gebhart/patrepeval huggingface dataset:
Adaptive wavelet thresholding for image denoising and compression (2000)

The first part of this paper proposes an adaptive, data-driven threshold for image denoising via wavelet soft-thresholding. The threshold is derived in a Bayesian framework, and the prior used on the wavelet coefficients is the generalized Gaussian distribution (GGD) widely used in image processing applications. The proposed threshold is simple and closed-form, and it is adaptive to each subband because it depends on data-driven estimates of the parameters. Experimental results show that the proposed method, called BayesShrink, is typically within 5% of the MSE of the best soft-thresholding benchmark with the image assumed known. It also outperforms SureShrink (Donoho and Johnstone 1994, 1995; Donoho 1995) most of the time. The second part of the paper attempts to further validate claims that lossy compression can be used for denoising. The BayesShrink threshold can aid in the parameter selection of a coder designed with the intention of denoising, and thus achieving simultaneous denoising and compression. Specifically, the zero-zone in the quantization step of compression is analogous to the threshold value in the thresholding function. The remaining coder design parameters are chosen based on a criterion derived from Rissanen's minimum description length (MDL) principle. Experiments show that this compression method does indeed remove noise significantly, especially for large noise power. However, it introduces quantization noise and should be used only if bitrate were an additional concern to denoising.
Imatinib Mesylate Efficiently Achieves Therapeutic Intratumor Concentrations in Vivo but Has Limited Activity in a Xenograft Model of Small Cell Lung Cancer (2004)

Orally administered imatinib rapidly reaches therapeutic concentrations in SCLC xenografts, suggesting the feasibility of combining imatinib with other novel or traditional chemotherapeutic agents in SCLC or other solid tumors. The c-Kit signaling pathway does not appear to play a critical role in SCLC proliferation and viability in vivo, however, suggesting that imatinib is unlikely to be effective as monotherapy for SCLC.
Decaprenylphosphoryl Arabinofuranose, the Donor of the d -Arabinofuranosyl Residues of Mycobacterial Arabinan, Is Formed via a Two-Step Epimerization of Decaprenylphosphoryl Ribose (2005)

The major cell wall polysaccharide of mycobacteria is a branched-chain arabinogalactan in which arabinan chains are attached to the 5 carbon of some of the 6-linked galactofuranose residues; these arabinan chains are composed exclusively of D-arabinofuranose (Araf) residues. The immediate precursor of the polymerized Araf is decaprenylphosphoryl-D-Araf, which is derived from 5-phosphoribose 1-diphosphate (pRpp) in an undefined manner. On the basis of time course, feedback, and chemical reduction experiment results we propose that decaprenylphosphoryl-Araf is synthesized by the following sequence of events. (i) pRpp is transferred to a decaprenyl-phosphate molecule to form decaprenylphosphoryl-beta-D-5-phosphoribose. (ii) Decaprenylphosphoryl-beta-D-5-phosphoribose is dephosphorylated to form decaprenylphosphoryl-beta-D-ribose. (iii) The hydroxyl group at the 2 position of the ribose is oxidized and is likely to form decaprenylphosphoryl-2-keto-beta-D-erythro-pentofuranose. (iv) Decaprenylphosphoryl-2-keto-beta-D-erythro-pentofuranose is reduced to form decaprenylphosphoryl-beta-D-Araf. Thus, the epimerization of the ribosyl to an arabinosyl residue occurs at the lipid-linked level; this is the first report of an epimerase that utilizes a lipid-linked sugar as a substrate. On the basis of similarity to proteins implicated in the arabinosylation of the Azorhizobium caulidans nodulation factor, two genes were cloned from the Mycobacterium tuberculosis genome and expressed in a heterologous host, and the protein was purified. Together, these proteins (Rv3790 and Rv3791) are able to catalyze the epimerization, although neither protein individually is sufficient to support the activity.
Prevalence and prognostic value of c-erbB2 expression in non-small cell lung cancer (NSCLC). (2003)

