gebhart/patrepeval huggingface dataset:
Primary structure of Escherichia coli ribosomal protein S1 and of its gene rpsA. (1982)

The primary structure of proteins S1, the largest protein component of the Escherichia coli ribosome, has been elucidated by determining the amino acid sequence of the protein (from E. coli MRE600) and the nucleotide sequence of the S1 gene (rpsA, of a K-12 strain). The two methods gave results in perfect agreement except of two positions where possible strain specific differences were found. Protein S1 (MRE600) is composed of 557 amino acid residues (no modified amino acids were detected) and has Mr 61,159. The DNA sequence for protein S1 (K-12) suggests 556 amino acid residues. A computer survey of the sequence revealed three regions in S1 with a high degree of internal homology. The ribosome binding domain of S1 (NH2 terminus) does not show any preponderance of basic amino acids. The two cysteine and the majority of tryptophan residues of S1 as well as two od the three homologous regions were located in its middle region which contains the nucleic acid binding domain. The pattern of degenerate codon usage in the S1 gene is nonrandom and similar to that reported for other ribosomal protein genes.
High-gain harmonic generation free-electron laser with variable wavelength (2005)

The external seed of the high-gain harmonic generation (HGHG) free-electron laser (FEL) determines the wavelength of the output radiation. Therefore, the tunability of such a laser depends upon the tunability of the seed. In this paper, we present and discuss an alternative scheme for the tunable HGHG FEL wherein the seed's wavelength is fixed and the variations in the wavelength of radiation are achieved by tuning the accelerator. As an illustration, we apply our proposed scheme to the deep ultraviolet free electron laser (DUV FEL) at Brookhaven National Laboratory demonstrating the ability to attain about a +/-10% variation in the wavelength's tuning range.
Aqueous Humor Dynamics (2014)

Normal visual function requires the shape of the globe to remain fixed and the optical pathway from the cornea to the retina to remain clear. The anterior portions of the larger processes have many capillary fenestrations and epithelial mitochondria, indicating specialization for aqueous humor production. The posterior chamber aqueous humor is modified by diffusion of molecules into or out of the surrounding tissue. The rate at which aqueous humor enters the anterior chamber in the normal human eye averages about ±2.5 ml/min. In the primate trabecular outflow pathway, the aqueous humor drains sequentially through the trabecular meshwork, Schlemm’s canal, collector channels, episcleral veins, and anterior ciliary veins and into the systemic circulation. The intraocular pressure (IOP) declines over the time interval, and with the aid of the Friedenwald tables, the change in the IOP allows one to infer the volume of aqueous humor displaced from the eye.
The RAMCloud Storage System (2015)

RAMCloud is a storage system that provides low-latency access to large-scale datasets. To achieve low latency, RAMCloud stores all data in DRAM at all times. To support large capacities (1PB or more), it aggregates the memories of thousands of servers into a single coherent key-value store. RAMCloud ensures the durability of DRAM-based data by keeping backup copies on secondary storage. It uses a uniform log-structured mechanism to manage both DRAM and secondary storage, which results in high performance and efficient memory usage. RAMCloud uses a polling-based approach to communication, bypassing the kernel to communicate directly with NICs; with this approach, client applications can read small objects from any RAMCloud storage server in less than 5μs, durable writes of small objects take about 13.5μs. RAMCloud does not keep multiple copies of data online; instead, it provides high availability by recovering from crashes very quickly (1 to 2 seconds). RAMCloud’s crash recovery mechanism harnesses the resources of the entire cluster working concurrently so that recovery performance scales with cluster size.
From Word Embeddings To Document Distances (2015)

