gebhart/patrepeval huggingface dataset:
Epidermolysis Bullosa Acquisita (Brunsting-Perry Pemphigoid Variant) Localized to the Face and Diagnosed With Antigen Identification Using Skin Deficient in Type VII Collagen (2017)

Brunsting-Perry pemphigoid is defined as an autoimmune vesiculobullous eruption typically localized on the head and neck region with minimal or no mucosal involvement. The disease tends to run a chronic and recurrent course with residual scarring. Histological features are characterized by subepidermal bullae and linear IgG deposits at the dermo-epidermal junction. We report a case of a 46-year-old lady who presented with typical features of Brunsting-Perry pemphigoid. Autoantibodies to type VII collagen were identified by using recessive dystrophic epidermolysis bullosa skin which lacks type VII collagen in an indirect immunofluorescence assay. As a result, we diagnosed our patient as having the Brunsting-Perry pemphigoid variant of epidermolysis bullosa acquisita (EBA). This finding led us to review the literature on target antigens in Brunsting-Perry pemphigoid. Only 11 out of the 58 cases reported to date had target antigens identified. Interestingly, type VII collagen was the second most common target antigen/autoantibody (4 cases) detected after BP180 (5 cases). However, 2 further cases of EBA localized to the face with typical features of Brunsting-Perry pemphigoid were found in the literature. Although the target antigens are heterogeneous in Brunsting-Perry pemphigoid, a significant number of cases represent a clinical presentation of localized EBA.
Anatomy of a Crash (2014)

Transportation networks constitute a critical infrastructure enabling the transfers of passengers and goods, with a significant impact on the economy at different scales. Transportation modes, whether air, road or rail, are coupled and interdependent. The frequent occurrence of perturbations on one or several modes disrupts passengers' entire journeys, directly and through ripple effects. The present paper provides a case report of the Asiana Crash in San Francisco International Airport on July 6th 2013 and its repercussions on the multimodal transportation network. It studies the resulting propagation of disturbances on the transportation infrastructure in the United States. The perturbation takes different forms and varies in scale and time frame : cancellations and delays snowball in the airspace, highway traffic near the airport is impacted by congestion in previously never congested locations, and transit passenger demand exhibit unusual traffic peaks in between airports in the Bay Area. This paper, through a case study, aims at stressing the importance of further data-driven research on interdependent infrastructure networks for increased resilience. The end goal is to form the basis for optimization models behind providing more reliable passenger door-to-door journeys.
Quantum Support Vector Machine for Big Data Classification (2014)

Supervised machine learning is the classification of new data based on already classified training examples. In this work, we show that the support vector machine, an optimized binary classifier, can be implemented on a quantum computer, with complexity logarithmic in the size of the vectors and the number of training examples. In cases where classical sampling algorithms require polynomial time, an exponential speedup is obtained. At the core of this quantum big data algorithm is a nonsparse matrix exponentiation technique for efficiently performing a matrix inversion of the training data inner-product (kernel) matrix.
Increased optic atrophy type 1 expression protects retinal ganglion cells in a mouse model of glaucoma. (2010)

OPA1 can directly modulate RGC survival, and increasing OPA1 expression may protect against RGC death in glaucomatous optic neuropathy.
Comparative genomic and functional analyses of Paenibacillus peoriae ZBSF16 with biocontrol potential against grapevine diseases, provide insights into its genes related to plant growth-promoting and biocontrol mechanisms (2022)

