gebhart/patrepeval huggingface dataset:
Snapshot of a DNA Polymerase while Incorporating Two Consecutive C5-Modified Nucleotides (2013)

Functional nucleotides are important in many cutting-edge biomolecular techniques. Often several modified nucleotides have to be incorporated consecutively. This structural study of KlenTaq DNA polymerase, a truncated form of Thermus aquaticus DNA polymerase, gives first insights how multiple modifications are processed by a DNA polymerase and, therefore, contribute to the understanding of these enzymes in their interplay with artificial substrates.
High Penetration Alerting Signal Design for Mobile Satellite Communications Systems (2014)

This paper presents a novel practical transmission signal design that enables a mobile satellite network to alert user terminals operating in a heavily power attenuated environment, such as inside buildings or in shadowed areas. In particular, we describe in detail a waveform design employing an orthogonal sequence modulated with p/2-BPSK and encoded with Reed-Solomon codes. The transmit waveform performance is characterized in terms of its Power Spectral Density (PSD) and Peak-to-Average Power Ratio (PAPR). The receiver performance is evaluated in terms of the symbol error rate and message error rate under the AWGN and Rician channels. Here we have examined the performance of conventional sequence detection as well as computationally efficient joint sequence detection with simple erasure decoding.
Synthesis of transition-metal carbonyl derivatives of magnesium (1972)

Novel transition-metal carbonyl derivatives of magnesium can be readily prepared by the reductive cleavage of numerous dimeric transition metal carbonyl complexes with magnesium amalgam in the presence of a Lewis base.
Method of forming single crystals of beta silicon carbide (1982)

A method of growing single crystals of beta SiC from solution using molten lithium as a solvent for polycrystalline SiC feed material. Reasonable growth rates are accomplished at temperatures in the range of about 1330/sup 0/C or about 1500/sup 0/C.
Adaptive digital equalization in the presence of chromatic dispersion, PMD, and phase noise in coherent fiber optic systems (2005)

Chromatic dispersion (CD) and polarization mode dispersion (PMD) severely limit the performance of optical transmission systems operating at and above 10 Gb/s. Electrical equalization techniques have been proposed to compensate dispersion in both coherent and intensity modulation/direct-detection (IM/DD) systems. We investigate the combined adaptive digital equalization of all-order PMD, CD, and laser phase noise in high-speed coherent optical transmission systems. Simultaneous equalization of these impairments has not been reported previously and is particularly important in modulation systems that exploit polarization to increase modulation efficiency. We propose a novel 4-dimensional equalizer structure for joint polarization modulation and M-ary differential phase shift keying (JPMDPSK) systems. The specific example considered is 40 Gb/s transmission with a 10 GBaud symbol rate, using DQPSK modulation on each axis of polarization. Our results show that the new four-dimensional equalizer can compensate channel dispersion of up to 1000 km of standard single-mode fiber, with less than 3 dB penalty in signal-to-noise ratio (SNR). This is a dramatic improvement over 40 Gb/s IM/DD systems. The feasibility of the very large scale integration (VLSI) of coherent receivers in current technology is also discussed.
Transformerless Partial Power Converter for Electric Vehicle Fast Charging Stations (2022)

This paper proposes a new transformerless partial power converter for the DC-DC stage of a Electric Vehicle (EV) fast charging station. Partial power converters (PPC) are very attractive for this purpose thanks to their high efficiency. Based on this concept, it is proposed a new transformerless PPC using an impedance network instead of the transformer used in classical PPC. The proposed solution allows similar efficiency compared to traditional PPC, but improved power density since no transformer is required. Simulation results show the effectiveness of the proposed converter in both cases of 400V and 800V DC-DC fast charging stations. Efficiency of the proposed converter has been evaluated, and results show high efficiency over a wide range of operation, with a maximum of 98%. It is conclude that the proposed transfromerless partial power converter is suitable for EV fast charging application.
Intraoperative monitoring of neuromuscular function with soft, skin-mounted wireless devices (2018)

