gebhart/patrepeval huggingface dataset:
278 Total Antioxidant Capacity, Hydrogen Peroxide, Malondialdehyde and Total Nitric Oxide Concentrations in Patients With Severe Persistent Allergic Asthma (2012)

BACKGROUND: There is no data available to adequately explain the alterations in total antioxidant capacity, hydrogen peroxide, malondialdehyde and total nitric oxide concentrations in severe persistent asthma and newly diagnosed allergic asthma patients. In the study below we have examined changes in total antioxidant capacity, hydrogen peroxide, malondialdehyde and total nitric oxide levels in severe persistent asthma and newly diagnosed allergic asthma patients and the association(s) between these variables. METHODS: The first group of patients included 6 male and 8 female subjects with severe persistent asthma, having a mean age of 42.4 years. A second group of subjects consisted of 14 newly diagnosed allergic asthma patients with a mean age of 43.8 years. All patients were followed in our clinic, and were evaluated by clinical status. A third group of 14 age-sex matched healthy controls were also included. Serum samples were collected and stored at –70 until use for the determination of total antioxidant capacity, hydrogen peroxide, malondialdehyde and total nitric oxide concentrations. Serum IgE levels, ANA, RF, hepatitis markers, C3, C4 and eosinophil levels were evaluated in all patients. All assays were carried out in duplicate. RESULTS: Total antioxidant capacity levels of Group IB, group II and group III were lower than the IA group. Total antioxidant capacity levels of groups II and III were higher than in group IB. Hydrogen peroxide concentrations in group IB were lower than in group IA, while concentrations in group II were higher than in group IB. The malondialdehyde concentration of group IB was lower than in all other groups. The malondialdehyde concentration of group III was higher than all other groups. The malondialdehyde concentration of group II was lower than in group III. The total nitric oxide level of group IB was lower than all other groups. The total nitric oxide level of group III was higher than all other groups, while that of group II was higher than for both groups IA/IB. CONCLUSIONS: To monitor the omalizumab treatment efficacy in the severe allergic asthma patients; total antioxidant capacity, hydrogen peroxide, malondialdehyde and total nitric oxide concentrations might be new markers.
Characterization of the manufacturability of ultrathin resist (1999)

A study was conducted to explore the manufacturability of ultrathin resist by focusing on two key issues, defects and etch resistance. Defects in ultrathin resist were characterized by optical inspection and scanning electron microscopy reviews. A number of representative defect types in the ultrathin resist/hardmask process were identified. With process optimization, defect density in ultrathin resist was reduced to levels that are comparable to that of a baseline 0.5 μm thick resist process on nontopographic wafers. Etch resistance sufficient for patterning metal–oxide–semiconductor transistor gate film stacks was demonstrated for a 100–150 nm thick resist layer.
The 2D Rancieite-type manganic acid and its Li-exchanged derivative: A new synthetic route for a better cycling behavior (1998)

Abstract The usual preparation route of lithiated Rancieite-type Manganese Oxide (Li-RMO) includes three steps: reduction of KMnO4 in acidic medium (1), followed by a further acidic treatment which ensures a complete K+/H+ exchange (2) and subsequent Li+/H+ ion-exchange reaction (3). The surface area of the as prepared Li-RMO is always several tens of m2g−1. Its initial capacity with respect to electrochemical Li intercalation is 220 mAh/g with an average voltage of 2.85V (vs Li). However, a rapid capacity fading is observed upon cycling, due to a dissolution of the material likely related to its large surface area. A new synthetic route is proposed leading to a material with a surface area less than 10 m2g−1. As expected, the cycling behavior of this new material is greatly improved.
Analog NMOS sampled-data recursive filter (1977)

