gebhart/patrepeval huggingface dataset:
Perspective: next generation isotope-aided methods for protein NMR spectroscopy (2018)

In this perspective, we describe our efforts to innovate the current isotope-aided NMR methodology to investigate biologically important large proteins and protein complexes, for which only limited structural information could be obtained by conventional NMR approaches. At the present time, it is widely believed that only backbone amide and methyl signals are amenable for investigating such difficult targets. Therefore, our primary mission is to disseminate our novel knowledge within the biological NMR community; specifically, that any type of NMR signals other than methyl and amide groups can be obtained, even for quite large proteins, by optimizing the transverse relaxation properties by isotope labeling methods. The idea of "TROSY by isotope labeling" has been cultivated through our endeavors aiming to improve the original stereo-array isotope labeling (SAIL) method (Kainosho et al., Nature 440:52-57, 2006). The SAIL TROSY methods subsequently culminated in the successful observations of individual NMR signals for the side-chain aliphatic and aromatic <sup>13</sup>CH groups in large proteins, as exemplified by the 82 kDa single domain protein, malate synthase G. Meanwhile, the expected role of NMR spectroscopy in the emerging integrative structural biology has been rapidly shifting, from structure determination to the acquisition of biologically relevant structural dynamics, which are poorly accessible by X-ray crystallography or cryo-electron microscopy. Therefore, the newly accessible NMR probes, in addition to the methyl and amide signals, will open up a new horizon for investigating difficult protein targets, such as membrane proteins and supramolecular complexes, by NMR spectroscopy. We briefly introduce our latest results, showing that the protons attached to <sup>12</sup>C-atoms give profoundly narrow <sup>1</sup>H-NMR signals even for large proteins, by isolating them from the other protons using the selective deuteration. The direct <sup>1</sup>H observation methods exhibit the highest sensitivities, as compared to heteronuclear multidimensional spectroscopy, in which the <sup>1</sup>H-signals are acquired via the spin-coupled <sup>13</sup>C- and/or <sup>15</sup>N-nuclei. Although the selective deuteration method was launched a half century ago, as the first milestone in the following prosperous history of isotope-aided NMR methods, our results strongly imply that the low-dimensional <sup>1</sup>H-direct observation NMR methods should be revitalized in the coming era, featuring ultrahigh-field spectrometers beyond 1 GHz.
Synthesis of spiro[isobenzofuran-1(3H),4'-piperidines] as potential central nervous system agents. 1 (1976)

Synthesis of 1'-methyl-3-phenylspiro[isobenzofuran-1(3H),4'-piperidine] (7a, HP 365) and the demethyl analogue 9a (HP 505) was prompted by recognition of an aminoalkyl(aryl)isobenzofuran moiety common to the antidepressants talopram (Lu 3-010) and trans-10,11-dihydro-5,10-epoxy-5-[3-(methylamino)propyl]-5H-dibenzo[a,d]cyclohepten-11-ol (MK-940). Convenient laboratory synthesis of 7a was provided by lithiation of 2-bromobenzhydryl methyl ether, followed by addition of 1-methyl-4-piperidone and acid-catalyzed cyclization. N-Dealkylation by standard methods afforded 9a. Synthesis of analogues was stimulated by discovery of marked inhibition of tetrabenazine-induced ptosis for lead compounds 7a and 9a. Optimal antitetrabenazine activity is associated with the 3-phenylspiro-[isobenzofuran-1(3H),4'-piperidine] moiety where nitrogen is basic. Modification of this moiety by introduction of large nitrogen substituents or a C-3 substituent greater than H significantly reduced antitetrabenazine activity. A series of analogues with aromatic substituents was investigated; however, few of these compounds were significantly more active than 7a and 9a. Compound 9a was selected for additional studies.
Electric Field Imaging Project (2016)

NDE historically has focused technology development in propagating wave phenomena with little attention to the field of electrostatics and emanating electric fields. This work is intended to bring electrostatic imaging to the forefront of new inspection technologies, and new technologies in general. The specific goals are to specify the electric potential and electric field including the electric field spatial components emanating from, to, and throughout volumes containing objects or in free space.
Three‐dimensional motion estimation of head in model‐based coding of moving facial images (1992)

