japan Proton Accelerator Research Complex (J-PARC) and the US Spallation Neutron Source. It is anticipated that this work will contribute significantly to the accurate determination of the coherent neutron scattering component for scatterers in various types of organic sample systems in SANS experiments at J-PARC, particularly for systems involving competition between the coherent and incoherent scattering intensity.
Novel mutations in reverse transcriptase of human immunodeficiency virus type 1 reduce susceptibility to foscarnet in laboratory and clinical isolates (1995)

Foscarnet (phosphonoformic acid) is a pyrophosphate analog that inhibits the replication of human immunodeficiency virus type 1 (HIV-1) in vitro and in patients with AIDS. HIV-1 resistance to foscarnet has not been reported despite long-term foscarnet therapy of AIDS patients with cytomegalovirus disease. We therefore attempted to select foscarnet-resistant HIV-1 in vitro by serial endpoint passage of virus in 400 microM foscarnet. After 13 cycles of passage in MT-2 cells, virus exhibiting > or = 8.5-fold foscarnet resistance was isolated. The reverse transcriptase (RT) from resistant virions exhibited a similar level of foscarnet resistance in enzyme inhibition assays (approximately 10-fold resistance). Foscarnet-resistant virus showed increased susceptibility to 3'-azido-3'-deoxythymidine (90-fold) and to the HIV-1-specific RT inhibitors TIBO R82150 (30-fold) and nevirapine (20-fold). DNA sequence analysis of RT clones from resistant virus revealed the coexistence of two mutations in all clones: Gln-161 to Leu (CAA to CTA) and His-208 to Tyr (CAT to TAT). Sequence analysis of six clinical HIV-1 isolates showing reduced susceptibility to foscarnet revealed the Tyr-208 mutation in two, the Leu-161 mutation in one, and a Trp-88-to-Ser or -Gly mutation in four isolates. Site-specific mutagenesis and production of mutant recombinant viruses demonstrated that the Leu-161, Ser-88, and Tyr-208 mutations reduced HIV-1 susceptibility to foscarnet 10.5-, 4.3-, and 2.4-fold, respectively, in MT-2 cells. In the crystal structure of HIV-1 RT, the Gln-161 residue lies in the alpha E helix beneath the putative deoxynucleoside triphosphate (dNTP) binding site. The Gln-161-to-Leu mutation may affect the structure of the dNTP binding site and its affinity for foscarnet. The location of the Trp-88 residue in the Beta5a strand of HIV-1 RT suggest that the Ser-88 mutation affects template-primer binding, as do several mutations that affect RT susceptibility to nucleoside analogs.
Anal Neoplasia in Women With Genital Dysplasia (2013)

Human papillomavirus (HPV) infection has been implicated in a variety of mucosal malignancies at genital as well as oral sites. Investigators used anal cytology and high resolution anoscopy followed by biopsies of abnormal areas to assess the incidence of anal neoplasia in 327 women with genital dysplasia.

Among 64 women …
On-line dead-time compensation technique for open-loop PWM-VSI drives (1999)

A new on-line dead-time compensation technique for low-cost open-loop pulsewidth modulation voltage-source inverter (PWM-VSI) drives is presented. Because of the growing numbers of open-loop drives operating in the low-speed region, the synthesis of accurate output voltages has become an important issue where low-cost implementation plays an important role. The so-called average dead-time compensation techniques rely on two basic parameters to compensate for this effect: the magnitude of the volt seconds lost during each PWM cycle and the direction of the current. In a low-cost implementation, it is impractical to attempt an on-line measurement of the volt-seconds error introduced in each cycle-instead an off-line measurement is favored. On the other hand, the detection of the current direction must be done on line. This becomes increasingly difficult at lower frequencies and around the zero crossings, leading to erroneous compensation and voltage distortion. This paper presents a simple and cost-effective solution to this problem by using an instantaneous back calculation of the phase angle of the current. Given the closed-loop characteristic of the back calculation, the zero crossing of the current is accurately obtained, thus allowing for a better dead-time compensation. Experimental results validating the proposed method are presented.
Supplementary Figure 1 from Inhibition of Cyclooxygenase-2 Suppresses Lymph Node Metastasis via Reduction of Lymphangiogenesis (2023)

Supplementary Figure 1 from Inhibition of Cyclooxygenase-2 Suppresses Lymph Node Metastasis via Reduction of Lymphangiogenesis
Photopolymerization of Pollen Based Biosourced Composites and Applications in 3D and 4D Printing (2021)

