gebhart/patrepeval huggingface dataset:
Phenotypic screening of a focused nucleoside library (2016)

Nucleoside analogues have been used as therapeutics for the treatment of cancer or viral infections for over 50 years. Despite this fact, agents with intriguing and improved efficacy, tolerability etc. have been discovered over the past decade. With this in mind, research was initiated to explore untapped potential of certain nucleoside scaffolds. It was envisioned to screen a focused in-house prepared nucleoside library phenotypically against a vast array of viruses as well as tumor cell lines.
Benchmarks and performance analysis of decimal floating-point applications (2007)

The IEEE P754 draft standard for floating-point arithmetic provides specifications for decimal floating-point (DFP) formats and operations. Based on this standard, many developers will provide support for DFP calculations. We present a benchmark suite for DFP applications and use this suite to evaluate the performance of hardware and software DFP solutions. Our benchmarks include banking, commerce, risk-management, tax, and telephone billing applications organized into a suite of five macro benchmarks. In addition to developing our own applications, we leverage open-source projects and academic financial analysis applications. The benchmarks are modular, making them easy to adapt for different DFP solutions. We use the benchmarks to evaluate the performance of the decNumber DFP library and an extended version of the SimpleScalar PISA architecture with hardware and instruction set support for DFP operations. Our analysis shows that providing processor support for high-speed DFP operations significantly improves the performance of DFP applications.
Synthesis of 2′-amino-LNA: a new strategyElectronic supplementary information (ESI) available: further experimental details and the structure of compound S11 (.pdb file). See http://www.rsc.org/suppdata/ob/b2/b208864a/ (2003)

In this paper we present revised and significantly improved synthetic routes to 2'-amino-LNA (locked nucleic acid). The optimal route is convergent with the synthesis of LNA monomers ("2'-oxy-LNA") via a common intermediate obtained by a mild deacetylation for the liberation of the 2'-hydroxy group to give compound 23 without the concomitant ring closure that affords the 2'-oxy-LNA skeleton. After inversion of the stereochemistry at C2' and triflate formation at the 2'-hydroxy group a new common intermediate 16 is obtained which gives easy access to a range of other analogues exemplified by the introduction of a sulfur nucleophile leading to the 2'-thio-LNA structure. After substitution of the triflate with azide a basic reduction affords the desired 2'-amino-LNA structure, i.e., compound 18. This new synthesis strategy towards 2'-amino-LNA improves the overall yield significantly and converges the syntheses of 2'-oxy-LNA and LNA analogues.
Single-Ended Quality Measurement of Noise Suppressed Speech Based on Kullback-Leibler Distances (2007)

In this paper, a single-ended quality measurement algorithm for noise suppressed speech is described.The proposed algorithm computes fast approximations of Kullback-Leibler distances between Gaussian mixture (GM) reference models of clean, noise corrupted, and noise suppressed speech and a GM model trained online on the test speech signal. The distances, together with a spectral flatness measure, are mapped to an estimated quality score via a support vector regressor. Experimental results show that substantial improvement in performance and complexity can be attained, relative to the current state-of-art single-ended ITU-T P.563 algorithm. Due to its modular architecture, the proposed algorithm can be easily configured to also perform signal distortion and background intrusiveness measurement, a functionality not available with current standard algorithms.
Stream Processing Based Intelligent Transport Systems (2007)

In this paper, we present a Fleet Management Center application implemented using a stream processing infrastructure we call System S. System S enables the deployment of large scale applications with mechanisms for sharing multi-party data sources, software components, and even intermediate results. This approach significantly reduces the cost of software integration, and ownership, the major factor in Intelligent Transportation Systems. In addition, the system includes an adaptive data source management that determines the list of relevant data sources based on the current locations of the entities monitored or managed by the applications.
Estimating the use of spectrum for defining and enforcing the spectrum access rights (2015)

