gebhart/patrepeval huggingface dataset:
A Novel Approach to Auto Image Annotation Based on Pairwise Constrained Clustering and Semi-Na&#239;ve Bayesian Model (2005)

Automatic image annotation has been intensively studied for content-based image retrieval recently. In this paper, we propose a novel approach for this task. Our approach first performs the segmentation of images into regions, followed by the clustering of regions, before learning the associations between concepts and region clusters using the set of training images with pre-assigned concepts. The main focus of this paper and our main contributions are as follows. First, in the learning stage, we perform clustering of regions into region clusters by incorporating pair-wise constraints derived by considering the language model underlying the annotations assigned to training images. Second, in the annotation stage, to alleviate the restriction of the independence assumption between region clusters, we develop a greedy selection and joining algorithm to find the independent sub-sets of region clusters and employ a semi-naïve Bayesian (SNB) model to compute the posterior probability of concepts given those independent sub-sets. Experimental results show that our proposed system utilizing these two strategies outperforms the state-of-the-art techniques in large image collection.
A novel constrained reduced-amide inhibitor of HIV-1 protease derived from the sequential incorporation of .gamma.-turn mimetics into a model substrate (1993)

C7 mimetics, designed to lock three amino acid residues of a peptide chain into a gamma-turn conformation, were introduced sequentially between the P3 to P2' positions of a model HIV-1 protease substrate I (resulting in compounds II-IV) to probe its conformational requirements in binding to HIV-1 protease. Of these, compound IIIa with the C7 mimetic replacing Asn-Tyr-Pro, corresponding to the P2 through P1' positions of substrate, was found to be an inhibitor with a Ki of 147 microM. Reduction of the amide bond in the C7 mimetic of IIIa resulted in a novel constrained reduced-amide mimetic VIa with a Ki of 430 nM. This corresponds to over a 300-fold improvement in inhibitory activity over the original C7 mimetic. The inhibitory activity of mimetic VIa was in addition found to be 44-fold better than a similar linear reduced-amide containing inhibitor V. The synthesis of these mimetics are described.
Kraft lignin as feedstock for chemical products: The effects of membrane filtration (2008)

Abstract The use of technical lignins as feedstock for chemical products will require improvements in purity, molecular mass distribution, and thermal behavior. Therefore, industrial black liquors from kraft pulping of softwood (spruce/pine) and hardwood (birch and Eucalyptus globulus ) have been subjected to fractionation according to molecular mass by ceramic membranes. After acidification and isolation of the lignin fractions, a variety of analytical methods have been applied to help understand their structure – property relationships. From all types of lignin, the chemical and polymeric properties of fractions isolated from the membrane permeates were more homogeneous. This demonstrates that technical kraft lignins, irrespective of origin, may constitute an interesting feedstock for products, such as carbon fibers, adhesives, and phenol-based polymers.
Promotion of Reprogramming to Ground State Pluripotency by Signal Inhibition (2008)

Induced pluripotent stem (iPS) cells are generated from somatic cells by genetic manipulation. Reprogramming entails multiple transgene integrations and occurs apparently stochastically in rare cells over many days. Tissue stem cells may be subject to less-stringent epigenetic restrictions than other cells and might therefore be more amenable to deprogramming. We report that brain-derived neural stem (NS) cells acquire undifferentiated morphology rapidly and at high frequency after a single round of transduction with reprogramming factors. However, critical attributes of true pluripotency--including stable expression of endogenous Oct4 and Nanog, epigenetic erasure of X chromosome silencing in female cells, and ability to colonise chimaeras--were not attained. We therefore applied molecularly defined conditions for the derivation and propagation of authentic pluripotent stem cells from embryos. We combined dual inhibition (2i) of mitogen-activated protein kinase signalling and glycogen synthase kinase-3 (GSK3) with the self-renewal cytokine leukaemia inhibitory factor (LIF). The 2i/LIF condition induced stable up-regulation of Oct4 and Nanog, reactivation of the X chromosome, transgene silencing, and competence for somatic and germline chimaerism. Using 2i /LIF, NS cell reprogramming required only 1-2 integrations of each transgene. Furthermore, transduction with Sox2 and c-Myc is dispensable, and Oct4 and Klf4 are sufficient to convert NS cells into chimaera-forming iPS cells. These findings demonstrate that somatic cell state influences requirements for reprogramming and delineate two phases in the process. The ability to capture pre-pluripotent cells that can advance to ground state pluripotency simply and with high efficiency opens a door to molecular dissection of this remarkable phenomenon.
Quantitative investigation of the multiphoton intrapulse interference phase scan method for simultaneous phase measurement and compensation of femtosecond laser pulses (2006)