The c-erbB2 oncoprotein is highly expressed in approximately one third of non-small cell lung cancer (NSCLC) patients. We determined the status of c-erbB2 expression in our patients with NSCLC and investigated its correlation with disease stage, histological type and response to treatment. Eighty-four patients were examined for the expression of c-erbB2 by immunohistochemistry using a polyclonal antibody. The scoring criteria of Clinical Trial Assay (CTA) were used to evaluate staining (0 to +3). c-erbB2 overexpression was determined in 35% of the cases. Tumors from higher stage disease (stage IIIb-IV) were more often c-erbB2 positive in adenocarcinoma (ADC) (p=0.04). In addition, there was an association between c-erbB2 score and disease stage in ADC patients (p=0.03). Our study did not demonstrate an association of c-erbB2 overexpression with response to chemotherapy. We conclude that c-erbB2 overexpression may be a prognostic marker for evaluating tumor progression in NSCLC patients but further studies must be performed with larger patient populations.
Heavy Metal Ion Adsorbents Formed by the Grafting of a Thiol Functionality to Mesoporous Silica Molecular Sieves:  Factors Affecting Hg(II) Uptake (1998)

A new approach to heavy metal ion adsorbents based on the covalent grafting of 3-mercaptopropylsilyl groups to the framework pore walls of mesoporous silica molecular sieves has been investigated with regard to hydroxyl group densities, channel dimensions, and morphologies. Two types of silicas were examined, namely, MCM-41 with an initially anionic silicate framework and HMS with an electrically neutral framework. The MCM-41 derivative was obtained through electrostatic S+X-I+ assembly, where S+ was a quaternary ammonium ion surfactant, X- was a halide, and I+ was the silica precursor derived from tetraethyl orthosilicate (TEOS) in acidic solution. HMS silicas were assembled by a S°I° pathway using alkylamines as surfactants (S°) and TEOS as the neutral silica source (I°). Prior to thiol functionalization of the mesostructures by a one-step grafting procedure, S+ was removed from MCM-41 by calcination, whereas for HMS, S° was removed by solvent extraction. The grafting process was much more effective for the functionalization of HMS than for MCM-41 owing to a higher surface concentration of surface hydroxyl groups. Consequently, the functionalized HMS derivative was able to bind quantitatively more Hg(II) ions from aqueous solution compared to MCM-41. The Hg(II) adsorption capacities for HMS were interpreted in terms of the size and accessibility of the framework pore structure.
Renal sympathetic nerve activity modulates afferent renal nerve activity by PGE2-dependent activation of α1- and α2-adrenoceptors on renal sensory nerve fibers (2007)

Increasing efferent renal sympathetic nerve activity (ERSNA) increases afferent renal nerve activity (ARNA). To test whether the ERSNA-induced increases in ARNA involved norepinephrine activating alpha-adrenoceptors on the renal sensory nerves, we examined the effects of renal pelvic administration of the alpha(1)- and alpha(2)-adrenoceptor antagonists prazosin and rauwolscine on the ARNA responses to reflex increases in ERSNA (placing the rat's tail in 49 degrees C water) and renal pelvic perfusion with norepinephrine in anesthetized rats. Hot tail increased ERSNA and ARNA, 6,930 +/- 900 and 4,870 +/- 670%.s (area under the curve ARNA vs. time). Renal pelvic perfusion with norepinephrine increased ARNA 1,870 +/- 210%.s. Immunohistochemical studies showed that the sympathetic and sensory nerves were closely related in the pelvic wall. Renal pelvic perfusion with prazosin blocked and rauwolscine enhanced the ARNA responses to reflex increases in ERSNA and norepinephrine. Studies in a denervated renal pelvic wall preparation showed that norepinephrine increased substance P release, from 8 +/- 1 to 16 +/- 1 pg/min, and PGE(2) release, from 77 +/- 11 to 161 +/- 23 pg/min, suggesting a role for PGE(2) in the norepinephrine-induced activation of renal sensory nerves. Prazosin and indomethacin reduced and rauwolscine enhanced the norepinephrine-induced increases in substance P and PGE(2). PGE(2) enhanced the norepinephrine-induced activation of renal sensory nerves by stimulation of EP4 receptors. Interaction between ERSNA and ARNA is modulated by norepinephrine, which increases and decreases the activation of the renal sensory nerves by stimulating alpha(1)- and alpha(2)-adrenoceptors, respectively, on the renal pelvic sensory nerve fibers. Norepinephrine-induced activation of the sensory nerves is dependent on renal pelvic synthesis/release of PGE(2).
Role of serum carbohydrate antigen 19-9 and carcinoembryonic antigen in distinguishing between benign and invasive intraductal papillary mucinous neoplasm of the pancreas (2010)