Abstract A model‐based image coding system basically consists of an “analysis” process at the transmitting side and a “synthesis” process at the receiving side. Images are coded by transmitting only information about changes in shape of a three‐dimensional (3‐D) model of an object prepared at both the transmitting and receiving sides. The essential elements in the “analysis” process are recognition of the object from moving images, estimation of the object motion, and detection of changes in its shape. This paper proposes a method of estimating the motion in 3‐D space of the head in model‐based image coding of moving facial images and confirms the validity of the method by computer simulations. First, the basic concept of model‐based coding is described. A discussion about the treatment of motion information in moving images is performed from the viewpoints of 3‐D motion of the object and shape changes of object components, and the outline of the basic idea to detect the motion and shape changes is presented. Then the 3‐D motion estimation method using the 3‐D shape model of the object and motion vectors in 2‐D space is described in detail. Computer simulations are performed on moving facial images, and the results show that the motion of the head in the input moving images is well reproduced as the motion of a 3‐D shape model. Finally, the relation between precision of depth coordinates and estimation results is considered, and it is demonstrated that the proposed method is effective for estimating 3‐D motion parameters in model‐based coding of moving facial images.
A preoperative diagnostic test that distinguishes benign from malignant thyroid carcinoma based on gene expression (2004)

Made available in DSpace on 2016-01-24T12:37:04Z (GMT). No. of bitstreams: 0 Previous issue date: 2004-04-01. Added 1 bitstream(s) on 2016-01-31T13:33:11Z : No. of bitstreams: 1 WOS000221365100023.pdf: 2529523 bytes, checksum: c9f93892aaabf2b3fe401e40ac44d484 (MD5)
Light Guidance Based on Topological Confinement Yielding Fiber Mode Counts Exceeding 50 (2021)

We exploit a novel waveguiding regime that enables low-loss guidance for high angular momentum modes while avoiding coupling to other modes, yielding a 25-m long fiber propagating > 52 modes with purity > 19 dB.
Estimating the size of the transitive closure in linear time (2002)

Computing transitive closure and reachability information in directed graphs is a fundamental graph problem with many applications. The fastest known algorithms run in O(sm) time for computing all nodes reachable from each of 1/spl les/s/spl les/n source nodes, or, using fast matrix multiplication, in O(n/sup 2.38/) time for computing the transitive closure, where n is the number of nodes and m the number of edges in the graph. In query optimization in database applications it is often the case that only estimates on the size of the transitive closure and on the number of nodes reachable from certain nodes are needed. We present an O(m) time randomized algorithm that estimates the number of nodes reachable from every node and the size of the transitive closure. We also obtain a O/spl tilde/(m) time algorithm for estimating sizes of neighborhoods in directed graphs with nonnegative weights, avoiding the O/spl tilde/(mn) time bound of explicitly computing these neighborhoods. Our size-estimation algorithms are much faster than performing the actual computations and improve significantly over previous estimation methods.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Box-Beam Burster Energy-Absorbing Terminal Bridge Pier Protection System (2003)

A new box-beam burster energy-absorbing terminal (BEAT) bridge pier (BEAT-BP) protection system was successfully crash tested according to the safety performance criteria presented in NCHRP Report 350. The system comprises two BEAT crash cushions and a frame that envelops the bridge piers. Because of the close proximity to the piers, the system has a footprint significantly smaller than those of the other available options. Three crash tests were considered necessary to evaluate the BEAT-BP protection system and were conducted successfully: a pickup truck critical impact point (CIP) transition test at a bridge pier (Test Designation 3-21), a pickup truck CIP test at the connection between the crash cushion and the tubular frame structure (Test Designation 3-38), and a pickup truck end-on test for the crash cushion (Test Designation 3-31). A total of four crash tests were conducted, including one failed test (Test BP-2). The BEAT-BP protection system performed satisfactorily in all three required crash tests, meeting all evaluation criteria set forth in the guidelines of NCHRP Report 350.
Reconstruction algorithm for tilted helical volumetric CT (2005)