MONOLITHIC INTEGRATION of precision audio frequency filters has been a difficult objective to reach. Active RC filters using numerous off-chip precision RC elements have been in use for years’. Transversal filters using CCD or BBD approaches occupy very large silicon areas when fully integrated with all peripheral circuits2. Fully integrated digital filters require precision linear A/D coders and also require a large silicon area . Analog sampled data recursive filters have been described previously, but these employed many off-chip precision components.
Molecular Dynamics Simulations of Perylene and Tetracene Librations: Comparison With Femtosecond Upconversion Data (2008)

In a prior manuscript by Xu et al. [Xu, J.; Shen, X.; Knutson, J. R. J. Phys. Chem. A 2003, 107, 8383], time-resolved fluorescence emission anisotropy measurements were performed on perylene and tetracene in hexadecane using an upconversion technique with approximately 100 fs resolution. The anisotropy transients contained previously unseen decay terms of approximately 300 fs. In perylene, their amplitude corresponded to the " r(o) defect" that has gathered interest over decades. We ascribed this term to a predominantly in-plane libration. In this manuscript, we present molecular dynamics simulations for the motions of perylene and tetracene using the CHARMm molecular dynamics program (version c29b2). Both rotational correlation functions contain subpicosecond decay terms that resemble experimental anisotropy decays. It was suggested that the r(o) defect might arise from excited-state distortions of perylene, so we conducted quantum mechanical calculations to show that such distortion does not significantly displace the oscillators. We compare the case of perylene, with a strongly allowed singlet emission transition, to that of the weakly allowed tetracene transition. In perylene, motion alone can explain subpicosecond anisotropy decay, while tetracene decay also contains vibrational coupling terms, as previously reported by Sarkar et al. [Sarkar, N.; Takeuchi, S.; Tahara, T. J. Phys. Chem. A 1999, 103, 4808].
Molecular characterization of COVID-19 therapeutics: luteolin as an allosteric modulator of the spike protein of SARS-CoV-2 (2021)

The interactions between the receptor binding domain (RBD) of SARS-CoV-2 and the angiotensin-converting enzyme 2 (ACE2) are crucial for viral entry and subsequent replication.
Regulation of Peripheral Inflammation by a Non-Viable, Non-Colonizing Strain of Commensal Bacteria (2022)

The gastrointestinal tract represents one of the largest body surfaces that is exposed to the outside world. It is the only mucosal surface that is required to simultaneously recognize and defend against pathogens, while allowing nutrients containing foreign antigens to be tolerated and absorbed. It differentiates between these foreign substances through a complex system of pattern recognition receptors expressed on the surface of the intestinal epithelial cells as well as the underlying immune cells. These immune cells actively sample and evaluate microbes and other particles that pass through the lumen of the gut. This local sensing system is part of a broader distributed signaling system that is connected to the rest of the body through the enteric nervous system, the immune system, and the metabolic system. While local tissue homeostasis is maintained by commensal bacteria that colonize the gut, colonization itself may not be required for the activation of distributed signaling networks that can result in modulation of peripheral inflammation. Herein, we describe the ability of a gut-restricted strain of commensal bacteria to drive systemic anti-inflammatory effects in a manner that does not rely upon its ability to colonize the gastrointestinal tract or alter the mucosal microbiome. Orally administered EDP1867, a gamma-irradiated strain of <i>Veillonella parvula</i>, rapidly transits through the murine gut without colonization or alteration of the background microbiome flora. In murine models of inflammatory disease including delayed-type hypersensitivity (DTH), atopic dermatitis, psoriasis, and experimental autoimmune encephalomyelitis (EAE), treatment with EDP1867 resulted in significant reduction in inflammation and immunopathology. <i>Ex vivo</i> cytokine analyses revealed that EDP1867 treatment diminished production of pro-inflammatory cytokines involved in inflammatory cascades. Furthermore, blockade of lymphocyte migration to the gut-associated lymphoid tissues impaired the ability of EDP1867 to resolve peripheral inflammation, supporting the hypothesis that circulating immune cells are responsible for promulgating the signals from the gut to peripheral tissues. Finally, we show that adoptively transferred T cells from EDP1867-treated mice inhibit inflammation induced in recipient mice. These results demonstrate that an orally-delivered, non-viable strain of commensal bacteria can mediate potent anti-inflammatory effects in peripheral tissues through transient occupancy of the gastrointestinal tract, and support the development of non-living bacterial strains for therapeutic applications.
User Friendly Robust MPC Tuning of Uncertain Paper-Making Processes∗∗This work was supported by an NSERC CRD project with Honeywell Vancouver as the industrial partner. (2015)