Peripheral nerves are often vulnerable to damage during surgeries, with risks of significant pain, loss of motor function, and reduced quality of life for the patient. Intraoperative methods for monitoring nerve activity are effective, but conventional systems rely on bench-top data acquisition tools with hard-wired connections to electrode leads that must be placed percutaneously inside target muscle tissue. These approaches are time and skill intensive and therefore costly to an extent that precludes their use in many important scenarios. Here we report a soft, skin-mounted monitoring system that measures, stores, and wirelessly transmits electrical signals and physical movement associated with muscle activity, continuously and in real-time during neurosurgical procedures on the peripheral, spinal, and cranial nerves. Surface electromyography and motion measurements can be performed non-invasively in this manner on nearly any muscle location, thereby offering many important advantages in usability and cost, with signal fidelity that matches that of the current clinical standard of care for decision making. These results could significantly improve accessibility of intraoperative monitoring across a broad range of neurosurgical procedures, with associated enhancements in patient outcomes.
Inhibitors of Src Homology-2 Domain Containing Protein Tyrosine Phosphatase-2 (Shp2) Based on Oxindole Scaffolds (2008)

Screening of the NCI diversity set of compounds has led to the identification of 5 (NSC-117199), which inhibits the protein tyrosine phosphatase (PTP) Shp2 with an IC50 of 47 microM. A focused library incorporating an isatin scaffold was designed and evaluated for inhibition of Shp2 and Shp1 PTP activities. Several compounds were identified that selectively inhibit Shp2 over Shp1 and PTP1B with low to submicromolar activity. A model for the binding of the active compounds is proposed.
Data Vaporizer - Towards a Configurable Enterprise Data Storage Framework in Public Cloud (2015)

We propose a novel cloud-based data storage solution framework named Data Vaporizer (DV). The proposed framework provides many unique features such as storing data over multiple clouds or storage zones, resistance against organized vendor attacks, maintaining data integrity and confidentiality through client-side processing, fault-tolerance against failure of one or more cloud storage locations and avoids vendor lock-in of data. Data Vaporizer is highly configurable to meet various client data encryption requirements, compliance to industry standards and fault tolerance constraints depending on the nature and sensitivity of the data. To enhance the level of security and reliability, especially to protect data against malicious attacks and secure key management in cloud, DV uses advanced techniques of secret sharing of the keys. The architecture and optimality of data placement and efficient key management algorithm of DV ensure that the solution is highly scalable. The data foot print and subsequent cost incurred by our storage solution is minimal, considering the benefits provided. The initial response for the adoption of DV in actual client scenarios is promising.
A new system of environmental noise identification and subjective evaluation (1999)

A new system of environmental noise identification including aircraft noise or traffic noise and its subjective evaluation based on the model of the human auditory-brain system [Y. Ando, Architectural Acoustics—Blending sound sources, sound fields, and listeners (AIP Press/ Springer-Verlag, New York, 1998)] is proposed. In order to discuss the subjective effects of environmental noise, following factors are calculated by use of the autocorrelation function (ACF) and interaural crosscorrelation function (IACF) of binaural signals; From the ACF analysis: (1) energy represented at the origin of the delay, Φ(0); (2) effective duration of the envelope of the normalized ACF, τe; (3) the delay time of the first peak, τ1; and (4) its amplitude, φ1 are extracted. From the IACF analysis: (5) IACC; (6) interaural delay time at which the IACC is defined, τIACC; and (7) width of the IACF at the τIACC, WIACC are extracted. For example, loudness is related with Φ(0) and τe, and directional information may be obtained from τIACC. Especially, a noise source may be identified by the all ACF factors are timbre. [Work was partially supported by the Research and Development Applying Advanced Computational Science and Technology, Japan, Science and Technology Corporation (ACT-JST), 1999.]
TCO-less 3D dye-sensitized solar cells consisting of charge separation sheet-Tandem, hybrid, cylinder and fiber cells- (2010)

Three dimensional transparent conductive oxide-less dye-sensitized solar cells (3D-TCO-less DSCs) consisting of a flexible porous titania sheet are reported. The flexible titania sheet is composed of a dye stained porous titania layer and a mesh sheet acting as the backbone. Flexible TCO-less DSCs, tandem DSCs, TCO-less cylinder DSCs and TCO-less cubic DSCs are fabricated and their fundamental photovoltaic performances are reported.
Real time pattern changing in atomic beam holography using phase shift by Stark effect (2000)

