gebhart/patrepeval huggingface dataset:
Development and Validation of Novel AAV2 Random Libraries Displaying Peptides of Diverse Lengths and at Diverse Capsid Positions (2011)

Libraries based on the insertion of random peptide ligands into the capsid of adeno-associated virus type 2 (AAV2) have been widely used to improve the efficiency and selectivity of the AAV vector system. However, so far only libraries of 7-mer peptide ligands have been inserted at one well-characterized capsid position. Here, we expanded the combinatorial AAV2 display system to a panel of novel AAV libraries, displaying peptides of 5, 7, 12, 19, or 26 amino acids in length at capsid position 588 or displaying 7-mer peptides at position 453, the most prominently exposed region of the viral capsid. Library selections on two unrelated cell types-human coronary artery endothelial cells and rat cardiomyoblasts-revealed the isolation of cell type-characteristic peptides of different lengths mediating strongly improved target-cell transduction, except for the 26-mer peptide ligands. Characterization of vector selectivity by transduction of nontarget cells and comparative gene-transduction analysis using a panel of 44 human tumor cell lines revealed that insertion of different-length peptides allows targeting of distinct cellular receptors for cell entry with similar efficiency, but with different selectivity. The application of such novel AAV2 libraries broadens the spectrum of targetable receptors by capsid-modified AAV vectors and provides the opportunity to choose the best suited targeting ligand for a certain application from a number of different candidates.
A Fast Neural Network Approach to Predict Lung Tumor Motion during Respiration for Radiation Therapy Applications (2015)

During radiotherapy treatment for thoracic and abdomen cancers, for example, lung cancers, respiratory motion moves the target tumor and thus badly affects the accuracy of radiation dose delivery into the target. A real-time image-guided technique can be used to monitor such lung tumor motion for accurate dose delivery, but the system latency up to several hundred milliseconds for repositioning the radiation beam also affects the accuracy. In order to compensate the latency, neural network prediction technique with real-time retraining can be used. We have investigated real-time prediction of 3D time series of lung tumor motion on a classical linear model, perceptron model, and on a class of higher-order neural network model that has more attractive attributes regarding its optimization convergence and computational efficiency. The implemented static feed-forward neural architectures are compared when using gradient descent adaptation and primarily the Levenberg-Marquardt batch algorithm as the ones of the most common and most comprehensible learning algorithms. The proposed technique resulted in fast real-time retraining, so the total computational time on a PC platform was equal to or even less than the real treatment time. For one-second prediction horizon, the proposed techniques achieved accuracy less than one millimeter of 3D mean absolute error in one hundred seconds of total treatment time.
Total Synthesis of the Potent Marine-Derived Elastase Inhibitor Lyngbyastatin 7 and in Vitro Biological Evaluation in Model Systems for Pulmonary Diseases (2015)

Lyngbyastatin 7 (1) is a marine cyanobacteria-derived lariat-type cyclic depsipeptide of which the macrocyclic core possesses modified amino acids, including a featured 3-amino-6-hydroxy-2-piperidone (Ahp) moiety and a (Z)-2-amino-2-butenoic acid (Abu) moiety. The first total synthesis of 1 was successfully established via 31 steps, and the conditions of several crucial steps were optimized to ensure smooth operations. The previously reported structural assignment and elastase inhibitory activity of the isolated natural product were confirmed. According to the extensive in vitro biological evaluation, compound 1 displayed low nanomolar IC50 in blocking elastase activity and strong ability in protecting bronchial epithelial cells against elastase-induced antiproliferation and abrogating the elastase-triggered induction of pro-inflammatory cytokine expression. Its overall performance was superior over sivelestat, the only approved small molecule drug targeting elastase, which indicated its potential in developing as a pharmacotherapeutic against elastase-mediated pathologies. The success in total synthesis, designed with a novel convergent strategy, not only overcame the supply issue for thorough preclinical studies but also paved the way for convenient synthesis of analogues with improved potency and druglike properties.
Potential of new SLLIMM&amp;#x2122;-nano Intelligent Molded Module for low power home appliance motor drives (2012)