In the static and exclusive spectrum allocation paradigm, the spectrum-access parameters for a service are chosen to mitigate potential harmful-interference and ensure minimum performance under worst-case conditions. The new dynamic spectrum-sharing paradigm necessitates dynamically defining and enforcing the spectrum-access rights while accommodating the dynamics of the RF environment and the spectrum-access scenarios. To enforce spectrum-access rights, we emphasize capturing the use of spectrum by an individual transceiver. We propose to articulate the spectrum-access rights in terms of the characterization of the spectrum used by an individual transceiver in the space, time, and frequency dimensions. In order to estimate the use of spectrum in real time, we employ a dedicated RF-sensor network that uses interference-tolerant algorithms to estimate the transceiver spectrum-access parameters and to characterize the propagation environment. We illustrate defining and enforcing a spectrum-access policy and we bring out its advantages for dynamic spectrum sharing.
Nano-biotechnology: carbon nanofibres as improved neural and orthopaedic implants (2004)

For the continuous monitoring, diagnosis, and treatment of neural tissue, implantable probes are required. However, sometimes such neural probes (usually composed of silicon) become encapsulated with non-conductive, undesirable glial scar tissue. Similarly for orthopaedic implants, biomaterials (usually titanium and/or titanium alloys) often become encapsulated with undesirable soft fibrous, not hard bony, tissue. Although possessing intriguing electrical and mechanical properties for neural and orthopaedic applications, carbon nanofibres/nanotubes have not been widely considered for these applications to date. The present work developed a carbon nanofibre reinforced polycarbonate urethane (PU) composite in an attempt to determine the possibility of using carbon nanofibres (CNs) as either neural or orthopaedic prosthetic devices. Electrical and mechanical characterization studies determined that such composites have properties suitable for neural and orthopaedic applications. More importantly, cell adhesion experiments revealed for the first time the promise these materials have to increase neural (nerve cell) and osteoblast (bone-forming cell) functions. In contrast, functions of cells that contribute to glial scar-tissue formation for neural prostheses (astrocytes) and fibrous-tissue encapsulation events for bone implants (fibroblasts) decreased on PU composites containing increasing amounts of CNs. In this manner, this study provided the first evidence of the future that CN formulations may have towards interacting with neural and bone cells which is important for the design of successful neural probes and orthopaedic implants, respectively.
Bottom-up design of de novo thermoelectric hybrid materials using chalcogenide resurfacing (2017)

Molecular engineering at the organic/inorganic interface enables robust bottom-up design of solution processable p- and n-type hybrid nanostructures for thermoelectrics.
Stable Lanthanide Luminescence Agents Highly Emissive in Aqueous Solution:  Multidentate 2-Hydroxyisophthalamide Complexes of Sm<sup>3+</sup>, Eu<sup>3+</sup>, Tb<sup>3+</sup>, Dy<sup>3+</sup> (2003)

Efficient lanthanide (Ln) luminescent probes require good ligand-to-metal energy transfer and high aqueous stability. A family of ligands based on 2-hydroxyisophthalamide chelating units is reported. These form highly stable, eight-coordinate Ln complexes. Several of these (Ln = Sm, Eu, Tb, Dy) emit in the visible region with good ligand-to-lanthanide energy transfer. The absolute quantum yields of the two Tb complexes studies (Phi = 0.59, 0.61) and high absorbance make these the brightest luminescent probes for time-resolved detection; the emission spectrum of one complex can be seen down to 10-15 M. The low overlap of the four different Ln complexes enables their simultaneous detection and discrimination.
Variation in Invasive and Noninvasive Measurements of Isovolumetric Bladder Pressure and Categorization of Obstruction According to Bladder Volume (2006)

This study shows that cuff interruption pressure varies in the expected manner with bladder volume and provides a consistent estimate of isovolumetric bladder pressure throughout a void. These data provide important guidance for interpreting noninvasive pressure flow studies and classifying obstruction on the proposed nomogram.
Proposal of a 8-layer DOI detector composed of same scintillation crystal elements (2009)