Femtosecond pulse characterization and compensation using multiphoton intrapulse interference phase scan (MIIPS) [Opt. Lett.29, 775 (2004)] was rigorously tested. MIIPS was found to have 3 mrad precision within the 90 nm bandwidth of the pulses. Group-velocity dispersion measurements of glass and quartz provided independent accuracy tests. Phase distortions from high-numerical-aperture objectives were measured and corrected using MIIPS, an important requirement for reproducible two-photon microscopy. Phase compensation greatly improved the pulse-shaping results through a more accurate delivery of continuous and binary phase functions to the sample. MIIPS measurements were possible through the scattering of biological tissue, a consideration for biomedical imaging.
Threshold-Based Time-of-Arrival Estimators in UWB Dense Multipath Channels (2008)

The need for accurate positioning has gained significant interest recently, especially in cluttered environments where signals from satellite navigation systems are not reliable. Positioning systems based on ultrawide bandwidth (UWB) technology have been considered for these environments because UWB signals are able to resolve multipath and penetrate obstacles. These systems usually obtain range measurements from time-of-arrival (TOA) estimation of the first path, which can be a challenge in dense multipath environments. In this paper, we analyze and compare the performance of matched filter (MF) and energy detector (ED) TOA estimators based on thresholding in UWB dense multipath channels. The main advantage of threshold-based estimators is that they have the potential for complete analog implementation and hence they are particularly attractive for applications that require low cost battery-powered devices. Closed-form expressions for the estimator bias and mean square error (MSE) are derived as a function of the signal- to-noise ratio. A comparison with results obtained from Monte Carlo simulation confirms the validity of our analytical approach. This analysis enables us to determine the threshold value that minimizes the MSE, a critical parameter for optimal estimator design. A simple criteria to determine the threshold value is also presented. It is shown that the estimation accuracy is mainly affected by the ambiguity in the selection of the correct peak at the output of the MF or ED, caused by the fading characteristics of the first path. We also evaluate the performance loss of ED estimators with respect to MF estimators. Finally, results based on experimental measurements in an indoor residential environment are presented in order to compare the performance of TOA estimators in realistic environments.
Reaction of organometallic reagents with ethyl trifluoroacetate and diethyl oxalate. Formation of trifluoromethyl ketones and .alpha.-keto esters via stable tetrahedral adducts (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of organometallic reagents with ethyl trifluoroacetate and diethyl oxalate. Formation of trifluoromethyl ketones and .alpha.-keto esters via stable tetrahedral adductsXavier CrearyCite this: J. Org. Chem. 1987, 52, 22, 5026–5030Publication Date (Print):October 1, 1987Publication History Published online1 May 2002Published inissue 1 October 1987https://pubs.acs.org/doi/10.1021/jo00231a036https://doi.org/10.1021/jo00231a036research-articleACS PublicationsRequest reuse permissionsArticle Views5324Altmetric-Citations157LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Microfabricated Broadband Components For Microwave Front Ends (2011)

Broadband components for microwave and millimeter-wave RF front ends enable increased flexibility and functionality, such as using one front end for multiple electronic warfare frequency bands or using frequency scanning to electronically steer the main beam of a radar array. This thesis explores the usefulness of a sequential copper deposition, microfabrication process known as the PolyStrataTM process for broadband passive elements in two frequency ranges: 4-18 GHz and 130-180 GHz.\nThe 4-18 GHz band research focuses on taking advantage of the low loss, low dispersion, high isolation, and relatively high power handling capability of the PolyStrataTM process by enabling passive parts of a MMIC to be moved off chip, thus saving expensive semiconductor wafer area. Specifically assembly structures referred to as sockets, inductors, and bias tees are designed, fabricated, and tested as a means of hybridly integrating MMICs, SMDs, and PolystrataTMlines. Measured data is in agreement with full-wave simulations and shows that PolyStrataTM integration introduces minimal parasitics and is therefore an attractive packaging technology.\nThe 130-180 GHz band research focuses on taking advantage of the accuracy and tight tolerances of the PolyStrataTM process to make frequency-scanning, traveling-wave, slotted waveguide arrays at G-band using a WR-05 compatible PolyStrataTM waveguide. The array achieves scanning greater than 1â¦/GHz, and more than 20â¦ steering with less than 15% fractional bandwidth. The a 20-element slot array has a beamwidth of 6.3â¦ near the center of the band (150 GHz). The array is 2 cm in length, has a mass of approximately 0.063 mg, can be connected to standard waveguide, and is scalable to a 2-D array.
Mycotoxin Biotransformation by Native and Commercial Enzymes: Present and Future Perspectives (2017)