<i>Paenibacillus peoriae</i> is a plant growth-promoting rhizobacteria (PGPR) widely distributed in various environments. <i>P. peoriae</i> ZBFS16 was isolated from the wheat rhizosphere and significantly suppressed grape white rot disease caused by <i>Coniella vitis</i>. Here, we present the complete genome sequence of <i>P. peoriae</i> ZBFS16, which consists of a 5.83 Mb circular chromosome with an average G + C content of 45.62%. Phylogenetic analyses showed that ZBFS16 belongs to the genus <i>P. peoriae</i> and was similar to <i>P. peoriae</i> ZF390, <i>P. peoriae</i> HS311 and <i>P. peoriae</i> HJ-2. Comparative analysis with three closely related sequenced strains of <i>P. peoriae</i> identified the conservation of genes involved in indole-3-acetic acid production, phosphate solubilization, nitrogen fixation, biofilm formation, flagella and chemotaxis, quorum-sensing systems, two-component systems, antimicrobial substances and resistance inducers. Meanwhile, <i>in vitro</i> experiments were also performed to confirm these functions. In addition, the strong colonization ability of <i>P. peoriae</i> ZBFS16 was observed in soil, which provides it with great potential for use in agriculture as a PGPR. This study will be helpful for further studies of <i>P. peoriae</i> on the mechanisms of plant growth promotion and biocontrol.
Psychosocial Mediators of a Nurse Intervention to Increase Skin Self-examination in Patients at High Risk for Melanoma (2006)

This prospective study examines psychosocial mediators of an efficacious skin self-examination (SSE) intervention that includes provision of a whole-body digital photography book depicting the entire skin surface. Individuals (n = 100) with established risk factors for melanoma were recruited from the Memorial Sloan-Kettering Cancer Center Pigmented Lesion Clinic during their initial dermatologist visit and were randomized to receive a photobook immediately (n = 49) or 4 months after intervention delivery (n = 51). Potential mediators included self-efficacy and response efficacy drawn from Social Cognitive Theory, melanoma worry, and SSE anxiety drawn from Self-Regulation Theory, and skin cancer knowledge, and skin awareness. Only self-efficacy was a significant mediator, accounting for 8% of the total effect of photobook enhancement on SSE adherence at 4 months.
Particle Effects On The Extinction And Ignition Of Flames In Normal- And Micro-Gravity (2003)

Reacting dusty flows have been studied to lesser extent than pure gas phase flows and sprays. Particles can significantly alter the ignition, burning and extinction characteristics of the gas phase due to the dynamic, thermal, and chemical couplings between the phases. The understanding of two-phase flows can be attained in stagnation flow configurations, which have been used to study spray combustion [e.g. 1] as well as reacting dusty flows [e.g. 2]. The thermal coupling between inert particles and a gas, as well as the effect of gravity, were studied in Ref. 3. It was also shown that the gravity can substantially affect parameters such as the particle velocity, number density, mass flux, and temperature. In Refs. 4 and 5, the effects of inert particles on the extinction of strained premixed and nonpremixed flames were studied both experimentally and numerically at 1-g and m-g. It was shown that large particles can cool flames more effectively than smaller particles. The effects of flame configuration and particle injection orientation were also addressed. It was shown that it was not possible to obtain a simple and still meaningful scaling that captured all the pertinent physics due to the complexity of the couplings between parameters. Also, the cooling by particles is more profound in the absence of gravity as gravity works to reduce the particle number density in the neighborhood of the flame. The efforts were recently shifted towards the understanding of the effects of combustible particles on extinction [6], the gas-phase ignition by hot particle injection [7], and the hot gas ignition of flames in the presence of particles that are not hot enough to ignite the gas phase by themselves.
Channel Formation in Long Laser Pulse Interaction with a Helium Gas Jet (1997)

Experimental realization of an electron density channel created by a low intensity laser in a helium gas jet is presented. The long (2.5 mm) plasma channel is fully ionized and thus prevents undesirable refraction effects for propagation and guiding of a subsequent high intensity laser pulse. The channel parameters are easily controlled and well suited for laser guiding. The radial plasma expansion and the temperature evolution have been measured and compared to hydrodynamic simulations which show that the plasma expansion is governed by a thermal wave during the laser pulse.
A CFD Analysis of the Effects of Two-Phase Flow in a Two-Stage Centrifugal Compressor (2015)

