gebhart/patrepeval huggingface dataset:
Structure of the O antigen of Escherichia coli K-12 and the sequence of its rfb gene cluster (1994)

Escherichia coli K-12 has long been known not to produce an O antigen. We recently identified two independent mutations in different lineages of K-12 which had led to loss of O antigen synthesis (D. Liu and P. R. Reeves, Microbiology 140:49-57, 1994) and constructed a strain with all rfb (O antigen) genes intact which synthesized a variant of O antigen O16, giving cross-reaction with anti-O17 antibody. We determined the structure of this O antigen to be -->2)-beta-D-Galf-(1-->6)-alpha-D-Glcp- (1-->3)-alpha-L-Rhap-(1-->3)-alpha-D-GlcpNAc-(1-->, with an O-acetyl group on C-2 of the rhamnose and a side chain alpha-D-Glcp on C-6 of GlcNAc. O antigen synthesis is rfe dependent, and D-GlcpNAc is the first sugar of the biological repeat unit. We sequenced the rfb (O antigen) gene cluster and found 11 open reading frames. Four rhamnose pathway genes are identified by similarity to those of other strains, the rhamnose transferase gene is identified by assay of its product, and the identities of other genes are predicted with various degrees of confidence. We interpret earlier observations on interaction between the rfb region of Escherichia coli K-12 and those of E. coli O4 and E. coli Flexneri. All K-12 rfb genes were of low G+C content for E. coli. The rhamnose pathway genes were similar in sequence to those of (Shigella) Dysenteriae 1 and Flexneri, but the other genes showed distant or no similarity. We suggest that the K-12 gene cluster is a member of a family of rfb gene clusters, including those of Dysenteriae 1 and Flexneri, which evolved outside E. coli and was acquired by lateral gene transfer.
Heuristic evaluation of ambient displays (2003)

We present a technique for evaluating the usability and effectiveness of ambient displays. Ambient displays are abstract and aesthetic peripheral displays portraying non-critical information on the periphery of a user's attention. Although many innovative displays have been published, little existing work has focused on their evaluation, in part because evaluation of ambient displays is difficult and costly. We adapted a low-cost evaluation technique, heuristic evaluation, for use with ambient displays. With the help of ambient display designers, we defined a modified set of heuristics. We compared the performance of Nielsen's heuristics and our heuristics on two ambient displays. Evaluators using our heuristics found more, severe problems than evaluators using Nielsen's heuristics. Additionally, when using our heuristics, 3-5 evaluators were able to identify 40--60% of known usability issues. This implies that heuristic evaluation is an effective technique for identifying usability issues with ambient displays.
Wnt/β-Catenin Signaling Defines Organizing Centers that Orchestrate Growth and Differentiation of the Regenerating Zebrafish Caudal Fin (2014)

Zebrafish regenerate their fins via the formation of a population of progenitor cells, the blastema. Wnt/β-catenin signaling is essential for blastemal cell proliferation and patterning of the overlying epidermis. Yet, we find that β-catenin signaling is neither active in the epidermis nor the majority of the proliferative blastemal cells. Rather, tissue-specific pathway interference indicates that Wnt signaling in the nonproliferative distal blastema is required for cell proliferation in the proximal blastema, and signaling in cells lining the osteoblasts directs osteoblast differentiation. Thus, Wnt signaling regulates epidermal patterning, blastemal cell proliferation, and osteoblast maturation indirectly via secondary signals. Gene expression profiling, chromatin immunoprecipitation, and functional rescue experiments suggest that Wnt/β-catenin signaling acts through Fgf and Bmp signaling to control epidermal patterning, whereas retinoic acid and Hedgehog signals mediate its effects on blastemal cell proliferation. We propose that Wnt signaling orchestrates fin regeneration by defining organizing centers that instruct cellular behaviors of adjacent tissues.
The alveolar space is the site of intense inflammatory and profibrotic reactions in the early phase of acute respiratory distress syndrome (1999)

These results strongly support the conclusion that during the early phase of ARDS, the lung is the site of an intense inflammatory process with sequential activation of cytokines, chemokines, and secretion of proteases, as well as concomitant collagen synthesis. The inflammation is mostly limited to the lung, with low levels of inflammatory mediators in the systemic circulation. Unlike clinical scoring systems (SAPS II and LIS), inflammatory markers differentiate patients with permeability and hydrostatic pulmonary edema.
Serum melatonin levels in melanoma patients after repeated oral administration (1994)

