gebhart/patrepeval huggingface dataset:
Biocomputing: informatics and genome projects. (1994)

D.W. Smith, Introduction. S.P. Clark, G.A. Evans, and H.R. Garner, Informatics and Automation Used in Physical Mapping of the Genome. D.W. Smith, J. Jorgensen, J.P. Greenberg, J. Keller, J. Rogers, H.R. Garner, and L.T. Eyck, Supercomputers, Parallel Processing, and Genome Projects. S. Henikoff, Comparative Sequence Analysis: Finding Genes. A.K. Knopka, Sequence and Codes: Fundamentals of Biomolecular Cryptology. C. Wills, Phylogenetic Analysis and Molecular Evolution. B.I. Cohen and F.E. Cohen, Predictions of Protein Secondary and Tertiary Structure. K. Yoshida, C.L. Smith, and R. Overbeek, A Primer on Rapid Prototyping of Genomic Databases in Prolog. D.W. Mount and B.R. Schatz, A Genomic Database of E. coli: Total Information on a Given Organism. A.R. Galper and D.L. Brutlag, Computational Simulations of Biological Systems. Index.
Multiple Metabolic Roles for the Nonphotosynthetic Plastid of the Green Alga Prototheca wickerhamii (2005)

The presence of plastids in diverse eukaryotic lineages that have lost the capacity for photosynthesis is well documented. The metabolic functions of such organelles, however, are poorly understood except in the case of the apicoplast in the Apicomplexa, a group of intracellular parasites including Plasmodium falciparum, and the plastid of the green alga Helicosporidium sp., a parasite for which the only host-free stage identified in nature so far is represented by cysts. As a first step in the reconstruction of plastid functions in a nonphotosynthetic, predominantly free-living organism, we searched for expressed sequence tags (ESTs) that correspond to nucleus-encoded plastid-targeted polypeptides in the green alga Prototheca wickerhamii. From 3,856 ESTs, we found that 71 unique sequences (235 ESTs) correspond to different nucleus-encoded putatively plastid-targeted polypeptides. The identified proteins predict that carbohydrate, amino acid, lipid, tetrapyrrole, and isoprenoid metabolism as well as de novo purine biosynthesis and oxidoreductive processes take place in the plastid of P. wickerhamii. Mg-protoporphyrin accumulation and, therefore, plastid-to-nucleus signaling might also occur in this nonphotosynthetic organism, as we identified a transcript which encodes subunit I of Mg-chelatase, the enzyme which catalyzes the first committed step in chlorophyll synthesis. Our data indicate a far more complex metabolism in P. wickerhamii's plastid compared with the metabolic pathways predicted to be located in the apicoplast of P. falciparum and the plastid of Helicosporidium sp.
Nanoheteroepitaxy: The Application of nanostructuring and substrate compliance to the heteroepitaxy of mismatched semiconductor materials (1999)

This article describes an approach to the heteroepitaxy of lattice mismatched semiconductors, that we call nanoheteroepitaxy. The theory developed here shows that the 3D stress relief mechanisms that are active when an epilayer is nucleated as an array of nanoscale islands on a compliant patterned substrate, will significantly reduce the strain energy in the epilayer and extend the critical thickness dramatically. Calculations show that with the scale of patterning that is achievable with advanced lithography (10–100 nm) we can eliminate mismatch dislocations from heterojunctions that are mismatched by as much as 4.2%.
Methadone in saliva (1991)

Journal Article Methadone in saliva Get access K Wolff, K Wolff Search for other works by this author on: Oxford Academic Google Scholar A Hay, A Hay Search for other works by this author on: Oxford Academic Google Scholar D Raistrick D Raistrick Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 37, Issue 7, 1 July 1991, Pages 1297–1298, https://doi.org/10.1093/clinchem/37.7.1297 Published: 01 July 1991
Correlation of nuclear morphometry with progression of breast cancer (1991)