The performance of a compressor is known to be affected by the ingestion of liquid droplets. Heat, mass and momentum transfer as well as the droplet dynamics are some of the important mechanisms that govern the two-phase flow. This paper presents numerical investigations of three-dimensional two-phase flow in a two-stage centrifugal compressor, incorporating the effects of the above mentioned mechanisms. The results of the two-phase flow simulations are compared with the simulation involving only the gaseous phase. The implications for the compressor performance, viz. the pressure ratio, the power input and the efficiency are discussed. The role played by the droplet-wall interactions on the rate of vaporization, and on the compressor performance is also highlighted.
A Model for the Structure of the Large-Pore Zeolite SSZ-31 (1997)

A model for the structure of the zeolite SSZ-31 is presented. The model is obtained by combining information from adsorption capacity measurements, transmission electron microscopy, and high-resolution X-ray diffraction. SSZ-31 is a one-dimensional large-pore zeolite with a framework density of 18.7 tetrahedral(T)-atoms per nm-3 and a bulk density of 1.87 g cm-3. The pore apertures are elliptical with major and minor axes of approximately 8.6 Å × 5.7 Å. SSZ-31 is an extreme example of a complex and highly faulted zeolite. The structure can be described as an intergrowth of four different but structurally related polymorphs.
Mucosal Th1‐ versus Th2‐Type Responses for Antibody‐ or Cell‐Mediated Immunity to Simian Immunodeficiency Virus in Rhesus Macaques (1999)

Simian immunodeficiency virus (SIV)-specific B cell responses and the Th1- or Th2-type profiles of cytokine expression were determined for rhesus macaques immunized with SIV antigens via the iliac lymph nodes (by use of a targeted lymph node [TLN] procedure) or orally with SIV p55gag plus cholera toxin (CT) as a mucosal adjuvant. Analysis of CD4+ T cells purified from SIV-stimulated peripheral blood mononuclear cells of immunized macaques revealed that Th2 cytokine production gradually increased after the second and third TLN immunization. Analysis of SIV-specific B cell responses revealed that peak SIV-specific IgA B cell responses followed the third TLN immunization and occurred during peak Th2-type T cell responses. Oral immunization of macaques with p55gag plus CT induced interferon-gamma-secreting Th1-type and select Th2-type cytokine-producing CD4+ T helper cells, which most likely accounted for the induction of p55-specific systemic IgG and mucosal IgA responses.
Induction of thymidine phosphorylase expression and enhancement of efficacy of capecitabine or 5?-deoxy-5-fluorouridine by cyclophosphamide in mammary tumor models (1999)

Thymidine phosphorylase (dThdPase) is an essential enzyme for the activation of the oral cytostatic drugs capecitabine (N(4)-pentyloxycarbonyl-5'-deoxy-5-fluorocytidine, Xeloda(trade mark)) and its intermediate metabolite doxifluridine [5'-deoxy-5-fluorouridine (5'-dFUrd, Furtulon((R)))] to 5-fluorouracil (5-FUra) in tumors. In a previous study, we found that several cytostatics were able to up-regulate tumor levels of dThdPase in a human colon cancer xenograft model. In the present study, we confirmed that the administration of cytostatics used for breast cancer treatment, such as taxanes and cyclophosphamide (CPA), up-regulated the tumor level of dThdPase in mammary tumor models as well. Because the dThdPase up-regulation was observed even when CPA was given orally, we investigated further the usefulness of combination therapy with the 2 oral drugs, 5'-dFUrd/capecitabine and CPA in mammary tumor models. Daily oral administration of CPA up-regulated human dThdPase levels in the tumor tissue of mice bearing a human mammary tumor xenograft, MX-1, whereas in the small intestine and liver, it did not affect levels of pyrimidine nucleoside phosphorylases (PyNPase) including dThdPase and uridine phosphorylase. The preferential up-regulation of PyNPase activity in the tumor by CPA administration was also confirmed in mice bearing a syngeneic murine mammary adenocarcinoma, A755. In both models, combination therapy of 5'-dFUrd/capecitabine with CPA showed synergistic antitumor activity, without significant potentiation of toxicity. In contrast, treatment with CPA and either 5-FUra or UFT (a mixture of tegafur and uracil) in combination showed only additive activity. Our results suggest that CPA and capecitabine/5'-dFUrd, both available for oral administration, would be good partners, and that clinical trials with this drug combination against breast cancer are warranted.
Silicon resonator sensors: interrogation techniques and characteristics (1988)