The goal of this study was to determine the effect of oral melatonin in divided doses on plasma melatonin levels in patients with metastatic melanoma. Hourly blood samples were obtained from five patients for 24 h prior to melatonin administration and for 24 h during oral administration of melatonin, 50 mg every 4 h. In two of the five patients, the expected nocturnal plasma melatonin peak was observed. Oral melatonin was well absorbed. Plasma melatonin levels exhibited six peaks and troughs, were two to four-fold higher during peaks than troughs, and remained more than 25 times higher than peak pretreatment melatonin levels, even during troughs. Divided oral doses of melatonin were well tolerated and maintained plasma melatonin levels 25-80 times higher than endogenous peak values.
Electron transport and full-band electron-phonon interactions in graphene (2008)

We developed a full-band Monte Carlo simulator to investigate electron transport in a single layer of graphite (graphene). The electron and phonon dispersion curves of graphene are first obtained by applying the tight-binding method to the two inequivalent atoms of the graphene unit cell, considering their nearest four neighbors. The electron-phonon scattering rates for interactions that conserve momentum and energy are then determined using Fermi’s golden rule and the deformation potential approximation. Average electron velocities due to external fields applied in different directions are calculated using these electron-phonon scattering rates and a semiclassical electron and electric field interaction. Graphene transport simulations at room temperature indicate large low-field graphene electron mobilities of approximately 4.0×104, 6.0×104, and 8.0×104 cm2/Vs along the ky (kx=0), kx=ky, and kx (ky=0) momentum directions, respectively. These low-field electron mobilities further suggest graphene field-effect mobilities of 1.3−2.6×104 cm2/Vs, which agree with experiments. Also, a large peak electron velocity of roughly 4.6×107 cm2/Vs at high fields is obtained.
Lipid peroxidation in human red cells. (1989)

In this review we have discussed the chemistry and biochemistry of lipid peroxidation as well as lipid repair mechanisms in human RBCs. We have presented findings relating to the effect of lipid peroxidation on the RBC membrane and on several properties that are determinants of RBC survival in vivo. Since we have not discussed how oxidative damage to membrane proteins or hemoglobin may affect RBC survival, the role of lipid oxidation must be considered in a broader perspective. Considerable evidence has recently been reported to indicate that oxidative hemoglobin denaturation plays an extremely important role in RBC survival. Since all cellular components are susceptible to peroxidative damage, it is likely that multiple reactions will be important with regard to RBC oxidant injury, just as they have been implicated in many degenerative processes, and that certain "compartments" of the membrane may be more susceptible than others due to congenital or acquired defects in membrane structure.
Role of the HTR1A serotonin receptor gene in Tourette syndrome and conduct disorder (1996)

Department of Medical Genetics, City of Hope Medical Center, Duarte, CA 91010, USA; Department of Psychiatry, Loma Linda University School of Medicine, CA, USA
Figuring Modernity: The New Woman and the Modern Girl in Republican China (2003)

�� This paper examines the cultural fi gures of the New Woman and the Modern Girl in Republican China (1911–1949). In addition to refl ecting the anxieties arising from a changing gender ideology, these contending images reveal anxieties associated with the concept of modernity and the modern nation project. The New Woman represents a positive view of linear modernity and hopes for a strong future China. The Modern Girl manifests in two distinct ways: as a self-absorbed woman searching for subjectivity and as a dangerous femme fatale who devours the urban male. Both of these manifestations reveal deep anxieties over the alienation and loss that accompany modernity. Literary works by Ding Ling, Mao Dun, Shi Zhecun, and others reveal that the fi gures of the New Woman and the Modern Girl cross political and canonical lines. They can best be distinguished by their use in depicting the hopes, fears, pleasures, and dangers of modernity.
Intracellular expression of single-chain variable fragments to inhibit early stages of the viral life cycle by targeting human immunodeficiency virus type 1 integrase (1996)

