gebhart/patrepeval huggingface dataset:
Rhizobium meliloti nifN (fixF) gene is part of an operon regulated by a nifA-dependent promoter and codes for a polypeptide homologous to the nifK gene product (1987)

An essential gene for symbiotic nitrogen fixation (fixF) is located near the common nodulation region of Rhizobium meliloti. A DNA fragment carrying fixF was characterized by hybridization with Klebsiella pneumoniae nif DNA and by nucleotide sequence analysis. The fixF gene was found to be related to K. pneumoniae nifN and was therefore renamed as the R. meliloti nifN gene. Upstream of the nifN coding region a second open reading frame was identified coding for a putative polypeptide of 110 amino acids (ORF110). By fragment-specific Tn5 mutagenesis it was shown that the nifN gene and ORF110 form an operon. The control region of this operon contains a nif promoter and also the putative nifA-binding sequence. For the deduced amino acid sequence of the nifN gene product a striking homology to the R. meliloti nifK protein was found. One cysteine residue and its adjacent amino acid sequence, which are highly conserved in the R. meliloti nifK, R. meliloti nifN, and K. pneumoniae nifN proteins, may play a role in binding the FeMo cofactor.
Abstract POSTER-THER-1428: Effects of atypical PKC inhibitors on ovarian cancer proliferation and RNA levels (2015)

Abstract Ovarian cancers are highly lethal tumors which account for approximately four percent of all women’s cancers and are the fifth leading cause of cancer-related death among women. At diagnosis the majority of patients have metastatic disease and the long-term survival remains low. Certain ovarian cancers are highly lethal tumors due to the emergence of therapy-resistant ovarian cancer cells. Protein kinase C-iota (PKC-ι) has been shown to aid in the ability of cancer cells to resist drug-induced apoptosis. Recently, it has been reported that PKC-ι which is located in chromosome 3 at 3q26.2 is the most common genomic amplicon as identified by comparative genomic hybridization [Proc Natl Acad Sci U S A 102:12519–12524(2005)]. Additionally, an increase in PKC-ι DNA copy number was associated with decreased progression-free survival of ovarian cancer patients. Moreover, only PKC-ι gene amplification is highly correlated with protein overexpression, tumor size, lymph node metastasis and clinical stage out of four genes studied on the 3q26 amplification [Genes Chromosomes Cancer 47:127-136(2008)]. The focus of this research was to determine the in-vitro efficacy of the pan-atypical PKC inhibitor, 2-acetyl-1,3-cyclopentanedione (ACPD; Diabetes. 2014 Apr 4) and the novel PKC-iota inhibitor, ICA-1, (1H-imidazole-4-carboxamide, 5-amino-1-[2,3-dihydroxy-4-[(phosphonooxy) methyl]cyclopentyl]-,[1R-(1α, 2β, 3 β, 4 α) [The Inter. J. Biochem. & Cell Biol. 43:784-794(2011)] on HEY ovarian cancer cell proliferation and RNA concentration. In contrast to ACPD which inhibits both PKC-ι and PKC-zeta (PKC-ζ), ICA-1 specifically inhibits the activity of PKC-ι but not (PKC-ζ). The effects of ACPD and ICA-1on HEY proliferation was quantified by Trypan blue exclusion assay. RNA was isolated from treated and untreated cells using the Rneasy Mini Kit and protocol. Total RNA concentration was estimated using the NanoDrop1000 Spectrophotometer. Results showed that incubation of HEY ovarian cancer cells with ICA-1(1 μm) decreased proliferation by 41% compared to controls at 72 hours post-treatment. ICA-1(2 μM) reduced RNA levels by 17% at 72 hours post-treatment compared to controls. In contrast, ACPD (2 μM) inhibited proliferation by 82% compared to controls and RNA levels were reduced by 97% at 24 hours post-treatment. These results suggest the potential of ICA-1 and ACPD as chemotherapeutic agents. Citation Format: Minjel Shah, Christopher Apostolatos, Hercules Apostolatos, Mildred Acevedo-Duncan. Effects of atypical PKC inhibitors on ovarian cancer proliferation and RNA levels [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr POSTER-THER-1428.
Papulacandins, a new family of antibiotics with antifungal activity. I. Fermentation, isolation, chemical and biological characterization of papulacandins A, B, C, D and E. (1977)