Worldwide mycotoxins contamination has a significant impact on animal and human health, and leads to economic losses accounted for billions of dollars annually. Since the application of pre- and post- harvest strategies, including chemical or physical removal, are not sufficiently effective, biological transformation is considered the most promising yet challenging approach to reduce mycotoxins accumulation. Although several microorganisms were reported to degrade mycotoxins, only a few enzymes have been identified, purified and characterized for this activity. This review focuses on the biotransformation of mycotoxins performed with purified enzymes isolated from bacteria, fungi and plants, whose activity was validated in in vitro and in vivo assays, including patented ones and commercial preparations. Furthermore, we will present some applications for detoxifying enzymes in food, feed, biogas and biofuel industries, describing their limitation and potentialities.
Processiveness of DNA polymerases. A comparative study using a simple procedure. (1979)

In this communication, we describe a simple procedure for analyzing the processiveness of DNA polymerases in general. By choosing conditions for which the number of incorporations per available primer is less than 1, we have reduced the probability of a primer molecule being utilized by the enzyme more than once. The primer-template used was poly(dA)300:oligo(dT)10, and the product was isolated by oligo(dT)-cellulose chromatography. The number of dTMP residues added per association was determined from the [3H]dThd + [3'-3H]dTMP/[3H]dThd ratio of the product after its digestion by micrococcal nuclease and spleen phosphodiesterase. Using this procedure, we have found that Escherichia coli DNA polymerase I, T4 DNA polymerase, and calf thymus alpha- and beta-DNA polymerase are "quasi-processive." Most of these enzymes add on the average approximately 10 to 15 nucleotides before dissociating from the template. T5 DNA polymerase, on the other hand, is processive, i.e. it continues to replicate a given template until it is very close to the 5' end of the template. With "nicked DNA-like" poly(dA):oligo(dT), the processiveness of E. coli DNA polymerase I is increased 2- to 2.5-fold. The significance of this increase in determining the "patch size" during DNA repair is discussed.
Phantom Limb Pain (2019)

In the United States (U.S.), 30,000 to 40,000 amputations are performed each year. Amputations can occur for many reasons including severe trauma, tumors, vascular disease, and infection. Pain after amputation of a limb is a common symptom and is separated into two types of pain including residual limb pain (RLP) and phantom limb pain (PLP). PLP is clinically defined as the perception of pain or discomfort in a limb that no longer exists. Although PLP most commonly presents as pathological sequelae in amputee patients, the underlying pathophysiology remains poorly understood. Furthermore, PLP can present along a wide clinical spectrum and varying severity of symptoms. The condition should be differentiated from other related but separate clinical conditions, including RLP. This latter condition, formerly known as stump is pain that originates from the actual site of the amputated limb. It is most common in the early post-amputation period and tends to resolve with wound healing. Unlike PLP, RLP is often a manifestation of an underlying source, such as nerve entrapment, neuroma formation, surgical trauma, ischemia, skin breakdown, or infection. Of note, more than half of people with PLP also have RLP. It is important to know the difference between the two because the causes and treatments for each differ, but also be aware that both of these elements can coexist at the same time. PLP and RLP represent an important challenge in medicine, in terms of epidemiology and therapeutic difficulties. Ninety-five percent of patients, indeed, report experiencing some amputation-related pain, with 79.9% reporting phantom pain and 67.7% reporting RLP. Again, these clinical manifestations can significantly worsen the health-related quality of life (HR-QOL) and in some cases are very difficult to manage.
Free energy increments for hydrogen bonds in nucleic acid base pairs (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFree energy increments for hydrogen bonds in nucleic acid base pairsDouglas H. Turner, Naoki Sugimoto, Ryszard Kierzek, and Scott D. DreikerCite this: J. Am. Chem. Soc. 1987, 109, 12, 3783–3785Publication Date (Print):June 1, 1987Publication History Published online1 May 2002Published inissue 1 June 1987https://pubs.acs.org/doi/10.1021/ja00246a047https://doi.org/10.1021/ja00246a047research-articleACS PublicationsRequest reuse permissionsArticle Views632Altmetric-Citations110LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Estrogen Receptor-α Is Developmentally Regulated during Osteoblast Differentiation and Contributes to Selective Responsiveness of Gene Expression (1998)

