gebhart/patrepeval huggingface dataset:
Isolation and characterization of two domains of human von Willebrand factor that interact with fibrillar collagen types I and III. (1987)

We have identified four discrete proteolytic fragments of von Willebrand factor (vWF) that define two collagen-binding domains. Two of the fragments tested, T 96 kDa and T 55 kDa, were generated by digestion with trypsin, and two, Fragments I and III, with Staphylococcus aureus V8 protease. The larger Fragment III, a disulfide-linked homodimer, extends between residues 1 and 1365 of the 2050-residue vWF subunit and comprises the sequence of all the others. T 96 kDa, also a disulfide-linked homodimer, extends between residues 449 and 728. T 55 kDa and Fragment I, both single-chain polypeptides, have a partial sequence overlap corresponding to residues 911-1114, and together extend from residue 730 to 1365. The ability of the fragments to interfere with the vWF-collagen interaction was evaluated by measuring inhibition of 125I-labeled vWF binding to fibrillar bovine collagen types I and III. All the four fragments tested inhibited binding. Native conformation was essential for expression of this function; denaturation with guanidine hydrochloride and reduction of disulfide bonds resulted in marked reduction or complete loss, respectively, of the inhibitory activity at all the concentrations tested. Two monoclonal antibodies were prepared, one directed against T 96 kDa and the other against Fragment I. Both antibodies partially inhibited vWF binding to collagen, and their inhibitory effect was enhanced when they were used together. 125I-Labeled Fragment I bound to collagen in a saturable manner, and the binding was completely blocked by both T 96 kDa and T 55 kDa. Thus, we have identified at least two distinct functional domains of vWF that concurrently mediate the vWF-collagen interaction. The two domains appear to share a common recognition site on collagen.
Three-dimensional solution structure of calcium-loaded porcine calbindin D9k determined by nuclear magnetic resonance spectroscopy (1992)

The three-dimensional solution structure of native, intact porcine calbindin D9k has been determined by distance geometry and restrained molecular dynamics calculations using distance and dihedral angle constraints obtained from 1H NMR spectroscopy. The protein has a well-defined global fold consisting of four helices oriented in a pairwise antiparallel manner such that two pairs of helix-loop-helix motifs (EF-hands) are joined by a linker segment. The two EF-hands are further coupled through a short beta-type interaction between the two Ca(2+)-binding loops. Overall, the structure is very similar to that of the highly homologous native, minor A form of bovine calbindin D9k determined by X-ray crystallography [Szebenyi, D. M. E., & Moffat, K. (1986) J. Biol. Chem. 261, 8761-8776]. A model structure built from the bovine calbindin D9k crystal structure shows several deviations larger than 2 A from the experimental distance constraints for the porcine protein. These structural differences are efficiently removed by subjecting the model structure to the experimental distance and dihedral angle constraints in a restrained molecular dynamics protocol, thereby generating a model that is very similar to the refined distance geometry derived structures. The N-terminal residues of the intact protein that are absent in the minor A form appear to be highly flexible and do not influence the structure of other regions of the protein. This result is important because it validates the conclusions drawn from the wide range of studies that have been carried out on minor A forms rather than the intact calbindin D9k.
Predicting ionizing radiation exposure using biochemically-inspired genomic machine learning (2018)