A robust tuning problem for a two-degree-of-freedom model predictive controller is explored for single-input, single-output uncertain paper-making processes. The objective is to achieve satisfactory closed-loop responses, as measured by overshoots, settling times and output oscillations with user-specified parametric uncertainties. As the output variation cannot be easily specified by the end users, two methods are proposed to connect a total variation specification to user-friendly indices, based on which two algorithms are designed to solve the tuning problem. An application to a process extracted from the pulp and paper industry is employed to verify the effectiveness of the proposed algorithms.
An Approach for Understanding Action Origami as Kinematic Mechanisms (2013)

Action origami is a field of origami dealing with models that are folded so that in their final, deployed state they exhibit motion. Hundreds of action origami models exist, many of which use complicated kinematics to achieve motion in their deployed state. Understanding the kinematics of action origami could result in a new source of concepts for deployable, movable engineering solutions. This paper presents an approach for evaluating and classifying the mechanisms that enable action origami motion. Approximately 300 action origami models are studied. Although disguised with artistic elements, it is found that most action origami models are based on a few fundamental mechanisms. A classification scheme is proposed, and a previously unused class of action origami is identified as an area for future origami art.
Improving Fracture Initiation Predictions on Arbitrarily Oriented Wells in Anisotropic Shales (2011)

Abstract The hydraulic fracturing stimulation of unconventional shale reservoirs requires the identification of sections along the well with good reservoir and completion quality. Completion quality depends on the poromechanical properties of the reservoir. Shales are known to exhibit anisotropic elastic properties. The elastic anisotropic of shales is of first order as it affects four key geomechanical steps: the in-situ stress field, the stress concentration around the borehole, the failure properties both in tension and compression and the geometry of the hydraulic fracture. Consequently, the initiation pressure of hydraulic fractures at the wellbore predicted by data and models taking into account the anisotropy can be lower or higher by up to 100% as compared to isotropic conditions. We performed a thorough sensitivity analysis of in-situ stress, material anisotropy and well orientation conditions for different scenarios for far field in-situ stress and near field borehole stress, under isotropic and anisotropic conditions. We consider three scenarios. Scenario-1 where both the far field in-situ stress and the near field borehole stress are computed under isotropic assumption. Scenario-2 where only the far field in-situ stress is computed using anisotropic assumption while keeping the isotropic solution for stress concentration is kept. Scenario-3 where both the far field in-situ stress and the stress concentration take into account the material anisotropy. In addition, for each scenario, we considered three different σH/σh cases. This study shows that the full anisotropic solution or scenario 3 is always the most appropriate one for predicting correct initiation pressures and the pressure is always lower for the anisotropic case. It is clear that the observed effects are magnified by the degree of anisotropy of the rock, i.e. each rock or formation will influence differently the initiation pressure. We conclude that the material anisotropy is affecting the in-situ stress model as well as the stress concentration around the borehole. Both effects need to be considered in order to account for the anisotropy. If the effect of the anisotropy is taken into account, for both the far and the near field, it will be possible to better predict the initiation pressure and better stimulate unconventional reservoirs.
Impact of wavelength dependency of LED and photodiode in visible light positioning (2017)

