gebhart/patrepeval huggingface dataset:
Treating astigmatism at the time of cataract surgery (2003)

An increasingly important goal of modern cataract and implant surgery is to obtain the most desirable refractive outcome for our patients, and in so doing, decrease their dependence upon spectacle correction. Refined spherical outcomes are now achieved by directing close attention to biometry technique, through the use of third generation intraocular lens (IOL) power formulae, and refinements in technology such as partial coherence interferometry. Similarly, improvements in astigmatic outcomes are now possible by focusing upon and obtaining more accurate preoperative cylinder measurements, careful surgical planning particularly in regard to incision(s) design, use of toric IOLs, and employing advanced postoperative enhancement techniques. Because of these refinements in technique and technology, the field of cataract and implant surgery has emerged as a true and recognized form of refractive surgery.
alpha Conotoxins Nicotinic Acetylcholine Receptor Antagonists as Pharmacological Tools and Potential Drug Leads (2001)

Conotoxins are small disulfide rich peptides from the venoms of marine cone snails. They target specific nicotinic acetylcholine receptor (nAChR) subtypes with high affinity and potency and are therefore valuable as neuropharmacological probes and potential drug leads. This article gives a general overview of the chemical and biological features of alpha-conotoxins, including their pharmacology, binding interactions and structure. A detailed analysis of recently reported three-dimensional structures from members of different subfamilies of the alpha-conotoxins, including those with 3/5, 4/3, 4/6 and 4/7 spacings of their two intracysteine loops is given. The structures are generally well defined and represent useful frameworks for the display of amino acid residues to target molecules.
Limited specificity of xenoantibodies in diabetic patients transplanted with fetal porcine islet cell clusters. Main antibody reactivity against α‐linked galactose‐containing epitopes (1994)

Abstract: The immunological specificity of antibodies formed as a result of xenotransplantation of fetal porcine islet‐like cell clusters to diabetic patients was characterized. High titer increases were recorded against porcine cells, solubilized membrane fractions of porcine cells, and purified MHC class I antigens. However, titer increases were also noted against ssDNA and dsDNA and against pig thyroglobulin but not against actin, myoglobin, or haptenated BSA. Antibody titers against tetanus toxoid were unaffected. The reactivity against porcine RBC could be completely blocked by absorption with pig thyroglobulin. Since pig thyroglobulin contains the galαl‐3gal antigen, the reactivity against RBC was most probably mainly due to antibodies against this oligosaccharide epitope. The reactivity against porcine mononuclear cells was only partially absorbed by pig thyroglobulin, indicating a heterogeneity of the clonal response. These conclusions were substantiated by data showing that the antigenic determinants on pig thyroglobulin were completely destroyed by treatment with α‐ but not with β‐galactosidase. Further studies showed that immune reactivity against pig RBCs, platelets, islet‐cells, endothelial cells and pig MHC class I molecules, caused by xenoimmunization, was almost completely blocked by either absorption of antibodies on a column of Sepharose beads coated with galα1‐3gal or by pretreatment of the antigen fractions with α‐galactosidase. Western blot experiments revealed that both the natural and xenoimmune antibodies reacted with a large number of different glycoproteins. There was no difference in heterogeneity of the response when comparisons were made between pre‐and posttransplantation sera, nor was there any difference of patterns caused by IgM or IgG antibodies. Absorption studies revealed that this epitope was present in a large number of different glycoproteins, a conclusion verified by staining with the eluate from a thyroglobulin‐immunosorbent column or with the eluate from the galα1‐3gal‐coupled Sepharose column. Our findings demonstrate that the xenoimmune response is mainly directed against oligosaccharide residues and that there is a limited clonal heterogeneity of antibodies in xenografted patients. There was no direct evidence of reactivity against any porcine proteins nor of specific immunization against porcine MHC peptides. The data form a basis for a future understanding of means to cope with and prevent the rejection of xenogeneic islet cells in man. We also suggest, based on the specificity found in xenoimmunized patients sera, that a major part of naturally occurring antibodies might be specifically reactive with carbohydrate antigens.
Identification and characterization of a neutralization site within the second variable region of human immunodeficiency virus type 1 gp120 (1992)