<b>Background:</b> Gene signatures derived from transcriptomic data using machine learning methods have shown promise for biodosimetry testing. These signatures may not be sufficiently robust for large scale testing, as their performance has not been adequately validated on external, independent datasets. The present study develops human and murine signatures with biochemically-inspired machine learning that are strictly validated using k-fold and traditional approaches. <b>Methods:</b> Gene Expression Omnibus (GEO) datasets of exposed human and murine lymphocytes were preprocessed via nearest neighbor imputation and expression of genes implicated in the literature to be responsive to radiation exposure (n=998) were then ranked by Minimum Redundancy Maximum Relevance (mRMR). Optimal signatures were derived by backward, complete, and forward sequential feature selection using Support Vector Machines (SVM), and validated using k-fold or traditional validation on independent datasets. <b>Results:</b> The best human signatures we derived exhibit k-fold validation accuracies of up to 98% ( <i>DDB2</i>, <i> PRKDC</i>, <i>TPP2</i>, <i>PTPRE</i>, and <i>GADD45A</i>) when validated over 209 samples and traditional validation accuracies of up to 92% ( <i>DDB2</i>, <i> CD8A</i>, <i> TALDO1</i>, <i> PCNA</i>, <i> EIF4G2</i>, <i> LCN2</i>, <i> CDKN1A</i>, <i> PRKCH</i>, <i> ENO1</i>, and <i>PPM1D</i>) when validated over 85 samples. Some human signatures are specific enough to differentiate between chemotherapy and radiotherapy. Certain multi-class murine signatures have sufficient granularity in dose estimation to inform eligibility for cytokine therapy (assuming these signatures could be translated to humans). We compiled a list of the most frequently appearing genes in the top 20 human and mouse signatures. More frequently appearing genes among an ensemble of signatures may indicate greater impact of these genes on the performance of individual signatures. Several genes in the signatures we derived are present in previously proposed signatures. <b>Conclusions:</b> Gene signatures for ionizing radiation exposure derived by machine learning have low error rates in externally validated, independent datasets, and exhibit high specificity and granularity for dose estimation.
<i>Stored Program Controlled Network</i>: Calling Card Service-Overall Description and Operational Characteristics (1982)

Conventionally, operator assistance is required for most nonsent paid telephone calls (calls that are billed to a number other than the calling number). Examples of these calls include collect, credit card, and bill-to-third-number. These three types of calls currently represent about two-thirds of all operator-handled toll calls. To reduce the need for operator assistance, a new service, Calling Card Service, enables customers to make credit card calls by dialing in the billing information without the assistance of an operator; it also provides an alternative to operator-assisted collect and bill-to-third-number calls. This new capability is made possible through changes in the Traffic Service Position System (TSPS) No. 1, and uses the Stored Program Controlled (SPC) Network. By providing customers with an alternative to operator assistance, Calling Card Service is helping the Bell Operating Companies (BOCS) and independent telephone companies stabilize operator work force requirements. This paper gives a basic description of Calling Card Service and the customer interface. It also describes the implementation in TSPS, and other areas of the SPC network, and discusses some of the effects on telephone company operations.
The impact of near-death experiences on persons who have not had them: A report of a preliminary study and two replications. (1995)

Three informal surveys of college students enrolled in a semester-long course on near-death experiences (NDEs) suggest that exposure to information about the NDE may bring about substantial changes in beliefs about NDEs, life after death, and God, as well as reduce fear of death and increase one's level of spirituality. These surveys and previous research point to the importance of conducting more systematic and large-scale studies of the impact of NDE materials on the general population.
Design of a real-time gesture recognition system: high performance through algorithms and software (2005)

The embedded systems group at Princeton University in New Jersey has developed, as an example of smart cameras, a gesture recognition system that can build a complete model of the torso and recognize gestures at 30 frames/s. Designing a real-time gesture recognition system is a complex task that involves many issues such as algorithm design, processing speed, system architecture, and video interface. In this article, the authors describe a method to manage the complexity by decomposing the entire process into different design and implementation phases.
Enhancing the signal-to-noise ratio of FTIR spectrometers by a digital J-Stop (2017)

Fourier transform infrared (FTIR) spectrometers have been widely used as very important analytical tools in various fields. Owing to the Jacquinot Stop (J-Stop), high throughput is a widely recognized advantage inherent to Fourier transform interferometers. However, there is a fundamental trade-off between the throughput and spectral resolution, which is primarily affected by the size of the J-Stop. So far, no effective optimization methods have been provided to break the trade-off. In this paper, we introduce a numeric technique of the digital J-Stop, which has been experimentally validated using the FTIR spectra collected from a commercial spectrometer. The result shows that the throughput can be increased by ~12 times, while the spectral resolution is also improved. In this way, the signal-to-noise ratio (SNR) gets improved by ~3 times.
Adeno-associated virus proteins: origin of the capsid components (1984)