An electrically controlled phase hologram has been used to change the reconstructed atomic image on a solid surface. The second order Stark effect of the laser-cooled metastable Ne atom was used to induce the phase shift during the atoms passage through the hologram. By controlling the applied electric voltage, the reconstructed pattern was switched according to the induced phase shift.
Abstract 600: Novel Assays to Determine in vivo Platelet Activation (2015)

In vivo platelet activation is associated with several pathologic entities, including acute coronary syndrome, essential thrombocythemia, anti-phospholipid antibody syndrome, diabetes and metabolic syndrome. The need for more robust biomarkers with which to assess platelet activation in vivo in human diseases is well recognized. Our lab has developed two novel assays to study in vivo platelet activation and rate of turnover. During platelet activation, malondialdehyde (MDA) is produced by the thromboxane synthase in amounts equimolar to thromboxane A2 and also non-enzymatically by lipid peroxidation resulting from the oxidative processes that accompany activation. MDA is a reactive dicarbonyl that reacts with amines, notably lysines on proteins, yielding covalent modifications of the proteins that then accumulate over the lifetime of the platelet. We developed an LC/MS/MS method for quantification of the most stable of three MDA adducts, the dilysyl-MDA crosslink, employing a [13C12] labeled internal standard. We found that activation of platelets with arachidonic acid leads to an increase in the levels of dilysyl-MDA crosslinks in platelets, which is inhibited by the thromboxane synthase inhibitor, ozagrel, by the cyclooxygenase inhibitor, aspirin, and by scavengers of reactive carbonyls, 3- methoxysalicylamine and Salicylamine. High platelet turnover has been associated with increased risk for thrombosis and failure of antiplatelet agents. We propose a novel approach to studying platelet turnover by labeling platelets in vivo by oral administration of aspirin containing a deuterium labeled acetyl group (d3-aspirin). We can measure the clearance of d3-labeled platelets by using LC/MS/MS to measure the tryptic peptide (SLK) of COX-1 labeled with d3. This approach avoids exposure to radioactivity and the artifact resulting from manipulation of platelets labeled ex vivo. The results of this study provide two novel assays with the potential to serve as markers of in vivo platelet activation and turnover, which may be useful in predicting thrombotic risk and efficacy of antiplatelet therapy in patients with medical conditions associated with platelet hyperactivity and high rate of platelet turnover.
Phase-locking in distributed arrays of Josephson oscillators (1987)

Arrays of Josephson junctions can be used as voltage tunable oscillators at millimeter and submillimeter wavelengths. However proper circuit design is required to achieve the phase-locking of the junctions required for coherent radiation. The design of arrays of Josephson junctions distributed over many wavelengths is discussed and data are presented on the strength of the phase-locking in these systems. With proper design and optimization substantial power at frequencies above 100 GHz is predicted.
Synthesis and Antitumor Activity of Various 6-Demethylmitomycins and 6-Demethyl-6-halomitomycins (1995)

A series of 6-demethylmitomycins and 6-demethyl-6-halomitomycins having various mitomycin skeletons were synthesized, taking into account the electronic effect toward the quinone moiety and the partition coefficients. Treatment of enones 15 and 16 with selenenamide or N-halosuccinimide-Et2NH afforded the 6-demethyl intermediates 17, 18, and 21-24 via the tandem Michael addition/retro-Mannich reaction sequence. Subsequent conversions into the mitomycin skeletons resulted in the formation of the desired derivatives 7a-c, 8a-c, 11a-c, and 12a,b. These mitomycin derivatives including 3a-c and 4a-c were evaluated for their anticellular activity against HeLa S3 cells and antitumor activity against Sarcoma 180 in mice. The anticellular activity of 1 and 3a-c depends on the substituent at the C-6 position and the order of increasing activity is H < CH3 < Br < Cl. A similar tendency was observed in their antitumor potency (ED50). The activities of 9 and 11a-c also follow a pattern similar to that of 1 and 3a-c. Compounds 4b,c, 8b,c, and 12b having both a halogen at the C-6 position and a methoxy group at the C-7 position did not show the activities because of the instability of the compounds. Interestingly, a correlation between the anticellular activity (IC50) and the partition coefficients (log kappa') determined by HPLC was observed within the compounds studied except the unstable compounds, while their antitumor activity (ED50 or T/C) did not correlate with the quinone reduction potential (E1/2). These results would indicate the importance of the C-6 substituents and the mitomycin skeletons for exhibiting both anticellular and antitumor activities.
Imaging the total wavefields by reflectivity estimation using amplitude-normalized wavefield decomposition: Field data example (2017)