This paper presents the new SLLIMM™-nano (Small Low-Loss Intelligent Molded Module) in an NDIP-26L transfer molded package, which has been developed for low power home appliance motor drives up to 100W without a heat sink. The module integrates STMicroelectronics' very fast 600V IGBT technology with the ST Turbo 2 ultra-fast soft recovery diodes, and the HVIC (high voltage gate driver IC) in BCD technology to provide an extremely compact solution, especially where space assembly is a key factor in designing the inverter system. A comparison analysis between IGBT and MOSFET based inverter solutions in a dishwasher water pump with sinusoidal FOC and 6-step 120° controls is presented in this work. By using the IGBT option with the sinusoidal FOC technique, better electrical and thermal behavior is achieved if the switching frequency adopted for the control strategy is relatively high. The IGBT choice is still the best if the 6-step 120° technique is adopted, especially at high T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">AMB</sub> and high PWM f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sw</sub> values. On the other hand, if the PWM f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sw</sub> and the power level involved are low, the MOSFET based inverter performs better than the IGBT with both control techniques.
Label‐Free Colorimetric Detection of Lead Ions with a Nanomolar Detection Limit and Tunable Dynamic Range by using Gold Nanoparticles and DNAzyme (2008)

In the presence of Pb2+, a cleaved enzyme–substrate complex releases ssDNA that adsorbs onto and stabilizes gold nanoparticles (AuNPs) against salt-induced aggregation. In the absence of Pb2+, the uncleaved complex can not stabilize the AuNPs, resulting in purple–blue AuNP aggregates (see figure). The sensor has a low detection limit of 3 nM, a high selectivity, and a tunable dynamic range.
Electoral, Partisan, and Corporate Socialism: Organisational Consolidation and Membership Mobilisation in Early Socialist Movements (1996)

It is generally accepted that the pathogenesis of hantavirus infections is the result of virus-mediated host immune response. Hantaviruses, and mainly Dobrava-Belgrade virus, are present in Greece, and cause to humans hemorrhagic fever with renal syndrome (HFRS). Serum IL-6, IL-8, IL-10, TNF-α and sTNFR1 levels were measured in 29 HFRS Greek patients. Significant higher sTNFR1, IL-6, IL-8 and IL-10 levels were observed in severe than in mild/moderate cases, while TNF-α did not seem to be associated with disease severity. Correlations between cytokine levels and their fluctuation over time after onset of the illness, along with comparisons from previously published data on the field, led in building an immune response pattern for HFRS.
Wavelength-Controlled Orthogonal Photolysis of Protecting Groups (2002)

The selective control of a chemical process by the use of an electromagnetic wave has been a challenging goal for several decades. In this article, we describe for the first time the use of a monochromatic light beam to differentiate two different reactive centers. A direct application of this concept is found in the chemistry of protecting groups. Two different photolabile protecting groups were tuned to be responsive to a specific wavelength (e.g., 254 or 420 nm). Using derivatives of the 2-nitroveratryl fragment (such as 10, sensitive at 420 nm) and 3',5'-dimethoxybenzoin fragment (such as 4, sensitive at 254 nm), it was shown that energy transfer phenomena did not erode the selectivity. Both the inter- and the intramolecular cases were studied and showed selectivities within the synthetically useful range. Hence, we could replace the traditional chemical orthogonality by a chromatic orthogonality.
Helium Diffusion Through Glass (1953)

Using the mass spectrometer as an analytical tool and as a means of rate measurement, the rates of helium diffusion through nine types of glass were measured. The temperature range covered was from –80° to 600°C. The highest rates were for fused silica and Vycor brand glass; the lowest were for the lead glasses. The rate at 100°C. decreased by a factor of one million as the percentage of glassformers (SiO 2 , B 2 O 3 , P 2 O 5 ) decreased in the glass composition. A few measurements are also given for hydrogen, deuterium, and neon rates through fused silica and estimates are made of the upper limit for argon, oxygen, and nitrogen at 700°C.
IOP1, a novel hydrogenase-like protein that modulates hypoxia-inducible factor-1α activity (2006)