Papulacandin, a new antibiotic complex, active against Candida albicans and several other yeasts, was isolated from a strain of Papularia sphaerosperma. The fermentation, isolation, physico-chemical properties and biological activity of the five structurally related papulacandins A, B, C, D and E are reported. Papulacandin B, the main component, was assigned the formula of C47H64O17.
Broadband gradient index microwave quasi-optical elements based on non-resonant metamaterials (2009)

Utilizing non-resonant metamaterial elements, we demonstrate that complex gradient index optics can be constructed exhibiting low material losses and large frequency bandwidth. Although the range of structures is limited to those having only electric response, with an electric permittivity always equal to or greater than unity, there are still numerous metamaterial design possibilities enabled by leveraging the non-resonant elements. For example, a gradient, impedance matching layer can be added that drastically reduces the return loss of the optical elements due to reflection. In microwave experiments, we demonstrate the broadband design concepts with a gradient index lens and a beam-steering element, both of which are confirmed to operate over the entire X-band (roughly 8-12 GHz) frequency spectrum.
Dynamic phase measurement of fast liquid crystal phase modulators (2022)

We present dynamic time-resolved measurements of a multi-pixel analog liquid crystal phase modulator driven at a 1 kHz frame rate. A heterodyne interferometer is used to interrogate two pixels independently and simultaneously, to deconvolve phase modulation with a wide bandwidth. The root mean squared optical phase error within a 30 Hz to 25 kHz bandwidth is <0.5° and the crosstalk rejection is 50 dB. Measurements are shown for a custom-built device with a flexoelectro-optic chiral nematic liquid crystal. However, the technique is applicable to many different types of optical phase modulators and spatial light modulators.
Real-time communication and admission control over responsive link (2008)

This paper presents a framework of real-time communica-tions over Responsive Link, which is one of the communi-cation standards for real-time networks. In the Responsive Link, each packet has a priority at the hardware level and higher-prioritized packets can overtake lower-prioritized packets on network switches. Although Responsive Link is suitable for real-time communication in multihop net-works, it is necessary for Responsive Link to be managed by software in order to establish the sufficient number of connections with timing constraints. In our approach, the communication delay of any connection is guaranteed by the admission control before the transmission to meet the timing constraints of any message which belong to the con-nection. We first introduce the notion of the virtual deadline assignment between two nodes lying side-by-side on the connection. We then propose an efficient admission control in which the virtual deadline is re-assigned. The simulation results show that the proposed methods improve the accep-tance ratio of establishing the connections compared to a orthodox method.
Impact Ionization across the band-edge discontinuity in superlattices and its applications to solid-state photomultipliers (1986)

We report the observation of a new avalanche phenomenon in superlattices. This effect is characterized by a large ratio of the multiplications for holes and electrons implying β ≫ α and is very different in nature from the previously studied band-edge discontinuity assisted ionization in quantum wells. The i region of our p + in + structures, grown by MBE, consists of an undoped (n ≃10 15 cm −3 ) Al 0.48 ln 0.52 As/Ga 0.47 ln 0.53 As superlattice. Six wafers with well and barrier thicknesses ranging from 100 to 470 Å and a number of periods varying from 20 to 50 were studied. In addition similar MBE structures with an AISb/GaSb superlattice were also grown. The electron and hole initiated gains ( M e and M h ) were determined using standard techniques. It was found that M h ≫ M e . Ionization ratios β/α in excess of 10 2 have been deduced which are the highest observed in any III–V material. All the experimental data can be explained in terms of a new mechanism, impact ionization across the band-edge discontinuity. There are concentrations of electrons and holes dynamically stored in the conduction and valence band wells which can easily approach 10 16 cm −3 in our structures, at fields ≲ 10 5 V/cm. Consider now a carrier (e.g., a hole) photoinjected into the structure; after gaining energy in the barrier layers it can impact-ionize one of the holes dynamically stored in the low gap layers out of the well across the valence band discontinuity. Electrons may of course impact-ionize electrons out of the wells but since ∆ E C (≃0.5 eV) is more than twice ∆ E v , the electron ionization rate is much smaller than the hole ionization rate which explains why the holes are multiplied much more than the electrons. New solid-state photomultipliers based on this phenomenon are discussed.
Preferential drug delivery to tumor cells than normal cells using a tunable niosome–chitosan double package nanodelivery system: a novel in vitro model (2020)