We present the Word Mover's Distance (WMD), a novel distance function between text documents. Our work is based on recent results in word embeddings that learn semantically meaningful representations for words from local cooccurrences in sentences. The WMD distance measures the dissimilarity between two text documents as the minimum amount of distance that the embedded words of one document need to travel to reach the embedded words of another document. We show that this distance metric can be cast as an instance of the Earth Mover's Distance, a well studied transportation problem for which several highly efficient solvers have been developed. Our metric has no hyperparameters and is straight-forward to implement. Further, we demonstrate on eight real world document classification data sets, in comparison with seven state-of-the-art baselines, that the WMD metric leads to unprecedented low k-nearest neighbor document classification error rates.
<title>Tunable RF optical source using harmonic carrier generation</title> (1997)

A tunable millimeter wave source is demonstrated using the frequency multiplication properties of a Mach-Zehnder modulator based analog fiber optic link. Extremely low phase noise millimeter wave output signals (minus 86 dBc/Hz at 1 kHz from a 40.96 GHz carrier) have been obtained using harmonic carrier generation by electrically overdriving the Mach-Zehnder modulator. This technique can be useful for high quality signal synthesis to 100 GHz, well beyond the modulation bandwidth of present optical modulators.
Early Arrest in B Cell Development in Transgenic Mice That Express the E41K Bruton’s Tyrosine Kinase Mutant Under the Control of the CD19 Promoter Region (1999)

Bruton's tyrosine kinase (Btk) is a nonreceptor protein kinase that is defective in X-linked agammaglobulinemia in humans and in X-linked immunodeficiency in mice. To study the effect of Btk activation in early B cell development in vivo, we have created transgenic mouse strains expressing Btk under the control of the human CD19 promoter region. The transgenic expression of wild-type human Btk corrected all X-linked immunodeficiency features in mice carrying a targeted disruption of the Btk gene. In contrast, expression of an activated form of Btk, the E41K mutant, resulted in an almost complete arrest of B cell development in the immature IgM+IgD- B cell stage in the bone marrow, irrespective of the presence of the endogenous intact Btk gene. Immature B cells were arrested at the progression from IgMlow into IgMhigh cells, which reflects the first immune tolerance checkpoint at which autoreactive B cells become susceptible to apoptosis. As the constitutive activation of Btk is likely to mimic B cell receptor occupancy by autoantigens in the bone marrow, our findings are consistent with a role for Btk as a mediator of B cell receptor-induced apoptotic signals in the immature B cell stage. Whereas the peripheral mature B cell pool was reduced to <1% of the normal size, significant numbers of IgM-secreting plasma cells were present in the spleen. Serum IgM levels were substantial and increased with age, but specific Ab responses in vivo were lacking. We conclude that the residual peripheral B cells were efficiently driven into IgM+ plasma cell differentiation, apparently without functional selection.
Overexpression of the Bcl-2 Protein Increases the Half-life of p21Bax (1995)

Bcl-2 and Bax are homologous proteins which can heterodimerize with each other. These proteins have opposing effects on cell survival when overexpressed in cells, with Bcl-2 blocking and Bax promoting apoptosis. Here we demonstrate that gene transfer-mediated elevations in Bcl-2 protein levels result in a marked increase in the steady-state levels of endogenous p21Bax protein as determined by immunoblotting in the Jurkat T-cell and 697 pre-B-cell leukemia cell lines, but not in several other cell lines including CEM T-cell leukemia, 32D.3 myeloid progenitor, PC12 pheochromocytoma, and NIH-3T3 fibroblasts. Steady-state levels of p21Bax protein were also elevated in the lymph nodes of Bcl-2 transgenic mice in which a BCL-2 transgene is expressed at high levels in B-cells. Northern blot analysis of BCL-2-transfected and control-transfected Jurkat and 697 leukemia cells revealed no Bcl-2-induced alterations in the steady-state levels of BAX mRNAs. In contrast, L-[35S]methionine pulse-chase analysis indicated a marked increase in the half-life (t1/2) of the p21Bax protein in BCL-2-transfected 697 cells compared to control-transfected cells (t1/2 > 24 h versus approximately 4 h), whereas the rate of Bax degradation was unaltered in Bcl-2-transfected CEM cells. The results demonstrate that levels of the proapoptotic p21Bax protein can be post-translationally regulated by Bcl-2, probably in a tissue-specific fashion, and suggest the existence of a feedback mechanism that may help to maintain the ratio of Bcl-2 to Bax protein in physiologically appropriate ranges.
Menu planning using the exchange diet system (2004)