Alterations in nuclear structure are the morphologic hallmark of cancer diagnosis. Nuclear size, shape, chromatin pattern, and nucleolar size and number have all been reported to change in breast cancer. Attempts to quantify nuclear alterations to establish grading systems, predict prognosis, and/or set guidelines for therapy have met with varied success. Therefore, the authors quantified the changes that occur with breast cancer with nuclear morphology in several different groups of patients: normal controls, intraductal carcinoma, invasive ductal carcinoma with negative nodes at mastectomy, and invasive ductal carcinoma with positive lymph nodes. Pleomorphism as measured by both nuclear area and intrasample variation increased with invasive histology and metastatic breast cancer. It is still unclear whether node-negative Stage II breast cancer requires adjuvant therapy. This issue would be less complicated if it were possible to identify those women at high risk of recurrence. Therefore, the authors retrospectively identified 30 women with node-negative Stage II infiltrating ductal carcinoma with a long follow-up period of 6 to 12 years. Computer-assisted morphometry of nuclei in routine hematoxylin and eosin-stained pathologic slides was done using the DynaCell Analysis System in a blinded fashion. DynaCell measures 15 nuclear parameters, including perimeter, area volume, roundness, and ellipticity. Although nuclear area and variance were related to breast cancer progression, nuclear morphometry did not predict successfully which patients would have recurrent disease in the women with Stage II, node-negative lesions at the time of mastectomy.
Efficient Zerotree-Based Image Compression With Directionlets (2007)

Publication in the conference proceedings of EUSIPCO, Poznan, Poland, 2007
Immunohistochemical analysis of Bin1/Amphiphysin II in human tissues: Diverse sites of nuclear expression and losses in prostate cancer (2002)

The Bin1/Amphiphysin II gene encodes at least seven alternately spliced adapter proteins that have been implicated in membrane dynamics and nuclear processes. Nuclear localized Bin1 polypeptides have tumor suppressor and proapoptotic activities, suggesting that Bin1 may suppress cancer in tissues where nuclear expression may occur. One question is the extent to which human tissues express nuclear Bin1 isoforms. A secondary issue has been the need for a specific antibody that can detect all the splice isoforms expressed by the human, mouse, and rat Bin1 genes. Using a novel mouse monoclonal antibody with these characteristics, we performed an immunohistochemical analysis of Bin1 expression in a panel of normal human tissues. We also compared the expression profile of Bin1 in normal or malignant tissues derived from human prostate, where Bin1 is a candidate tumor suppressor gene. In brain, a distinct nuclear staining pattern overlapped with a cytosolic staining pattern present in certain layers of the cerebral cortex and cerebellum. Bone marrow cells displayed mainly nuclear localization whereas peripheral lymphoid cells exhibited mainly cytosolic localization. In several epithelial tissues, nuclear or nucleocytosolic staining patterns were displayed by basal cells in skin, breast, or prostate, whereas cytosolic or plasma membrane-associated staining patterns were noted in gastrointestinal cells. Interestingly, a striking gradient of expression was observed in gastrointestinal epithelia, particularly in the large intestine, with the strongest staining displayed by cells destined to undergo apoptosis at the villus tip. In prostate, Bin1 staining was frequently absent in cases of primary prostate adenocarcinoma. This study used a novel reagent to document the extent of expression of nuclear Bin1 isoforms, which exhibit cancer suppression and proapoptotic activity in human cells.
Structure of cutinase gene, cDNA, and the derived amino acid sequence from phytopathogenic fungi (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure of cutinase gene, cDNA, and the derived amino acid sequence from phytopathogenic fungiWilliam F. Ettinger, Sushil K. Thukral, and Pappachan E. KolattukudyCite this: Biochemistry 1987, 26, 24, 7883–7892Publication Date (Print):December 1, 1987Publication History Published online1 May 2002Published inissue 1 December 1987https://pubs.acs.org/doi/10.1021/bi00398a052https://doi.org/10.1021/bi00398a052research-articleACS PublicationsRequest reuse permissionsArticle Views410Altmetric-Citations72LEARN 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
Seizures, sensorineural deafness, ataxia, mental retardation, and electrolyte imbalance (SeSAME syndrome) caused by mutations in KCNJ10 (2009)