Abstract Background We previously described the properties of a targeted drug delivery system (DDS) in a cell-free system. Here, in this comparative cell-based study (normal and tumor cells), we provide a quantitative analysis of the extracellular diffusion and intracellular localization of this DDS. This DDS consists of fluorescence-labeled paclitaxel encapsulated in non-ionic surfactant vesicles/niosomes embedded in a thermo-sensitive cross-linked chitosan hydrogel with an affinity for the MUC1 mucin surface antigen overexpressed on tumor cells, and designed for a sustained and controlled, localized delivery of embedded drugs. We evaluated DDS in our novel in vitro model using MatTek’ glass-bottom culture plates and compared human cancer cell lines (OV2008 epithelial origin carcinoma and U373 glioma, both overexpressing MUC1) with human normal epithelial control cell lines (IMMC3 and IOSE-121 using differential contrast and confocal microscopy. Results Tumor cells incubated in the presence of chitosan alone or DDS-containing chitosan–niosome–paclitaxel–BODIPY 564/570, showed a prominent granular accumulation on their surface when compared to the normal cells. Quantitation of gray value light intensity of the extracellular region of chitosan alone treated OV2008 and IOSE-121 controls done by analysis of multiple radial line segments, 4 µm each, using ImageJ software showed 2 times higher intensity around the OV2008 than around normal IOSE-121 controls ( p < 0.05). In the DDS-treated OV2008 cells, extracellular fluorescence intensity measured at different diffusion distances outside of the cells, in three different zones showed the difference in means of fluorescence intensity in these zones ( p < 0.05) with the highest level of fluorescence near the cell surface indicating a concentration gradient, most likely driven by the high affinity of chitosan to the MUC1 receptor. Also, as chitosan alone accumulated two times more along the edge of tumor cells compared to normal cells, we found intracellular fluorescence intensity quantified at time intervals to be also 2 times higher in OV2008 than in normal IMCC3 cells ( p < 0.05). Conclusion Based on the observation of the DDS preferentially targeting tumor cells, there is a potential implication for the localized delivery of therapeutic drug doses to solid tumors or post-surgical solid tumors cavities containing residual tumor cells.
Privacy-preserving querying mechanism on privately encrypted personal health records (2017)

The affordability of cloud data storage has made it simpler for users to store and access data online from any location or operating system. These services may be used by users to store sensitive data, such as personal health records or financial data. Many service providers offer features such as analyzing the users’ private data to generate useful reports for medical data. Storing such sensitive data on the cloud raises many privacy concerns. While encryption can ensure data confidentiality, it introduces the challenge of analyzing the privately encrypted data while preserving the privacy of the users and the querying entity. In this paper, we address this problem by proposing a network protocol that would allow a third party, such as a health organization, to query privately encrypted data without relying on a trusted entity. The protocol we propose preserves the privacy of the users and the querying entity. The protocol relies on homomorphic, threshold cryptography, and randomization to allow for secure, distributed, and privacy-preserving queries. We evaluate the performance of our protocol and report on the results of the implementation.
Discovery of Small Molecule CD40–TRAF6 Inhibitors (2015)

The CD154-CD40 receptor complex plays a pivotal role in several inflammatory pathways. Attempts to inhibit the formation of this complex have resulted in systemic side effects. Downstream inhibition of the CD40 signaling pathway therefore seems a better way to ameliorate inflammatory disease. To relay a signal, the CD40 receptor recruits adapter proteins called tumor necrosis factor receptor-associated factors (TRAFs). CD40-TRAF6 interactions are known to play an essential role in several inflammatory diseases. We used in silico, in vitro, and in vivo experiments to identify and characterize compounds that block CD40-TRAF6 interactions. We present in detail our drug docking and optimization pipeline and show how we used it to find lead compounds that reduce inflammation in models of peritonitis and sepsis. These compounds appear to be good leads for drug development, given the observed absence of side effects and their demonstrated efficacy for peritonitis and sepsis in mouse models.
7-μm-cutoff PtSi infrared detector for high sensitivity MWIR applications (1995)