Serum CA19-9 is a useful non-invasive preoperative tool for differentiating between invasive and benign IPMN, and should be taken into account in the decision to offer surgery. Patients with an IPMN and positive tumour markers have a high risk of malignant disease.
Application of a Theory of Enzyme Specificity to Protein Synthesis (1958)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Recent progress in CdTe and CdZnTe detectors (2001)

Cadmium telluride (CdTe) and cadmium zinc telluride (CdZnTe) have been regarded as promising semiconductor materials for hard X-ray and /spl gamma/-ray detection. The high atomic number of the materials (Z/sub Cd/=48, Z/sub Te/=52) gives a high quantum efficiency in comparison with Si. The large bandgap energy (Eg/spl sim/1.5 eV) allows us to operate the detector at room temperature. However, a considerable amount of charge loss in these detectors produces a reduced energy resolution. This problem arises due to the low mobility and short lifetime of holes. Recently, significant improvements have been achieved to improve the spectral properties based on the advances in the production of crystals and in the design of electrodes. In this paper we summarize 1) advantages and disadvantages of CdTe and CdZnTe semiconductor detectors and 2) the technique for improving energy resolution and photopeak efficiencies. Applications of these imaging detectors in future hard X-ray and /spl gamma/-ray astronomy missions are briefly discussed.
Energy Storage That May Be Too Good to Be True: Comparison Between Wayside Storage and Reversible Thyristor Controlled Rectifiers for Heavy Rail (2013)

There has been substantial interest in the traction community for using wayside energy storage systems (ESSs) to better use train braking energy, thus reducing energy costs and peak power as well as voltage stabilization. An alternative solution to reach the same goals is using recuperating (also called reversible) traction power substations such as reversible thyristor controlled rectifiers (RTCRs). This article compares advantages and disadvantages of ESSs of three most common types?flywheels, batteries, and supercapacitors?and recuperating substations. The analysis takes into account size, capital cost, the ?round trip? energy losses, and energy savings for heavy rail applications.
Plantazolicin A and B: Structure Elucidation of Ribosomally Synthesized Thiazole/Oxazole Peptides from Bacillus amyloliquefaciens FZB42 (2011)

The structures of the ribosomally synthesized peptide antibiotics from Bacillus amyloliquefaciens FZB42, plantazolicin A and B, have been elucidated by high resolving ESI-MSMS, 2D (1)H-(13)C-correlated NMR spectroscopy as well as (1)H-(15)N-HMQC/(1)H-(15)N-HMBC NMR experiments. (15)N-labeling prior to the experiments facilitated the structure determination, unveiling a hitherto unusual number of thiazoles and oxazoles formed from a linear 14mer precursor peptide. This finding further extends the number of known secondary metabolites from B. amyloliquefaciens and represents a new type of secondary metabolites from the genus Bacillus.
Twice weekly 5-azacytidine infusion in dissmeinated metastatic cancer: a phase II study. (1977)

A phase II study of 5-azacytidine given twice weekly as a rapid iv infusion was performed on 116 patients with different metastatic cancers of refractory lymphomas at a dose of 150 mg/m2 twice weekly x 6. Ninety-one patients were evaluable. Dose modifications were carried out depending on previous treatment status. Nausea and vomiting was a major side effect; significant granulocytopenia was observed in 35 patients. Responses were observed in only four patients. Our results indicate little effectiveness of this drug. The severe toxicity prevented escalation to potentially more effective dose levels.
Dairy Herd Management Types Assessed from Indicators of Health, Reproduction, Replacement, and Milk Production (1996)

Variables related to health, reproduction, replacement, and milk production in 111 Danish dairy herds were studied with factor analysis. The objectives were to identify management types and to assess the relevance of those types for herd milk production. Median herd size and total milk production were 59 cows and 7100 kg of energy-corrected milk, respectively. Based on cow data, 22 herd variables were defined. A factor analysis identified 10 first-order factors and 5 second-order factors. The latter factors were valid indicators of replacement intensity, variability of milk production, potential for peak milk production, disease, and a complex pattern related to herd size and age, cow size, and live cattle sales. The potential for peak milk production, replacement intensity, and variability of milk production were strong predictors of herd milk production. Interactions with herd size were important. The derived factor scoring coefficients allowed assessment of the management type of a given herd.
Phenylalanine ammonia lyase in the management of phenylketonuria: the relationship between ingested cinnamate and urinary hippurate in humans. (1982)