Estrogen responsiveness of bone is a fundamental regulatory mechanism operative in skeletal homeostasis. We examined the expression of estrogen receptor-alpha (ER) messenger RNA (mRNA) in cultured rat calvarial-derived osteoblasts during progressive development of the osteoblast phenotype. Levels of ER message were compared with the expression of traditional osteoblastic markers that have been mapped throughout the differentiation process of these cells. ER transcripts, measured using semiquantitative RT-PCR analysis, were expressed at low levels in early stage proliferating osteoblasts and increased at confluence upon initial expression of bone cell phenotypic genes. A 23-fold up-regulation of ER mRNA expression coincided with the initiation of alkaline phosphatase activity (day 8). ER mRNA levels progressively increased 70-fold, reaching a maximum level on days 22-25 in fully differentiated osteoblasts when osteocalcin expression peaked, but declined precipitously by day 32 in osteocytic cells. Analysis of RNA isolated directly from rat calvaria confirmed these in vitro results and demonstrated that ER message levels become more abundant postnatally as bone becomes more mineralized. We also examined the responsiveness of osteoblasts to 17beta-estradiol (17beta-E2) at two periods of maturation: the nodule-forming stage (day 14) and the late mineralization stage (day 30). Estradiol suppressed the levels of alkaline phosphatase, osteocalcin, osteonectin, and ER mRNAs on day 14, but up-regulated these messages on day 30. In contrast, 17beta-E2 treatment regulated the steady state levels of transforming growth factor-beta1 and type I procollagen mRNAs only in the late mineralization stage, whereas histone H4 message was unaffected by the steroid at either stage of differentiation. Thus, the observed developmental expression of ER mRNA correlates with progressive osteoblast differentiation and may be a contributing factor to differential regulation of bone cell gene expression by 17beta-E2.
Selected Properties of Polar, Ionic and Metallic Fluids in the Supercritical Region (1972)

Abstract A survey is given of selected properties of polar, ionic and metallic fluids in critical and supercritical regions. New experimental data of the following properties and phenomena in this range are presented and discussed: The static dielectric constant of water, the infrared and Raman spectra of water, ion dissociation of water and ammonia, electrolytic conductance of supercritical bismuth trichloride, electronic conductance and metal‐nonmetal transition in dense gaseous metals.
Specific Modification of Arginine Residues in Proteins with Ninhydrin1 (1976)

Ninhydrin (1)2,3-indantrione monohydrate) was shown to react with the guanidino group of Nalpha-benzyloxycarbonylarginine under mild conditions (pH 8.0, 25 degrees). When ribonuclease A [EC 3.1.4.22] was reacted with ninhydrin under similar conditions, rapid inactivation took place with concomitant modification of arginine and lysine residues. Specific modification of arginine residues in the enzyme could be achieved by reversible blocking of amino groups with citraconic anhydride. Ribonuclease T1 [EC 3.1.4.8] was also inactivated rapidly by ninhydrin under similar conditions. In this case, the single arginine residue (Arg-77) and the amino groups of the N-terminal alanine and lysine-41 appeared to be specifically modified. Other amino acid residues did not appear to be significantly modified by ninhydrin in either of these enzymes. Ninhydrin thus can be used for the specific modification of arginine residues in proteins under mild conditions by reversibly blocking amino and, possibly, thiol groups.
Identification of a mouse brain cDNA that encodes a protein related to the Alzheimer disease-associated amyloid beta protein precursor. (1992)

We have isolated a cDNA from a mouse brain library that encodes a protein whose predicted amino acid sequence is 42% identical and 64% similar to that of the amyloid beta protein precursor (APP). This 653-amino acid protein, which we have termed the amyloid precursor-like protein (APLP), appears to be similar to APP in overall structure as well as amino acid sequence. The amino acid homologies are concentrated within three distinct regions of the two proteins where the identities are 47%, 54%, and 56%. The APLP cDNA hybridizes to two messages of approximately 2.4 and 1.6 kilobases that are present in mouse brain and neuroblastoma cells. Polyclonal antibodies raised against a peptide derived from the C terminus of APLP stain the cytoplasm in a pattern reminiscent of Golgi staining. In addition to APP, APLP also displays significant homology to the Drosophila APP-like protein APPL and a rat testes APP-like protein. These data indicate that the APP gene is a member of a strongly conserved gene family. Studies aimed at determining the functions of the proteins encoded by this gene family should provide valuable clues to their potential role in Alzheimer disease neuropathology.
Novel N-terminal amino acid sequence required for retention of a hepatitis B virus glycoprotein in the endoplasmic reticulum. (1989)

The preS1 surface glycoprotein of hepatitis B virus is targeted to the endoplasmic reticulum (ER) and is retained in this organelle when expressed in the absence of other viral gene products. The protein is also acylated at its N terminus with myristic acid. Sequences responsible for its ER retention have been identified through examination of mutants bearing lesions in the preS1 coding region. These studies reveal that such sequences map to the N terminus of the molecule, between residues 6 and 19. Molecules in which this region was present remained in the ER; those in which it had been deleted were secreted from the cell. Although all deletions which allowed efficient secretion also impaired acylation of the polypeptide, myristylation alone was not sufficient for ER retention: point mutations which eliminated myristylation did not lead to secretion. These data indicate that an essential element for ER retention resides in a 14-amino-acid sequence that is unrelated to previously described ER retention signals.