We describe members of 4 kindreds with a previously unrecognized syndrome characterized by seizures, sensorineural deafness, ataxia, mental retardation, and electrolyte imbalance (hypokalemia, metabolic alkalosis, and hypomagnesemia). By analysis of linkage we localize the putative causative gene to a 2.5-Mb segment of chromosome 1q23.2-23.3. Direct DNA sequencing of KCNJ10, which encodes an inwardly rectifying K(+) channel, identifies previously unidentified missense or nonsense mutations on both alleles in all affected subjects. These mutations alter highly conserved amino acids and are absent among control chromosomes. Many of these mutations have been shown to cause loss of function in related K(+) channels. These findings demonstrate that loss-of-function mutations in KCNJ10 cause this syndrome, which we name SeSAME. KCNJ10 is expressed in glia in the brain and spinal cord, where it is believed to take up K(+) released by neuronal repolarization, in cochlea, where it is involved in the generation of endolymph, and on the basolateral membrane in the distal nephron. We propose that KCNJ10 is required in the kidney for normal salt reabsorption in the distal convoluted tubule because of the need for K(+) recycling across the basolateral membrane to enable normal activity of the Na(+)-K(+)-ATPase; loss of this function accounts for the observed electrolyte defects. Mice deficient for KCNJ10 show a related phenotype with seizures, ataxia, and hearing loss, further supporting KCNJ10's role in this syndrome. These findings define a unique human syndrome, and establish the essential role of basolateral K(+) channels in renal electrolyte homeostasis.
THE SURGICAL MANAGEMENT OF ATRIAL FIBRILLATION (1997)

Atrial fibrillation is the most common dysrhythmia encountered in clinical practice. For some patients, satisfactory rate control is not possible by pharmacologic means. This led us to develop a surgical approach to its cure, which in turn has led to a deeper understanding of the electrophysiologic basis of atrial fibrillation and to the development of a surgical procedure that is highly effective in restoring sinus rhythm with an acceptable mortality and morbidity. We review these findings as well as the clinical results obtained with the Maze procedure.
Lymphokine-activated killer cell activity of CD4-CD8- TCR alpha beta + thymocytes. (1993)

Functions of CD4-8-TCR alpha beta+ thymocytes, which are characterized by predominant usage of V beta 8.2 TCR, have remained unclear. In this study, we found that the CD4-8-TCR alpha beta + thymocytes expressed NK1.1 Ag and IL-2R beta-chain but not IL-2R alpha-chain. When the CD4-8- TCR alpha beta + thymocytes were cultured in the presence of IL-2, the CD4-8-TCR alpha beta + thymocytes vigorously proliferated. After 7 days of culture in the presence of 1000 U/ml of IL-2, approximately half of the CD4-8-TCR alpha beta + thymocytes lost NK1.1 Ag. However, the remaining half of the CD4-8-TCR alpha beta + cells showed increasing levels of NK1.1 Ag and acquired killer activity against tumor cells such as YAC-1, P815, and EL-4. These cells also killed syngeneic as well as allogeneic thymocytes. The LAK activity by the NK1.1+ CD4-8-TCR alpha beta + thymocytes was not inhibited by anti-NK1.1, anti-TCR alpha beta, or anti-CD44 mAb but was partially inhibited by anti-LFA-1 mAb. These findings indicate that the CD4-8-TCR alpha beta + thymocyte population can be divided into two population on the basis of NK1.1 expression after culture in the presence of IL-2. The NK1.1 Ag expression on the cultured CD4-8-TCR alpha beta + seems to be correlated to acquisition of LAK activity, although the NK1.1 Ag itself may not be directly involved in the target cell recognition. The present data suggest that the CD4-8- TCR alpha beta + thymocyte population is a functional T cell lineage which may serve as cells of immune defense and/or immune regulation.
Helical epitopes determined by low‐stringency antibody screening of a combinatorial peptide library (1997)

Combinatorial phage display peptide libraries are routinely used to map epitopes of specific monoclonal antibodies. In this study we illustrate that these libraries can be used in the analysis of protein structure. By screening libraries at low stringency, a collection of phages can be obtained. These are characterized by the fact that they are recognized by a given monoclonal antibody yet with various affinities. Comparing the random peptides of these phages indicates the common essential residues necessary for antibody recognition. Aligning the inserts based on the detected homology has revealed structural motifs that correspond to secondary protein structures. The envelope protein of HIV-1 has been studied using this approach. A combinatorial phage display library containing a 20 mer random peptide in protein III of the filamentous phage fd-tet has been used to analyze two different monoclonal antibodies directed against gp120. Our results provide experimental evidence that indicate that the C1 domain of gp120 contains an alpha helix.
Exploring the design space for adaptive graphical user interfaces (2006)

