gebhart/patrepeval huggingface dataset:
New anthracyclines, feudomycins, produced by the mutant from Streptomyces coeruleorubidus ME130-A4. (1981)

Various blocked mutants were isolated from Streptomyces coeruleorubidus ME130-A4 by NTG and UV treatments. Among them, mutant strain 4N-140 produced new anthracycline feudomycins A and B having new aglycones in which the side chain at C-9 position of daunomycinone was ethyl and acetonyl, respectively. New aglycones feudomycinones C and D having methyl at C-9 and additional groups at C-10 of daunomycinone were also isolated from this strain.
Practical algorithm for the inversion of an experimental input-output color map for color correction (2003)

We introduce the iteratively clustered interpolation algorithm to compute a structured printer inverse look-up table from irregularly sampled experimental color data. The algorithm is based on a gradient optimization method, with initial points generated through an iterative technique. Experimental results with a digital color printer are provided to illustrate the algorithm.
Sizing and placement of charge recycling transistors in MTCMOS circuits (2007)

A downside of using Multi-Threshold CMOS (MTCMOS) technique for leakage reduction is the energy consumption during transitions between sleep and active modes. Previously, a charge recycling (CR) MTCMOS architecture was proposed to reduce the large amount of energy consumption that occurs during the mode transitions in power-gated circuits. Considering the RC parasitics of the virtual ground and VDD lines, proper sizing and placement of charge-recycling transistors is key to achieving the maximum power saving. In this paper, we show that the sizing and placement problems of charge-recycling transistors in CR-MTCMOS can be formulated as a linear programming problem, and hence, can be efficiently solved using standard mathematical programming packages. The proposed sizing and placement techniques allow us to employ the CR-MTCMOS solution in large row-based standard cell layouts while achieving nearly the full potential of this power-gating architecture, i.e., we achieve 44% saving in switching energy due to the mode transition in CR-MTCMOS compared to standard MTCMOS.
Analysis of the upstream regions governing expression of the chicken cardiac troponin T gene in embryonic cardiac and skeletal muscle cells. (1988)

The chicken gene encoding cardiac troponin T (cTNT) is expressed in both cardiac and skeletal muscle during early embryonic development, but is specifically repressed in skeletal muscle during fetal development. To determine if the cis-acting sequences governing transcription of a single gene in these two related cell types are the same, we have transfected promoter/upstream segments of the cTNT gene coupled to the bacterial chloramphenicol acetyltransferase gene into primary cultures of early embryonic cardiac and skeletal muscle cells. Using this assay system, chloramphenicol acetyltransferase activity directed by the cTNT promoter/upstream region was between two and three orders of magnitude higher in cardiac or skeletal muscle cells than in fibroblast cells, indicating that cis elements responsible for cell-specific expression reside in this region of the cTNT gene. Deletion experiments showed that a 67-nucleotide DNA segment residing between 268 and 201 nucleotides upstream of the cTNT transcription initiation site is required for cTNT promoter activity in embryonic cardiac cells. This region is not required in embryonic skeletal muscle cells because a cTNT promoter construction containing only 129 upstream nucleotides is transcriptionally active in these cells. These results demonstrate that different cis-acting sequences are required for cTNT expression in early embryonic cardiac and skeletal muscle cells. Nonessential regions residing farther upstream, on the other hand, affected the level of expression of these minimum regions in a similar manner in both cell types. The data from these experiments indicate, therefore, that transcription of the cTNT promoter in early embryonic cardiac and skeletal muscle cells is governed both by common and divergent regulatory elements in cis and in trans.
The diode-array velocimeter (1994)

Diode-array velocimetry is an optical technique for measuring turbulent flows. It involves timing the passage of seed particles through a small section of a light beam by imaging the light they scatter onto one or more photodiode arrays. The arrays have a few carefully shaped elements, the shapes and positions of which are used to control the measurement-volume geometry and thus select the measurement made. Measurement volumes sensitive to velocity, position and acceleration may be designed. Measurements in highly turbulent and reversing flows are possible. A diode-array velocimeter (DAV) for one-component velocity measurements has been developed to demonstrate this concept. This uses a single laser beam to illuminate particles and a photodiode array with two rectangular elements to sense their motion. The sensitivity of this DAV to electrical noise in the photodiode circuitry decreases with reduction in measurement-volume size. The angle response is closely cosinusoidal to about 60°. Changes to the photodiode-array design could substantially increase this limit. Measurements of mean velocity, normal turbulence stress and velocity skewness made with this DAV in two attached boundary-layer flows compare well with hot-wire measurements. Useful DAV measurements were made as close as 0.2 mm from the wall. DAV measurements made in a separated flow formed downstream of a fence are also presented. These show all the expected features of the separated shear layer and recirculation including the sub-boundary layer formed beneath the backflow. Histograms measured in the reversing part of this flow show a hole near zero velocity that is a consequence of the imperfections in the DAV angle response and limitations on the maximum transit time. These are not fundamental problems, however, and the hole could be minimized or eliminated by using a different photodiode array design and/or measurement strategy.
Efficient Inner Product Approximation in Hybrid Spaces (2019)