Previously, we developed a 4-layer depth of interaction (DOI) detector. It is composed of four layers of a scintillation crystal array and a position sensitive photomultiplier tube (PS-PMT) and by removing some reflectors between the crystal elements in the array, we control scintillation light distribution on the PS-PMT so that the responses of all crystal elements are discriminated. We also proposed a 2-layer DOI encoding method that uses the crystal elements cut as a triangular prism and proved its capability. Combining these two methods, here we propose an 8-layer DOI encoding method. The method makes it possible that the 8-layer DOI detector is consisted of same scintUlation crystal elements, that is to say, any scintillation crystals. The method was demonstrated with the Lu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2x</sub> G <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d2</sub> (LGSO, x = 0.9) crystals. The obtained results indicated the possibility of the proposed method.
Efficient Learning on Point Clouds with Basis Point Sets (2019)

With an increased availability of 3D scanning technology, point clouds are moving into the focus of computer vision as a rich representation of everyday scenes. However, they are hard to handle for machine learning algorithms due to their unordered structure. One common approach is to apply occupancy grid mapping, which dramatically increases the amount of data stored and at the same time loses details through discretization. Recently, deep learning models were proposed to handle point clouds directly and achieve input permutation invariance. However, these architectures often use an increased number of parameters and are computationally inefficient. In this work we propose basis point sets (BPS) as a highly efficient and fully general way to process point clouds with machine learning algorithms. The basis point set representation is a residual representation that can be computed efficiently and can be used with standard neural network architectures and other machine learning algorithms. Using the proposed representation as the input to a simple fully connected network allows us to match the performance of PointNet on a shape classification task, while using three orders of magnitude less floating point operations. In a second experiment, we show how the proposed representation can be used for registering high resolution meshes to noisy 3D scans. Here, we present the first method for single-pass high-resolution mesh registration, avoiding time-consuming per-scan optimization and allowing real-time execution.
Generation of Airway Epithelial Cell Air-Liquid Interface Cultures from Human Pluripotent Stem Cells (2022)

Diseases of the conducting airway such as asthma, cystic fibrosis (CF), primary ciliary dyskinesia (PCD), and viral respiratory infections are major causes of morbidity and mortality worldwide. In vitro platforms using human bronchial epithelial cells (HBECs) have been instrumental to our understanding of the airway epithelium in health and disease. Access to HBECs from individuals with rare genetic diseases or rare mutations is a bottleneck in lung research. Induced pluripotent stem cells (iPSCs) are readily generated by "reprogramming" somatic cells and retain the unique genetic background of the individual donor. Recent advances allow for the directed differentiation of iPSCs to lung epithelial progenitor cells, alveolar type 2 cells, as well as the cells of the conducting airway epithelium via basal cells, the major airway stem cells. Here we outline a protocol for the maintenance and expansion of iPSC-derived airway basal cells (hereafter iBCs) as well as their trilineage differentiation in air-liquid interface (ALI) cultures. iBCs are maintained and expanded as epithelial spheres suspended in droplets of extracellular matrix cultured in a primary basal cell medium supplemented with inhibitors of TGF-ß and BMP signaling pathways. iBCs within these epithelial spheres express key basal markers TP63 and NGFR, can be purified by fluorescence activated cell sorting (FACS), and when plated on porous membranes in standard ALI culture conditions, differentiate into a functional airway epithelium. ALI cultures derived from healthy donors are composed of basal, secretory and multiciliated cells and demonstrate epithelial barrier integrity, motile cilia, and mucus secretion. Cultures derived from individuals with CF or PCD recapitulate the dysfunctional CFTR-mediated chloride transport or immotile cilia, the respective disease-causing epithelial defects. Here, we present a protocol for the generation of human cells that can be applied for modeling and understanding airway diseases.
Evaluation of the Monotonic Lagrangian Grid and Lat-Long Grid for Air Traffic Management (2011)

