gebhart/patrepeval huggingface dataset:
Applications of catalyzed cytoplasmic disulfide bond formation (2019)

Disulfide bond formation is an essential post-translational modification required for many proteins to attain their native, functional structure. The formation of disulfide bonds, otherwise known as oxidative protein folding, occurs in the endoplasmic reticulum and mitochondrial inter-membrane space in eukaryotes and the periplasm of prokaryotes. While there are differences in the molecular mechanisms of oxidative folding in different compartments, it can essentially be broken down into two steps, disulfide formation and disulfide isomerization. For both steps, catalysts exist in all compartments where native disulfide bond formation occurs. Due to the importance of disulfide bonds for a plethora of proteins, considerable effort has been made to generate cell factories which can make them more efficiently and cheaper. Recently synthetic biology has been used to transfer catalysts of native disulfide bond formation into the cytoplasm of prokaryotes such as Escherichia coli. While these engineered systems cannot yet rival natural systems in the range and complexity of disulfide-bonded proteins that can be made, a growing range of proteins have been made successfully and yields of homogenously folded eukaryotic proteins exceeding g/l yields have been obtained. This review will briefly give an overview of such systems, the uses reported to date and areas of future potential development, including combining with engineered systems for cytoplasmic glycosylation.
WKYMVm hexapeptide, a strong formyl peptide receptor 2 agonist, attenuates hyperoxia-induced lung injuries in newborn mice (2019)

The hexapeptide WKYMVm, which is a strong formyl peptide receptor (FPR) 2 agonist, exhibits pro-angiogenic, anti-inflammatory and anti-apoptotic properties. However, its therapeutic efficacy in bronchopulmonary dysplasia (BPD) has not been tested to date. Here, we investigated whether WKYMVm attenuates hyperoxia-induced lung inflammation and ensuing injuries by upregulating FPR2. The proliferation and tube formation ability of human umbilical vein endothelial cells (HUVECs), along with the level of extracellular signal regulated kinase (ERK) phosphorylation, were evaluated in vitro. Newborn mice were randomly exposed to 80% oxygen or room air for 14 days starting at birth. WKYMVm (2.5 mg/kg) was intraperitoneally administrated daily from postnatal day (P) 5 to P8. At P14, mice were sacrificed for histopathological and morphometric analyses. Along with upregulation of FPR2 and p-ERK, WKYMVm promoted HUVEC cell proliferation and tube formation in vitro. Additionally, WKYMVm promoted proliferation of human pulmonary microvascular endothelial cells (HULEC-5a) and murine pulmonary endothelial and epithelial cells in vitro. WKYMVm significantly attenuated hyperoxia-induced lung inflammation, as evidenced by increased inflammatory cytokines, neutrophils, and alveolar macrophages, and resultant lung injuries, which included impaired alveolarization and angiogenesis, an increased number of apoptotic cells, and reduced levels of growth factors in vivo, such as vascular endothelial growth factor and hepatocyte growth factor. WKYMVm attenuates hyperoxia-induced lung injuries and lung inflammation by upregulating FPR2 and p-ERK.
Ascosteroside, a New Antifungal Agent from Ascotricha amphitricha. I. Taxonomy, Fermentation and Biological Activities. (1996)

Ascosteroside, a novel antifungal compound, was isolated from the culture broth of Ascotricha amphitricha. This compound is an alpha-linked glycoside of a lanostane type triterpenoid. It is active against yeasts such as Candida albicans and Saccharomyces cerevisiae and against filamentous fungi but shows no activity against bacteria. It is not toxic to mammalian cells at concentrations up to 150 microM. In a mouse model, the compound afforded protection comparable to that of ketoconazole.
Truncations of Titin Causing Dilated Cardiomyopathy (2012)

