gebhart/patrepeval huggingface dataset:
Native and Non-native Secondary Structure and Dynamics in the pH 4 Intermediate of Apomyoglobin (2000)

The partly folded state of apomyoglobin at pH 4 represents an excellent model for an obligatory kinetic folding intermediate. The structure and dynamics of this intermediate state have been extensively examined using NMR spectroscopy. Secondary chemical shifts, (1)H-(1)H NOEs, and amide proton temperature coefficients have been used to probe residual structure in the intermediate state, and NMR relaxation parameters T(1) and T(2) and ¿(1)H¿-(15)N NOE have been analyzed using spectral densities to correlate motion of the polypeptide chain with these structural observations. A significant amount of helical structure remains in the pH 4 state, indicated by the secondary chemical shifts of the (13)C(alpha), (13)CO, (1)H(alpha), and (13)C(beta) nuclei, and the boundaries of this helical structure are confirmed by the locations of (1)H-(1)H NOEs. Hydrogen bonding in the structured regions is predominantly native-like according to the amide proton chemical shifts and their temperature dependence. The locations of the A, G, and H helix segments and the C-terminal part of the B helix are similar to those in native apomyoglobin, consistent with the early, complete protection of the amides of residues in these helices in quench-flow experiments. These results confirm the similarity of the equilibrium form of apoMb at pH 4 and the kinetic intermediate observed at short times in the quench-flow experiment. Flexibility in this structured core is severely curtailed compared with the remainder of the protein, as indicated by the analysis of the NMR relaxation parameters. Regions with relatively high values of J(0) and low values of J(750) correspond well with the A, B, G, and H helices, an indication that nanosecond time scale backbone fluctuations in these regions of the sequence are restricted. Other parts of the protein show much greater flexibility and much reduced secondary chemical shifts. Nevertheless, several regions show evidence of the beginnings of helical structure, including stretches encompassing the C helix-CD loop, the boundary of the D and E helices, and the C-terminal half of the E helix. These regions are clearly not well-structured in the pH 4 state, unlike the A, B, G, and H helices, which form a native-like structured core. However, the proximity of this structured core most likely influences the region between the B and F helices, inducing at least transient helical structure.
Regulation and plasticity of intestinal stem cells during homeostasis and regeneration (2016)

The intestinal epithelium is the fastest renewing tissue in mammals and has a large flexibility to adapt to different types of damage. Lgr5<sup>+</sup> crypt base columnar (CBC) cells act as stem cells during homeostasis and are essential during regeneration. Upon perturbation, the activity of CBCs is dynamically regulated to maintain homeostasis and multiple dedicated progenitor cell populations can reverse to the stem cell state upon damage, adding another layer of compensatory mechanisms to facilitate regeneration. Here, we review our current understanding of how intestinal stem and progenitor cells contribute to homeostasis and regeneration, and the different signaling pathways that regulate their behavior. Nutritional state and inflammation have been recently identified as upstream regulators of stem cell activity in the mammalian intestine, and we explore how these systemic signals can influence homeostasis and regeneration.
Substrate Specificities of the Soluble and Particulate Methane Mono-oxygenases of Methylosinus trichosporium OB3b (1984)

The intracellular location of methane mono-oxygenase (MMO) (soluble or particulate) in Methylosinus trichosporium OB3b is dependent on the availability of copper in the growth medium. Raising the Cu2+ concentration from 1 μm to 5 μm effected a transition from soluble to particulate MMO activity, and changes in major cell polypeptides were observed on SDS-polyacrylamide gels. Organisms containing soluble MMO oxidized a wide range of substrates including n-alkanes, n-alkenes, aromatic and alicyclic compounds. By contrast, organisms containing particulate MMO did not oxidize aromatic or alicyclic compounds. These observations provide further evidence that the two types of MMO are fundamentally different.
Phase I trial of gemcitabine (Gemzar®), 24 h infusion 5-fluorouracil and folinic acid in patients with inoperable pancreatic cancer (1999)