The three primary capsid proteins (A, B, and C) of adeno-associated viruses have been shown previously to contain overlapping amino acid sequences (R. McPherson and J. Rose, J. Virol. 46:523-529, 1983). In the present study we demonstrate definitively that these proteins are encoded in the right half of the adeno-associated virus 2 genome, and one or both of the smallest adeno-associated RNA species (2.3- or 2.6-kilobase RNA) account for their synthesis. Protein A (90 kilodaltons) apparently initiates from a site within the intervening sequence, which is intact in the larger (unspliced) 2.6-kilobase mRNA, and may read through one or more termination codons, including a strong stop signal (UAA) that lies 31 bases downstream from the end of the intervening sequence. Proteins B (72 kilodaltons) and C (60 kilodaltons) are not derived from protein A but apparently originate from independent, in-frame initiations that lie downstream from the splice junction. It thus seems likely that production of the three adeno-associated virus capsid proteins involves at least two mRNA species. The B and C proteins presumably arise from the spliced 2.3-kilobase RNA, whereas protein A should be generated by the 2.6-kilobase RNA or a hitherto unidentified spliced RNA species.
A novel visual immunoassay for coeliac disease screening (1999)

The sensitivity and specificity of the visual system are greater than those of most ELISA systems and are similar to those observed with IgA antiendomysium antibodies when tested in the same population. Moreover, it is inexpensive, quick, simple to perform and easy to interpret, i.e. it requires no qualified personnel. It is for these features, together with the outstanding sensitivity and specificity, that we propose this immunoassay as a new test for reliable coeliac disease screening.
Human-guided grasp measures improve grasp robustness on physical robot (2010)

Humans are adept at grasping different objects robustly for different tasks. Robotic grasping has made significant progress, but still has not reached the level of robustness or versatility shown by human grasping. It would be useful to understand what parameters (called grasp measures) humans optimize as they grasp objects, how these grasp measures are varied for different tasks, and whether they can be applied to physical robots to improve their robustness and versatility. This paper demonstrates a new way to gather human-guided grasp measures from a human interacting haptically with a robotic arm and hand. The results revealed that a human-guided strategy provided grasps with higher robustness on a physical robot even under a vigorous shaking test (91%) when compared with a state-of-the-art automated grasp synthesis algorithm (77%). Furthermore, orthogonality of wrist orientation was identified as a key human-guided grasp measure, and using it along with an automated grasp synthesis algorithm improved the automated algorithm's results dramatically (77% to 93%).
EXPANDING CONCEPTIONS OF STATISTICAL LITERACY: AN ANALYSIS OF PRODUCTS FROM STATISTICS AGENCIES (2003)

This paper reports the results of an exploratory study of the characteristics of key information products released by statistics agencies. Such products are central to debates and decisions in the public arena, but have received little attention in the literature on statistical literacy, statistics education, or adult numeracy. Based on a qualitative analysis of Internet-based products of six national and international statistics agencies, the paper sketches the characteristics of five product types (Indicators, Press releases, Executive summaries, Reports, and Aggregate data) and of the environment in which they are found. The paper discusses implications for the specification of the skills needed for accessing, filtering, comprehending, and critically evaluating information in these products. Directions for future research and educational practice are outlined. First published May 2003 at Statistics Education Research Journal: Archives
Can an antibody-combining site be mimicked synthetically? The possible surface simulation synthesis of two antibody-combining sites complementary to two antigenic sites of lysozyme. (1977)