The hypothesis that the action of an oral preparation of the enzyme phenylalanine ammonia lyase, used to lower blood phenylalanine levels in phenylketonuria, is by removal of phenylalanine from hydrolysed protein in the lumen of the gut has been examined. Phenylalanine ammonia lyase mediates the conversion of phenylalanine to cinnamate. If cinnamate is produced in the gut it will be absorbed and converted to hippurate in the liver. However, treatment with phenylalanine ammonia lyase does not result in raised urinary hippurate ammonia lyase does not result in raised urinary hippurate levels while ingestion of cinnamate does.
Radiographic Changes in Algodystrophy of the Hand (1991)

It is not certain to what extent the radiographic features of post-traumatic algodystrophy can be differentiated from disuse atrophy following trauma. A semi-quantitative scoring system has been devised, grading the dominant features seen on radiography in both conditions following Colles' fracture. The technique had intra- and inter-observer errors of 14% and 17% respectively. When applied prospectively 7 weeks after Colles' fractures, there was a significantly greater score in patients with algodystrophy (p less than 0.001) than those without. Analysis of the scores was performed to identify a score for the optimal identification of algodystrophy. At a score of four or greater, 87.5% of patients with algodystrophy were positively identified with a positive predictive value of 83%. It is suggested that use of this scoring system will aid in the early diagnosis of algodystrophy.
Treatment of murine lupus with anti-CD4 monoclonal antibodies. (1993)

Extensive studies in lupus-prone mice strongly suggest that mAbs to CD4 may be effective in SLE. By virtue of their selectivity for distinct cells within the immune system, anti-CD4 mAbs may be both more potent and less toxic than current therapies for SLE. In addition, their potential to block the host immune response to therapy may provide a critical advantage for anti-CD4 compared to other forms of mAb therapy. The problem of generalized immune suppression remains a significant obstacle to the use of anti-CD4 in humans, but it may be minimized by the use of mAb fragments or mAb isotypes that can reversibly inhibit immune function without depleting CD4+ T cells.
Structural and molecular determinants of HIV-1 Gag binding to the plasma membrane (2015)

Targeting of the Gag polyprotein to the plasma membrane (PM) for assembly is a critical event in the late phase of immunodeficiency virus type-1 (HIV-1) infection. Gag binding to the PM is mediated by interactions between the myristoylated matrix (MA) domain and PM lipids. Despite the extensive biochemical and in vitro studies of Gag and MA binding to membranes over the last two decades, the discovery of the role of phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] in Gag binding to the PM has sparked a string of studies aimed at elucidating the molecular mechanism of retroviral Gag-PM binding. Electrostatic interactions between a highly conserved basic region of MA and acidic phospholipids have long been thought to be the main driving force for Gag-membrane interactions. However, recent studies suggest that the mechanism is rather complex since other factors such as the hydrophobicity of the membrane interior represented by the acyl chains and cholesterol also play important roles. Here we summarize the current understanding of HIV-1 Gag-membrane interactions at the molecular and structural levels and briefly discuss the underlying forces governing interactions of other retroviral MA proteins with the PM.
Human Sperm Binding Is Mediated by the Sialyl-Lewis x Oligosaccharide on the Zona Pellucida (2011)

Human fertilization begins when spermatozoa bind to the extracellular matrix coating of the oocyte, known as the zona pellucida (ZP). One spermatozoan then penetrates this matrix and fuses with the egg cell, generating a zygote. Although carbohydrate sequences on the ZP have been implicated in sperm binding, the nature of the ligand was unknown. Here, ultrasensitive mass spectrometric analyses revealed that the sialyl-Lewis(x) sequence [NeuAcα2-3Galβ1-4(Fucα1-3)GlcNAc], a well-known selectin ligand, is the most abundant terminal sequence on the N- and O-glycans of human ZP. Sperm-ZP binding was largely inhibited by glycoconjugates terminated with sialyl-Lewis(x) sequences or by antibodies directed against this sequence. Thus, the sialyl-Lewis(x) sequence represents the major carbohydrate ligand for human sperm-egg binding.
Persistent and improved functional gain in mdx dystrophic mice after treatment with L‐arginine and deflazacort (2006)