Gemcitabine (Gemzar) has a significant impact upon survival and quality of life for patients with pancreatic cancer, compared with 5-fluorouracil (5-FU). This phase I study was initiated to define the recommended dose of 5-FU delivered as a 24 h infusion in combination with gemcitabine (1000 mg/m2) and folinic acid (200 mg/m2) in patients with inoperable pancreatic cancer, treated on an outpatient basis. Drugs were administered weekly for 4 weeks out of 6 weeks. Sixteen chemonaive patients (median age 59 years, range 51-66) were enrolled, 15 had stage IV and one stage III disease. The median Karnofsky performance score (KPS) was 70 (range 60-80). Six patients received 5-FU 750 mg/m2, eight received 5-FU 1000 mg/m2 and two received 5-FU 1250 mg/m2. The maximum tolerated dose of 5-FU was 1000 mg/m2. Hepatotoxicity was dose limiting. One patient who received 5-FU 1250 mg/m2 died as a result of hepatorenal failure. There was one partial response, nine patients had stable disease for more than 3 months and 13 patients had improved KPS. The median time to progressive disease was 31 weeks (range 5-50 weeks). A phase 11 trial is underway to further assess the activity of this combination at the recommended dose of 750 mg/m2 5-FU.
Active Learning with Support Vector Machine Applied to Gene Expression Data for Cancer Classification (2004)

There is growing interest in the application of machine learning techniques in bioinformatics. The supervised machine learning approach has been widely applied to bioinformatics and gained a lot of success in this research area. With this learning approach researchers first develop a large training set, which is a time-consuming and costly process. Moreover, the proportion of the positive examples and negative examples in the training set may not represent the real-world data distribution, which causes concept drift. Active learning avoids these problems. Unlike most conventional learning methods where the training set used to derive the model remains static, the classifier can actively choose the training data and the size of training set increases. We introduced an algorithm for performing active learning with support vector machine and applied the algorithm to gene expression profiles of colon cancer, lung cancer, and prostate cancer samples. We compared the classification performance of active learning with that of passive learning. The results showed that employing the active learning method can achieve high accuracy and significantly reduce the need for labeled training instances. For lung cancer classification, to achieve 96% of the total positives, only 31 labeled examples were needed in active learning whereas in passive learning 174 labeled examples were required. That meant over 82% reduction was realized by active learning. In active learning the areas under the receiver operating characteristic (ROC) curves were over 0.81, while in passive learning the areas under the ROC curves were below 0.50.
Fgf-4expression during gastrulation, myogenesis, limb and tooth development in the mouse (1992)

Fgf-4, initially isolated as a transforming gene from human tumors, is a member of the Fibroblast Growth Factor (FGF) family. It has previously been shown by northern blot hybridization analysis to be expressed in teratocarcinoma and embryonic stem cells, suggesting that it plays a role in embryonic development. We have carried out an RNA in situ hybridization analysis of Fgf-4 expression in the developing mouse embryo, from fertilization through the 14th day of gestation (E14.5). Our results show that Fgf-4 RNA is first detected at the late blastocyst stage in cells that give rise to all of the embryonic lineages (inner cell mass cells). During the early stages of gastrulation, expression becomes restricted to the primitive streak where mesoderm and definitive endoderm are formed. Expression continues in the distal (rostral) two-thirds of the streak through approx. E10, and then is detected in the tail bud, which replaces the streak as the primary source of mesoderm. Additional sites of expression are found after the three primary germ layers are established and organogenesis begins. Fgf-4 RNA is detected transiently in the branchial arch units, the somitic myotome, the apical ectodermal ridge of the developing limb bud and the tooth bud, suggesting that the gene has multiple roles during embryogenesis. These results are compared with the expression patterns of other FGF genes. Taken together, the data suggest that individual members of the gene family are expressed sequentially in developmental pathways such as mesoderm formation and myogenesis, and play a role in specific epithelial-mesenchymal interactions.
Generation and phenotypic characterization of new human ovarian cancer cell lines with the identification of antigens potentially recognizable by HLA-restricted cytotoxic T cells (1997)

