gebhart/patrepeval huggingface dataset:
Exploring Peptide Ligase Orthologs in Actinobacteria—Discovery of Pseudopeptide Natural Products, Ketomemicins (2016)

We recently identified a novel peptide ligase (PGM1), an ATP-grasp-ligase, that catalyzes amide bond formation between (S)-2-(3,5-dihydroxy-4-methoxyphenyl)-2-guanidinoacetic acid and ribosomally supplied oligopeptides in pheganomycin biosynthesis. This was the first example of an ATP-grasp-ligase utilizing peptides as nucleophiles. To explore the potential of this type of enzyme, we performed a BLAST search and identified many orthologs. The orthologs of Streptomyces mobaraensis, Salinispora tropica, and Micromonospora sp. were found in similar gene clusters consisting of six genes. To probe the functions of these genes, we heterologously expressed each of the clusters in Streptomyces lividans and detected novel and structurally similar pseudotripeptides in the broth of all transformants. Moreover, a recombinant PGM1 ortholog of Micromonospora sp. was demonstrated to be a novel dipeptide ligase catalyzing amide bond formation between amidino-arginine and dipeptides to yield tripeptides; this is the first report of a peptide ligase utilizing dipeptides as nucleophiles.
Aflibercept Action in a Rabbit Model of Chronic Retinal Neovascularization: Reversible Inhibition of Pathologic Leakage With Dose-Dependent Duration (2018)

This model mimics a chronic human disease in its stability and persistence, and the antileak action of aflibercept is fully reversible with a dose-dependent duration. Therefore, this large eye model is uniquely suitable for investigations into the efficacy and duration of action of novel formulations and pharmacotherapies for retinal vascular diseases, and for studying the underlying pathobiology of retinal angiogenesis.
Special session 11B: Hot topic hardware security: Design, test and verification issues (2010)

Security is rapidly becoming a critical factor in the IC design and test cycle. To provide higher levels of assurance and trust to designers, manufacturers and end users of integrated circuits (ICs), there is a need to integrate security measures during design, validation, and manufacturing test covering all aspects of security threats in hardware. These threats include secret information leakage, malicious hardware modifications in an untrusted foundry, hardware IP piracy and reverse engineering efforts. This session will have three presentations focusing on the design, validation, and test challenges for attack-resistant secure hardware systems.
Two Dimensional 32×32 InGaAs/InP Photodiode Arrays and Dark Current Characteristics Limited by the Diffusion and Generation-Recombination (2006)

In the 2 dimensional InGaAs/InP photodiode arrays on semi-insulating InP the dark current is limited by the diffusion and generation- recombination. The static dark current of the InGaAs/InP PiN photodiode arrays is proportional to the number of the pixels in the array. In PiN InGaAs photodiode array structure, the diffusion currents of the each pixel due to the thermally generated minority carriers diffusing into the depletion region are accumulated to reach total leakage current. This phenomenon of pixel number dependent leakage current is due to the accumulation of the contributed diffusion current as much as ~0.02 pA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> from the each pixel photodiode comprising the array.
Supplementary Figure S1 from PTEN Regulates Glutamine Flux to Pyrimidine Synthesis and Sensitivity to Dihydroorotate Dehydrogenase Inhibition (2023)

&lt;p&gt;Supplementary Figure S1. Loss of Pten increases proliferation.&lt;/p&gt;
AKR-501 Activates the Thrombopoietin Receptor through Interaction with the Transmembrane Domain (2008)