With the development of volumetric computed tomography (VCT), technical challenges in image reconstruction increases significantly. Majorities of the proposed algorithms are for helical acquisition in which the gantry is perpendicular to the rotation axis. In many clinical applications, however, the gantry needs to be tilted to avoid direct X-ray exposure to the sensitive organs. If appropriate correction is not rendered, degraded image quality will result. There are two effects when the CT gantry is tilted with respect to the z-axis. The first is that the detector rotation axis and the reconstruction axis is no longer the same. The second effect is that in helical acquisition, the patient table does not travel perpendicular to the detector center plane. These two effects have been studied in the past. Complication arises, however, when the cone beam geometry is first rebinned to a set of parallel samples prior to the filtered backprojection. Under such conditions, the source locations for each projection map to a segment of the source-helix instead of a single point. In this paper, we derive a close-form reconstruction algorithm. We separate the entire process into two components. The first component assumes the detector center plane coincides with the reconstruction plane. The second component deals with the two separate planes. The key step in the reconstruction is that for each pixel, the original coordinate is first mapped to a new coordinate before the backprojection. For validation, we conducted extensive phantom and clinical experiments. Results have shown that the proposed algorithm can successfully remove image artifacts. Since the correction is implemented as part of the backprojection process, little impact on spatial resolution is observed.
Interactions of Staphylokinase with Human Platelets (1995)

The interactions of recombinant staphylokinase (SakSTAR) with human platelets were investigated in a buffer milieu, in a human plasma milieu in vitro, and in plasma from patients with acute myocardial infarction (AMI) treated with SakSTAR. In a buffer milieu, the activation rate of plasminogen by SakSTAR or streptokinase (SK) was not significantly altered by addition of platelets. Specific binding of SakSTAR or SK to either resting or thrombin-activated platelets was very low. ADP-induced or collagen-induced platelet aggregation in platelet-rich plasma (PRP) was 94 +/- 2.7% or 101 +/- 1.7% of control in the presence of 0.1 to 20 microM SakSTAR, with corresponding values of 95 +/- 2.8% or 90 +/- 4.6% of control in the presence of 0.1 to 4 microM SK. No effects were observed on platelet disaggregation. ATP secretion following collagen-induced platelet aggregation was 4.3 +/- 0.26 microM for SakSTAR (at concentrations of 0.1 to 20 microM) and 4.4 +/- 0.35 microM for SK (at concentrations of 0.1 to 4 microM), as compared to 3.4 +/- 0.70 microM in the absence of plasminogen activator. Fifty % lysis in 2 h (C50) of 60 microliters 125I-fibrin labeled platelet-poor plasma (PPP) clots prepared from normal plasma or from plasma of patients with Glanzmann thrombasthenia and immersed in 0.5 ml normal plasma, was obtained with 12 or 16 nM SakSTAR and with 49 or 40 nM SK, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Self-Monitoring Navigation Agent via Auxiliary Progress Estimation (2019)

The Vision-and-Language Navigation (VLN) task entails an agent following navigational instruction in photo-realistic unknown environments. This challenging task demands that the agent be aware of which instruction was completed, which instruction is needed next, which way to go, and its navigation progress towards the goal. In this paper, we introduce a self-monitoring agent with two complementary components: (1) visual-textual co-grounding module to locate the instruction completed in the past, the instruction required for the next action, and the next moving direction from surrounding images and (2) progress monitor to ensure the grounded instruction correctly reflects the navigation progress. We test our self-monitoring agent on a standard benchmark and analyze our proposed approach through a series of ablation studies that elucidate the contributions of the primary components. Using our proposed method, we set the new state of the art by a significant margin (8% absolute increase in success rate on the unseen test set). Code is available at this https URL .
A Metric-First Scheme for MIMO Signal Decoding with Branch Length Threshold (2008)

In this paper, we propose a near maximum likelihood (ML) scheme for the decoding of multiple input multiple output systems. Based on the metric-first search method and by employing Schnorr-Euchner enumeration and branch length thresholds, the proposed scheme provides a higher efficiency than other conventional near ML decoding schemes. From simulation results, it is confirmed that the proposed scheme has lower computational complexity than other near ML decoders while maintaining the bit error rate very close to the ML performance. The proposed scheme in addition possesses the capability of allowing flexible tradeoffs between the computational complexity and BER performance.
On the Design of a Processor Working Over Encrypted Data (2018)