Integration of viral DNA into a chromosome of the infected host cell is required for efficient replication of a retroviral genome, and this reaction is mediated by the virus-encoded enzyme integrase (IN). As IN plays a pivotal role in establishing infection during the early stages of the retroviral life cycle, it is an attractive target for therapeutic intervention. However, the lack of effective antiviral drug therapy against this enzyme has led to the testing of other novel approaches towards its inhibition. In these studies, a panel of anti-human immunodeficiency virus type 1 (anti-HIV-1) IN hybridomas has been used in the construction of single-chain variable antibody fragments (SFvs). The monoclonal antibodies produced by these hybridomas, and derived SFvs, bind to different domains within IN. We now demonstrate that intracellular expression of SFvs which bind to IN catalytic and carboxy-terminal domains results in resistance to productive HIV-1 infection. This inhibition of HIV-1 replication is observed with SFvs localized in either the cytoplasmic or nuclear compartment of the cell. The expression of anti-IN SFvs in human T-lymphocytic cells and peripheral blood mononuclear cells appears to specifically neutralize IN activity prior to integration and, thus, has an effect on the integration process itself. These data support our previous studies with an anti-HIV-1 reverse transcriptase SFv and demonstrate further that intracellularly expressed SFvs can gain access to viral proteins of the HIV-1 preintegration complex. This panel of anti-HIV-1 IN SFvs also provides the tools with which to dissect the molecular mechanism(s) directly involved in integration within HIV-1-infected cells.
The cystic fibrosis transmembrane conductance regulator is a dual ATP and chloride channel. (1994)

The cystic fibrosis transmembrane conductance regulator (CFTR) belongs to a superfamily of proteins implicated in the transport of ions, proteins, and hydrophobic substances. Recent studies have demonstrated that CFTR is a protein kinase A-sensitive anion channel regulated by ATP. In the present study, patch-clamp techniques were used to assess the role of CFTR in the transport of Cl- and ATP. The stable transfection of mouse mammary carcinoma cells, C127i, with the cDNA for human CFTR resulted in the appearance of a diphenylamine-2-carboxylate-inhibitable Cl- channel, which was activated by cAMP under whole-cell and cell-attached conditions and by protein kinase A plus ATP under excised, inside-out conditions. CFTR expression was also associated with the electrodiffusional movement of ATP as indicated by the cAMP activation of ATP currents measured under whole-cell conditions. In excised, inside-out patches, it was demonstrated that ATP currents were mediated by ATP-conductive channels, which were also activated by protein kinase A and blocked by the Cl- channel blocker diphenylamine-2-carboxylate under excised, inside-out conditions. Single-channel currents observed in the presence of asymmetrical Cl-/ATP concentrations indicated that the same conductive pathway was responsible for both ATP and Cl- movement. Thus, CFTR is a multifunctional protein with more than one anion transport capability and may modify signal transduction pathways for Cl- or other secretory processes by the selective delivery of nucleotides to the extracellular domain.
Cell adhesion molecule uvomorulin expression in human breast cancer cell lines: relationship to morphology and invasive capacities. (1991)

Loss of cell-cell adhesion in carcinoma cells may be an important step in the acquisition of an invasive, metastatic phenotype. We have examined the expression of the epithelial-specific cell adhesion molecule uvomorulin (E-cadherin, cell-CAM 120/80, L-CAM) in human breast cancer cell lines. We find that fibroblastoid, highly invasive, vimentin-expressing breast cancer cell lines do not express uvomorulin. Of the more epithelial-appearing, less invasive, keratin-expressing breast cancer cell lines, some express uvomorulin, and some do not. We examined the morphologies of the cell lines in the reconstituted basement membrane matrix Matrigel and measured the ability of the cells to traverse a Matrigel-coated filter as in vitro models for detachment of carcinoma cells from neighboring cells and invasion through basement membrane into surrounding tissue. Colonies of uvomorulin-positive cells have a characteristic fused appearance in Matrigel, whereas uvomorulin-negative cells appear detached. Cells which are uvomorulin negative and vimentin positive have a stellate morphology in Matrigel. We show that uvomorulin is responsible for the fused colony morphology in Matrigel since treatment of uvomorulin-positive MCF-7 cells with an antibody to uvomorulin caused the cells to detach from one another but did not induce invasiveness in these cells, as measured by their ability to cross a Matrigel-coated polycarbonate filter in a modified Boyden chamber assay. Two uvomorulin-negative, vimentin-negative cell lines are also not highly invasive as measured by this assay. We suggest that loss of uvomorulin-mediated cell-cell adhesion may be one of many changes involved in the progression of a carcinoma cell to an invasive phenotype.
Size Effects of Surface Roughness to Superhydrophobicity (2014)