A central means by which mammalian cells respond to low oxygen tension is through the activation of the transcription factor HIF-1 (hypoxia-inducible factor-1). Under normoxic conditions, HIF-1alpha (the alpha subunit of HIF-1) is targeted for rapid degradation by the ubiquitin-proteasome pathway. Under hypoxic conditions, this degradation is inhibited, thereby leading to the stabilization and activation of HIF-1alpha. Here, we report the identification of IOP1 (iron-only hydrogenase-like protein 1), a protein homologous with enzymes present in anaerobic organisms that contain a distinctive iron-sulfur cluster. IOP1 is present in a broad range of cell types. Knockdown of IOP1 using siRNA (small interfering RNA) in mammalian cells increases protein levels of HIF-1alpha under both normoxic and hypoxic conditions, and augments hypoxia-induced HRE (hypoxia response element) reporter gene and endogenous HIF-1alpha target gene expressions. We find that IOP1 knockdown up-regulates HIF-1alpha mRNA levels, thereby providing a mechanism by which knockdown induces the observed effects. The results collectively provide evidence that IOP1 is a component of the protein network that regulates HIF-1alpha in mammalian cells.
Comparative efficacy of alemtuzumab and&amp;nbsp;established treatment in the management of&amp;nbsp;multiple sclerosis (2015)

Alemtuzumab is the newest disease-modifying therapy approved for the treatment of relapsing multiple sclerosis. Alemtuzumab is an anti-CD52 targeted antibody that causes lysis of T and B lymphocytes, monocytes, natural killer cells, macrophages, and dendritic cells. Following its administration, a prolonged T-cell lymphopenia results with emergence of a reconstituted immune system that differs in its composition from that pretreatment. In clinical trials, alemtuzumab has shown impressive efficacy with regard to clinical and radiological outcomes in relapsing multiple sclerosis, along with sustained long-term beneficial effects, and it is attractive for its once-yearly administration. Despite this, the occurrence of serious secondary autoimmune disorders, infections, and a potential risk of malignancy necessitates a careful evaluation of risks versus benefits for an individual patient prior to its use. The requirement of patient commitment to the intense mandatory monitoring program is also a factor to be considered when incorporating alemtuzumab into the treatment regimen.
Proteolytic Cleavage of Extracellular Secreted α-Synuclein via Matrix Metalloproteinases (2005)

Although alpha-synuclein is the main structural component of the insoluble filaments that form Lewy bodies in Parkinson disease (PD), its physiological function and exact role in neuronal death remain poorly understood. In the present study, we examined the possible functional relationship between alpha-synuclein and several forms of matrix metalloproteinases (MMPs) in the human dopaminergic neuroblastoma (SK-N-BE) cell line. When SK-N-BE cells were transiently transfected with alpha-synuclein, it was secreted into the extracellular culture media, concomitantly with a significant decrease in cell viability. Also the addition of nitric oxide-generating compounds to the cells caused the secreted alpha-synuclein to be digested, producing a small fragment whose size was similar to that of the fragment generated during the incubation of alpha-synuclein with various MMPs in vitro. Among several forms of MMPs, alpha-synuclein was cleaved most efficiently by MMP-3, and MALDI-TOF mass spectra analysis showed that alpha-synuclein is cleaved from its C-terminal end with at least four cleavage sites within the non-Abeta component of AD amyloid sequence. Compared with the intact form, the protein aggregation of alpha-synuclein was remarkably facilitated in the presence of the proteolytic fragments, and the fragment-induced aggregates showed more toxic effect on cell viability. Moreover, the levels of MMP-3 were also found to be increased significantly in the rat PD brain model produced by the cerebral injection of 6-hydroxydopamine into the substantia nigra. The present study suggests that the extracellularly secreted alpha-synuclein could be processed via the activation of MMP-3 in a selective manner.
One-Trip, Multizone Gravel-Packing Technique for Low-Pressure, Shallow Wells (1990)

Summary This paper describes a one-trip, multizone gravel-packing technique designed for use in short-zoned, shallow, low-pressure wells. The system, which allows several zones to be completed with a single gravel-pack assembly, has been adapted for use in both standard and thermal applications.
Covalent Immobilization of Proteins on Carbon Nanotubes Using the Cross-Linker 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide—a Critical Assessment (2008)