Abstract Pollen have the potential to be effective plant‐based biorenewable reinforcing fillers for polymers due to their chemical stability and unique micro‐ or nano‐structured surfaces. Pollen‐polymer composites can form the basis for a new class of light‐weight and sustainable materials if compatible polymer‐filler systems can be engineered through photopolymerization, but this idea is previously unexplored. The first demonstration of photopolymerization and 3D printing with the incorporation of pine pollen as filler in poly(ethylene glycol) diacrylate are presented. The filler properties affecting the related depth of cure and the mechanical, thermal, and functional properties are examined in detail. In addition, the lithography technique is applied to the photocomposites for the production of 3D patterns. 4D printing behavior is also possible through the water swelling and dehydration induced actuation of the 3D printed composites with spatial resolution features. This work is expected to provide a new way to a field for photopolymerization reactions in natural material‐resin composites and thereby to expand potential applications in 3D and 4D printing.
Properties of metal-insulator transition and electron spin relaxation in GaN:Si (2011)

We investigate the properties of doping-induced metal-insulator transition in GaN:Si by means of electron spin resonance and the Hall effect. While increasing the doping concentration, Si-related bands are formed below the bottom of the GaN conduction band. The ${D}^{0}$ band of single-occupied Si donor sites is centered 27 meV below the bottom of the GaN conduction band, and the ${D}^{\ensuremath{-}}$ band of double-occupied Si states is centered at 2.7 meV below the bottom of the GaN conduction band. Strong damping of the magnetic moment occurs due to filling of the ${D}^{\ensuremath{-}}$ states at Si concentrations approaching the metal-insulator transition. Simultaneously, shortening of electron spin relaxation time due to limited electron lifetime in the single-occupied ${D}^{0}$ band is observed. The metal-insulator transition occurs at the critical concentration of uncompensated donors equal to about 1.6 $\ifmmode\times\else\texttimes\fi{}$ 10${}^{18}$ cm${}^{\ensuremath{-}3}$. Electronic states in metallic samples beyond the metal-insulator transition demonstrate the nonmagnetic character of double-occupied states.
White LEDs for General Lighting Applications (2010)

A range of high-performance LED modules for General Lighting has been designed to meet requirements of LED lamps. The Red-white approach using efficiency-optimized phosphor-converted and red LEDs delivers warm-white emission of highest quality and efficacy.
Abstract 17185: Sympathetic Reinnervation is Required for Mammalian Cardiac Regeneration (2015)

Rationale: Established animal models of tissue and limb regeneration demonstrate a critical dependence on concurrent reinnervation by the peripheral nervous system. The abundance of autonomic nerves in the mammalian heart suggests they play a similar role in the response to cardiac injury. Objective: To test the hypothesis that reinnervation is required for innate neonatal cardiac regeneration. Methods and Results: Crossing Wnt1:cre transgenic mice with a double-tandem (td) tomato reporter strain identified all neural crest-derived cell lineages including the peripheral autonomic nerves in the heart. Whole mount epi-fluorescence microscopy facilitated the clear resolution of subepicardial autonomic nerves in the mouse ventricles providing unprecedented detail of the subepicardial neuroanatomy of the mouse heart. We confirmed that sympathetic nerve structures envelop the entire heart, and importantly, exhibit robust re-growth into the regenerating myocardium following resection of the left ventricular apex in neonatal mice. While innervated hearts regenerate with minimal scarring to the left ventricular myocardium, we report that innate cardiac regeneration was inhibited following sympathectomy, as determined by cross-sectional percentage of viable LV myocardium (n=9, 0.87±1.4% vs. n=6, 14.05±4.4% ; p&lt;0.01). Conclusions: Ablation of post-ganglionic sympathetic nerves blocks the innate regenerative capacity of neonatal mouse hearts. Therefore, the innate ability of the neonatal mouse heart to undergo regeneration in response to injury is dependent on sympathetic innervation of the ventricular myocardium. This finding has significant implications for adult regeneration following myocardial infarction where nerve growth is hindered by age related influences and scar tissue.
Effects of NH3 and N2 additions to hot filament activated CH4/H2 gas mixtures (2002)