Water droplets placed on a superhydrophobic surface act like soft balls that can easily deform, roll and bounce, leading to various novel behaviors such as self-cleaning and anti-icing. Thousands of plant and animal species have been observed to have superhydrophobic surfaces and all these surfaces seem to have roughness sizes in the micro-submicron range. The classical models don not predict this kind of specified size phenomenon. Here we review some recent findings, which show that scaling down the surface roughness into the micro-submicron range is a unique and elegant strategy to not only achieve superhydrophobicity, but also increase its stability against environmental disturbances. We further demonstrate that these findings can guide fabrication of stable and extreme liquid-repellant surfaces.
Phenotypic and Functional Evidence for the Expression of CXCR4 Receptor During Megakaryocytopoiesis (1999)

Abstract The identification of stromal cell–derived factor (SDF)-1 as a chemoattractant for human progenitor cells suggests that this chemokine and its receptor might represent critical determinants for the homing, retention, and exit of precursor cells from hematopoietic organs. In this study, we investigated the expression profile of CXCR4 receptor and the biological activity of SDF-1 during megakaryocytopoiesis. CD34+ cells from bone marrow and cord blood were purified and induced to differentiate toward the megakaryocyte lineage by a combination of stem-cell factor (SCF) and recombinant human pegylated megakaryocyte growth and development factor (PEG-rhuMGDF). After 6 days of culture, a time where mature and immature megakaryocytes were present, CD41+ cells were immunopurified and CXCR4mRNA expression was studied. High transcript levels were detected by a RNase protection assay in cultured megakaryocytes derived from cord blood CD34+ cells as well as in peripheral blood platelets. The transcript levels were about equivalent to that found in activated T cells. By flow cytometry, a large fraction (ranging from 30% to 100%) of CD41+cells showed high levels of CXCR4 antigen on their surface, its expression increasing in parallel with the CD41 antigen during megakaryocytic differentiation. CXCR4 protein was also detected on peripheral blood platelets. SDF-1 acts on megakaryocytes by inducing intracellular calcium mobilization and actin polymerization. In addition, in in vitro transmigration experiments, a significant proportion of megakaryocytes was observed to respond to this chemokine. This cell migration was inhibited by pertussis toxin, indicating coupling of this signal to heterotrimeric guanine nucleotide binding proteins. Although a close correlation between CD41a and CXCR4 expession was observed, cell surface markers as well as morphological criteria indicate a preferential attraction of immature megakaryocytes (low level of CD41a and CD42a), suggesting that SDF-1 is a potent attractant for immature megakaryocytic cells but is less active on fully mature megakaryocytes. This hypothesis was further supported by the observation that SDF-1 induced the migration of colony forming unit–megakaryocyte progenitors (CFU-MK) and the expression of activation-dependent P-selectin (CD62P) surface antigen on early megakaryocytes, although no effect was observed on mature megakaryocytes and platelets. These results indicate that CXCR4 is expressed by human megakaryocytes and platelets. Furthermore, based on the lower responses of mature megakaryocytes and platelets to SDF-1 as compared with early precursors, these data suggest a role for this chemokine in the maintenance and homing during early stages of megakaryocyte development. Moreover, because megakaryocytes are also reported to express CD4, it becomes important to reevaluate the role of direct infection of these cells by the human immunodeficiency virus (HIV)-1 in HIV-1–related thrombocytopenia.
Biocatalysis as the strategy of choice in the exhaustive enantiomerically controlled synthesis of conduritols (1991)

An approach to several conduritols, both naturally occurring and unnatural derivatives, is described. The key strategy of this potentially exhaustive approach relies on the bio-oxidation of chloro- or bromobenzene to their corresponding cis-diols. Subsequent synthetic manipulations enjoy extensive use of symmetry considerations in the introduction of functionalities. Complete stereo- and enantio-control is achieved in the preparation of conduritols E 5 and F 6, aminoconduritols A-1 7 and F-4 9, fluorodeoxyconduritol F 13, chlorodeoxyconduritol F 14, and deoxyconduritol E 15. A detailed discussion of the stereoelectronic parameters that control opening of epoxy alkenes of type 33 or 37 is advanced. Full experimental details are provided for all compounds.
Crystal structure of Boc‐Ala‐Aib‐Ala‐Aib‐Aib‐methyl ester, a pentapeptide fragment of the channel‐forming ionophore suzukacillin (1983)