Abstract AKR-501 (1-(3-Chloro-5-{[4-(4-chloro-2-thienyl)-5-(4-cyclohexylpiperazin-1-yl) thiazol-2-yl]carbamoyl}-2-pyridyl)piperidine-4-carboxylic acid, formerly known as YM-477) is an orally-active full agonist of the thrombopoietin (TPO) receptor, c-Mpl. Human c-Mpl consists of an N-terminal extracellular domain containing a membrane-distal cytokine receptor homology region (CRH-1) which is the site of TPO binding, as well as a membrane-proximal CRH region (CRH-2) with yet to be identified functions. The C-terminal end of c-Mpl contains the transmembrane domain (TM), and a cytoplasmic signal transduction domain. It has previously been demonstrated that AKR-501 does not interfere with TPO binding to c-Mpl at the CRH-1 domain, and that AKR-501 is highly species-specific with action only with human and chimpanzee c-Mpl. In the current study, we sought to define the AKR-501 binding domain on c-Mpl by constructing a series of human and mouse chimera c-Mpl receptors in order to evaluate which domain(s) of human c-Mpl confers growth stimulation in response to AKR-501. We found that Ba/F3 cells expressing a chimeric c-Mpl that contained both human CRH-2 and TM responded to AKR-501 and stimulated growth to the same extent as TPO. Other chimeras with only human CRH-2 could not, suggesting that TM is critical for AKR-501 action. A construct was then built to substitute the mouse TM leucine amino acid residue at position 499 with the corresponding human histidine amino acid; this residue is conserved between humans and chimpanzee, but is not found in other species. We found the mouse c-Mpl with a His499 substitution was sufficient to support AKR-501 stimulated growth of Ba/F3 cells. Thus, we concluded that the c-Mpl TM appears essential for AKR-501 activity, and the species specific activity of AKR-501 depends on His499 in the TM.
Relationships among CFTR expression, HCO 3 − secretion, and host defense may inform gene- and cell-based cystic fibrosis therapies (2016)

Cystic fibrosis (CF) is caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel. Airway disease is the major source of morbidity and mortality. Successful implementation of gene- and cell-based therapies for CF airway disease requires knowledge of relationships among percentages of targeted cells, levels of CFTR expression, correction of electrolyte transport, and rescue of host defense defects. Previous studies suggested that, when ∼10-50% of airway epithelial cells expressed CFTR, they generated nearly wild-type levels of Cl(-) secretion; overexpressing CFTR offered no advantage compared with endogenous expression levels. However, recent discoveries focused attention on CFTR-mediated HCO3 (-) secretion and airway surface liquid (ASL) pH as critical for host defense and CF pathogenesis. Therefore, we generated porcine airway epithelia with varying ratios of CF and wild-type cells. Epithelia with a 50:50 mix secreted HCO3 (-) at half the rate of wild-type epithelia. Likewise, heterozygous epithelia (CFTR(+/-) or CFTR(+/∆F508)) expressed CFTR and secreted HCO3 (-) at ∼50% of wild-type values. ASL pH, antimicrobial activity, and viscosity showed similar relationships to the amount of CFTR. Overexpressing CFTR increased HCO3 (-) secretion to rates greater than wild type, but ASL pH did not exceed wild-type values. Thus, in contrast to Cl(-) secretion, the amount of CFTR is rate-limiting for HCO3 (-) secretion and for correcting host defense abnormalities. In addition, overexpressing CFTR might produce a greater benefit than expressing CFTR at wild-type levels when targeting small fractions of cells. These findings may also explain the risk of airway disease in CF carriers.
Control system for high power solid State microwave generators 2.45 GHz band (2010)

The paper presents development and implementation of the four high power microwave sources system used for testing phased 2.45 GHz antenna array. Each module has maximum output power of 200 watts and covers frequency band between 2.35 and 2.6 GHz. System provides possibility of independent setup of frequency, amplitude and phase of each generator (depends on mode of operation).
PF-06651600, a Dual JAK3/TEC Family Kinase Inhibitor (2019)

PF-06651600 was developed as an irreversible inhibitor of JAK3 with selectivity over the other three JAK isoforms. A high level of selectivity toward JAK3 is achieved by the covalent interaction of PF-06651600 with a unique cysteine residue (Cys-909) in the catalytic domain of JAK3, which is replaced by a serine residue in the other JAK isoforms. Importantly, 10 other kinases in the kinome have a cysteine at the equivalent position of Cys-909 in JAK3. Five of those kinases belong to the TEC kinase family including BTK, BMX, ITK, RLK, and TEC and are also inhibited by PF-06651600. Preclinical data demonstrate that inhibition of the cytolytic function of CD8<sup>+</sup> T cells and NK cells by PF-06651600 is driven by the inhibition of TEC kinases. On the basis of the underlying pathophysiology of inflammatory diseases such as rheumatoid arthritis, inflammatory bowel disease, alopecia areata, and vitiligo, the dual activity of PF-06651600 toward JAK3 and the TEC kinase family may provide a beneficial inhibitory profile for therapeutic intervention.
Abstract 374: Development of tumor-targeted near infrared dyes for fluorescence guided surgery (2012)