Many emerging use cases of data mining and machine learning operate on large datasets with data from heterogeneous sources, specifically with both sparse and dense components. For example, dense deep neural network embedding vectors are often used in conjunction with sparse textual features to provide high dimensional hybrid representation of documents. Efficient search in such hybrid spaces is very challenging as the techniques that perform well for sparse vectors have little overlap with those that work well for dense vectors. Popular techniques like Locality Sensitive Hashing (LSH) and its data-dependent variants also do not give good accuracy in high dimensional hybrid spaces. Even though hybrid scenarios are becoming more prevalent, currently there exist no efficient techniques in literature that are both fast and accurate. In this paper, we propose a technique that approximates the inner product computation in hybrid vectors, leading to substantial speedup in search while maintaining high accuracy. We also propose efficient data structures that exploit modern computer architectures, resulting in orders of magnitude faster search than the existing baselines. The performance of the proposed method is demonstrated on several datasets including a very large scale industrial dataset containing one billion vectors in a billion dimensional space, achieving over 10x speedup and higher accuracy against competitive baselines.
Reduced Cell Surface Expression of CCR5 in CCR5Δ32 Heterozygotes Is Mediated by Gene Dosage, Rather Than by Receptor Sequestration (2002)

Macrophage tropic (M-tropic) human immunodeficiency virus (HIV) infection of primary human T cells and macrophages requires optimal cell surface expression of the chemokine receptor CCR5 in addition to CD4. Natural mutations of CCR5 that impair surface expression bestow in the homozygous state complete resistance to M-tropic HIV infection. ccr5Delta32 is the major prototype of such mutants. ccr5Delta32 heterozygosity is associated with delayed onset of AIDS and reduced risk of initial transmission, and this correlates with reduced levels of CCR5 and reduced infectability of CD4+ cells. In addition to gene dosage, sequestration of wild type (WT) CCR5 by mutant protein has been proposed as a mechanism to explain reduced surface expression of CCR5 in cells from ccr5Delta32 and CCR5-893(-) heterozygotes. However, here we demonstrate that a molar excess of ccr5Delta32 or related deletion mutants does not significantly impair the cell surface density of co-expressed WT receptor either in human epithelial cells or Jurkat T cells. Further, ligand-dependent signaling and M-tropic HIV usage of WT receptor are also unaffected. Nascent WT receptor does associate with ccr5Delta32 and related mutant proteins and with other unrelated CC and CXC chemokine receptors under transient labeling conditions. However, using confocal microscopy, we demonstrate that in the steady state, WT and truncated CCR5 proteins segregate into nonoverlapping subcellular compartments. These findings together with the observed and known variability in the cell surface density of CCR5 on quiescent PBLs lead us to conclude that reduced CCR5 gene dosage rather than receptor sequestration is the major determinant of reduced CCR5 expression in cells from ccr5Delta32 heterozygotes.
3D Bioprinting Human Chondrocytes with Nanocellulose–Alginate Bioink for Cartilage Tissue Engineering Applications (2015)

The introduction of 3D bioprinting is expected to revolutionize the field of tissue engineering and regenerative medicine. The 3D bioprinter is able to dispense materials while moving in X, Y, and Z directions, which enables the engineering of complex structures from the bottom up. In this study, a bioink that combines the outstanding shear thinning properties of nanofibrillated cellulose (NFC) with the fast cross-linking ability of alginate was formulated for the 3D bioprinting of living soft tissue with cells. Printability was evaluated with concern to printer parameters and shape fidelity. The shear thinning behavior of the tested bioinks enabled printing of both 2D gridlike structures as well as 3D constructs. Furthermore, anatomically shaped cartilage structures, such as a human ear and sheep meniscus, were 3D printed using MRI and CT images as blueprints. Human chondrocytes bioprinted in the noncytotoxic, nanocellulose-based bioink exhibited a cell viability of 73% and 86% after 1 and 7 days of 3D culture, respectively. On the basis of these results, we can conclude that the nanocellulose-based bioink is a suitable hydrogel for 3D bioprinting with living cells. This study demonstrates the potential use of nanocellulose for 3D bioprinting of living tissues and organs.
Finding a new vaccine in the ricin protein fold (2004)