Gentry's breakthrough of Fully Homomorphic Encryption (FHE) in 2009 revolutionized the field of secure computation. Since then, most applications of homomorphic encryption have been oriented towards offloading computations to the cloud in a secure fashion. Indeed, the user usually does not have full confidence in the cloud provider and wants to keep its data secrecy. A similar situation appears in most embedded systems, where information leakages through hardware or software side-channel attacks might compromise data confidentiality. In this work, we attempt to leverage Homomorphic Encryption in a different threat model, adapted to CPS (Cyber-Physical Systems) use cases. The main challenge is that, even today's most promising FHE schemes remain orders of magnitude too big to fit in a constrained system. To address this issue, we show how a trade-off can be achieved by securing a noise reduction module against side-channel leakages. This approach is described and evaluated on FPGA using the BGV scheme, a very efficient homomorphic scheme based on Ring-LWE encryption. We conclude that such homomorphic encryption can fit in an embedded system, while offering reasonable performances with respect to the security provided.
Study of capillary transit time distribution in coherent hemodynamics spectroscopy (2014)

A recently proposed analytical hemodynamic model 1 [S. Fantini, NeuroImage85, 202–221 (2014)] is able to predict the changes of oxy, deoxy, and total hemoglobin concentrations (model outputs) given arbitrary changes in blood flow, blood volume, and rate of oxygen consumption (model inputs). One assumption of this model is that the capillary compartment is characterized by a single blood transit time. In this work, we have extended the original model by considering a distribution of capillary transit times and we have compared the outputs of both models (original and extended) for the case of sinusoidal input signals at different frequencies, which realizes the new technique of coherent hemodynamics spectroscopy (CHS). For the calculations with the original model, we have used the mean value of the distribution of capillary transit times considered in the extended model. We have found that, for distributions of capillary transit times having mean values around 1 s and a standard deviation less than about 45% of the mean value, the original and extended models yield the same CHS spectra (i.e., model outputs versus frequency of oscillation) within typical experimental errors. For wider capillary transit time distributions, the two models yield different CHS spectra. By assuming that Poiseuille's law is valid in the capillary compartment, we have related the distribution of capillary transit times to the distributions of capillary lengths and capillary speed of blood flow to calculate the average capillary and venous saturations. We have found that, for standard deviations of the capillary transit time distribution that are less than about 80% of the mean value, the average capillary saturation is always larger than the venous saturation. By contrast, the average capillary saturation may be less than the venous saturation for wider distributions of the capillary transit times.
Vinblastine 20′ Amides: Synthetic Analogues That Maintain or Improve Potency and Simultaneously Overcome Pgp-Derived Efflux and Resistance (2017)

A series of 180 vinblastine 20′ amides were prepared in three steps from commercially available starting materials, systematically exploring a typically inaccessible site in the molecule enlisting a powerful functionalization strategy. Clear structure–activity relationships and a structural model were developed in the studies which provided many such 20′ amides that exhibit substantial and some even remarkable enhancements in potency, many that exhibit further improvements in activity against a Pgp overexpressing resistant cancer cell line, and an important subset of the vinblastine analogues that display little or no differential in activity against a matched pair of vinblastine sensitive and resistant (Pgp overexpressing) cell lines. The improvements in potency directly correlated with target tubulin binding affinity, and the reduction in differential functional activity against the sensitive and Pgp overexpressing resistant cell lines was found to correlate directly with an impact on Pgp-derived efflux.
An Autonomous Resource Block Assignment Scheme for OFDMA-Based Relay-Assisted Cellular Networks (2011)

Terminal relaying offers an effective means for improving the performance of OFDMA-based wireless networks. However, \revrr{with the increase in the number of relaying terminals (RTs), their coordination becomes a cumbersome task.} To address this drawback, in this paper an autonomous scheme is proposed whereby the RTs assign resource blocks (RBs) to incoming wireless terminals (WTs) in a way that minimizes the number of hit occurrences at which the same RB is assigned to multiple WTs. The proposed scheme uses cyclic group generators to determine the sequence of RBs to be assigned by each RT. This scheme is particularly beneficial in terminal relaying systems in which the distribution of the WTs is nonuniform and the channel quality indicators are not available. Simulation results show that the proposed scheme performs significantly better than currently available autonomous assignment schemes.
Applications of Non-Linear Optics. (1990)