The wavelength dependency of LEDs and photodiodes in RSS-based Visible Light Positioning systems is sometimes omitted in the calculations. This study investigates the consequences on the accuracy of this approach. A simulation-based assessment is performed, where a single link is considered. The received signal strength is used to estimate the distance between LED and photo-diode. Results are obtained for different phosphor coated LEDs and photodiodes. It is shown that neglecting the wavelength dependency results in distance estimation errors in the order of 10 %. This severe degradation would undermine the achievable accuracy of VLP systems (order of centimeters). The result shows that regardless the used photodiode, LEDs with a high correlated color temperature are more prone to distance estimation errors in comparison with low correlated color temperature LEDs.
Control of protein activity by photoinduced spin polarized charge reorganization (2021)

Abstract Considerable electric fields are present within living cells, and the role of bioelectricity has been well established at the organismal level. Yet little is known about electric-field effects on protein function. Here we use phototriggered charge injection from a site-specifically attached ruthenium photosensitizer to directly demonstrate the effects of charge redistribution within a protein. We find that binding of an antibody to phosphoglycerate kinase (PGK) is increased two folds under illumination. Remarkably, illumination is found to suppress the enzymatic activity of PGK by a factor as large as three. These responses are sensitive to the photosensitizer position on the protein. Surprisingly, left (but not right) circularly polarized light elicits these responses, indicating that the electrons involved in the observed dynamics are spin polarized, due to spin filtration by protein chiral structures. Our results directly establish the contribution of electrical polarization as an allosteric signal within proteins. Future experiments with phototriggered charge injection will allow delineation of charge rearrangement pathways within proteins and will further depict their effects on protein function. Significance Statement The role of well-placed charges within proteins in mediating biological functions, from protein-protein association to enzyme kinetics, is well documented. Here we go beyond this static picture and show that charge motions can exert significant effects on protein function. Injecting charge from a photosensitizer, we demonstrate a three-fold decrease in enzymatic activity and a two-fold increase of antibody-antigen binding. These effects depend on the specific position of the photosensitizer on the protein. Our results point to charge reorganization as a form of allostery that complements known allosteric mechanisms such as conformational changes and dynamics.
Audio-Visual Fusion and Tracking With Multilevel Iterative Decoding: Framework and Experimental Evaluation (2010)

Speech is a natural interface for human communication. However building human-computer interfaces in unconstrained intelligent spaces still remains a challenging task. Incorporating video information is shown to improve the performance of many audio applications. Similarly, information from the microphones is useful in computer vision tasks. One of the first steps in enabling natural human-computer interaction is person tracking. In this paper, we present a new approach to person tracking using both audio and visual information. We develop a multilevel framework to combine the audio and visual cues to track multiple persons in a meeting room equipped with cameras and microphone arrays. We discuss in detail the multilevel iterative decoding based audio-visual person tracker (MID-AVT). Extensive experimental evaluation of the MID-AVT and comparison to other audio-visual tracking techniques is also presented. The dataset consists of real meeting recordings with sensor configurations similar to those used in the CLEAR 2006 and CLEAR 2007 evaluation workshops. The overall accuracy of the tracker was 75%. The MID-AVT framework performed slightly better than particle filter-based tracker when accurate camera and microphone calibration was available. However, the MID-AVT is also shown to be robust to sensor calibration errors while the particle filtering framework fails. In addition to the audio-visual person tracking results, we also track the active speaker at every instance of time and the results are presented.
Maternal CD4 + T cells protect against severe congenital cytomegalovirus disease in a novel nonhuman primate model of placental cytomegalovirus transmission (2015)

Elucidation of maternal immune correlates of protection against congenital cytomegalovirus (CMV) is necessary to inform future vaccine design. Here, we present a novel rhesus macaque model of placental rhesus CMV (rhCMV) transmission and use it to dissect determinants of protection against congenital transmission following primary maternal rhCMV infection. In this model, asymptomatic intrauterine infection was observed following i.v. rhCMV inoculation during the early second trimester in two of three rhCMV-seronegative pregnant females. In contrast, fetal loss or infant CMV-associated sequelae occurred in four rhCMV-seronegative pregnant macaques that were CD4(+) T-cell depleted at the time of inoculation. Animals that received the CD4(+) T-cell-depleting antibody also exhibited higher plasma and amniotic fluid viral loads, dampened virus-specific CD8(+) T-cell responses, and delayed production of autologous neutralizing antibodies compared with immunocompetent monkeys. Thus, maternal CD4(+) T-cell immunity during primary rhCMV infection is important for controlling maternal viremia and inducing protective immune responses that prevent severe CMV-associated fetal disease.
Supplementary Table 2 from Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor (2023)