Two monoclonal antibodies designated BAT085 and G3-136 were raised by immunizing BALB/c mice with gp120 purified from human immunodeficiency virus type 1 (HIV-1) IIIB-infected H9 cell extracts. Among three HIV-1 laboratory isolates (IIIB, MN, and RF), BAT085 neutralized only IIIB infection of CEM-SS cells, whereas G3-136 neutralized both IIIB and RF. These antibodies also neutralized a few primary HIV-1 isolates in the infection of activated human peripheral blood mononuclear cells. In indirect immunofluorescence assays, BAT085 bound to H9 cells infected with IIIB or MN, while G3-136 bound to H9 cells infected with IIIB or RF, but not MN. Using sequence-overlapping synthetic peptides of HIV-1 IIIB gp120, the binding site of BAT085 and G3-136 was mapped to a peptidic segment in the V2 region (amino acid residues 169 to 183). The binding of these antibodies to immobilized gp120 was not inhibited by the antibodies directed to the principal neutralization determinant in the V3 region or to the CD4-binding domain of gp120. In a competition enzyme-linked immunosorbent assay, soluble CD4 inhibited G3-136 but not BAT085 from binding to gp120. Deglycosylation of gp120 by endo-beta-N-acetylglucosaminidase H or reduction of gp120 by dithiothreitol diminished its reactivity with G3-136 but not with BAT085. These results indicate that the V2 region of gp120 contains multiple neutralization determinants recognized by antibodies in both a conformation-dependent and -independent manner.
Ubiquitin Lives Up to Its Name (2002)

The cleanup protein has been known to be present in all higher organisms, but now researchers are discovering that it has a hand in everything from directing protein traffic to regulating gene activity
Metal Halide Analogues of Chalcogenides:  A Building Block Approach to the Rational Synthesis of Solid-State Materials (1998)

Principles of solid-state structure and bonding that relate metal-halide and metal-chalcogenide materials are described through a comparison of binary AXn salts. Structural variation is rationalized by a comparison of the size and charge of the respective ions, the d-electron count of the cations, and the type of A−X, A−A, and X−X bonding interactions. These general bonding considerations are exploited for the construction of new metal-halide structure types that are patterned after known chalcogenide structures such as metal-halide analogues of silicates, aluminosilicates, phosphates, and phosphonates.
Nanoparticle-Directed Crystallization of Calcium Carbonate (2001)

The crystallization of CaCO3 in the presence of monolayer-protected gold nanoparticles is investigated here. It is found that crystals of CaCO3 grow around the gold nanoparticles, which act as nucleation templates, resulting in metal–organic–inorganic hybrid materials (see Figure). Control of the shape (spherical or needle-like) and polymorph (vaterite or aragonite) is also demonstrated.
An Efficient Synthesis of 4-Aryl-1,2,3,4-Tetrahydroisoquinolines (1994)

Abstract An efficient synthesis of 4-aryl substituted 1,2,3,4-tetrahydroisoquinolines is described. Suzuki coupling of 4-bromoisoquinoline with arylboronic acids gives the 4-arylisoquinolines which can be reduced with NaBH3CN to the 1,2,3,4-tetrahydroisoquinolines.
The type I IFN induction pathway constrains Th17-mediated autoimmune inflammation in mice (2008)

IFN-beta, a type I IFN, is widely used for the treatment of MS. However, the mechanisms behind its therapeutic efficacy are not well understood. Using a murine model of MS, EAE, we demonstrate that the Th17-mediated development of autoimmune disease is constrained by Toll-IL-1 receptor domain-containing adaptor inducing IFN-beta-dependent (TRIF-dependent) type I IFN production and its downstream signaling pathway. Mice with defects in TRIF or type I IFN receptor (IFNAR) developed more severe EAE. Notably, these mice exhibited marked CNS inflammation, as manifested by increased IL-17 production. In addition, IFNAR-dependent signaling events were essential for negatively regulating Th17 development. Finally, IFN-beta-mediated IL-27 production by innate immune cells was critical for the immunoregulatory role of IFN-beta in the CNS autoimmune disease. Together, our findings not only may provide a molecular mechanism for the clinical benefits of IFN-beta in MS but also demonstrate a regulatory role for type I IFN induction and its downstream signaling pathways in limiting Th17 development and autoimmune inflammation.
Micromixing with Linked Chains of Paramagnetic Particles (2004)

Paramagnetic colloidal particles aggregate into linear chains under an applied external magnetic field. These particles can be chemically linked to create chains that can be magnetically actuated to manipulate microscopic fluid flow. The flexibility of the chain can be adjusted by varying the length of the linker molecule. In this paper, we describe the use of a suspension of linked paramagnetic chains in a rotating magnetic field to perform microscale mixing. The effect of chain rotation and flexibility on the diffusion of molecules is studied by observing the mixing of an acid and base in a microchannel. We show that, as the chain rotation frequency increases, there is marked increase in the effective mixing between fluid streams; however, a maximum frequency exists and above this frequency the chains are no longer effective in mixing. More flexible chains are more effective at mixing over a larger range of frequencies.
FER overexpression is associated with poor postoperative prognosis and cancer-cell survival in non-small cell lung cancer. (2013)