TTN truncating mutations are a common cause of dilated cardiomyopathy, occurring in approximately 25% of familial cases of idiopathic dilated cardiomyopathy and in 18% of sporadic cases. Incorporation of sequencing approaches that detect TTN truncations into genetic testing for dilated cardiomyopathy should substantially increase test sensitivity, thereby allowing earlier diagnosis and therapeutic intervention for many patients with dilated cardiomyopathy. Defining the functional effects of TTN truncating mutations should improve our understanding of the pathophysiology of dilated cardiomyopathy. (Funded by the Howard Hughes Medical Institute and others.).
Towards synchronization of live virtual machines among mobile devices (2013)

The mobile computing experience would improve if users could switch seamlessly from one device to another, with both data and computation state preserved across the switch without apparent delay. This paper proposes VMsync, a system for synchronizing the state of live virtual machines (VMs) among mobile devices. VMsync seeks to incrementally transfer changes in an active VM on one device to standby VMs in other devices, so as to maintain a consistent VM image and minimize switching latency. However, constraints of the mobile environment make these goals difficult to achieve and raise many research questions. We present our preliminary design for VMsync and a feasibility study aimed at determining how much data would need to be transferred under different mobile workloads and synchronization policies. For example, through experiments with a Xen VM running Android and playing a YouTube video, we show that sending dirty memory pages transfers 3 times more data than sending only the bytes that actually changed in those pages. Overall, we conclude that VMsync is a feasible approach deserving of further research.
(Invited) Techniques for the Dry Transfer of Epitaxial Graphene onto Arbitrary Substrates (2010)

Graphene can be formed via a variety of methods, each providing various benefits. Epitaxial graphene (EG) grown on the carbon-face of SiC has been shown to exhibit high carrier mobilities, in comparison to other growth techniques, while remaining amenable to wafer-scale graphene fabrication. Therefore, the transfer of large area (>mm2) graphene films to substrates amenable for specific applications is desirable. We demonstrate the dry transfer of EG from the C-face of 4H-SiC onto SiO2, GaN and Al2O3 substrates via two approaches using either 1) thermal release tape, 2) a PMMA/thermal release tape bilayer or 3) a spin-on, chemically-etchable dielectric. We will report on the impact that these transfer processes has upon the electrical properties of the transferred EG films.
Inhomogeneous magnetization transfer imaging: Concepts and directions for further development (2022)

Off-resonance radio frequency irradiation can induce the ordering of proton spins in the dipolar fields of their neighbors, in molecules with restricted mobility. This dipolar order decays with a characteristic relaxation time, T<sub>1D</sub> , that is very different from the T<sub>1</sub> and T<sub>2</sub> relaxation of the nuclear alignment with the main magnetic field. Inhomogeneous magnetization transfer (ihMT) imaging is a refinement of magnetization transfer (MT) imaging that isolates the MT signal dependence on dipolar order relaxation times within motion-constrained molecules. Because T<sub>1D</sub> relaxation is a unique contrast mechanism, ihMT may enable improved characterization of tissue. Initial work has stressed the high correlation between ihMT signal and myelin density. Dipolar order relaxation appears to be much longer in membrane lipids than other molecules. Recent work has shown, however, that ihMT acquisitions may also be adjusted to emphasize different ranges of T<sub>1D</sub> . These newer approaches may be sensitive to other microstructural components of tissue. Here, we review the concepts and history of ihMT and outline the requirements for further development to realize its full potential.
Magnetic field-assisted electrochemical discharge machining (2010)

