gebhart/patrepeval huggingface dataset:
Synthetic peptides analogous to the fimbrillin sequence inhibit adherence of Porphyromonas gingivalis (1992)

Fimbriae are important in the adherence of many bacterial species to the surfaces they eventually colonize. Porphyromonas (Bacteroides) gingivalis fimbriae appear to mediate adherence to oral epithelial cells and the pellicle-coated tooth surface. The role and contribution of fimbriae in the binding of P. gingivalis to hydroxyapatite (HAP) coated with saliva as a model for the pellicle-coated tooth surface were investigated. 3H-labeled P. gingivalis or the radioiodinated purified fimbriae were incubated with 2 mg of HAP beads coated with whole human saliva (sHAP) and layered on 100% Percoll to separate unbound from sHAP-bound components. The radioactivity of the washed beads was a measure of the bound components. The binding of P. gingivalis 2561 (381) cells and that of purified fimbriae were concentration dependent and saturable at approximately 10(8) cells and 40 micrograms of fimbriae added, respectively. The addition of fimbriae inhibited binding of P. gingivalis to sHAP beads by 65%, while the 75-kDa protein, which is another major surface component of P. gingivalis 2561, did not show significant inhibition, suggesting that the fimbriae are important in adherence. Encapsulated and sparsely fimbriated P. gingivalis W50 did not bind to sHAP beads. On the basis of the predicted sequence of the fimbrillin, a structural subunit of fimbriae, a series of peptides were synthesized and used to localize the active fimbrillin domains involved in P. gingivalis adherence to sHAP beads. Peptides from the carboxyl-terminal one-third of the fimbrillin strongly inhibited P. gingivalis binding to sHAP beads. Active residues within the sequence of inhibitory peptide 226-245 (peptide containing residues 226 to 245) and peptide 293-306 were identified by using smaller fragments prepared either by trypsin cleavage of the peptide 226-245 or by synthesis of smaller segments of peptide 293-306. Hemagglutinin activity, lectinlike binding, and ionic interaction did not seem to be involved in this binding since lysine, arginine, carbohydrates, and calcium ions failed to affect the binding of P. gingivalis. The observation that poly-L-lysine, bovine serum albumin, and defatted bovine serum albumin, even at high concentrations, only partially blocked the binding of P. gingivalis indicates that hydrophobic interactions are not the major forces involved in P. gingivalis binding to sHAP beads. Protease inhibitors such as EDTA, leupeptin, pepstatin, 1,10-phenanthroline, and phenylmethylsulfonyl fluoride did not interfere with the binding of P. gingivalis. However, the binding of P. gingivalis to trypsin- or chymotrypsin-pretreated sHAP beads was reduced.(ABSTRACT TRUNCATED AT 400 WORDS)
Degradation of Cardiac Troponin I in Serum Complicates Comparisons of Cardiac Troponin I Assays (1999)

The availability of serum cTnI epitopes is markedly affected by the extent of ligand degradation. The N-terminal half of the cTnI molecule was found to be the most stable region in human serum. Differential degradation of cTnI is a key factor in assay-to-assay variation.
CogSense: A Cognitively Inspired Framework for Perception Adaptation (2021)

This paper proposes the CogSense system, which is inspired by sense-making cognition and perception in the mammalian brain to perform perception error detection and perception parameter adaptation using probabilistic signal temporal logic. As a specific application, a contrast-based perception adaption method is presented and validated. The proposed method evaluates perception errors using heterogeneous probe functions computed from the detected objects and subsequently solves a contrast optimization problem to correct perception errors. The CogSense probe functions utilize the characteristics of geometry, dynamics, and detected blob image quality of the objects to develop axioms in a probabilistic signal temporal logic framework. By evaluating these axioms, we can formally verify whether the detections are valid or erroneous. Further, using the CogSense axioms, we generate the probabilistic signal temporal logic-based constraints to finally solve the contrast-based optimization problem to reduce false positives and false negatives.
Improved production of heme using metabolically engineered <i>Escherichia coli</i> (2022)

Heme has recently attracted much attention due to its promising applications in the food and healthcare industries. However, the current titers and productivities of heme produced by recombinant microorganisms are not high enough for a wide range of applications. In this study, the process for the fermentation of the metabolically engineered Escherichia coli HAEM7 strain was optimized for the high-level production of heme. To improve the production of heme, different carbon sources, iron concentration in the medium, pH control strategies, induction points, and iron content in the feeding solution were examined. Moreover, strategies of increasing cell density, regular iron supplementation, and supply of excess feeding solution were developed to further improve the production of heme. In the optimized fermentation process, the HAEM7 strain produced 1.03 g/L heme with productivity of 21.5 mg/L/h. The fermentation process and strategies reported here will expedite establishing industry-level production of heme.
Enhanced smart window based on electrochromic (EC) polymers (2003)