This work is focused on individual menu planning for non-therapeutic adult diets. A step-by-step methodology for modeling the problem as a mixed integer linear problem is proposed and tested with four different subjects by reading their preferences, building the model in Excel and solving it with a commercial MILP solver. The preference function to be maximized is the sum of the piece wise linear approximations of the quadratic frequency-preference function for each of the menu items available for assignment.
Quantifying comparison of large detrital geochronology data sets (2016)

The increase in detrital geochronological data presents challenges to existing approaches to data visualization and comparison, and highlights the need for quantitative techniques able to evaluate and compare multiple large data sets. We test five metrics commonly used as quantitative descriptors of sample similarity in detrital geochronology: the Kolmogorov-Smirnov (K-S) and Kuiper tests, as well as Cross-correlation, Likeness, and Similarity coefficients of probability density plots (PDPs), kernel density estimates (KDEs), and locally adaptive, variable-bandwidth KDEs (LA-KDEs). We assess these metrics by applying them to 20 large synthetic data sets and one large empirical data set, and evaluate their utility in terms of sample similarity based on the following three criteria. (1) Similarity of samples from the same population should systematically increase with increasing sample size. (2) Metrics should maximize sensitivity by using the full range of possible coefficients. (3) Metrics should minimize artifacts resulting from sample-specific complexity. K-S and Kuiper test p-values passed only one criterion, indicating that they are poorly suited as quantitative descriptors of sample similarity. Likeness and Similarity coefficients of PDPs, as well as K-S and Kuiper test D and V values, performed better by passing two of the criteria. Cross-correlation of PDPs passed all three criteria. All coefficients calculated from KDEs and LA-KDEs failed at least two of the criteria.
Identification of a double-stranded RNA virus by using polymerase chain reaction and magnetic separation of the synthesized DNA segments (1990)

A double-nested polymerase chain reaction assay (PCR), followed by magnetic separation of the PCR-synthesized DNA segments, was developed to detect a double-stranded RNA virus, infectious pancreatic necrosis virus from salmonid fish. Viral RNA was extracted from cell cultures and used for cDNA synthesis. The cDNA produced was used as a template in a double PCR. The sensitivity of this double PCR was approximately 0.8 pg of template double-stranded RNA. The DNA segment produced from the first PCR was also used as a template in a second PCR with a set of two 5'-labeled primers, one with biotin and the other with 32P. The PCR segment that was then synthesized was separated from the solution by using streptavidin-coated, superparamagnetic beads. The levels of radioactivity measured in the magnetically separated fractions were significantly higher in the positive samples than they were in the negative samples.
Determination of blood clot composition in real-time by laser scattering method (2002)

Blood clots are composed of different substances and their composition percentage can be a good indicator for determination of their cause or clotting mechanism. In order to see the possibility of real-time composition determination, the laser scattering characteristic of blood clots located in whole blood is theoretically calculated and compared with an experimental measurement. It is found that there is a good agreement between theory and experiment, and the major composition of blood clots in flowing whole blood can be determined in real-time by laser scattering method.
Assessment of the Analgesic Effect of Centhaquin in Mouse Tail Flick and Hot-Plate Tests (2011)

This is the first report demonstrating the analgesic activity of centhaquin. The α(2)-adrenergic, imidazoline and opioid receptors are involved in mediating centhaquin analgesia. Endothelin ET(A) receptors do not play a role in centhaquin analgesia; centhaquin does not augment morphine analgesia.
Computer-Aided Design Methods for Additive Fabrication of Truss Structures (2002)