To combine imaging information of up- and downgoing wavefields using primaries and multiples, we have developed an imaging framework based on the subsurface impulse response. The latter is expressed at every depth level by a Fredholm integral equation defined in terms of the amplitude-normalized upgoing pressure and downgoing vertical velocity wavefields. The subsurface impulse response can be obtained by inverting the matrix form of the integral equation. By performing a multidimensional deconvolution (MDD) of the upgoing components by the downgoing components, this procedure gives the reflectivity matrix. By assuming locally reacting media or lateral shift invariance, we can describe how the MDD can reduce to simpler deconvolution imaging conditions. Based on an example acquired with dual-sensor towed streamers and simultaneous sources, we have developed a real data application of imaging the total up- and downgoing wavefields by reflectivity inversion. The total upgoing wavefield used in the imaging scheme is composed of the scattered energy from primaries and multiples. The primary reflected wavefield is generated by a direct downgoing source wavefield, which is mostly passing the acquisition surface at offsets smaller than the nearest data channel. Hence, the most relevant part of the direct wavefield is not measured in the studied example. From near-field pressure measurements, we predict the missing direct arrivals needed to image the primary reflected wavefield; we then synthesize the total downgoing wavefield by adding the downgoing scattered energy. By downward extrapolating the total up- and downgoing wavefields, a structural image is obtained by extracting the zero-spatial and temporal lags of the reflectivity matrix (computed by MDD of the decomposed wavefields). The obtained image is compared with the results computed from deconvolution imaging conditions. Furthermore, calculating the reflectivity matrix naturally allows for extracting the angle-dependent information of the subsurface.
P95 Assessment of F/HN-pseudotyped Lentivirus as a Clinically Relevant Vector For Lung Gene Therapy (2012)

<h3>Rational</h3> Our ongoing efforts to improve pulmonary gene transfer thereby enabling gene therapy for the treatment of lung diseases such as cystic fibrosis (CF) has led to the development of a lentiviral vector (SIV) pseudotyped with the Sendai virus envelope proteins F and HN. <h3>Objectives</h3> Here, we begin to place this vector onto a translational pathway to the clinic, by addressing some key milestones that have to be achieved. <h3>Main results</h3> These include: (1) a single dose produces lung expression for the life-time of the mouse (approximately 2 years), (2) only brief contact time is needed to achieve transduction, (3) repeated daily administration leads to a dose-related increase in gene expression, (4) repeated monthly administration to mouse lower airways is feasible without loss of gene expression, (5) there is no evidence of chronic toxicity during a 2 year study period, (6) F/HN-SIV transduction generates persistent gene expression in human differentiated airway cultures, and human lung slices and transduces freshly obtained primary human airway epithelial cells. <h3>Conclusions</h3> The data support F/HN-pseudotyped SIV as a promising vector for pulmonary gene therapy for a number of diseases including CF and we are now undertaking the necessary refinements to progress this vector into clinical trials.
An Architecture for IP/LDP Fast Reroute Using Maximally Redundant Trees (MRT-FRR) (2016)

This document defines the architecture for IP and LDP Fast Reroute
using Maximally Redundant Trees (MRT-FRR). MRT-FRR is a technology
that gives link-protection and node-protection with 100% coverage in
any network topology that is still connected after the failure.
Asymmetric trimethine 3H-indocyanine dyes: efficient synthesis and protein labeling (2010)

We present an efficient method to synthesize three new asymmetric trimethine cyanine dyes containing only one carboxylic acid group for bioconjugation. Two of them have better protein labeling performance than other conventional cyanine dyes due to their particular structure design.
[Combination of anti-EGFR and anti-HER2 antibodies: hope in pancreatic cancer treatment]. (2007)