Resonance enhanced multiphoton ionization and cavity ring down spectroscopies have been used to provide spatially resolved measurements of relative H atom and CH3 radical number densities, and NH column densities, in a hot filament (HF) reactor designed for diamond chemical vapor deposition and here operating with a 1% CH4/n/H2 gas mixture—where n represents defined additions of N2 or NH3. Three-dimensional modeling of the H/C/N chemistry prevailing in such HF activated gas mixtures allows the relative number density measurements to be placed on an absolute scale. Experiment and theory both indicate that N2 is largely unreactive under the prevailing experimental conditions, but NH3 additions are shown to have a major effect on the gas phase chemistry and composition. Specifically, NH3 additions introduce an additional series of “H-shift” reactions of the form NHx+H⇌NHx−1+H2 which result in the formation of N atoms with calculated steady state number densities &amp;gt;1013 cm−3 in the case of 1% NH3 additions in the hotter regions of the reactor. These react, irreversibly, with C1 hydrocarbon species forming HCN products, thereby reducing the concentration of free hydrocarbon species (notably CH3) available to participate in diamond growth. The deduced reduction in CH3 number density due to competing gas phase chemistry is shown to be compounded by NH3 induced modifications to the hot filament surface, which reduce its efficiency as a catalyst for H2 dissociation, thus lowering the steady state gas phase H atom concentrations and the extent and efficiency of all subsequent gas phase transformations.
Endogenous mink (Mustela vison) type C virus isolated from sarcoma virus-transformed mink cells (1978)

A previously described type virus stock (designated PP-1R), isolated by cocultivating baboon cells with mink cells transformed by Kirsten sarcoma virus (64J1), has been further cloned and characterized. End point-diluted stocks of PP-1R have been obtained that are free of focus-forming activity and lack both Kirsten sarcoma and primate type C viral sequences. Nucleic acid hybridization experiments show that the cloned virus (MiLV) is an endogenous, genetically transmitted virus of the mink (Mustela vison). MiLV replicates in canine, feline, and 64J1 mink cells but not in an untransformed mink cell line. Multiple viral gene copies can be detected in the DNA of normal mink cells in culture and in normal mink tissues; related endogenous viral genes are also detected in several related Mustela species. The virus codes for a p30 protein very closely related antigenically to that of feline leukemia virus but contains p15 and p12 proteins that are antigenically distinct. The mink cell line, Mv1Lu, and its Kirsten sarcoma-transformed derivatives, 64J1, express relatively low levels of type C viral RNA related to MiLV and normally do not produce detectable levels of MiLV p30 protein or complete, infectious viral particles. Infection of sarcoma virus-transformed mink cells with baboon type C virus, however, can augment the level of expression of endogenous mink viral RNA and can result in the synthesis and packaging of mink viral RNA and p30 antigen in extracellular virions. Since the Mv1Lu cell line and its tranformed derivatives have become widely used in studies of retroviruses, the possibility of activating endogenous mink viral genes should be considered by investigators working with these cells.
Stream Register Files with Indexed Access (2005)

Many current programmable architecture designed to exploit data parallelism require computation to be structured to operate on sequentially accessed vectors or streams of data. Applications with less regular data access patterns perform sub-optimally on such architectures. We present a register file for streams (SRF) that allows arbitrary, indexed accesses. Compared to sequential SRF access, indexed access captures more temporal locality, reduces data replication in the SRF, and provides efficient support for certain types of complex access patterns. Our simulations show that indexed SRF access provides speedups of 1.03x to 4.1x and memory bandwidth reductions of up to 95% over sequential SRF access for a set of benchmarks representative of data-parallel applications with irregular accesses. Indexed SRF access also provides greater speedups than caches for a number of application classes despite significantly lower hardware costs. The area overhead of our indexed SRF implementation is 11%-22% over a sequentially accessed SRF, which corresponds to a modest 1.5%-3% increase in the total die area of a typical stream processor.
Copper-Catalyzed Low-Voltage Cathodic Electroluminescence at Anodized Aluminium Electrode (1984)

Electroluminescence is observed at several semiconductor-electrolyte interfaces during the reduction of hydrogen peroxide, persulphate and oxygen. 1-3 This luminescence is presumably caused by the electron-hole recombination in a semiconductor.
Study on organosilicon positive resist. II. Organosilicon positive photoresist (OSPR–1334) and its application to bilayer resist system (1992)

Abstract A new alkali‐developable organosilicon positive photoresist (OSPR–1334) and a bilayer resist process with OSPR–1334 has been developed. OSPR–1334 is composed of poly( p ‐hydroxybenzylsilsesquioxane) and naphthoquinone diazide. The sensitivity and the resolution are almost the same as those of conventional novolac‐based resists when aqueous tetrakis (2‐hydroxyethyl) ammonium hydroxide is used as a developer. Also, OSPR–1334 has excellent resistance to O 2 RIE. The etching rate is 3.6 nm/min, while that of polyimide resins or hard‐baked novolac‐based resists is 100 nm/min. OSPR–1334 is suitable for use as the top layer of the bilayer resist system. OSPR–1334, after O 2 RIE, can be eliminated by dissolving an unchanged layer followed by spinning out or filtrating a changed surface layer. Submicron patterns with a high aspect ratio can easily be obtained with this bilayer resist process.
ChemInform Abstract: MCM‐41 as a Support for Small Platinum Particles: A Catalyst for Low‐ Temperature Carbon Monoxide Oxidation. (1996)