&lt;p&gt;Table S2: Oligos used in the study&lt;/p&gt;
Cloning and Expression of the Clostridium thermohydrosulfuricum -Amylase-pullulanase Gene in Escherichia coli (1989)

An alpha-amylase-pullulanase gene from Clostridium thermohydrosulfuricum DSM 3783 was cloned in Escherichia coli on a 7.0 kb EcoRI fragment using a lambda vector. The gene produced, from an indigenous promoter, active thermostable alpha-amylase-pullulanase, seemingly mostly a soluble intracellular enzyme in E. coli. Gel filtration separated the active enzyme produced into three peaks, each having both alpha-amylase and pullulanase activities. Immunoblotting after SDS-PAGE revealed more than ten alpha-amylase-pullulanase specific polypeptides; the biggest of these had an Mr of about 165,000, whereas the smallest enzymically active polypeptide had an Mr of about 100,000. Despite the marked degeneration of its constituent polypeptides, the apparent temperature optimum of the enzyme (80-85 degrees C) was only some 5 degrees C lower and the heat stability the same as that of the extracellular alpha-amylase-pullulanase produced by the native host. Oligonucleotide probes prepared according to the NH2-terminal amino acid sequences of the enzyme and its satellite polypeptide (a polypeptide associated with the extracellular enzyme of the native host) hybridized to different regions of the 7.0 kb DNA insert.
Edge-directed interpolation (2002)

We present a new method for digitally interpolating images to higher resolution. It consists of two phases: rendering and correction. The rendering phase is edge-directed. From the low resolution image data, we generate a high resolution edge map by first filtering with a rectangular center-on-surround-off filter and then performing piecewise linear interpolation between the zero crossings in the filter output. The rendering phase is based on bilinear interpolation modified to prevent interpolation across edges, as determined from the estimated high resolution edge map. During the correction phase, we modify the mesh values on which the rendering is based to account for the disparity between the true low resolution data, and that predicted by a sensor model operating on the high resolution output of the rendering phase. The overall process is repeated iteratively. We show experimental results which demonstrate the efficacy of our interpolation method.
Recommendations for laparoscopic liver resection: a report from the second international consensus conference held in Morioka. (2015)

The use of laparoscopy for liver surgery is increasing rapidly. The Second International Consensus Conference on Laparoscopic Liver Resections (LLR) was held in Morioka, Japan, from October 4 to 6, 2014 to evaluate the current status of laparoscopic liver surgery and to provide recommendations to aid its future development. Seventeen questions were addressed. The first 7 questions focused on outcomes that reflect the benefits and risks of LLR. These questions were addressed using the Zurich-Danish consensus conference model in which the literature and expert opinion were weighed by a 9-member jury, who evaluated LLR outcomes using GRADE and a list of comparators. The jury also graded LLRs by the Balliol Classification of IDEAL. The jury concluded that MINOR LLRs had become standard practice (IDEAL 3) and that MAJOR liver resections were still innovative procedures in the exploration phase (IDEAL 2b). Continued cautious introduction of MAJOR LLRs was recommended. All of the evidence available for scrutiny was of LOW quality by GRADE, which prompted the recommendation for higher quality evaluative studies. The last 10 questions focused on technical questions and the recommendations were based on literature review and expert panel opinion. Recommendations were made regarding preoperative evaluation, bleeding controls, transection methods, anatomic approaches, and equipment. Both experts and jury recognized the need for a formal structure of education for those interested in performing major laparoscopic LLR because of the steep learning curve.