This paper presents computer-aided design methods to create truss structures manufactured with additive fabrication to enhance a part’s mechanical properties. It describes the overall design process for the truss structure, and then discusses how parametric modeling and solid modeling techniques, finite element methods, and optimization approaches are applied to design the truss structure. Examples and some potential applications will be discussed.
Fast Random Number Generation With Bandwidth-Enhanced Chaotic Semiconductor Lasers at 8$\,\times\,$50 Gb/s (2012)

We propose a scheme for fast random number generation with bandwidth-enhanced chaotic semiconductor lasers. Chaotic laser intensity output and its time-delayed signal are sampled at 50 GigaSample per second and converted into eight-bit values. The order of the eight-bit samples of the time-delayed signal is reversed, and bitwise exclusive-or operation is executed between the bit-order-reversed samples and the original eight-bit samples. With this method, it is not necessary to eliminate any of the bits in eight-bit samples in order to obtain good-quality random bit sequences. The equivalent generation rate of 8×50 Gb/s is achieved in an experiment using bandwidth-enhanced chaotic semiconductor lasers.
A Ripple-Mitigating and Energy-Efficient Fuel Cell Power-Conditioning System (2007)

We describe an energy-efficient, fuel-cell power-conditioning system (PCS) for stationary application, which reduces the variations in the current drawn from the fuel-cell stack and can potentially meet the $40/kW cost target. The PCS consists of a zero-ripple boost converter (ZRBC) followed by a soft-switched and multilevel high-frequency (HF) inverter and a single-phase cycloconverter. The ZRBC comprises a new zero-ripple filter (ZRF), which significantly reduces the input low- and high-frequency current ripples, thereby potentially enhancing the durability of the stack. A new phase-shifted sinewave modulation of the multilevel HF inverter is proposed, which results in the zero-voltage switching (ZVS) of all four switches without the use of any auxiliary circuit components. For such a sine wave modulation technique, >90% ZVS range is obtained per line cycle for about 70% of the rated load. Further, the line-frequency switching of the cycloconverter (at close to unity power factor) results in extremely low switching losses. The intermediate dc bus facilitates the inclusion of power systems based on other forms of alternative-energy techniques (e.g., photovoltaic/high-voltage stack). A 5 kW prototype of the proposed PCS is built, which currently achieves a peak efficiency of 92.4%. We present a detailed description of the operation of the PCS along with its key features and advantages. Finally, experimental results showing the satisfactory performance and the operation of the PCS are demonstrated.
High Strength Rapid Payout Fiber Optic Cable Assembly. (1979)

Abstract : This report summarizes preliminary results obtained in the investigation of the feasibility of a fiber optic cable payout assembly capable of high speed payout with simultaneous optical transmission. The results of both cable design studies and payout assembly (dispenser) design studies are described. Experimental results for both optical attenuation and payout performance are provided. (Author)
Ear Recognition based on 2D Images (2007)

Research of ear recognition and its application is a new subject in the field of biometrics authentication. Ear normalization and alignment is a fundamental module in the ear recognition system. Traditional manually normalization method is not suitable for an automatic recognition system. In this paper, an automatic ear normalization method is proposed based on improved Active Shape Model (ASM). This algorithm is applied on the USTB ear database for ear normalization. Then Full-space Linear Discriminant Analysis (FSLDA) is applied for ear recognition on the normalized ear images with different rotation variations. Experiments are performed on USTB ear image database. Recognition rates show that based on the right ear images, the acceptable head rotation range for ear recognition is between the right rotation of 20 degree to the left rotation of 10 degree.
Platelet inhibitory activity and pharmacokinetics of prasugrel (CS-747) a novel thienopyridine P2Y<sub>12</sub> inhibitor: A multiple-dose study in healthy humans (2006)