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.
MicroRNA-506 as a tumor suppressor in anaplastic thyroid carcinoma by regulation of WNT and NOTCH signaling pathways. (2023)

MiR-506 regulated EMT, cell migration, and chemoresistance through regulation of WNT and NOTCH signaling pathways in ATC cells. Therefore, after confirmation with animal studies, it can be introduced as an efficient novel therapeutic factor for ATC tumors.
Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data (2012)

Human microbiome research characterizes the microbial content of samples from human habitats to learn how interactions between bacteria and their host might impact human health. In this work a novel parametric statistical inference method based on object-oriented data analysis (OODA) for analyzing HMP data is proposed. OODA is an emerging area of statistical inference where the goal is to apply statistical methods to objects such as functions, images, and graphs or trees. The data objects that pertain to this work are taxonomic trees of bacteria built from analysis of 16S rRNA gene sequences (e.g. using RDP); there is one such object for each biological sample analyzed. Our goal is to model and formally compare a set of trees. The contribution of our work is threefold: first, a weighted tree structure to analyze RDP data is introduced; second, using a probability measure to model a set of taxonomic trees, we introduce an approximate MLE procedure for estimating model parameters and we derive LRT statistics for comparing the distributions of two metagenomic populations; and third the Jumpstart HMP data is analyzed using the proposed model providing novel insights and future directions of analysis.
Percutaneous Coronary Intervention (PCI) Reprograms Circulating Extracellular Vesicles from ACS Patients Impairing Their Cardio-Protective Properties (2021)

Extracellular vesicles (EVs) are promising therapeutic tools in the treatment of cardiovascular disorders. We have recently shown that EVs from patients with Acute Coronary Syndrome (ACS) undergoing sham pre-conditioning, before percutaneous coronary intervention (PCI) were cardio-protective, while EVs from patients experiencing remote ischemic pre-conditioning (RIPC) failed to induce protection against ischemia/reperfusion Injury (IRI). No data on EVs from ACS patients recovered after PCI are currently available. Therefore, we herein investigated the cardio-protective properties of EVs, collected after PCI from the same patients. EVs recovered from 30 patients randomly assigned (1:1) to RIPC (EV-RIPC) or sham procedures (EV-naive) (NCT02195726) were characterized by TEM, FACS and Western blot analysis and evaluated for their mRNA content. The impact of EVs on hypoxia/reoxygenation damage and IRI, as well as the cardio-protective signaling pathways, were investigated in vitro (HMEC-1 + H9c2 co-culture) and ex vivo (isolated rat heart). Both EV-naive and EV-RIPC failed to drive cardio-protection both in vitro and ex vivo. Consistently, EV treatment failed to activate the canonical cardio-protective pathways. Specifically, PCI reduced the EV-naive Dusp6 mRNA content, found to be crucial for their cardio-protective action, and upregulated some stress- and cell-cycle-related genes in EV-RIPC. We provide the first evidence that in ACS patients, PCI reprograms the EV cargo, impairing EV-naive cardio-protective properties without improving EV-RIPC functional capability.
Charge-Transfer in Silicon Governs the Pattern of Dissociative Attachment of Hydrogen Halides: HCl, HBr, and HI (2016)

The dissociative attachment of hydrogen halides, HCl, HBr, and HI, on Si(100) was studied by scanning tunneling microscopy, and modeled by molecular dynamics computations based on density functional theory. The relative yields of on-dimer (OD), inter-dimer (ID), and inter-row (IR) products, reported here for the first time, were unaltered by temperature change, indicative of barrier-free reaction. Inter-dimer reaction was found experimentally to be overwhelmingly the favored reaction path at all temperatures, 175–300 K. This is a preference that theory accounts for by a combination of kinematics favoring the initial approach of H, and subsequent charge-displacement directing the halogen atom to an inter-dimer site. Molecular dynamics, with statistical sampling of the initial collision-geometry at the surface, showed that the light H-atom invariably was the first to engage with the surface, forming H–Si. This bond-formation resulted in directional charge-transfer to a neighboring Si dimer-pair of the same dimer-row. As a consequence this neighboring Si became attractive to the incoming electrophilic halogen-atom, accounting for the observed strong preference for the inter-dimer outcome.