For decades, researchers have presented different adaptive user interfaces and discussed the pros and cons of adaptation on task performance and satisfaction. Little research, however, has been directed at isolating and understanding those aspects of adaptive interfaces which make some of them successful and others not. We have designed and implemented three adaptive graphical interfaces and evaluated them in two experiments along with a non-adaptive baseline. In this paper we synthesize our results with previous work and discuss how different design choices and interactions affect the success of adaptive graphical user interfaces.
Effect of Guar Gum on Mineral Balances in NIDDM Adults (1989)

The self-selected diet of 16 subjects with non-insulin-dependent diabetes mellitus (NIDDM) was supplemented for 6 mo with either a granolalike bar containing 35.5 g carbohydrate and 6.6 g guar gum/bar or a placebo bar containing carbohydrate but no guar gum. Subjects consumed a mean of 4.8 bars/day. Average guar gum consumption at the end of the study was 31.7 g/day. One week before and at the end of the study, subjects were admitted to a metabolic ward and fed a controlled diet similar to their self-selected diet. Food, feces, and urine were composited for analysis of iron, zinc, copper, calcium, magnesium, and manganese. Eight subjects consuming the guar gum supplement and 6 subjects consuming the placebo bar completed collections for mineral balance. Neither consumption of guar gum nor placebo bar significantly changed apparent mineral balance for iron, copper, zinc, calcium, manganese, or magnesium from prestudy levels to 6-mo levels, and no significant differences were observed between the two groups. With the exception of copper, men consumed significantly more minerals than women. We conclude that consumption of guar gum by patients with NIDDM does not adversely affect apparent mineral balance.
Three-dimensional rigorous simulation of EUV defective masks using modal method by Fourier expansion (2006)

In Extreme Ultraviolet Lithography, the electromagnetic modelling of the mask allows determining the influence of the mask structure on the electromagnetic field. That makes it possible to take into account the presence of a defect modifying the multi-layer stack<sup>1,2</sup>. The method used throughout this paper is the MMFE (Modal Method by Fourier Expansion) also known as the RCWA (Rigorous Coupled Wave Analysis). Modal methods allow computing the electromagnetic field just above the EUV mask or the near field. Modal methods are well adapted for EUV mask simulation due to materials and structure size. The previous works performed on 2D simulation with MMFE<sup>3</sup> have shown the influence of a defect inside a EUV mask structure. In this article, the method is extended to address 3D structures. The printability of a spherical shaped defect is analyzed depending on the deposition process used. The influence of a 3D defect position regarding the position of a line absorber is also shown.
Identification of a New Class of Nonpeptidic Inhibitors of Cruzain (2008)

Cruzain is the major cysteine protease of Trypanosoma cruzi, which is the causative agent of Chagas disease and is a promising target for the development of new chemotherapy. With the goal of developing potent nonpeptidic inhibitors of cruzain, the substrate activity screening (SAS) method was used to screen a library of protease substrates initially designed to target the homologous human protease cathepsin S. Structure-based design was next used to further improve substrate cleavage efficiency by introducing additional binding interactions in the S3 pocket of cruzain. The optimized substrates were then converted to inhibitors by the introduction of cysteine protease mechanism-based pharmacophores. Inhibitor 38 was determined to be reversible even though it incorporated the vinyl sulfone pharmacophore that is well documented to give irreversible cruzain inhibition for peptidic inhibitors. The previously unexplored beta-chloro vinyl sulfone pharmacophore provided mechanistic insight that led to the development of potent irreversible acyl- and aryl-oxymethyl ketone cruzain inhibitors. For these inhibitors, potency did not solely depend on leaving group p K a, with 2,3,5,6-tetrafluorophenoxymethyl ketone 54 identified as one of the most potent inhibitors with a second-order inactivation constant of 147,000 s (-1) M (-1). This inhibitor completely eradicated the T. cruzi parasite from mammalian cell cultures and consequently has the potential to lead to new chemotherapeutics for Chagas disease.
Transformation System for Hypocrea jecorina ( Trichoderma reesei ) That Favors Homologous Integration and Employs Reusable Bidirectionally Selectable Markers (2010)