Although an increase in nitric oxide (NO) in muscle is reported to improve the outcome of deflazacort treatment for mdx mouse muscular dystrophy, the genetic homologue of Duchenne muscular dystrophy (DMD), the impact such treatment on the functional outcomes of the disease, including fiber susceptibility to exercise-induced injury, is not established. Experiments were designed to test whether treatment with deflazacort and L-arginine (a substrate for NO synthase, NOS) would change the extent of fiber injury induced by 24 h of voluntary exercise. The impact of exercise-related injury to induce a secondary regenerative response by muscle was also examined as corroborating evidence of muscle damage. Dystrophic mdx mice were treated for 3 wk with placebo, deflazacort, or deflazacort plus either L-arginine or N(G)-nitro-L-arginine methyl ester (a NOS inhibitor). Deflazacort, especially combined with L-arginine, spared quadriceps muscle from injury-induced regeneration (myf5 expression) compared with placebo treatment, despite an increase in membrane permeability immediately after exercise (assessed by Evans blue dye infiltration). Deflazacort alone prevented the typical progressive loss of function (measured as voluntary distance run over 24 h) that was observed 3 months later in placebo-treated mice. Therefore, combined deflazacort plus L-arginine treatment spared mdx dystrophic limb muscle from exercise-induced damage and the need for regeneration and induced a persistent functional improvement in distance run. Results suggest a potential new treatment option for improving the quality of life for boys with DMD.
The Complement Component C1s Is the Protease That Accounts for Cleavage of Insulin-like Growth Factor-binding Protein-5 in Fibroblast Medium (2000)

Cultured fibroblasts secrete an 88-kDa serine protease that cleaves insulin-like growth factor binding protein-5 (IGFBP-5). Because IGFBP-5 has been shown to regulate IGF-I actions, understanding the chemical identity and regulation of this protease is important for understanding how IGF-I stimulates anabolic functions. The protease was purified from human fibroblast-conditioned medium by hydrophobic interaction, lectin affinity, and heparin Sepharose affinity chromatography followed by SDS-polyacrylamide gel electrophoresis. An 88-kDa band was excised and digested with lysyl-endopeptidase. Sequencing of the high pressure liquid chromatography-purified peptides yielded the complement components C1r and C1s. To confirm that C1r/C1s accounted for the proteolytic activity in the medium, immunoaffinity chromatography was performed. Most of the protease activity adhered to the column, and the eluant was fully active in cleaving IGFBP-5. SDS-polyacrylamide gel electrophoresis with silver staining showed two bands, and IGFBP-5 zymography showed a single 88-kDa band. Amino acid sequencing confirmed that the 88-kDa band contained only C1r and C1s. C1r in the fibroblast medium underwent autoactivation, and the activated form cleaved C1s. C1s purified from the conditioned medium cleaved C(4), a naturally occurring substrate. The purified protease cleaved IGFBP-5 but had no activity against IGFBP-1 through -4. C1 inhibitor, a protein known to inhibit activated C1s, was shown to inhibit the cleavage of IGFBP-5 by the protease in the conditioned medium. In summary, human fibroblasts secrete C1r and C1s that actively cleave IGFBP-5. The findings define a mechanism for cleaving IGFBP-5 in the culture medium, thus allowing release of IGF-I to cell surface receptors.
Structural Insights into the Tumor-Promoting Function of the MTDH-SND1 Complex (2014)

Metadherin (MTDH) and Staphylococcal nuclease domain containing 1 (SND1) are overexpressed and interact in diverse cancer types. The structural mechanism of their interaction remains unclear. Here, we determined the high-resolution crystal structure of MTDH-SND1 complex, which reveals an 11-residue MTDH peptide motif occupying an extended protein groove between two SN domains (SN1/2), with two MTDH tryptophan residues nestled into two well-defined pockets in SND1. At the opposite side of the MTDH-SND1 binding interface, SND1 possesses long protruding arms and deep surface valleys that are prone to binding with other partners. Despite the simple binding mode, interactions at both tryptophan-binding pockets are important for MTDH and SND1's roles in breast cancer and for SND1 stability under stress. Our study reveals a unique mode of interaction with SN domains that dictates cancer-promoting activity and provides a structural basis for mechanistic understanding of MTDH-SND1-mediated signaling and for exploring therapeutic targeting of this complex.