Previous attempts to produce a vaccine for ricin toxin have been hampered by safety concerns arising from residual toxicity and the undesirable aggregation or precipitation caused by exposure of hydrophobic surfaces on the ricin A-chain (RTA) in the absence of its natural B-chain partner. We undertook a structure-based solution to this problem by reversing evolutionary selection on the 'ribosome inactivating protein' fold of RTA to arrive at a non-functional, compacted single-domain scaffold (sequence RTA1-198) for presentation of a specific protective epitope (RTA loop 95-110). An optimized protein based upon our modeling design (RTA1-33/44-198) showed greater resistance to thermal denaturation, less precipitation under physiological conditions and a reduction in toxic activity of at least three orders of magnitude compared with RTA. Most importantly, RTA1-198 or RTA1-33/44-198 protected 100% of vaccinated animals against supra-lethal challenge with aerosolized ricin. We conclude that comparative protein analysis and engineering yielded a superior vaccine by exploiting a component of the toxin that is inherently more stable than is the parent RTA molecule.
Excimer formation using low-energy electron-beam excitation (1998)

Excimer formation in dense gas targets is studied using a 10 to 20 keV electron beam for the excitation of rare gases. A SiN<SUB>x</SUB> ceramic foil, only 300 nm thick but strong and completely vacuum tight is used as an entrance window. The electrons loose only 4 to 6% of their energy in this foil. The low electron energy allows a table top setup without high voltage or x-ray radiation hazards. First applications of the system for excimer physics research and the development of novel vacuum ultraviolet light sources are described.
Clinical Validity of Detecting Circulating Tumor Cells by AdnaTest Assay Compared With Direct Detection of Tumor mRNA in Stabilized Whole Blood, as a Biomarker Predicting Overall Survival for Metastatic Castration-Resistant Prostate Cancer Patients (2016)

Circulating tumor cell (CTC) number measured with the CellSearch assay is prognostic for survival in metastatic castration-resistant prostate cancer before and after therapy. Using a standard operating protocol for sample collection, processing, and analysis, we compared detection rates of CellSearch performed using US Food and Drug Administration-cleared methodology with a second positive selection assay, AdnaTest, and a nonselection polymerase chain reaction (PCR)-based (direct detection PCR [DDPCR]) assay in 55 blood samples from 47 men with progressive metastatic castration-resistant prostate cancer. AdnaTest requires processing within 4 hours of the draw and detects KLK3, PSMA, and EGFR transcripts in cells captured on magnetic beads. The DDPCR assay can be processed up to 7 days after a draw and detects KLK2, KLK3, HOXB13, GRHL2, and FOXA1 genes. AdnaTest and DDPCR were considered positive if at least 1 transcript was detected. AdnaTest detected CTCs in 34 samples (62%; 95% confidence interval [CI], 48%-75%), of which 23 (68%) had unfavorable CTC counts by CellSearch. A positive DDPCR result was seen in 38 cases (69%; 95% CI, 55%-81%), including 24 (63%) with unfavorable CellSearch CTC counts. CellSearch found unfavorable CTC counts in 25 samples (45%; 95% CI, 33%-58%). Sensitivities were similar between the AdnaTest and DDPCR assays, and both were more sensitive than CellSearch. Concordance probability estimates (possible values, 0.5-1.0) associating the biomarker result with survival were similar: 0.77 (SE, 0.07) for AdnaTest, 0.72 (SE, 0.08) for DDPCR, and 0.76 (SE, 0.06) for CellSearch. Overall detection rates between the AdnaTest and DDPCR assays were similar, and both were superior to CellSearch. The DDPCR assay required the lowest blood volume, least on-site processing, and longest stability for batch processing.
Speech-Centric Multimodal User Interface Design in Mobile Technology (2008)

Multimodal user interface (MUI) allows users to interact with a computer system through multiple human- computer communication channels or modalities. Users have the freedom to choose one or more modalities at the same time. MUI is especially important in mobile devices due to the limited display and keyboard size. In this chapter, we provide a survey of the MUI design in mobile technology with a speech-centric view based on our research and experience in this area (e.g., MapPointS and MiPad). In the context of several carefully chosen case studies, we discuss the main issues related to the speechcentric MUI in mobile devices, current solutions, and future directions.
Enhancement of field emission properties of cyanoacrylate–carbon nanotube arrays by laser treatment (2004)

Cyanoacrylate–carbon nanotube arrays are prepared by embedding carbon nanotube (CNT) arrays grown on silicon substrate in cyanoacrylate adhesive. Upon laser treatment, enhanced field emission properties are obtained. Moreover, the binding force between the carbon nanotubes and the substrate is strengthened by the cyanoacrylate adhesive. When the field emission current is large enough at high electric field, the carbon nanotubes cannot be pulled out of the substrate by electric field force. A large field emission current can be obtained from cyanoacrylate–carbon nanotube arrays at relatively low voltage just by decreasing the distance between the anode and the cathode.
Extended multiple feature-based classifications for adaptive loop filtering (2019)