A large contrast ratio and rapid switching EC polymer device which consists of a laminated two-layer structure between two electrodes was prepared. The new design consists of an ITO glass electrode, a cathodic EC polymer film, a gel electrolyte and a counter-electrode that replaces the anodic EC polymer and ITO electrode. Several types of EC polymers, such as, poly[3,3-dimethyl-3,4-dihydro-2H-thieno(3,4-b)(1,4)dioxepine] (PProDOT-(CH<sub>3</sub>)<sub>2</sub>) and poly[3,4-(2,2-dimethylpropylenedioxy)-pyrrole] (PProDOP-(CH<sub>3</sub>)<sub>2</sub>) were synthesized as cathodic EC polymers. A carbon-based counter-electrode was prepared for comparison with an Au-based counter-electrode. Screen-printing was utilized for the carbon-based counter-electrode. Lithography and sputtering were used for the Au patterned glass counter-electrodes. Several kinds of polymer gel electrolytes were prepared for solid-state applications. Color change of high contrast ratio of visible light transmittance (>ΔΤ55%)of the device is rapidly obtained (0.5-1s) when even less than 2.5V is applied. The repeatability of color changeable EC polymer windows was estimated by the method of electrochemistry and spectrophotometry. This "smart window" technology can be used in many applications where a rapid color change between transparent and color states is required.
Phase I trial of chemoradiotherapy with the combination of S‐1 plus cisplatin for patients with unresectable locally advanced squamous cell carcinoma of the head and neck (2010)

The aim of the present study was to determine the maximum tolerated dose (MTD) of S-1 in combination with chemoradiotherapy (CRT) in patients with unresectable locally advanced squamous cell carcinoma of the head and neck, and evaluate the difference in pharmacokinetics of S-1 when administered as a suspension via a feeding tube or orally as a capsule. Chemotherapy consisted of administration of S-1 twice daily on days 1-14 at escalating doses of 40, 60 and 80 mg/m(2) per day, and cisplatin at 20 mg/m(2) per day on days 8-11, repeated twice at a 5-week interval. Single daily radiation of 70 Gy in 35 fractions was given concurrently starting on day 1. Two additional cycles of chemotherapy were planned after the completion of CRT. Before starting CRT, each patient received S-1 via two different administration methods. Twenty-two patients were enrolled. The MTD was reached with S-1 at 80 mg/m(2) per day, with two of six patients experiencing febrile neutropenia lasting more than 4 days. All four patients whose creatinine clearance was decreased to <60 mL/min after the first cycle of chemotherapy developed febrile neutropenia lasting more than 4 days. Pharmacokinetic analysis revealed that the 5-fluorouracil area under the curve did not significantly differ by the administration route. S-1 at 60 mg/m(2) per day for 14 days was well tolerated with concurrent CRT. Administration of S-1 as a suspension or by whole capsule can be considered therapeutically interchangeable. Although these data are preliminary, activity was highly promising, and this approach warrants further investigation.
CONTINUOUS COMMISIONING BASED ON EXTENDED FAULT DETECTION AND DIAGNOSIS (2012)

Buildings seldom perform as intended, resulting in energy use much higher than predicted from design. State-of-the-art HVAC fault detection and diagnosis (FDD) systems report component failures that may corrupt energy efficiency, however FDD does not detect component performance degradation and energy waste from poor designed control sequences. This paper introduces energy related extensions to our pre- vious HFM-FDD system, with which energy consump- tion/production is modeled and simulated in HFM (Heat Flow Model) nodes. The inconsistency between simulated energy data and measured data indicates component performance degradation. In addition, al- ternative control strategies (control algorithms, set- points, etc.) are modeled in the HFM simulation engine to test energy optimization opportunities. All energy calculations can be averaged with short term real data histories. Full year energy evaluations can be produced using standard or local weather files. These extensions that include air and water flow nodes support continu- ous commissioning® (CCx) with operation optimiza- tion. The HFM-FDD with energy and control modeling extension is designed as generic as possible, and re- quires minimal engineering efforts because of model based software generation techniques. Results using structure and data from a complex HVAC system of a real building are included.
Distributed compressive wide-band spectrum sensing (2009)

We consider a compressive wide-band spectrum sensing scheme for cognitive radio networks. Each cognitive radio (CR) sensing receiver transforms the received analog signal from the licensed system in to a digital signal using an analog-to-information converter. The autocorrelation of the compressed signal is then collected from each CR at a fusion center. A compressive sampling recovery algorithm that exploits joint sparsity is then employed to reconstruct an estimate of the signal spectrum and used to make a decision on signal occupancy. We compare the performance of this distributed compressive spectrum sensing scheme with a compressive spectrum sensing scheme at a single CR and show the performance gains obtained from spatial diversity.
Blind identification of multipath channels: a parametric subspace approach (2001)