The Air Traffic Monotonic Lagrangian Grid (ATMLG) is used to simulate a 24 hour period of air traffic flow in the National Airspace System (NAS). During this time period, there are 41,594 flights over the United States, and the flight plan information (departure and arrival airports and times, and waypoints along the way) are obtained from an Federal Aviation Administration (FAA) Enhanced Traffic Management System (ETMS) dataset. Two simulation procedures are tested and compared: one based on the Monotonic Lagrangian Grid (MLG), and the other based on the stationary Latitude-Longitude (Lat- Long) grid. Simulating one full day of air traffic over the United States required the following amounts of CPU time on a single processor of an SGI Altix: 88 s for the MLG method, and 163 s for the Lat-Long grid method. We present a discussion of the amount of CPU time required for each of the simulation processes (updating aircraft trajectories, sorting, conflict detection and resolution, etc.), and show that the main advantage of the MLG method is that it is a general sorting algorithm that can sort on multiple properties. We discuss how many MLG neighbors must be considered in the separation assurance procedure in order to ensure a five-mile separation buffer between aircraft, and we investigate the effect of removing waypoints from aircraft trajectories. When aircraft choose their own trajectory, there are more flights with shorter duration times and fewer CD&R maneuvers, resulting in significant fuel savings.
Novel Antibody-Drug Conjugate with Anti-CD26 Humanized Monoclonal Antibody and Transcription Factor IIH (TFIIH) Inhibitor, Triptolide, Inhibits Tumor Growth via Impairing mRNA Synthesis (2019)

Here, we report a novel antibody drug conjugate (ADC) with the humanized anti-CD26 monoclonal antibody YS110 and triptolide (TR-1). YS110 has an inhibitory activity against the CD26-positive tumor growth via the immunological and direct pathway, such as intra-nuclear transportation of CD26 and YS110, and suppressed transcription of RNA polymerase II (Pol II) subunit POLR2A. The ADC conjugated with YS110 and an antitumor compound triptolide (TR-1), which is an inhibitor for TFIIH, one of the general transcription factors for Pol II was developed. YS110 and triptolide were crosslinked by the heterobifunctional linker succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC) and designated Y-TR1. Antitumor efficacy of Y-TR1 against malignant mesothelioma and leukemia cell lines were assessed by the in vitro cell viability assay and in vivo assay using xenografted mouse models. Y-TR1 showed significant cytotoxicity against CD26-positive cell lines but not CD26-negative counterparts in a dose-dependent manner via suppression of mRNA synthesis by impairment of the Pol II activity. The tumors in xenografted mice administered Y-TR1 was smaller than that of the unconjugated YS110 treated mice without severe toxicity. In conclusion, the novel compound Y-TR1 showed antitumor properties against CD26-positive cancer cell lines both in vitro and in vivo without toxicity. The Y-TR1 is a unique antitumor ADC and functions against Pol II.
Tiling light sheet selective plane illumination microscopy using discontinuous light sheets (2018)

Abstract Tiling light sheet selective plane illumination microscopy (TLS-SPIM) improves 3D imaging ability of SPIM by using a real-time optimized tiling light sheet. However, the imaging speed decreases, and size of the raw image data increases proportionally to the number of tiling positions in TLS-SPIM. The decreased imaging speed and the increased raw data size could cause significant problems when TLS-SPIM is used to image large specimens at high spatial resolution. Here, we present a novel method to solve the problem. Discontinuous light sheets created by scanning coaxial beam arrays synchronized with camera exposures are used for 3D imaging to decrease the number of tiling positions required at each image plane without sacrificing the spatial resolution. We investigate the performance of the method via numerical simulation and discuss the technical details of the method.
A novel cone beam breast CT scanner: system evaluation (2007)