Recent progress in video compression is seemingly reaching its limits making it very hard to improve coding efficiency significantly further. The adaptive loop filter (ALF) has been a topic of interest for many years. ALF reaches high coding gains and has motivated many researchers over the past years to further improve the state-of-the-art algorithms. The main idea of ALF is to apply a classification to partition the set of all sample locations into multiple classes. After that, Wiener filters are calculated and applied for each class. Therefore, the performance of ALF essentially relies on how its classification behaves. In this paper, we extensively analyze multiple feature-based classifications for ALF (MCALF) and extend the original MCALF by incorporating sample adaptive offset filtering. Furthermore, we derive new block-based classifications which can be applied in MCALF to reduce its complexity. Experimental results show that our extended MCALF can further improve compression efficiency compared to the original MCALF algorithm.
Injection Rate Measurement of a Gaseous Fuel Injector Using a Beam Cut Method (2008)

Injection rate of a gaseous fuel injector was calculated by measuring the needle valve lift history. In our lab, a gaseous fuel injection rate meter using 1-dimensional pipe flow was developed. In the present study, the measurement accuracy of the injection rate meter was examined by comparing the theoretical injection rate estimated from the needle valve lift history. The needle valve lift was measured using an optical method. A small beam cut plate is attached to the needle valve of the gaseous fuel injector. A laser beam passes through the beam cut plate, and the variation of the beam intensity was measured with a photo sensor. From the beam intensity, the needle valve lift history was estimated. One-dimensional, compressible, inviscid, adiabatic flow was assumed, and the instantaneous mass flow rate through the needle valve sheet, the injector sack, and the injection hole was estimated. The estimated injection rate was compared with that obtained with the gaseous fuel injection rate meter. The estimated and measured injection rates agree relatively well even at transient duration. It is shown that the injection rate meter has high reliability and accuracy.
Discovery and Validation of Protein Abundance Differences between Follicular Thyroid Neoplasms (2008)

Distinguishing between benign follicular thyroid adenoma (FTA) and malignant follicular thyroid carcinoma (FTC) by cytologic features alone is not possible. Molecular markers may aid distinguishing FTA from FTC in patients with indeterminate cytology. The aim of this study is to define protein abundance differences between FTC from FTA through a discovery (proteomics) and validation (immunohistochemistry) approach. Difference gel electrophoresis (DIGE) and peptide mass fingerprinting were performed on protein extracts from five patients with FTC and compared with six patients with FTA. Individual gel comparisons (i.e., each FTC extract versus FTA pool) were also performed for the five FTC patients. Immunohistochemical validation studies were performed on three of the identified proteins. Based on DIGE images, 680 protein spots were matched on individual gels. Of these, 102 spots showed statistically significant differences in abundance between FTC and FTA in the individual gel analyses and were therefore studied further. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to identify 54 of these protein spots. Three candidates involved in protein folding (heat shock protein gp96, protein disulfide isomerase A3, and calreticulin) were studied by immunohistochemistry. Moderate calreticulin immunohistochemical staining was the best single marker with a high negative predictive value (88%); combining all three markers (any marker less than moderate staining) had the best positive predictive value (75%) while still retaining a good negative predictive value (68%). With DIGE, we identified 54 proteins differentially abundant between FTC and FTA. Three of these were validated by immunohistochemistry. These findings provide further insights into the diagnosis, prognosis, and pathophysiology of follicular-derived thyroid neoplasms.
Recent advances in understanding and managing hairy cell leukemia (2018)

Hairy cell leukemia is a rare B-cell malignancy that is characterized by an indolent course. It was initially described as a distinct entity in 1958. Before the establishment of modern treatment, median survival was only 4 years. Since then, major advances in the treatment and understanding of the biology and genomic landscape of hairy cell leukemia have been made. This review summarizes the present understanding of hairy cell leukemia with particular focus on the development of novel and targeted approaches to treatment.
Hydrothermal Gelation of Aqueous Cellulose Nanocrystal Suspensions (2016)

We report the facile preparation of gels from the hydrothermal treatment of suspensions of cellulose nanocrystals (CNCs). The properties of the hydrogels have been investigated by rheology, electron microscopy, and spectroscopy with respect to variation in the temperature, time, and CNC concentration used in preparation. Desulfation of the CNCs at high temperature appears to be responsible for the gelation of the CNCs, giving highly porous networks. The viscosity and storage modulus of the gels was shown to increase when samples were prepared at higher treatment temperature. Considering the wide natural abundance and biocompatibility of CNCs, this simple, green approach to CNC-based hydrogels is attractive for producing materials that can be used in drug delivery, insulation, and as tissue scaffolds.