Abstract t ‐Buthyoxycarbonyl‐ L ‐alanyl‐α‐aminiosobutyryl‐ L ‐alanyl‐α‐aminoisobutyryl‐α‐aminoisobutyric acid methyl ester ( t ‐Boc‐ L ‐Ala‐Aib‐ L ‐Ala‐Aib‐Aib‐OMe), C 24 H 43 N 5 O 8 , an end‐protected pentapeptide with a sequence corresponding to the 6th through the 10th residues in suzukacillin, crystallizes in the orthorhombic space group P 2 1 2 1 2 1 with a = 11.671, b = 14.534, c = 17.906 Å and z = 4. The molecule exists as a right‐handed 3 10 ‐helix with a pitch of 6.026 Å. The helix is stabilized by three 4 → 1 hydrogen bonds with the NH groups of Ala(3), Aib(4), and Aib(5) hydrogen bonding to the carbonyl oxygens of t ‐Boc, Ala(1), and Aib(2), respectively. The helical molecules arrange themselves in a head‐to‐tail fashion along the a direction in such a way that the NH groups of Ala(1) and Aib(2) hydrogen bond to the carbonyl oxygens of Aib(4) and Aib(5), respectively, of a translationally related molecule. The helical columns thus formed close‐pack nearly hexagonally to form the crystal.
Observer Variation in the Diagnosis of Follicular Variant of Papillary Thyroid Carcinoma (2004)

The histopathologic diagnosis of follicular variant of papillary thyroid carcinoma (FVPCA) can be difficult. Recent reports have suggested that this neoplasm may be frequently overdiagnosed by pathologists. We examined the observer variation in the diagnosis of FVPCA in 87 tumors by 10 experienced thyroid pathologists. The criteria that the reviewers considered most helpful for making a diagnosis of FVPCA were also assessed. A concordant diagnosis of FVPCA was made by all 10 reviewers with a cumulative frequency of 39%. In this series, 24.1% of the patients had metastatic disease (n = 21). In the cases with metastatic disease, a diagnosis of FVPCA was made by all 10 reviewers with a cumulative frequency of 66.7%, and 7 of the reviewers made a diagnosis of FVPCA with a cumulative frequency of 100%. The most important criteria used to diagnose FVPCA included the presence of cytoplasmic invaginations into the nucleus (pseudo-inclusions), abundant nuclear grooves, and ground glass nuclei. These results suggest that although the diagnosis of FVPCA is variable even among experienced thyroid pathologists, most reviewers agreed on this diagnosis for patients with metastatic disease. The use of well-defined histopathologic features should improve the consistency in diagnosing FVPCA. Since most cases with metastatic disease had obvious invasion, caution should be used in making a diagnosis of FVPCA in the absence of the major histopathologic features or clear-cut invasive growth.
Global and Target Analysis of Complex Decay Phenomena (1985)

ABSTRACT: Methodologies for the simultaneous analysis of multiple total-intensity, anisotropy, and excited-state reactions are developed. Alternatives to the standard sums-of-exponentials fitting are proposed for both anisotropy and excited-state reaction data. Both simulation studies and real-data examples show these methods to be superior to single curve analysis.
Epinephrine: the drug of choice for anaphylaxis. A statement of the World Allergy Organization (2008)

Anaphylaxis is an acute and potentially lethal multi-system allergic reaction. Most consensus guidelines for the past 30 years have held that epinephrine is the drug of choice and the first drug that should be administered in acute anaphylaxis. Some state that properly administered epinephrine has no absolute contraindication in this clinical setting. A committee of anaphylaxis experts assembled by the World Allergy Organization has examined the evidence from the medical literature concerning the appropriate use of epinephrine for anaphylaxis. The Committee strongly believes that epinephrine is currently underutilized and often dosed suboptimally to treat anaphylaxis, is under-prescribed for potential future self-administration, that most of the reasons proposed to withhold its clinical use are flawed, and that the therapeutic benefits of epinephrine exceed the risk when given in appropriate i.m. doses.