Our recent determination of the complete antigenic structure of native lysozyme was made possible by our introduction of the "surface simulation" synthetic concept. The remarkable success afforded by this strategy in the synthetic construction of antigenic sites prompted us to investigate whether it can be applied to mimic antibody-combining sites. Two peptides, designed to be complementary to antigenic sites 2 and 3 of lysozyme, were synthesized and their immunochemistry was studied. Each of the two complementary peptides exhibited an appreciable inhibitory activity towards the reaction of lysozyme with its antisera. Peptide immunoadsorbents bound only lysozyme and not antibody or myoglobin. Neither of the two peptides had any immunochemical activity in the myoglobin or bovine serum albumin immune systems. Furthermore, it was shown that three control synthetic peptides of myoglobin, of similar charge but different sequence, had no inhibitory effect on the lysozyme immune reaction. The evidence indicates that the antibody-combining sites sgainst antigenic sites 2 and 3 of native lysozyme were successfully mimicked synthetically, at least in terms of binding function.
Intragel photoreduction of aryl halides by green-to-blue upconversion under aerobic conditions (2015)

The first proof of concept for the application of intragel green-to-blue photon upconversion to a chemical reaction is reported.
Microstructural Evolution Of Iron Oxyfluoride/Carbon Nanocomposites Upon Electrochemical Cycling (2016)

High electrochemical performance iron oxyfluoride conversion electrode undergoes complex electrochemical reaction mechanisms upon cycling. In this work, a combination of selected area electron diffraction (SAED) and scanning transmission electron microscopy/electron energy loss spectroscopy (STEM/EELS) analysis techniques have been used to understand the conversion-reconversion mechanisms of FeO0.7F1.3/C upon cycling. Considerable changes have been observed with cycling. For the fully delithiated electrodes, the nanometer scale intermixing of amorphous rutile and nanocrystalline rocksalt phases is stable up to 20 cycles; however, upon further cycling the amount of amorphous rutile phase decreased and amount of rocksalt phase increased gradually, implying incomplete reconversion reactions with increasing cycle number. In addition, a progressive growth of solid electrolyte interphase (SEI) layer was observed with cycling, which is mainly composed of LiF. Interestingly, Fe2+ and Fe nanoparticles were found trapped in the SEI layer with increasing cycle number. Upon cycling, the combined progressive increase in Fe2+ content and insulating LiF (from SEI and conversion product) give rise to the observed capacity loss.
A Succinct Method for Preparing the Stork−Jung Vinylsilane Robinson Annulation Reagent (2004)

The Stork-Jung vinylsilane reagent (1) is prepared in two steps and in good overall yield. This provides rapid and efficient access to a useful methyl vinyl ketone surrogate.
No-reference video quality metric for HDTV based on H.264/AVC bitstream features (2011)

No-reference video quality metrics are becoming ever more popular, as they are more useful in real-life applications compared to full-reference metrics. Many proposed metrics extract features related to human perception from the individual video frames. Hence the video sequences have to be decoded first, before the metrics can be applied. In order to avoid decoding just for quality estimation, we therefore present in this contribution a no-reference metric for HDTV that uses features directly extracted from the H.264/AVC bitstream. We combine these features with the results from subjective tests using a data analysis approach with partial least squares regression to gain a prediction model for the visual quality. For verification, we performed a cross validation. Our results show that the proposed no-reference metric outperforms other metrics and delivers a correlation between the quality prediction and the actual quality of 0.93.
A Tn <i>7</i> -Like Transposon Is Present in the <i>glmUS</i> Region of the Obligately Chemoautolithotrophic Bacterium <i>Thiobacillus ferrooxidans</i> (1998)

The region downstream of the Thiobacillus ferrooxidans ATCC 33020 atp operon was examined, and the genes encoding N-acetylglucosamine-1-uridyltransferase (glmU) and glucosamine synthetase (glmS) were found. This atpEFHAGDC-glmUS gene order is identical to that of Escherichia coli. The T. ferrooxidans glmS gene was shown to complement E. coli glmS mutants for growth on minimal medium lacking glucosamine. A Tn7-like transposon, Tn5468, was found inserted into the region immediately downstream of the glmS gene in a manner similar to the site-specific insertion of transposon Tn7 within the termination region of the E. coli glmS gene. Tn5468 was sequenced, and Tn7-like terminal repeat sequences as well as several open reading frames which are related to the Tn7 transposition genes tnsA, tnsB, tnsC, and tnsD were found. Tn5468 is the closest relative of Tn7 to have been characterized to date. Southern blot hybridization indicated that a similar or identical transposon was present in three T. ferrooxidans strains isolated from different parts of the world but not in two Thiobacillus thiooxidans strains or a Leptospirillum ferrooxidans strain. Since T. ferrooxidans is an obligately acidophilic autotroph and E. coli is a heterotroph, ancestors of the Tn7-like transposons must have been active in a variety of physiologically different bacteria so that their descendants are now found in bacteria that occupy very different ecological niches.
Spontaneous isotropy breaking: A mechanism for CMB multipole alignments (2005)