Electrochemical discharge machining (ECDM) is an effective unconventional method for micromachining in non-conducting materials, such as glass, quartz and some ceramics. However, since the spark discharge performance becomes unpredictable as the machining depth increases, it is hard to achieve precision geometry and efficient machining rate in ECDM drilling. One of the main factors for this is the lack of sufficient electrolyte flow in the narrow gap between the tool and the workpiece. In this study a magnetohydrodynamic (MHD) convection, which enhances electrolyte circulation has been applied to the ECDM process in order to upgrade the machining accuracy and efficiency. During electrolysis in the presence of a magnetic field, the Lorenz force induces the charged ions to form a MHD convection. The MHD convection then forces the electrolyte into movement, thus enhancing circulation of electrolyte. Experimental results show that the MHD convection induced by the magnetic field can effectively enhance electrolyte circulation in the micro-hole, which contributes to higher machining efficiency. Micro-holes in glass with a depth of 450 µm are drilled in less than 20 s. At the same time, better electrolyte circulation can prevent deterioration of gas film quality with increasing machining depth, while ensuring stable electrochemical discharge. The improvement in the entrance diameter thus achieved was 23.8% while that in machining time reached 57.4%. The magnetic field-assisted approach proposed in the research does not require changes in the machining setup or electrolyte but has proved to achieve significant enhancement in both accuracy and efficiency of ECDM.
A Fundamental Limitation of Small Diameter Single-Walled Carbon Nanotube Synthesis—A Scaling Rule of the Carbon Nanotube Yield with Catalyst Volume (2013)

Understanding the fundamental mechanisms and limiting processes of the growth of single-walled carbon nanotube (SWCNT) would serve as a guide to achieve further control on structural parameters of SWCNT. In this paper, we have studied the growth kinetics of a series of SWCNT forests continuously spanning a wide range of diameters (1.9-3.2 nm), and have revealed an additional fundamental growth limiting process where the mass of the individual SWCNT is determined by the individual catalyst volume. Calculation of the conversion rate of carbon atoms into CNTs per Fe atom is 2 × 10² atoms per second. This rate limiting process provides an important understanding where the larger diameter SWCNT would grow faster, and thus be more suited for mass production.
Target Trailing With Safe Navigation for Maritime Autonomous Surface Vehicles (2013)

This software implements a motion-planning module for a maritime autonomous surface vehicle (ASV). The module trails a given target while also avoiding static and dynamic surface hazards. When surface hazards are other moving boats, the motion planner must apply International Regulations for Avoiding Collisions at Sea (COLREGS). A key subset of these rules has been implemented in the software. In case contact with the target is lost, the software can receive and follow a reacquisition route, provided by a complementary system, until the target is reacquired. The programmatic intention is that the trailed target is a submarine, although any mobile naval platform could serve as the target. The algorithmic approach to combining motion with a (possibly moving) goal location, while avoiding local hazards, may be applicable to robotic rovers, automated landing systems, and autonomous airships. The software operates in JPL s CARACaS (Control Architecture for Robotic Agent Command and Sensing) software architecture and relies on other modules for environmental perception data and information on the predicted detectability of the target, as well as the low-level interface to the boat controls.
Delivery of multipurpose prevention drug combinations from electrospun nanofibers using composite microarchitectures (2014)

Electrospun fabrics with high drug loading create multicomponent systems that benefit from the independent control of the nanofibrous microarchitecture. Our findings are significant because they will inform the design and production of composite electrospun fabrics for the co-delivery of physicochemically diverse drugs that may be useful for multipurpose prevention.
Dielectric Properties of Modified Lead Zinc Niobate Ceramic (1985)

Crystal structures, dielectric properties and electrical resistivities for partially substituted lead zinc niobate [Pb(Zn 1/3 Nb 2/3 )O 3 ] ceramic were investigated. This ceramic, sintered at 1000–1050°C, was composed mainly of perovskite phase and showed a high dielectric constant (3500–5000) and a high resistivity (approximately 10 13 Ω·cm) when partial substitutions of the Pb site by Ba or Sr and the (Zn 1/3 Nb 2/3 ) site by Ti in the Pb(Zn 1/3 Nb 2/3 )O 3 were carried out. The reason why the perovskite phase was stable in the sintered body is explained qualitatively by introducing the concepts of an electronegativity difference and a tolerance factor.
Real-time new event detection for video streams (2008)