AbstractThis double-blind, placebo-controlled trial evaluated the safety, pharmacodynamics, and pharmacokinetics of prasugrel (CS-747, LY640315), a novel thienopyridine P2Y12 ADP receptor antagonist, during multiple oral dosing in healthy subjects. Eighteen subjects received placebo, or prasugrel 2.5 or 10 mg, orally, daily for 10 days. Adverse events were recorded and blood samples for measurement of platelet aggregation, bleeding time, and prasugrel metabolite concentrations were obtained. Two bleeding events were experienced in the prasugrel 10 mg dose group and one in the placebo group. Neither of the events was considered serious. ADP-induced platelet aggregation accumulated over the 10-day study period, reaching a steady state by days 2–4 following administration of prasugrel 10 mg daily. Limited inhibition of platelet aggregation was obtained with prasugrel 2.5 mg. In the 10-mg dose group at day 5, 4 h postdose, with 20 µM ADP as the agonist, inhibition of platelet aggregation was 61.2 ± 5.6 vs. 17.9 ± 6.2% in the placebo group (P < 0.01). Recovery of platelet aggregation was observed 48 h after the last dose of prasugrel 10 mg, but was only partial, consistent with irreversible platelet inhibition. The mean bleeding time was prolonged by day 5 at 4 h postdose in all subjects in the prasugrel 10 mg dose group (prasugrel 10 mg, 1058 ± 412 s vs. placebo, 196 ± 74 s; P < 0.001). The maximum plasma concentration of metabolites increased with prasugrel dose and there was no accumulation of metabolites over the 10-day study period. This study indicated that prasugrel 10 mg daily for 10 days was well tolerated and at steady-state provided sustained high levels of inhibition of platelet aggregation.KeywordsPrasugrelCS-747plateletsphase 1thienopyridine
Iterative reconstruction algorithm for optoacoustic imaging (2002)

Optoacoustic imaging is based on the generation of thermoelastic stress waves by heating an object in an optically heterogeneous medium with a short laser pulse. The stress waves contain information about the distribution of structures with preferential optical absorption. Detection of the waves with an array of broadband ultrasound detectors at the surface of the medium and applying a backprojection algorithm is used to create a map of absorbed energy inside the medium. With conventional reconstruction methods a large number of detector elements and filtering of the signals are necessary to reduce backprojection artifacts. As an alternative this study proposes an iterative procedure. The algorithm is designed to minimize the error between measured signals and signals calculated from the reconstructed image. In experiments using broadband optical ultrasound detectors and in simulations the algorithm was used to obtain three-dimensional images of multiple optoacoustic sources. With signals from a planar array of 3x3 detector elements a significant improvement was observed after about 10 iterations compared to the simple radial backprojection. Compared to conventional methods using filtered backprojection, the iterative method is computationally more intensive but requires less time and instrumentation for signal acquisition.
Differential accumulation of a protein kinase homolog in <i>Trypanosoma brucei</i> (1994)

Using degenerate oligonucleotide primers derived from conserved regions in the catalytic domains of protein kinases, we have identified transcripts of the protein kinase families in Trypanosoma brucei by the polymerase chain reaction technique. From the cDNAs synthesized from poly(A)+ RNA purified from the bloodstream form of the pathogen, we have obtained seven distinct partial cDNA sequences. Deduced amino acid sequences of these seven clones contain conserved regions characteristic of catalytic domains of eukaryotic protein serine/threonine kinases. DNA gel blots showed that one of the clones, TbPK-A4 is most likely a member of a subfamily in the protein kinase gene family, whereas the other six are probably each encoded by a single gene in the genome of T. brucei. The full-length cDNA of TbPK-A1 was cloned, sequenced, and found to encode an open reading frame of 350 amino acid residues. Its gene (designated KFR1) demonstrated high sequence similarity to KSS1 and FUS3 from Saccharomyces cerevisiae and rat MAP kinase at the amino acid level. There are a 3- to 4-fold higher level of KFR1 transcript and a 2-fold increase of KFR1 protein in the bloodstream form when compared with the insect form of T. brucei. This preferential expression of KFR1 in the bloodstream form of T. brucei may play a role in controlling the cell cycle and thus the growth rate of the organism.