PtSi Schottky infrared detectors with extended cutoff wavelengths of 5.7, 6.6, and 7.3 μm have been demonstrated by incorporating a thin p+ layer at the PtSi-Si interface for high sensitivity medium wavelength infrared imaging applications. The response uniformity of the 7-μm cutoff detector was studied.
Initial experimental results from a relativistic magnetron driven by transparent cathodes (2008)

The relativistic magnetron has been studied as a high power microwave source since the 1970's. Its most salient properties are its simplicity and its frequency agility. Recently, researchers at the University of New Mexico proposed that a transparent cathode can significantly improve the output characteristics of magnetrons. Since then, a comprehensive study using particle-in-cell simulations has elaborated the many benefits of using this cathode. This talk will enumerate the various benefits of operating a relativistic magnetron using a transparent cathode. In addition, the initial results of experiments at the University of New Mexico on an A6 magnetron driven by a short-pulse Sinus-6 accelerator will be presented. Planned experiments on an A6 magnetron using a longer pulse (50 ns) accelerator at UNM will also be described. Details will also be provided regarding the redesign of the longer pulse accelerator.
Expanding the Phenotypic Spectrum of the CACNA1A Gene T666M Mutation (2003)

The T666M mutation is the most frequent CACNA1A mutation in FHM; it was found in 5 of 33 FHM families at our laboratory, and in 19 of 39 families with a known mutation reported in the literature (including the present study). Screening for the T666M mutation should therefore be the first step when screening families with FHM. There is a remarkable clinical heterogeneity among families with the T666M mutation.
Epitope Mapping of Antibodies against Prostate-specific Antigen with Use of Peptide Libraries (2002)

Most of the cyclic peptides selected with PSA MAbs are specific for the MAb used for selection and do not resemble any sequence on the antigen. Peptides reactive with two MAbs recognizing the same epitope can be obtained by sequential panning. This method can be used to predict the location of some epitopes, but additional methods are needed to confirm the result.
A Digital Self-Tuning Tracking Controller for (1994)

A new digital self-tuning tracking controller for the permanent-magnet synchronous motor is presented, providing for either velocity or position trajectory tracking when both the electrical and mechanical parameters of the motor are unknown. A time-scale simplification leads to a discrete-time design model that is reduced order and that evolves in the slower mechani- cal time scale. A new piecewise-linear parameterization of the motor torque-angle characteristic functions and cogging allows for arbitrarily accurate identification of higher-order harmonics, without requiring more computation than traditional single- term sinusoidal descriptions. Experimental results demonstrate that good performance is achieved even with very poor initial parameter knowledge.
Preparation and Properties of a Therapeutic Inter‐Alpha‐Trypsin Inhibitor Concentrate from Human Plasma (1994)

Inter-alpha-trypsin inhibitor (ITI) is a serine protease inhibitor found in human plasma. Its antiprotease activity is due to bikunin which is effective in various types of experimental shock and pancreatitis. Therefore ITI, which releases bikunin by proteolytic cleavage, could be of therapeutic interest. A method for the large-scale isolation of ITI from human plasma is described. ITI was purified from the prothrombin complex concentrate (PCC) by diethylaminoethyl-Sepharose fast-flow chromatography followed by a chromatographic step on immobilized heparin designed to remove C4, factor X and protein C. With this procedure, which was performed under mild conditions, a homogeneous preparation of native ITI was obtained, as demonstrated by electrophoretic and chromatographic analyses. ITI maintained its biological activity, as exhibited by its specific antitryptic activity of 420 +/- 65 IU/g. In order to decrease or eliminate the risk of transmission of viral disease due to lipid-enveloped viruses, the process incorporated a solvent-detergent treatment. Animal studies on the final product revealed no adverse side-effects in terms of toxicity, thrombogenicity or hypotension. This preparation appears suitable for therapeutic evaluation in animal experimental models.
An In Vitro Evaluation of Condoms as Barriers to a Small Virus (1997)