Online detection of video clips that present previously unseen events in a video stream is still an open challenge to date. For this online new event detection (ONED) task, existing studies mainly focus on optimizing the detection accuracy instead of the detection efficiency. As a result, it is difficult for existing systems to detect new events in real time, especially for large-scale video collections such as the video content available on the Web. In this paper, we propose several scalable techniques to improve the video processing speed of a baseline ONED system by orders of magnitude without sacrificing much detection accuracy. First, we use text features alone to filter out most of the non-new-event clips and to skip those expensive but unnecessary steps including image feature extraction and image similarity computation. Second, we use a combination of indexing and compression methods to speed up text processing. We implemented a prototype of our optimized ONED system on top of IBM's System S. The effectiveness of our techniques is evaluated on the standard TRECVID 2005 benchmark, which demonstrates that our techniques can achieve a 480-fold speedup with detection accuracy degraded less than 5%.
Use of two reflective photodetectors for measuring all four Stokes parameters of light (1991)

It has been shown previously that all four Stokes parameters of light can be measured using an arrangement of four photodetectors. 1 Three of the four detectors are partially reflective and steer the beam in a nonplanar path to the fourth absorbing detector. In this paper schemes that employ only two reflective detectors for measuring all four Stokes parameters are described. The detectors are set for oblique reflection and with noncoincident planes of incidence. Recording the 2 × 1 output signal vector for two angular positions (45° apart) of the two-detector assembly around the incident beam axis provides sufficient information to determine the 4 × 1 Stokes vector. Mechanical rotation can be avoided by using a Faraday rotator in front of a stationary arrangement of two detectors. Another novel scheme uses intermittent optical feedback, with a normal-incidence back-reflecting mirror and a light chopper, to modulate the output signals of the two detectors in a square-wave fashion. The two square waves provide enough data to determine fully the most general state of partial elliptical polarization of incident light. The appropriate instrument matrix and its determinant are derived explicitly, and all possible discrete singularity conditions are shown to be readily avoidable. Implementations in fiber-optic form are also discussed.
A sensory feedback system for grasping pressure in a myoelectric hand (1988)

A critical aspect of replacing even a small portion of lost hand function is to provide accurate sensory information to the individual with a myoelectric limb. A prototype system was developed to enhance this sensory information transfer by using a technique in which the feedback modality (pressure) was the same as that of the grasping pressure. A pilot study which compared the developed system to an electrocutaneous feedback system as well as to a no-feedback condition (vision only) found that the pressure-pressure concept reduced grasping-pressure replication errors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Estimation of Photovoltaic Soiling Using Environmental Parameters: A Comparative Analysis of Existing Models (2022)

Abstract Soiling is the process where dust, dirt, and organic/inorganic contaminants accumulate on the surface of a photovoltaic (PV) module. It impacts the energy generation of PV systems and causes significant economic losses. It can be monitored through soiling estimation models, which evaluate its impact depending on a number of environmental parameters. The main focus of this study is to compare four existing estimation models in Jaén, Spain, and to analyze their performance in an environment different than that where each of them is developed. The results indicate that all models can reproduce accurately the seasonality of soiling in Jaén, if a cleaning threshold of 0.3 mm day −1 is considered. The models’ performance is found to be influenced not only by the mass concentration but also by the optical properties of each component of the atmospheric particulate matter, with an overestimation up to 4% in high organic carbon concentration periods. The natural cleaning role of rainfalls and its influence on the modeling error are also discussed through the paper.
Anti-alpha-fodrin antibodies in Sjögren's syndrome in children. (2001)

The pathogenesis of juvenile SS seems to be the same as that of adult SS, although subjective symptoms of dryness are less frequent in juvenile cases. This discrepancy may indicate that SS is a slowly progressive disease with a long time span. The anti-alpha-fodrin antibody is likely to be a reliable diagnostic marker for juvenile SS.
Carbon catabolite regulation of rebeccamycin production inSaccharothrix aerocolonigenes (1989)