This study describes a simple method for long-term establishment of human ovarian tumor lines and prediction of T-cell epitopes that could be potentially useful in the generation of tumor-specific cytotoxic T lymphocytes (CTLs). Nine ovarian tumor lines (INT.Ov) were generated from solid primary or metastatic tumors as well as from ascitic fluid. Notably all lines expressed HLA class I, intercellular adhesion molecule-1 (ICAM-1), polymorphic epithelial mucin (PEM) and cytokeratin (CK), but not HLA class II, B7.1 (CD80) or BAGE. While of the 9 lines tested 4 (INT.Ov1, 2, 5 and 6) expressed the folate receptor (FR-alpha) and 6 (INT.Ov1, 2, 5, 6, 7 and 9) expressed the epidermal growth factor receptor (EGFR); MAGE-1 and p185HER-2/neu were only found in 2 lines (INT.Ov1 and 2) and GAGE-1 expression in 1 line (INT.Ov2). The identification of class I MHC ligands and T-cell epitopes within protein antigens was achieved by applying several theoretical methods including: 1) similarity or homology searches to MHCPEP; 2) BIMAS and 3) artificial neural network-based predictions of proteins MAGE, GAGE, EGFR, p185HER-2/neu and FR-alpha expressed in INT.Ov lines. Because of the high frequency of expression of some of these proteins in ovarian cancer and the ability to determine HLA binding peptides efficiently, it is expected that after appropriate screening, a large cohort of ovarian cancer patients may become candidates to receive peptide-based vaccines.
Determination of protein secondary structure by Fourier transform infrared spectroscopy: A critical assessment (1993)

The ultimate goal of structural studies of proteins is to gain insight into protein three-dimensional structure at highresolution level. This can often be accomplished by the application of techniques such as X-ray crystallography or multidimensional nuclear magnetic resonance (NMR) spectroscopy. However, high-resolution studies of proteins are not always feasible. For example, crystallographic studies require high-quality single crystals which for many proteins (e.g., the vast majority of membrane proteins) are not available. Furthermore, the question arises as to whether the relatively “static” structure in single crystals adequately represents the protein conformation in a complex and dynamic environment of living cells. There is a growing realization [e.g., Martinek et al. (1989)l that in vivo most proteins act in an interfacial environmeht where they form dynamic complexes with biological membranes, nucleic acids, polysaccharides, or other proteins. Aqueous buffers, from which protein crystals are usually grown, do not necessarily mimic well the conditions of protein functioning in vivo. NMR offers a somewhat better flexibility in studying protein structure in “biologically relevant” environments. However, the interpretation of NMR spectra of larger proteins is very complex, and the assignment of interproton distances generated by the NMR experiment is not always feasible; at present the technique is restricted to small proteins of less than approximately 15-20 kDa.
Light‐dependent subcellular movement of photoreceptor proteins (1988)

The intracellular localization of photoreceptor-specific proteins 33 kd, beta-transducin, and 48 kd, as determined by immunocytochemistry, is transient and dependent on the lighting environment to which the retina is exposed. Western analysis of the proteins in isolated rod outer segments from mouse retina demonstrates that beta-transducin actually moves from the outer segment to the inner segment in response to light and that 48 kd moves simultaneously in the opposite direction. The light-induced movements appear to be initiated by the absorption of light by rhodopsin because red light, which does not bleach rhodopsin, does not produce this redistribution of photoreceptor proteins. Time course analysis of these movements suggests that the light-induced shift is detectable at the earliest time examined (30 seconds). The bidirectional movement suggests that the photoreceptor cells have at least two distinct dynein-like or kinesin-like translocator molecules that act as microtubule-based motors. This movement appears to be a basic mechanism by which photoreceptor cells rapidly and radically alter the subcellular concentrations of photoreceptor-specific proteins, which in turn may affect the rapid changes in membrane potential that occur during phototransduction.
Melanoma and the Problem of Malignancy (2004)