Abstract : Spatial mode-multiplexing is used to transmit several communication channels on a single multimode optical fiber. Each channel is encoded by an orthogonal pattern produced by a spatial light modulator. A photorefractive medium holographically decodes the output speckle pattern at a receiver station. A ring and star architectures for interconnection networks is demonstrated. Typical crosstalk to signal ratios, for fully interconnected 3 processor networks, are -24 and -26 dB for the ring and star respectively. Keywords: Fiber optics; Optical communications.
On-line step-size calculation using signal power estimation-tone grouping for frequency-domain equalizer of DMT-based systems (2005)

Based on the signal power estimation (SPE), a tone grouping (TG) approach is proposed to on-line calculate the subchannel step-size for FEQ of DMT systems. It is a reliable method that the SNR loss caused by the misadjustment of LMS algorithm is Iimited to less than 0.25-dB per tone. Consequently, an SPE-TG look-up table (LUT), which consists of 15 groups from Z6 to 2-', is designed for DMT ADSL systems (as a vehicle). Finally, the simulation results show that the data rate difference between floating step-size and SPE-TG is less than f0.21%.
BAYESIAN MODELING OF THE UNITED STATES RENAL DATA SYSTEM PRE-TRANSPLANT VARIABLES ACCURATELY PREDICTS GRAFT SURVIVAL (2010)

Stevens, K. A.1; Phinney, S.2; Graybill, C.2; Gillern, S.2; Salifu, M.3; Jindal, R.2; Brown, T.4; Elster, E.4 Author Information
Pitch‐based gender identification with two‐stage classification (2011)

Abstract In this paper, we address the speech‐based gender identification problem. Mel‐Frequency Cepstral Coefficients (MFCC) of voice samples are typically used as the features for gender identification. However, MFCC‐based classification incurs high complexity. This paper proposes a novel pitch‐based gender identification system with a two‐stage classifier to ensure accurate identification and low complexity. The first stage of the classifier identifies and labels all the speakers whose pitch clearly indicates the gender of the speaker; the complexity of this stage is very low since only threshold‐based decision rule on a scalar (i.e., pitch) is used. The ambiguous voice samples from all the other speakers (which cannot be classified with high accuracy by the first stage, and can be regarded as suspicious speakers or difficult cases) are forwarded to the second‐stage for finer examination; the second‐stage of our classifier uses Gaussian Mixture Model to accurately isolate voice samples based on gender. Experiment results show that our system is speech language/content independent, microphone independent, and robust against noisy recording conditions. Our system is extremely accurate with probability of correct classification of 98.65%, and very efficient with about 5 s required for feature extraction and classification. Copyright © 2011 John Wiley & Sons, Ltd.
Thyroid Hormone Regulates Type I Deiodinase Messenger RNA in Rat Liver (1990)

Conversion of the prohormone T4 to the active hormone T3 is catalyzed by 5'-deiodinases, enzymes that have not been purified. Previous studies have shown that modulating thyroid status results in changes in type I deiodinase activity in the rat liver. We have quantitated type I deiodinase mRNA in liver by an expression assay using Xenopus laevis oocytes. We report here that changes in enzyme activity correlate closely with changes in levels of the mRNA for this enzyme, indicating that thyroid hormone regulates type I deiodinase at a pretranslational step. Using the oocyte system to express size-fractionated mRNA, we have also determined that the mRNA coding for this protein is between 1.9-2.4 kilobases in length. It has been proposed that protein disulfide isomerase (PDI) is closely related to the rat type I 5'-deiodinase. Our results indicate that this is not the case, since injection of in vitro transcribed PDI mRNA into oocytes did not result in expression of deiodinase activity, and the deiodinase mRNA could be physically separated from the 2.8-kilobase mRNA species hybridizing to rat PDI cRNA by size fractionation.