Abstract Surgical resection of malignant disease is currently one of the most common and effective cancer treatments. Unfortunately, quantitative tumor resection is limited by a surgeon's ability to distinguish diseased tissue from adjacent healthy tissue. Fluorescence guided surgery has emerged as a tool to aid surgeons in the identification and removal of malignant tissue. While non-targeted fluorescent dyes injected near the primary tumor mass have been shown to passively accumulate in tumors and lymph nodes, the resulting tumor to background ratios are often poor and boundaries between malignant and normal tissue difficult to define. To circumvent these problems, our lab has developed high affinity tumor-specific ligands that can bind to either the prostate specific membrane antigen (PSMA) or the folate receptor (FR); i.e. cell surface molecules that are over-expressed on a number of cancers. In this study, we link these tumor targeting ligands to near infrared (NIR) dyes and explore their use in fluorescence guided surgery. In vitro, all FR and PSMA targeted NIR dyes were found to have binding affinities in the low nanomolar range. Binding was quantitatively blocked with 100-fold excess of free ligand. Upon injection into mice with metastatic disease, the targeted NIR dyes allowed clear distinction of tumor tissue from adjacent healthy tissue. Surgical resection could be conducted until all fluorescent tissue was removed. All resected fluorescent lesions were later confirmed by histology to be malignant. Of the NIR dyes tested, the 800 nm dyes were found to have the greatest fluorescence intensity through porcine tissue, indicating their superior ability to reveal buried tumor nodules. Collectively, these tumor-specific NIR dyes demonstrate significant potential for use in fluorescent guided surgery by aiding in the complete resection of diseased tissue. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 374. doi:1538-7445.AM2012-374
Iccosomes and the secondary antibody response. (1991)

Iccosomes derived from follicular dendritic cells (FDC) are believed to play an important role in dispersion of antigen necessary for induction of anamnestic responses. Because FDC are aberrant and iccosome release has not been observed in aged mice, we hypothesized that these animals would be impaired in their ability to mount anamnestic responses. To test this, anamnestic responses were compared in aged and control mice. To ensure the presence of functional lymphocytes, some aged mice were reconstituted with T- and B-memory cells obtained from control mice. Anamnestic responses in aged mice were markedly depressed even when given functional memory cells. To more directly relate the impaired antibody response of aged mice to FDC function, antigen-bearing FDC from either aged or control mice were incubated with T- and B-memory cells from control mice to induce an anamnestic response. Antigen retained by FDC from aged mice was much less immunogenic than antigen retained by FDC from control mice. Since iccosome formation does not appear in aged mice, iccosome-like fragments were generated by sonicating FDC from aged mice and tested for their ability to induce an anamnestic response. This procedure restored the ability of antigen retained on FDC from aged mice to induce a normal anamnestic response. These data support the concept that the inability to form and disperse iccosomes contributes to the impaired ability of aged mice to mount anamnestic antibody responses and provides further support for the role of iccosomes in anamnestic responses.
Clinician Adoption of an Artificial Intelligence Algorithm to Detect Left Ventricular Systolic Dysfunction in Primary Care. (2022)

Clinicaltrials.gov Identifier: NCT04000087.
Contribution à l'étude du système quinaire Ca++K+H+NO3PO4−−−H2O. I. Le diagramme de solubilité du système quaternaire Ca++K+H+PO4−−−H2O à 25° (1956)

Abstract 1° Le diagramme de solubilité du système ternaire K +  H +  PO 4 ‐‐‐  H 2 O est établi pour une temperature de 25°. II comprend les courbes de saturation des composés suivants.
Stabilization of Dichloromethane-Induced Protein Denaturation During Microencapsulation (1998)