Of the overt biological properties exhibited by malignant cells two appear to command particular attention; these are (1) the transmigratory ability which empowers these cells to invade surrounding tissues and results in their metastatic and destructive potential, and (2) their ability to evade detection by the immune system of the host. Both of these characteristics may well involve several disparate mechanisms. However, it may be that there are some metabolic features that are common to malignant neoplasms which could go some way to explaining one of these behavioural anomalies. It is proposed that abnormalities of oxidative metabolism of cancer cells, resulting in the generation of reactive oxygen species, are responsible for the inhibition of the functions of vicinal antigen-presenting cells and, thus, the failure of the immune system to recognize tumour-specific antigens likely to be expressed by malignant cells as part of their transmigratory capability.
Near-equilibrium growth of micropipe-free 6H-SiC single crystals by physical vapor transport (1998)

A process for growing micropipe-free single crystals has been developed by using the modified Lely method. The process parameters were kept close to thermal equilibrium. The maximum average thermal gradient inside the growth furnace leading to micropipe-free growth was 5 K/cm. A gradient of 7.5 K/cm already resulted in a strong defect formation and produced a high density of micropipes (&amp;gt;200 cm−2). The highest achieved growth rate providing micropipe-free growth was 0.27 mm/h. For the employed parameter range, 6H-SiC single boule crystals were grown on both the C face and the Si face of 6H-SiC Lely platelets. The grown crystals are electrically and optically characterized.
Electrophilic methane conversion (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleElectrophilic methane conversionGeorge A. OlahCite this: Acc. Chem. Res. 1987, 20, 11, 422–428Publication Date (Print):November 1, 1987Publication History Published online1 May 2002Published inissue 1 November 1987https://doi.org/10.1021/ar00143a006RIGHTS & PERMISSIONSArticle Views1148Altmetric-Citations119LEARN 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 InReddit PDF (800 KB) Get e-Alerts Get e-Alerts
A Radioactive Hapten-Binding Assay for Measuring Antibodies to the Pentapeptide Determinant of Peptidoglycan (1975)

Abstract A major portion of the humoral immune response to peptidoglycans is directed against the non-cross-linked pentapeptide side chains of these ubiquitous bacterial antigens. At present, no specific and sensitive assay for pentapeptide antibody determination is available. Therefore, a radioimmunoassay has been developed which employs the synthetic pentapeptide hapten L-Ala-γ-d-Glu-l-Lys-d-Ala-d-Ala, labeled by the active ester method of Bolton and Hunter to high specific activities (6.74 to 18.18 µCi/µg) with 125I, and used as a reagent for measuring pentapeptide antibody. A-variant streptococcal antisera, known to contain pentapeptide antibodies as shown by quantitative precipitation, would bind more than 95% of the radiolabeled hapten in contrast to 2 to 3% by preimmune rabbit sera. Specificity of the binding reaction was demonstrated by inhibition experiments employing various synthetic oligopeptides related or unrelated to the pentapeptide in the radioimmunoassay. Binding curves established with serial dilutions of peptidoglycan antiserum were linear from 15 to 500 µg/ml of antibody permitting pentapeptide antibody measurement within this range. Comparative data on pentapeptide antibody determinations by quantitative precipitation and radioimmunoassay are given and the time course of the production of this antibody in 14 rabbits hyperimmunized with A-variant streptococcal vaccine is reported.
Activity of Monosaccharide Lipid A Analogues in Human Monocytic Cells as Agonists or Antagonists of Bacterial Lipopolysaccharide (1999)