Functionalization of carbon nanotubes (CNTs) with proteins is often a key step in their biological applications, particularly in biosensing. One popular method has used the cross-linker 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) to covalently conjugate proteins onto carboxylated CNTs. In this article, we critically assess the evidence presented in these conjugation studies in the literature. As CNTs have a natural affinity for diverse proteins through hydrophobic and electrostatic interactions, it is therefore important to differentiate protein covalent attachment from adsorption in the immobilization mechanism. Unfortunately, many studies of conjugating proteins onto CNTs using EDC lacked essential controls to eliminate the possibility of protein adsorption. In studies where the attachment was claimed to be covalent, discrepancies existed and the observed immobilization appeared to be due to adsorption. So far, bond analysis has been lacking to ascertain the nature of the attachment using EDC. We recommend that this approach of covalent immobilization of proteins on CNTs be re-evaluated and treated with caution.
REST Enabled Wireless Sensor Networks for Seamless Integration with Web Applications (2011)

The use of Internet Protocol (IP) technology in Wireless Sensor Network (WSN) is a key prerequisite for the realization of the Internet of Things (IoT) vision. The IPv6 over Low power Wireless Personal Area Networks (6LoWPAN) standard enables the use of IPv6 in networks of constrained devices. 6LowPAN enables the use of Service Oriented Architectures (SOAs) in WSN. The Internet Engineering Task Force (IETF) has defined the Constrained Application Protocol (CoAP), a web transfer protocol which provides several Hypertext Transfer Protocol (HTTP) functionalities, re-designed for constrained embedded devices. CoAP allows WSN applications to be built on top of Representational State Transfer (REST) architectures. This considerably eases the IoT application development and facilitates the integration of constrained devices with the Web. This work describes the prototype design and development of a Web platform which integrates a REST/CoAP WSN with a REST/HTTP Web application and allows a user to visualize WSN measurements in the Web browser. Since the WSN Web integration relies on a non-transparent gateway/server, we also show how to provide transparent cross-protocol resource access by means of an HTTP-CoAP proxy. The paper describes the major building blocks, functionalities and the implementation approach.
Iodine<sup>125</sup> interstitial brachytherapy in the treatment of carcinoma of the lung (1992)

In a prospective study, 14 patients with primary non-oat cell lung carcinoma were treated with intraoperative Iodine125 (I125) implantation of the lung tumor via lateral thoracotomy or median sternotomy. Staging mediastinal node dissection was performed in each case. Patients were selected when wedge or segmental resections were not technically feasible, such that lobectomy or completion pneumonectomy would have been required or pulmonary function studies were poor. Doses ranged from 8,000 cGy at the periphery to 20,000 cGy at the center. With a minimum 12 month follow-up, mean and median survivals were 16.7 and 15.1 months, respectively. Local control was achieved in 10 of 14 patients (71%) with all local failures occurring in pathologic stage III patients. When separated according to tumor size, local control was obtained in six of seven tumors of less than 3 cm and four of five tumors of 3-5 cm. Both cases with masses greater than 5 cm failed locally. There was one operative mortality and two postoperative complications. All other patients were discharged within one week of surgery. There was no radiation pneumonitis. I125 lung brachytherapy is an excellent alternative treatment for T1 and T2 tumors when medical conditions preclude curative resection.
Absence of co-stimulation and not the intensity of TCR signaling is critical for the induction of T cell unresponsivenessin vivo (1999)

Understanding the mechanisms of T cell activation versus induction of unresponsiveness is of critical importance for the rational modulation of immune responses. Efficient T cell activation is critical for vaccination purposes, while the inhibition of T cell responses is potentially important for the ablation of autoimmune diseases. Modulation of co-stimulation and changing TCR-mediated signaling using altered peptide ligands (APL) have been shown to result in clonal T cell unresponsiveness. This study compares for the first time the efficiency of the two approaches for the induction of CD8+ T cell unresponsiveness in vivo for naive and memory T cells using TCR-transgenic mice. The results demonstrate that inhibition of CD28-mediated co-stimulation in the presence of a strong TCR-mediated signal most efficiently induces T cell unresponsiveness. In contrast, APL that are capable of weak TCR triggering fail to interfere with T cell responsiveness in vivo and are ignored by T cells. Thus, short-term blockage of CD28 during antigenic stimulation rather than the use of APL is the most promising way to actively down-modulate responsiveness of naive CD8+ T cells at least in the particular TCR-transgenic mouse model analyzed in this study.
Benefits and Issues on the Integration of GPS with a Wireless Communications Link (1997)