This paper describes the denaturation of protein drugs by dichloromethane (DCM) during the primary emulsification step of the microencapsulation process using biodegradable polymer matrix for controlled-release application. It was found that interaction of proteins such as tetanus toxoid (TT), diphtheria toxoid (DT), ovine growth hormone (oGH), and human chorionic gonadotropin-based antifertility vaccine (beta-hCG-TT) with DCM during primary emulsification stages of particle formulation led to the precipitation of the proteins at the aqueous organic interface with concomitant reduction in their immunoreactivity. On the other hand, the B subunit of E. coli enterotoxin (LTB) was found to be comparatively stable toward the denaturing action of DCM. Attempts were made to overcome the DCM-induced denaturation by incorporation of stabilizers during the primary emulsification step of the particle formulation. Of the many additives tested to overcome the DCM-induced denaturation of proteins, serum albumins and polyvinyl alcohol (PVA) showed promising results in terms of retention of the immunoreactivity of the protein. TT stabilized by the incorporation of serum albumin during the primary emulsification step not only showed immunoreactivity in vitro, but also invoked antibody titers in rats comparable to those obtained for the native protein molecules. Incorporation of 2.5% of serum albumins in the internal aqueous phase not only protected the protein from the degradative action of DCM but also led to stabilized primary emulsion, which is necessary for uniform entrapment of protein drugs in the polymer matrix.
Enhancement of Progenitor Cell Division in the Dentate Gyrus Triggered by Initial Limbic Seizures in Rat Models of Epilepsy (2000)

These observations indicate that a mechanism in epileptogenesis boosts dentate progenitor cell division, but progenitor cells may become unreactive to prolonged generalized seizures. Pyramidal neuronal degeneration is not necessary for triggering the upregulation. It is suggested that newly born granule cells may play a role in the network reorganization that occurs during epileptogenesis.
Classical scaling of the quantum capacitances for molecular wires (2007)

Detailed calculations demonstrate that the quantum capacitances of nonspherical, rodlike molecular wires scale with their dimensions according to a linear law much like that obeyed by classical, macroscopic spherical capacitors. Further, this linear isoperimetric scaling law leads to a particularly simple formula that relates a molecule's electron affinity directly to its ionization potential and its spatial dimensions.
Similarities Between Gait Adaptations in Preoperative and Postoperative Total Hip Replacement Patients (1997)

Abstract Gait adaptations among postoperative total hip replacement (THR) patients may be a response to the prosthesis and changes in the reconstructed joint mechanics or may be a learned response from an adaptation that was present preoperatively. Similarities have been reported between gait adaptations in preoperative and postoperative patients for THRs (1), but this was demonstrated in cross-sectional data and not longitudinal data. These gait adaptations may have implications on hip joint loading, rehabilitation protocols and can result in additional compensations at other joints. This longitudinal study tested the hypothesis that gait adaptations present preoperatively persist postoperatively.
Blue Fluorescence and Bipolar Transport Materials Based on Anthracene and Their Application in OLEDs (2012)

Abstract The phenomenon of organic electroluminescence (EL) was first discovered from studies on anthracene crystals in the 1960s. Since then, its derivatives have been studied extensively in applications such as organic light‐emitting diodes (OLEDs) and organic thin‐film transistors because of their excellent EL, transport, and good electrochemical properties. A blue fluorescence emitter based on anthracene is also important in constructing hybrid tandem white OLEDs for lighting applications. This article provides a review about the development of blue host OLED materials based on molecules designed and derived from the core structure of anthracene and their application as bipolar charge‐carrier transport materials in OLEDs. The recent development of efficient, stable, blue‐doped p‐i‐n OLEDs with simplified device architecture based on the single common host 2‐methyl‐9,10‐di(2‐napthyl)anthracene, with its stable thin‐film morphology, large band gap energy, high fluorescence quantum yield, and ambipolar charge‐carrier transport properties, is also highlighted.
Visualizing Fluorescence: Using a Homemade Fluorescence “Microscope” To View Latent Fingerprints on Paper (2010)