The lipid A portion of bacterial lipopolysaccharide (LPS) plays a central role in the production of endotoxic mediators. Different responses between human and murine macrophages to lipid A-like structures have been indicated. We investigated a series of structurally related monosaccharide lipid A analogues for their potency to activate human macrophage U937 cells and peripheral blood mononuclear cells for production of tumor necrosis factor-alpha and interleukin-6 compared with their potency to activate murine macrophage RAW264.7 cells. Two of the analogues were found to have sufficient potency to activate the human cells as well as the murine cells. These analogues comprise D-glucosamine, phosphoryl groups, and acyl groups of defined carbon chain lengths (C(14) and C(12)) in a ratio of 1:1:3. This ratio of molecular constituents is proportional to that of the complete disaccharide structure of lipid A (2:2:6). Other analogues with two or four C(14) acyl groups and with three acyl groups but including a C(10) or a C(16) acyl group, which are active to murine cells, showed no LPS-agonistic activity, but did show LPS-antagonistic activity, to human cells. An LPS-antagonistic analogue in the murine cells also showed antagonistic activity in human cells. These results reveal that lipid A analogues recognized as being LPS agonists by human macrophages have common structural features in monosaccharide and disaccharide structures which are more strict than those required for recognition by murine macrophages and that broad lipid A-like structures are recognized as being LPS antagonists by human cells but are recognized by murine cells as being either LPS agonists or antagonists.
Performance Evaluation for Multi-arm Manipulation of Hollow Suspended Organs (2008)

This paper presents a unified mathematical framework for modeling and evaluating the performance of multiple robotic arms that operate on hollow suspended organs. This framework is applied to a novel two-armed hybrid robotic system being developed for ophthalmic vitreous surgeries. Four cases are designated to capture the general movements required for any surgical procedure associated with hollow suspended organs. Dexterity measures, based on multiple characteristic lengths, are presented for procedures corresponding to these manipulation cases. Simulation results of the dual-arm robotic system for ophthalmic surgery are presented for all four manipulation cases. A comparison of this robotic system with current surgical tools shows a significant improvement in intraocular dexterity.
Veltuzumab, an anti-CD20 mAb for the treatment of non-Hodgkin's lymphoma, chronic lymphocytic leukemia and immune thrombocytopenic purpura. (2009)

Veltuzumab is a humanized, second-generation anti-CD20 mAb currently under development by Immunomedics Inc for the potential treatment of B-cell non-Hodgkin's lymphoma (NHL) and chronic lymphocytic leukemia (CLL). Licensee Nycomed is developing veltuzumab for the potential treatment of rheumatoid arthritis and immune thrombocytopenic purpura (ITP). Veltuzumab contains 90 to 95% human antibody sequences with identical antigen framework regions to epratuzumab (a humanized anti-CD22 mAb) and similar antigen-binding determinants to rituximab (chimeric, anti-CD20 mAb and the first-line treatment of aggressive and indolent NHL). In vitro studies have demonstrated that veltuzumab has enhanced binding avidities and a stronger effect on complement-dependent cytotoxicity compared with rituximab in selected cell lines. In dose-finding phase I/II clinical trials in patients with low-grade NHL, intravenous veltuzumab demonstrated a substantial rate of complete responses in concurrence with shorter and more tolerable infusions compared with rituximab. Currently there has been no evidence of an immune response to repeated administrations, and no serious adverse events related to veltuzumab treatment in patients with NHL. Veltuzumab is undergoing clinical trials using a low-dose subcutaneous formulation in patients with NHL, CLL and ITP. Prospective, randomized clinical trials are needed to clarify the role veltuzumab will play in a market where the therapy of B-cell lymphoproliferative disorders is dominated by rituximab.
Bacteriological studies on the coagulation of evaporated milk (1915)

The value of milk as a food has led to many attempts at its preservation until at the present time various kinds of dried and canned milks are manufactured. The canned milks, because of the water contained in them, are open to bacteriological changes unless the action of microorganisms is overcome by either killing those present or by making the conditions unsuited to their growth.