The purpose of the study is to characterize the imaging performance of the recently built novel cone beam breast CT (CBBCT) scanner. This CBBCT scanner system has one x-ray source and one flat panel detector (Varian's PaxScan 4030CB) mounted on a rotating assembly. A patient table is mounted above the rotating tube/detector assembly. The table has a hole through it that allows a woman's breast to hang pendant in the imaging volume at the rotation axis. The tube/detector assembly rotates around the rotation axis and acquires multiple 2D projection images of the uncompressed breast located at the rotation axis in 10 seconds. Slip ring technology allows continuous rotation of the x-ray tube/detector assembly concentric to the opening in the table to achieve multiple circle scans. Also, it has a controlled vertical motion during the rotation to perform a spiral scan over 20 cm of travel. The continuous 360° rotation is designed to have speeds up to 1 rev/sec. This system was validated through a series of breast-imaging phantom studies and and patient studies. The results show that the image quality of the CBBCT scanner is excellent and all phantom masses (tissue-equivalent carcinomas) and calcifications as well as human subjects' masses, calcifications and abnormalities can be detected faithfully using the CBBCT technique with a glandular dose level less than or equal to that of a single two-view mammography exam. The results indicate that the CBBCT imaging system has much better detectability of small breast tumors compared to the conventional mammography system.
Single-grating laser pulse stretcher and compressor (1994)

Stretching and compressing of laser pulses is demonstrated with a single-grating apparatus. A laser pulse of 110 fs is stretched to 250 ps and then recompressed to 115 fs. The apparatus exploits a two-level structure: one level for stretching and the other for compressing. This single-grating configuration shows significant simplification in structure and alignment over existing multiple-grating systems. Such a stretcher-compressor is particularly suitable for use with chirped-pulse amplification in which laser wavelength tuning is desirable. Only one rotational adjustment is rquired to restore the alignment of the entire stretcher and compressor when the laser wavelength is changed.
ChemInform Abstract: A Predictably Selective Aliphatic C—H Oxidation Reaction for Complex Molecule Synthesis. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Structure and Functional Evaluation of Tendon–Skeletal Muscle Constructs Engineered <i>in Vitro</i> (2006)

During muscle contraction, the integrity of the myotendinous junction (MTJ) is important for the transmission of force from muscle to tendon. We evaluated the contractile and structural characteristics of 3-dimensional (3-D) skeletal muscle constructs co-cultured with engineered self-organized tendon constructs (n = 4), or segments of adult (n = 4) or fetal (n = 5) rat-tail tendon. We hypothesized that the co-culture of tendon and muscle would produce constructs with viable muscle-tendon interfaces that remain intact during generation of force. Construct diameter (lm) and maximum isometric force (microN) were measured, and specific force (kPa) was determined. After measure of force, constructs were loaded at a constant strain rate until failure and surface strains were recorded optically across the tendon, the muscle and the interface and used to determine the tangent modulus (passive stiffness) of the construct. Frozen samples were used for Trichrome Masson staining and immunofluorescent analysis of the MTJ-specific protein paxillin. No differences were observed between the groups with respect to diameter, maximum force, or specific force. The MTJ was robust and withstood tensile loading beyond the physiological strain range. The majority of the constructs failed in the muscle region. At the MTJ, there is an increase in the expression and localization of paxillin. In conclusion, using 3 sources of tendon tissue, we successfully engineered 3-D muscle-tendon constructs with functionally viable MTJ, characterized by structural features and protein expression patterns resembling neonatal MTJs in vivo.
An optimal superimposed training sequence for channel estimation in OFDM systems (2008)

In this work an iterative time domain Least Squares (LS) based channel estimation method using superimposed training (ST) for an Orthogonal Frequency Division Multiplexing (OFDM) system over frequency selective fading channels is proposed. The performance of the channel estimator is analyzed in terms of the Mean Square Estimation Error (MSEE) and its impact on the uncoded Bit Error Rate (BER) of the OFDM system is studied. The selection criterion for the training sequences is proposed by jointly optimizing the MSEE and the BER of the OFDM system. A chirp based sequence satisfying the selection criterion is proposed and compared with the other sequences found in the literature. The sequence is generalized to incorporate the use of guard subcarriers in the OFDM based system. The proposed sequence offers fairness through providing equal interference in all the data carriers unlike earlier proposals. Experimental studies are carried to study the performance of the proposed scheme and also its comparison with the existing schemes is presented. Also, the proposed scheme is applied to the IEEE 802.16e OFDM standard, its suitability is examined and a case is made with the required design of the sequence.