Abstract : The NAVSTAR Global Positioning System (GPS) provides worldwide positioning service to 2- Dimensional, 95 percentile accuracies of 100 meters for the Standard Positioning Service (SPS) for civilians and about 15 meters for the Precise Positioning Service (PPS) available to authorized users only. In the past, GPS has been combined with other instruments, such as Inertial Navigation Systems (INS) and Doppler radars for navigation, and precise frequency standards for timing, to produce more robust and accurate integrated systems. Within the past few years, significant advances have been made in GPS receiver and wireless communication (comm) technologies. Handheld devices for GPS and Personal Communication Service (PCS) have decreased in size and cost, yet increased in capability and battery life. This paper analyzes the benefits and discusses conceptual design issues associated with a tight integration of GPS with II wireless communication link for both military and civilian users. In addition to providing a means for data and voice communication, the comm link can provide GPS initialization data that could significantly improve GPS acquisition and navigation (nav) performance, especially in stressed (interference prone) environments.
Toxicity of staphylococcal enterotoxins potentiated by lipopolysaccharide: major histocompatibility complex class II molecule dependency and cytokine release (1993)

The biological effects of staphylococcal enterotoxins (SE), potentiated by bacterial lipopolysaccharide (LPS), were studied with mice. Control animals survived the maximum dose of either SE or LPS, while mice receiving both agents died. SEA was 43-fold more potent than SEB and 20-fold more potent than SEC1. The mechanism of toxicity was further examined with transgenic mice deficient in major histocompatibility complex class I or II expression. Class II-deficient mice were resistant to SEA or SEB. However, class I-deficient animals were less susceptible to SEA (30% lethality) than wild-type mice (93% lethality). In vitro stimulation of T cells from the three mouse phenotypes by SEA correlated well with toxicity. T cells from transgenic or wild-type mice were similarly responsive to SEA when presented by irradiated, wild-type mononuclear cells. These data confirmed that the toxicity of SE was mainly exerted through a mechanism dependent on the expression of major histocompatibility complex class II molecules. Toxicity was also linked to stimulated cytokine release. Levels in serum of tumor necrosis factor alpha, interleukin-6, and gamma interferon peaked 2 to 4 h after the potentiating dose of LPS but returned to normal within 10 h. Concentrations of interleukin-1 alpha were also maximal after 2 h but remained above the background for up to 22 h. Relative to the levels in mice given only SEA or LPS, the levels in serum of tumor necrosis factor alpha, interleukin-6, and gamma interferon increased 5-, 10-, and 15-fold, respectively, after injections of SEA plus LPS. There was only an additive effect of SEA and LPS on interleukin-1 alpha concentrations.
Intraoperative Recording of the Bulbocavernosus Reflex (1997)

We demonstrated that it is feasible, under certain anesthetic regimes, to intraoperatively monitor the BCR in both children and adults (24 d to 74 yr of age) who did not have significantly affected function in sacral nervous structures.
Interleaved cyclic redundancy check (CRC) code (2004)

In this paper, we investigate interleaved cyclic redundancy check (CRC) code. The interleaved CRC can be obtained by merging independent small message blocks into one large block (merged interleaving) or by dividing the original message block into independent small sub blocks (divided interleaving) and then by alternatively dividing the resulting message block(s) using same generator polynomial. The interleaved CRC increases both the detection span and the detectable error patterns. New applications of the interleaved CRC as the error detection scheme or stopping criteria in interleaved error correction coding and iterative decoding schemes are proposed. Since each individual codeword of interleaved CRC code is mutually independent, it is possible to generate CRC in interleaved manner and to check CRC in parallel manner.