We describe an inexpensive handheld fluorescence imager (low-magnification microscope), constructed from poly(vinyl chloride) pipe and other inexpensive components for use as a teaching tool to understand the principles of fluorescence detection. Optical filters are used to select the excitation and emission wavelengths and can be easily interchanged to accommodate different fluorescent samples. As a demonstration, we used the fluorescence imager to view lawsone-dyed fingerprints on paper, which fluoresce red when illuminated with green light. This emission can be seen by viewing the sample through the instrument by eye, or the fluorescence can be captured by a camera. The entire imager can be built for less than $300.
Epidemiology and Clinical Presentation in Esophageal Cancer (2007)

The esophagus begins at the level of the cricopharyngeus and traverses the length of the neck to pass through the mediastinum. It then pierces the right crus of the diaphragm and after a short abdominal component joins the stomach at the cardia. For descriptive purposes the esophagus is referred to as cervical (∼6 cm), thoracic (∼25 cm), and abdominal (∼4 cm). Surgeons often refer to the esophagus in divisions of one-third, upper, middle, and distal, as this better relates to the operative options in esophagectomy.
Inactivation of Legionella pneumophila by hypochlorite and an organic chloramine (1987)

The susceptibility of a strain of Legionella pneumophila to disinfection by an organic halamine, free chlorine, and a mixture of the organic halamine and free chlorine was assessed. The organic halamine was found to have superior stability in solution and to exhibit adequate disinfectant potential over a period of 1 month of repeated reinoculations of fresh bacteria. The combined halamine exhibited great potential for use in maintaining closed-cycle cooling water systems free of L. pneumophila.
iPHACE: integrative navigation in pharmacological space (2010)

iPHACE is available at http://cgl.imim.es/iphace/ (EU site) and http://agave.health.unm.edu/iphace/ (US mirror).
Re-evaluating Evaluation (2018)

Progress in machine learning is measured by careful evaluation on problems of outstanding common interest. However, the proliferation of benchmark suites and environments, adversarial attacks, and other complications has diluted the basic evaluation model by overwhelming researchers with choices. Deliberate or accidental cherry picking is increasingly likely, and designing well-balanced evaluation suites requires increasing effort. In this paper we take a step back and propose Nash averaging. The approach builds on a detailed analysis of the algebraic structure of evaluation in two basic scenarios: agent-vs-agent and agent-vs-task. The key strength of Nash averaging is that it automatically adapts to redundancies in evaluation data, so that results are not biased by the incorporation of easy tasks or weak agents. Nash averaging thus encourages maximally inclusive evaluation -- since there is no harm (computational cost aside) from including all available tasks and agents.
Exposure bracketing via automatic exposure selection (2015)

Exposure bracketing is widely used to generate high dynamic range (HDR) images. Exposure bracketing often consists of an image taken by the auto-exposure setting of a camera as well as two other images taken at ±n exposure levels away from the auto-exposure setting where n is manually selected or specified. The images in the bracket are then blended to generate an HDR image. This paper presents an automatic exposure selection method that relieves the user from setting the exposure level, thus allowing HDR images to be generated with no user intervention. This is achieved by using the camera characteristics function and the scene information. The results obtained indicate the HDR images generated by using this method outperform the manual selection of exposure level in terms of two widely used image quality measures.
Web applications and dynamic reconfiguration in UNIX servers (2003)

In recent years, several large UNIX SMP Servers have added support for dynamic resource management through partitioning and dynamic resource reconfiguration. In this paper we study the ability of Dynamic Reconfiguration (DR) to accommodate fluctuating workloads and changes in operational priorities for a commercial web application. We use a WebSphere HTTP server, a WebSphere Application Server, and a DB2 Database for the application. This combination represents a popular platform for commercial computing deployments, and supports a number of common web-based application scenarios. In our study, we treat this application as a black box to provide a realistic measurement of the efficacy of the DR technology in UNIX Servers. We also use nonparametric estimation techniques to obtain an ab initio and unbiased study of the jitters in our experimental data. Our main conclusions are: (1) Resource allocations for the application (even for a complex and function-rich middleware system such as WebSphere) can be efficiently managed by DR, without the need for explicit accommodation of the DR features by the application, and (2) To obtain efficient resource utilization, the resource management system has to empirically monitor the throughput obtained from the application, rather than rely primarily on long time-scale estimations.