Few condoms allowed any virus penetration. The median amount of penetration for latex condoms when extrapolated to expected actual use conditions was 1 x 10(-5) ml (volume of semen). Thus, even for the few condoms that do allow virus penetration, the typical level of exposure to semen would be several orders of magnitude lower than for no condom at all.
Fluorescence line-narrowing detection in chromatography and electrophoresis (2000)

A review of the basic aspects of fluorescence line-narrowing spectroscopy (FLNS) and its coupling with thin-layer chromatography (TLC) and polyacrylamide gel electrophoresis (PAGE) for off-line high-resolution low temperature spectral characterization is discussed. This is followed by a description of the on-line interfacing of capillary electrophoresis (CE) and capillary electrochromatography (CEC) with FLN detection. CE/ CEC-FLNS instrumentation and its applications for spectral identification of closely related analytes are also presented. Future prospects of micro and capillary high performance liquid chromatography (HPLC) with on-line high-resolution low temperature spectroscopic identification are considered.
Immersive Audio Delivery Using Joint Object Coding (2016)

Immersive audio experiences (3D audio) are an important element of next-generation audio entertainment systems. This paper presents joint object coding techniques that enable the delivery of object-based immersive audio content (e.g. Dolby Atmos) at low bit rates. This is achieved by conveying a multi-channel downmix of the immersive content using perceptual audio coding algorithms together with parametric side information that enables the reconstruction of the audio objects from the downmix in the decoder. An advanced joint object coding tool is part of the AC-4 system recently standardized by ETSI. Joint object coding is also used in a backwards compatible extension of the Dolby Digital Plus system. Listening test results illustrate the performance of joint object coding in these two applications.
PPPS-2013: Nanoelectroablation for human carcinoma therapy (2013)

We have developed a low energy direct current pulsed electric field therapy for tissue ablation. This therapy applies 100 ns long electric pulses 30 kV/cm in amplitude using a contact electrode and triggers apoptosis in the treated tissue. Here we review the progress that has been made in understanding the mechanisms and targets of nanosecond pulsed electric fields (nsPEF) when applied to cells and tissues. This work began in 2001 in the laboratory of Karl Schoenbach who collaborated with biologists Stephen Beebe and Stephen Buescher to demonstrate the permeabilization of intracellular organelles. Since then over 100 papers have been published studying the cellular responses to nsPEF. We discuss these targets and cellular responses and introduce some new results from our group using nanoelectroablation to treat human pancreatic carcinoma in a murine xenograft model system. We have determined that 500 pulses 100 ns long and 30 kV/cm in amplitude are sufficient to ablate human pancreatic carcinomas growing in immunosuppressed mice and these ablated tumors do not recur for at least 300 days. We have also determined that the reactive oxygen species generation that is triggered within a minute after nsPEF treatment is Ca <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> -dependent. In order bring this therapy into the clinic for the treatment of human tumors we are developing both a pulse generator as well as delivery electrodes to target the tumors to be treated. We will describe the NanoBlate <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> Model NB-1 100 ns pulse generator and the first human clinical trial data using nanoelectroablation to ablate basal cell carcinomas without scarring.
Impedance-Based Online Estimation of Nodal Inertia and Primary Frequency Regulation Capability (2022)

Accurate estimation of inertia and primary frequency regulation (PFR) capability is important to ensure frequency stability in low-inertia power systems. This paper investigates how the inertia and PFR capability of a power source node can be evaluated using a non-invasive online estimation method from the impedance perspective. Based on small perturbation injection, a novel approximate relationship between the impedance and corresponding frequency response transfer function (FR(s)) is deduced. The features of the FR(s)’s magnitude response curve, i.e., resonance frequency and DC gain, are then used to develop an overall implementation framework for nodal inertia and PFR capability estimation in real time. This method provides new insights with respect to obtain the synchronous and non-synchronous converter interfaced generator's inertia constant and PFR capability for grid operators via impedance calculation and measurements. Case studies on a modified 9-bus system and NETS-NYPS 68-bus system demonstrate the effectiveness of the proposed impedance-based estimation approach.