Hypocrea jecorina is an industrially important filamentous fungus due to its effective production of hydrolytic enzymes. It has received increasing interest because of its ability to convert lignocellulosic biomass to monomeric sugars, which can be converted into biofuels or platform chemicals. Genetic engineering of strains is a highly important means of meeting the requirements of tailor-made applications. Therefore, we report the development of a transformation system that allows highly efficient gene targeting by using a tmus53 (human LIG4 homolog) deletion strain. Moreover, it permits the unlimited reuse of the same marker by employing a Cre/loxP-based excision system. Both marker insertion and marker excision can be positively selected for by combining resistance to hygromycin B and loss of sensitivity to fluoroacetamide. Finally, the marker pyr4, also positively selectable for insertion and loss, can be used to remove the cre gene.
Effect of recombinant human interleukin‐11 on rat megakaryopoiesis and thrombopoiesis in vivo: comparative study with interleukin‐6 (1993)

The ability of recombinant human interleukin-11 (IL-11) to stimulate rat megakaryopoiesis and thrombopoiesis in vivo was investigated. Once daily subcutaneous injections of IL-11 at doses of 2, 8 and 20 micrograms/rat for 5 d caused dose-dependent increases in platelet counts. The chronic administration of 20 micrograms/rat/d for 14 d resulted in biphasic increases in platelet counts with peaks at days 8 and 15 of up to 30% over the control, continuing for more than 5 d after cessation of IL-11 injections. Moreover, a striking increase in megakaryocytic size and ploidy in bone marrow in response to IL-11 was elicited. IL-11 induced a dose-dependent elevation in bone marrow cell numbers but not in splenic weight and cell numbers. Modifications of these parameters were noted as soon as 24 h after the first IL-11 injections. IL-11 had a same potency of thrombopoietic effect in rats as compared with IL-6. However, elevation of acute phase protein such as immunosuppressive acidic protein was 2.2-fold in rats given 20 micrograms/d of IL-6 over those receiving a same dose of IL-11 (470 v 210 micrograms/ml). In addition, the rate of body-weight increase in rats receiving IL-11 for 5 d as well as 14 d did not differ from that in control animals. In IL-6 treated rats, the increase in body weight was significantly slower than the controls, which was observed even in the group given 8 micrograms/d of IL-6. These results suggest that IL-11 may be an effective strategy for the treatment of thrombocytopenia.
Proteomic Mapping of 4-Hydroxynonenal Protein Modification Sites by Solid-Phase Hydrazide Chemistry and Mass Spectrometry (2007)

The modification of proteins by the cytotoxic, reactive aldehyde 4-hydroxynonenal (HNE) is known to alter protein function and impair cellular mechanisms. In order to identify susceptible amino acid sites of HNE modification within complex biological mixtures by microcapillary liquid chromatography and linear ion trap tandem mass spectrometry, we have developed a solid-phase capture and release strategy that utilizes reversible hydrazide chemistry to enrich HNE-modified peptides. To maximize the detection of fragment ions diagnostic of HNE modification, both neutral loss-dependent acquisition of MS/MS/MS spectra and the pulsed Q dissociation operation mode were employed. When the solid-phase hydrazide enrichment strategy was applied to a yeast lysate treated with HNE, 125 distinct amino acid sites of HNE modification were mapped on 67 different proteins. The endogenous susceptibility of many of these proteins to HNE modification was demonstrated by analyzing HNE-treated yeast cell cultures with a complementary biotin hydrazide enrichment strategy. Further analysis revealed that the majority of amino acid sites susceptible to HNE modification were histidine residues, with most of these sites being flanked by basic amino acid residues, and predicted to be solvent exposed. These results demonstrate the effectiveness of this novel strategy as a general platform for proteome-scale identification of amino acid sites susceptible to HNE modification from within complex mixtures.