Unresectable pancreatic cancer is still an extremely dismal prognosis. The conventional therapy using chemotherapy has no real effect on survival and new treatments are needed. EGFR and HER2 have been reported to be implicated and upregulated in pancreatic cancer tumorigenesis. The use of monoclonal antibodies (mAb) targeting these two receptors seems a relevant strategy for a new therapy. In a pre-clinical study, we demonstrated the therapeutic effect of the combination of two humanized Ab used in clinic, trastuzumab (Ab anti-HER2) and matuzumab (Ab anti-EGFR) in vivo in different carcinoma types. This Ab combination induced an important tumoral growth delay associated with some complete responses in two pancreatic carcinoma models expressing low HER2 level and in an ovarian model. Following all these results, a clinical trial is planned in pancreatic cancer.
The Synthesis, Photophysical and Photobiological Properties and <i>in vitro</i> Structure‐Activity Relationships of a Set of Silicon Phthalocyanine PDT Photosensitizers (1997)

Four silicon phthalocyanine photosensitizers have been prepared and studied in an effort to learn more about the structural features that a silicon phthalocyanine must have in order to be a good photodynamic therapy (PDT) photosensitizer. The compounds that have been studied are the known phthalocyanines HOSiPcOSi(CH3)2-(CH2)3N(CH3)2, Pc 4; and SiPc[OSi(CH3)2(CH2)3N(CH3)2]2, Pc 12; and the new photosensitizers HOSiPcOSi(CH3)2- (CH2)3N(CH2CH3)(CH2)2N(CH3)2, Pc 10; and SiPc[OSi (CH3)2(CH2)3N(CH2CH3)(CH2)2N(CH3)2]2, Pc 18. The triplet lifetimes of the four photosensitizers, their singlet oxygen quantum yields, their ability to photoenhance the generation of lipid peroxidation products in human erythrocyte ghosts, their ability to partition into V79 cells and their ability to photokill V79 and L5178Y-R cells have been determined. It is concluded that the presence of a small axial ligand (e.g. an OH ligand) is not necessary for efficient photosensitization, the presence of two aminosiloxy ligands generally provides at least as good photosensitization as one such ligand, and the presence of an elongated diaminosiloxy axial ligand rather than a short aminosiloxy ligand is less desirable. Further, it is concluded that the presence of structural features leading to improvement in the association between the photosensitizers and important cellular targets are more useful than those leading to improvements in their already acceptable photophysical and photochemical properties.
Three-dimensional Reconstruction of Functional Fascicular Groups inside a Segment of Common Peroneal Nerve (2009)

The virtual human plan has been the hot point of recent research. The objective of this study is to explore the possibility of three-dimensional (3D) reconstruction of functional fascicular groups inside short segmental peripheral nerve. A 5 cm length of common peroneal nerve was horizontally sliced at 0.25 mm intervals, and each section was stained with acetycholinesterase histochemical staining. The 2D panorama images were acquired by high-resolution digital camera under 100 x microscope and mosaic software; different functional fascicular groups were distinguished and marked. The topographic database was then matched using image processing software, through the 3D reconstruction achieved using 3D reconstruction software (Amira 3.1). The reconstructed 3D images could be rotated or zoomed in any direction and the intercross and recombination processes of nerve bundles could be observed. Based on the serial histological sections and computer technology, the 3D microstructure of short segmental peripheral nerve functional fascicular groups was reconstructed. These results provide the possibility of 3D reconstruction of long segmental peripheral nerve functional fascicular groups.
Extraction and Evaluation of Fibers from Sugar Cane (1992)

Sugar cane fiber bundles were extracted from the separated rind of cane stalks using alkaline treatments. The amount of lignin removed depended on alkaline concentration and time and pressure of treatment; agitation and vigorous boiling also affected the lignin removal. A severity factor R was calculated to compare the delignification conditions. Alkali concentration significantly affected the mechanical properties of the fiber bundles. Tenacity, toughness, and linear density were higher for the fibers extracted at the lower concentration, as were bending rigidity and hysteresis.
Fast and distributed dynamic sensing of strain using Sweep-Free Brillouin Optical Time-Domain Analysis (SF-BOTDA) (2011)

A frequency-sweep-free method for distributed Brillouin sensing is used to reconstruct the Brillouin gain spectrum of optical fibers at high speed. We experimentally demonstrate distributed strain measurements induced by 140Hz vibrations, with a spatial resolution of 5m.