Interferometric and noninterferometric optical-fibre sensing systems for resonator vibrations are described. The quality factor variation with pressure, the temperature dependence of resonant frequency and the acceleration sensitivity are given for a double-ended tuning-fork based acceleratometer.
3-Hydroxy-3H-1,2,3-triazolo[4,5-b]pyridine (2001)

[39968-33-7] C5H4N4O (MW 136.13) InChI = 1S/C5H4N4O/c10-9-5-4(7-8-9)2-1-3-6-5/h1-3,10H InChIKey = FPIRBHDGWMWJEP-UHFFFAOYSA-N (coupling additive for peptide synthesis1-4) Alternate Name: HOAt; 7-aza-1-hydroxybenzotriazole. Physical Data: mp: sample decomposes at temperatures above 205 °C. Solubility: sol DMF. Form Supplied in: white solid; commercially available. Purification: by crystallization from ethanol or water. Handling, Storage, and Precautions: is very stable, not hygroscopic, and can be stored indefinitely. HOAt solutions in DMF (0.3 M) can be stored in an inert atmosphere for weeks. Syntheses of peptides carried out with freshly prepared and 4-week old solutions show similar quality for the crude product.5 Violent decomposition may occur when dried at elevated temperatures.
Nucleation and growth characteristics of electroplated Cu on plasma enhanced atomic layer deposition-grown RuTaN direct plate barriers (2011)

A study has been carried out to understand the mechanism that enables plasma enhanced atomic layer deposition (PEALD)-grown RuTaN barriers to support direct (seedless) copper electroplating. In particular, the effects of changing the liner surface chemistry on the subsequent plated copper nucleation behavior have been evaluated. Amperometric measurements and short pulse plating experiments were carried out directly on PEALD-grown RuTaN barriers. To enhance copper nucleation, a liner surface cleaning protocol was developed and evaluated. In order to understand the effect of intrinsic liner composition and conductivity on the film microstructure and subsequent plated copper nucleation, a study of copper nucleation density as it relates to the Ru:Ta ratio in the liner was carried out. The thickness extendibility of these direct plate liners was also explored. These liners were also tested for potential use in sub-45-nm copper metallization applications.
Automatic Discovery of Non-Compositional Compounds (2001)

This chapter contains section titled: Introduction, Objective Functions, Search, Predictive Value Functions, Iteration, Credit Estimation, Single-Best Translation, Experiments, Related Work, Conclusion
Challenges in Peptide-Spectrum Matching: a Robust and Reproducible Statistical Framework for Removing Low-Accuracy, High-Scoring Hits (2019)

Abstract Workflows for large-scale (MS)-based shotgun proteomics can potentially lead to costly errors in the form of incorrect peptide spectrum matches (PSMs). To improve robustness of these workflows, we have investigated the use of the precursor mass discrepancy (PMD) to detect and filter potentially false PSMs that have, nonetheless, a high confidence score. We identified and addressed three cases of unexpected bias in PMD results: time of acquisition within a LC-MS run, decoy PSMs, and length of peptide. We created a post-analysis Bayesian confidence measure based on score and PMD, called PMD-FDR. We tested PMD-FDR on four datasets across three types of MS-based proteomics projects: standard (single organism; reference database), proteogenomics (single organism; customized genomic-based database plus reference), and metaproteomics (microorganism community; customized conglomerate database). On a ground truth dataset and other representative data, PMD-FDR was able to detect 60-80% of likely incorrect PSMs (false-hits) while losing only 5% of correct PSMs (true-hits). PMD-FDR can also be used to evaluate data quality for results generated within different experimental PSM-generating workflows, assisting in method development. Going forward, PMD-FDR should provide detection of high-scoring but likely false-hits, aiding applications which rely heavily on accurate PSMs, such as proteogenomics and metaproteomics.
Silver nanoparticle ink technology: state of the art (2016)