A new antitumor antibiotic named rebeccamycin was isolated from fermentations of an actinomycete, Saccharothrix aerocolonigenes. A defined medium was developed to study the regulation of synthesis of rebeccamycin by S. aerocolonigenes. In glucose medium formation of rebeccamycin was detected only after glucose was depleted. Examination of eleven different carbon sources revealed that carbon catabolite regulation is a major control mechanism for rebeccamycin production.
Spin-Seebeck thermoelectric converter (2014)

Thermoelectric conversion (TEC) technologies, which convert heat into electricity, have received a great attention, because they are expected to be a powerful approach to utilize wasted thermal energy. Here we present novel thermoelectric converters based on the spin Seebeck effect (SSE), and show their scaling law which is largely different from that of conventional TEC devices. We experimentally demonstrate that the TEC output signals straightforwardly increase with the size of the converters. This scaling law enables us to implement simple-structured thermoelectric converters by using productive film-coating methods. Such coating-based TEC techniques may pave the way for a wide range of applications using a variety of heat sources.
Developing novel anti-diabetic drugs for geriatric population: prospecting for lead compounds among botanical formulations of traditional medicine (2014)

Diabetes has attained pandemic proportions since decades and the trend of its spread shows no sign of receding. Other than high morbidity and mortality, diabetes and its complications causes tremendous cost to the individual, family, and governments. Definite causes of diabetes are not defined though there are numerous pathways described as leading to the destruction of beta cells in the pancreas and development of insulin resistance. Single agents and combination therapies are able to achieve target glycemic goals for limited periods of time and only in a subset of patients with Type 2 Diabetes Mellitus. There is renewed interest in multi-ingredient synergistic formulations for management of polygenic syndromes and conditions like diabetes. Drug discovery and development should be explored among rationally designed, carefully standardized, synergistic traditional herbal formulations and botanical drug products with robust scientific evidence. There are many Ayurvedic drugs available in the Indian market, claiming effective management for diabetes. Drug discovery is a process involving humongous cost, effort and time. Any lead followed in this direction needs to be selected with great scrutiny and caution.
Transform-data-by-example (TDE) (2018)

Today, business analysts and data scientists increasingly need to clean, standardize and transform diverse data sets, such as name, address, date time, and phone number, before they can perform analysis. This process of data transformation is an important part of data preparation, and is known to be difficult and time-consuming for end-users. Traditionally, developers have dealt with these longstanding transformation problems using custom code libraries. They have built vast varieties of custom logic for name parsing and address standardization, etc., and shared their source code in places like GitHub. Data transformation would be a lot easier for end-users if they can discover and reuse such existing transformation logic. We developed Transform-Data-by-Example ( TDE ), which works like a search engine for data transformations. TDE "indexes" vast varieties of transformation logic in source code, DLLs, web services and mapping tables, so that users only need to provide a few input/output examples to demonstrate a desired transformation, and TDE can interactively find relevant functions to synthesize new programs consistent with all examples. Using an index of 50K functions crawled from GitHub and Stackoverflow, TDE can already handle many common transformations not currently supported by existing systems. On a benchmark with over 200 transformation tasks, TDE generates correct transformations for 72% tasks, which is considerably better than other systems evaluated. A beta version of TDE for Microsoft Excel is available via Office store 1 . Part of the TDE technology also ships in Microsoft Power BI.
New algorithms for widefield SAR image formation (2004)

The widefield polar format algorithm, the Stolt polar algorithm, and the differential Doppler algorithm use variations of a new along-track alignment and formatting system (ATAFS) to generate fine-resolution images from synthetic aperture radar (SAR) data. ATAFS introduces a spatially variant modification of the SAR phase history storage format to remove the formatting inaccuracies of the conventional polar format algorithm and enables full image quality over large scenes without range curvature distortion or image defocus. These new algorithms are well-suited for processing fine resolution spotlight and ultra-wideband SAR data. Their image quality performance is comparable to that of the range migration algorithm (RMA). Unlike RMA, the new algorithms operate on data stabilized to a fixed reference point to remove the azimuth chirp (the Doppler bandwidth of the reference point) before it compromises processor efficiency.