We introduce a class of models in which statistical isotropy is broken spontaneously in the CMB by a nonlinear response to long-wavelength fluctuations in a mediating field. These fluctuations appear as a gradient locally and pick out a single preferred direction. The nonlinear response imprints this direction in a range of multipole moments. We consider two manifestations of isotropy breaking: additive contributions and multiplicative modulation of the intrinsic anisotropy. Since the Wilkinson microwave anisotropy probe (WMAP) exhibits an alignment of power deficits, an additive contribution is less likely to produce the observed alignments than the usual isotropic fluctuations, a fact which we illustrate with an explicit cosmological model of long-wavelength quintessence fluctuations. This problem applies to other models involving foregrounds or background anisotropy that seek to restore power to the CMB. Additive models that account directly for the observed power exacerbate the low power of the intrinsic fluctuations. Multiplicative models can overcome these difficulties. We construct a proof of principle model that significantly improves the likelihood and generates stronger alignments than WMAP in 30%--45% of realizations.
Origin and biology of cancer metastasis (1989)

Metastasis, the spread of cells from a primary neoplasm to distant sites where they grow, contributes to the death of most cancer patients. The process of metastasis is not random. Rather, the process consists of a series of linked, sequential steps that must be completed by tumor cells if a metastasis is to develop. Thus, metastatic cells must succeed in invasion and embolization, survive in the circulation, arrest in a distant capillary bed, and extravasate into and multiply in organ parenchyma. Although some of the steps in this process contain stochastic elements, as a whole metastasis favors the survival and growth of a few subpopulations of cells that preexist within the parent neoplasm. Moreover, metastases can have a clonal origin, and different metastases can originate from the proliferation of single cells. The outcome of metastasis depends on the interaction of metastatic cells with different organ environments. Organ-specific metastases have been demonstrated in a variety of experimental tumor systems, and even within one organ, site-specific tumor growth can be found. The conclusion that metastasis is a highly selective process that is influenced by both the intrinsic properties of tumor cells and by host factors is optimistic. A selective process is regulated and therefore can be studied and then manipulated.
A novel technique for reducing polarization noise in optical-time domain reflectometers for single-mode fibers (1985)

A novel technique is proposed for reducing polarization noise of backscattering in ordinary single-mode fibers. The technique is based on the depolarization of light due to propagation in highly birefringent polarization-holding fiber. Performance of the technique is examined theoretically and experimentally. The experimental results show the usefulness of the technique for an optical-time domain reflectometer.
Theoretical and Practical Aspects of Electron-Gun Design for Color Picture Tubes (1975)

This paper provides some insight into the theoretical and practical constraints imposed on the designer of electron guns for color picture tubes.
Manufacturing Process of Blended Delta-Shaped Wing Model (2013)

Aerodynamicists have long acknowledged the blended wing body (BWB) aircraft design could produce great aerodynamic advantages due to the integration of the delta wing structure with the thick center body. Therefore the wind tunnel test campaign is crucial to gain information of the flow field that governs the delta-shaped wing which has frequently baffled the aerodynamicists. In such, the wind tunnel test required acceptable quality of delta-shaped wing model for results validity. Consequently, the manufacturing process as well as the selection of the appropriate machinery tools, must be wisely designed and performed. The modular 3D concept in associating with CAD/CAM technology was utilised in the process. Finally, the actual flow cycle of manufactures blended BWB aircraft model was sucessfully established. The objective of this paper is to highlight those complexity manufacturing process and techniques involved in order to produce a good blended delta-shaped wind tunnel model.