Printed electronics will bring to the consumer level great breakthroughs and unique products in the near future, shifting the usual paradigm of electronic devices and circuit boards from hard boxes and rigid sheets into flexible thin layers and bringing disposable electronics, smart tags, and so on. The most promising tool to achieve the target depends upon the availability of nanotechnology-based functional inks. A certain delay in the innovation-transfer process to the market is now being observed. Nevertheless, the most widely diffused product, settled technology, and the highest sales volumes are related to the silver nanoparticle-based ink market, representing the best example of commercial nanotechnology today. This is a compact review on synthesis routes, main properties, and practical applications.
adiation-~nduced Proton (1998)

In order to understand the physics of radiation-induced proton density decay in thin SiO, films, we performed ab initio Hartree-Fock calculations of the potential energy curves for the interaction between model oxide clusters and H in two charge states. The calculated results led to two separate proposed mechanisms for proton density decay in thin SiO, films: (1) electronic excitation involving hot phonon levels of the ground electronic state at low photon-energy radiation and (2) electron capture by protons at high photon-energy radiation. The proposed mechanisms qualitatively explain recent experimental observations.
Measurement of Thermophysical Properties of Thin Film Shape Memory Alloys Using the 3-Omega Method (2005)

The excellent mechanical properties of thin film shape memory alloys like Nickel-Titanium (NiTi) have led to their widespread use in MEMS-based micropumps, microactuators, microgrippers, etc. Shape memory based micropumps and actuators have superior work densities compared to other technologies. Characterization of thermophysical properties of these materials is important for modeling the behavior of NiTi-based microdevices. For example, the frequency response of shape-memory based microactuators depends on the rate of dissipation of thermal energy, which is a strong function of the thermal properties of the thin film. While bulk thermal properties of NiTi have been reported before, there exists very little work on measuring these properties for the thin film form. This paper uses the 3-ω method for measurement of thermal conductivity of NiTi thin films. NiTi is sputtered on a Silicon substrate, followed by patterning of a metal heater line. Front-to-backside alignment and Deep Reactive Ion Etching (DRIE) of the substrate results in a free standing thin film of NiTi. A sinusoidal electric current is passed through the metal heater, and the third harmonic of the voltage is measured using a lock-in amplifier. This is used to determine the temperature oscillation in the metal heater, which provides the thin film thermal conductivity using a recently developed analytical model for 3-ω measurements in a two-dimensional free standing thin film. The measured values are found to be much lower than the known bulk thermal conductivity of NiTi. This highlights the importance of thin film property measurements instead of using bulk properties. Data obtained in this work is likely to be useful for improved modeling of thin film shape memory based microdevices.
Solids Formation After the Expansion of Supercritical Mixtures (1989)

The continuous formation of solids following the rapid expansion of a highly compressible supercritical mixture is an interesting alternative to conventional crystallization methods. Phase separation is caused by a mechanical perturbation which propagates rapidly and hence gives rise to essentially uniform conditions within the supersaturated medium. In this study, a systematic investigation of the influence of pre- and post-expansion conditions upon the crystallinity and particle size of Naphthalene and Lovastatin powders obtained by the rapid expansion of supercritical mixtures was performed. Naphthalene particles were produced continuously by expanding carbon dioxide-rich mixtures into a crystallizer whose temperature, pressure and composition were independently controlled. The mixture was expanded through a laser-drilled nozzle within which fluid residence times were less than 10-5 seconds. Naphthalene powders were found to be crystalline in all cases studied. Particle size of the solid product was consistently found to be a sensitive function of pre- and post-expansion temperature and of pre-expansion Naphthalene concentration, suggesting the possibility of an accurate control of product characteristics through small changes in process variables. The Lovastatin product formed upon the expansion of Lovastatin/CO2 supercritical mixtures consisted of aggregates of sub-micron crystal units. Mean particle sizes in the range of 126-255 nm were measured for these units. The average particle size was found to be relatively insensitive to changes in solute concentration, or in pre- and post-expansion temperature for the conditions investigated in this study.