In this paper, blind identification of single-input multiple-output (SIMO) systems using second-order statistics (SOS) only is considered. Using the assumption of a specular multipath channel, we investigate a parametric variant of the so-called subspace method. Nonparametric subspace-based methods require precise estimation of the model order; overestimation of the model order leads to inconsistent channel estimates. We show that the parametric subspace method gives consistent channel estimates when only an upper bound of the channel order is known. A new algorithm, which exploits parametric information on the channel structure, is presented. A statistical performance analysis of the proposed parametric subspace criterion is presented; limited Monte Carlo experiments show that the proposed algorithm is second-order optimal for a large class of channels.
EMAPII Monoclonal Antibody Ameliorates Influenza A Virus-Induced Lung Injury (2018)

Influenza A virus (IAV) remains a major worldwide health threat, especially to high-risk populations, including the young and elderly. There is an unmet clinical need for therapy that will protect the lungs from damage caused by lower respiratory infection. Here, we analyzed the role of EMAPII, a stress- and virus-induced pro-inflammatory and pro-apoptotic factor, in IAV-induced lung injury. First, we demonstrated that IAV induces EMAPII surface translocation, release, and apoptosis in cultured endothelial and epithelial cells. Next, we showed that IAV induces EMAPII surface translocation and release to bronchoalveolar lavage fluid (BALF) in mouse lungs, concomitant with increases in caspase 3 activity. Injection of monoclonal antibody (mAb) against EMAPII attenuated IAV-induced EMAPII levels, weight loss, reduction of blood oxygenation, lung edema, and increase of the pro-inflammatory cytokine TNF alpha. In accordance with the pro-apoptotic properties of EMAPII, levels of caspase 3 activity in BALF were also decreased by mAb treatment. Moreover, we detected EMAPII mAb-induced increase in lung levels of M2-like macrophage markers YM1 and CD206. All together, these data strongly suggest that EMAPII mAb ameliorates IAV-induced lung injury by limiting lung cell apoptosis and shifting the host inflammatory setting toward resolution of inflammation.
Genetic Definition and Sequence Analysis of <i>Arabidopsis</i> Centromeres (1999)

High-precision genetic mapping was used to define the regions that contain centromere functions on each natural chromosome in Arabidopsis thaliana. These regions exhibited dramatic recombinational repression and contained complex DNA surrounding large arrays of 180-base pair repeats. Unexpectedly, the DNA within the centromeres was not merely structural but also encoded several expressed genes. The regions flanking the centromeres were densely populated by repetitive elements yet experienced normal levels of recombination. The genetically defined centromeres were well conserved among Arabidopsis ecotypes but displayed limited sequence homology between different chromosomes, excluding repetitive DNA. This investigation provides a platform for dissecting the role of individual sequences in centromeres in higher eukaryotes.
Synthesis of hollow Y zeolite for catalytic applications (2018)

Mainly motivated by catalytic applications, the design of zeolites with diverse and well controlled morphologies remains a topic of intense research and development. In this sense, it is worth highlighting FAU-type materials that are extensively used in industrial catalytic and adsorption processes. The design of multimodal pore Y zeolite materials have been then emerging in order to combine the catalytic features of the zeolite and improved transport properties. In the literature, we can distinguish between two different approaches
for multimodal pore systems: creation of hierarchical structures with intraparticle mesopores and synthesis of nanocrystals (< 100 nm) with interparticle mesopores. Both approaches yield Y zeolite materials with smaller zeolite domains and concomitant larger external surface area.
Here, we propose an alternative approach that consists in synthesizing a new class of crystalline materials: hollow Y zeolite crystals which possess a large central cavity and similar size and shape to the parent crystals. In contrast to classical hierarchical zeolite materials, following this procedure, it can be obtained a smaller zeolite domain, i.e. the walls are thinner while the external surface remains approximatively the same. So far,
hollow single crystals have mainly been created from MFI-type zeolites thanks to a natural gradient of composition. The dissolution/recrystallization approach cannot be directly applied to as-synthesized Y zeolites, because the homogeneous distribution of aluminum throughout the crystals prevents a preferential dissolution of the core as opposed to the surface.
We report for the first time, a top-down pathway for the synthesis of original hollow Y zeolite from parent crystals in which a gradient of composition has been artificially created. Materials were obtained by a three-step process based on successive dealumination/realumination reactions followed by a selective dissolution of crystal cores.

See this article for further informations : Pagis et al., CrystEngComm, 2018, 20, 1564 - 1572
The role of polymer nanolayer architecture on the separation performance of anion‐exchange membrane adsorbers: I. Protein separations (2011)

This contribution describes the preparation of strong anion-exchange membranes with higher protein binding capacities than the best commercial resins. Quaternary amine (Q-type) anion-exchange membranes were prepared by grafting polyelectrolyte nanolayers from the surfaces of macroporous membrane supports. A focus of this study was to better understand the role of polymer nanolayer architecture on protein binding. Membranes were prepared with different polymer chain graft densities using a newly developed surface-initiated polymerization protocol designed to provide uniform and variable chain spacing. Bovine serum albumin and immunoglobulin G were used to measure binding capacities of proteins with different size. Dynamic binding capacities of IgG were measured to evaluate the impact of polymer chain density on the accessibility of large size protein to binding sites within the polyelectrolyte nanolayer under flow conditions. The dynamic binding capacity of IgG increased nearly linearly with increasing polymer chain density, which suggests that the spacing between polymer chains is sufficient for IgG to access binding sites all along the grafted polymer chains. Furthermore, the high dynamic binding capacity of IgG (>130 mg/mL) was independent of linear flow velocity, which suggests that the mass transfer of IgG molecules to the binding sites occurs primarily via convection. Overall, this research provides clear evidence that the dynamic binding capacities of large biologics can be higher for well-designed macroporous membrane adsorbers than commercial membrane or resin ion-exchange products. Specifically, using controlled polymerization leads to anion-exchange membrane adsorbers with high binding capacities that are independent of flow rate, enabling high throughput. Results of this work should help to accelerate the broader implementation of membrane adsorbers in bioprocess purification steps.
A High Performance Current-Mode Instrumentation Amplifier with Level Shifter for Single Power Biomedical Applications (2014)

In this paper, a high performance current-mode instrumentation amplifier has been proposed with low noise, low power and high CMRR features. The proposed design can adjust the gain with an external resistor for the processing of various biomedical signals. To reduce the noise of the amplifier, two design methods including PMOS input and lateral pnp BJT input have been implemented to improve the prior arts. To meet the single power supply need, a biomedical voltage level shifter is also proposed for low cost CMOS implementation. Based on the post-layout simulation results, the presented current-mode amplifier achieves high CMRR over 120 dB, power consumption of 61 uW at 1.8-V supply using standard 0.18-um CMOS technology.
Polyaniline in Corrision-Resistant Coatings (1998)

During the past two decades, one of the most active fields of solid-state science has been that of electrically conductive polymers. Electrically conductive polymers are polymers which, though insulators as prepared, can be converted to polymers having many or all of the properties of a metal through appropriate chemical/electrochemical oxidation or reduction. Typical applications considered for electrically conductive polymers have been in areas such as rechargeable batteries and electrochromic devices. Recently it has been reported that polyaniline, in its electrically conductive, protonated form, displays excellent performance as a coating for preventing the corrosion of carbon steel. The present research has shown that in fact, the non-conductive, unprotonated form of polyaniline displays even better performance in corrosion prevention than the conductive form. Moreover, it has been shown that polyaniline can be blended with other polymers (e.g., polyimides) to improve their corrosion resistance performance, or used as a hardener for epoxides or diisocyanates to give very good corrosion resistant coatings. Polyaniline performance is discussed in terms of its ability to form dense, adherent films, and create a basic surface on carbon steel.
Structural insights into ligand‐induced activation of the insulin receptor (2007)

The current model for insulin binding to the insulin receptor proposes that there are two binding sites, referred to as sites 1 and 2, on each monomer in the receptor homodimer and two binding surfaces on insulin, one involving residues predominantly from the dimerization face of insulin (the classical binding surface) and the other residues from the hexamerization face. High-affinity binding involves one insulin molecule using its two surfaces to make bridging contacts with site 1 from one receptor monomer and site 2 from the other. Whilst the receptor dimer has two identical site 1-site 2 pairs, insulin molecules cannot bridge both pairs simultaneously. Our structures of the insulin receptor (IR) ectodomain dimer and the L1-CR-L2 fragments of IR and insulin-like growth factor receptor (IGF-1R) explain many of the features of ligand-receptor binding and allow the two binding sites on the receptor to be described. The IR dimer has an unexpected folded-over conformation which places the C-terminal surface of the first fibronectin-III domain in close juxtaposition to the known L1 domain ligand-binding surface suggesting that the C-terminal surface of FnIII-1 is the second binding site involved in high-affinity binding. This is very different from previous models based on three-dimensional reconstruction from scanning transmission electron micrographs. Our single-molecule images indicate that IGF-1R has a morphology similar to that of IR. In addition, the structures of the first three domains (L1-CR-L2) of the IR and IGF-1R show that there are major differences in the two regions governing ligand specificity. The implications of these findings for ligand-induced receptor activation will be discussed. This review summarizes the key findings regarding the discovery and characterization of the insulin receptor, the identification and arrangement of its structural domains in the sequence and the key features associated with ligand binding. The remainder of the review deals with a description of the receptor structure and how it explains much of the large body of biochemical data in the literature on insulin binding and receptor activation.