Here, we show that overexpression of fer tyrosine kinase (FER), a non-receptor tyrosine kinase, predicts poor postoperative outcome and might be involved in cancer-cell survival in non-small cell lung cancer (NSCLC). Systematic screening using in silico analyses and quantitative RT-PCR revealed that FER was overexpressed in about 10% of NSCLC patients. Evaluation of FER expression using immunohistochemistry (IHC) on tissue microarrays was consistent with the mRNA level detected using quantitative RT-PCR. In analyses of 135 NSCLC patients who had undergone potential curative resection, we found that FER overexpression detected using IHC had no association with clinicopathological features such as age, sex, smoking history, histological type, disease stage, T factor, N factor, adjuvant chemotherapy history, or EGFR mutation, but was correlated with poor postoperative survival periods. A multivariate Cox regression analysis showed that this prognostic impact was independent of other clinicopathological features. In functional analyses of FER in vitro, FER exhibited a transforming activity, suggesting that it possesses oncogenic functions. We also found that human lung cancer NCI-H661 cells, which exhibited FER-outlier expression, were led to apoptosis by the knockdown of FER using RNA interference. FER overexpression might serve as a prognostic biomarker and be involved in cancer-cell survival in NSCLC.
Molecular cloning and nucleotide sequence of the streptavidin gene (1986)

Using synthetic oligonucleotides as probes we have cloned the streptavidin gene from a genomic library of Streptomyces avidinii. Nucleotide sequence analysis indicated that a 2 Kb DNA-fragment contained the entire coding region, a signal peptide region and the 3' and 5' flanking regions of the gene. The deduced amino acid sequence shows several interrupted blocks of homology with the amino acid sequence of chicken egg-white avidin. Analysis of the secondary structure suggests a high content of beta-structure in both proteins and considerable overall structural similarity between them.
Combined suppressive and extinction writing using M and M A centers in Li-doped NaF (1976)

The photodichroism and dispersion of M and MA centers in Li-doped NaF are used in a gray-scale image recording, reading, and storage scheme, combining extinction and suppressive writing. Improved sensitivity, contrast, and the use of the same wavelength for writing and reading are the principal advantages.
Generating product configuration knowledge bases from precise domain extended UML models (2000)

The Unified Modeling Language (UML) is an emerging standard conceptual modeling language in Software Engineering processes. UML provides extension mechanisms (stereotypes) to adapt the general modeling language to specific application domains. In addition, UML comprises the standardized expression language Object Constraint Language (OCL) to model additional invariants. In this paper we show how UML can be extended using the standardized extension mechanisms to fit the needs of the domain of knowledge-based product configuration. Starting from a conceptual product model, we define the semantics of the employed extensions based upon a logic theory of configuration in a way that the resulting knowledge bases can be processed by a specialized inference engine. We show especially how the built-in expression language OCL can be employed to enhance the expressiveness of the conceptual models and how such expressions can be translated to the logical model. Finally, we describe a prototype implementation of the presented ideas based on commercial tools.
Increased surface phosphatidylserine is an early marker of neuronal apoptosis (1997)

Neuronal apoptosis is the subject of intense investigation and is beginning to be understood in some molecular detail. In the present study, we show that PC12 cells, like certain other cell types, redistribute phosphatidylserine (PS) from the inner leaflet to the outer leaflet of the plasma membrane early in the process of apoptosis. The externalised PS can be readily visualised by incubating intact cells with a fluorescent derivative of the protein annexin V. When apoptosis is blocked with an inhibitor of interleukin-1beta-converting-enzyme-like proteases, the increased annexin binding is also blocked. Fluorescent annexin V binding provides a rapid and convenient way to identify apoptotic neurones.
Compositional effects on the thermo-optic coefficients of potassium aluminophosphate glasses (2003)

The central wavelength of lightwave devices such as gratings is sensitive to temperature, due to the temperature dependence of the devices' optical path lengths. One way to solve this problem is to use an athermal device. Phosphate glasses are ideal hosts for such devices as they exhibit negative thermo-optic coefficient (dn/dT), which counters the effect of expansion. For this study, fourteen different compositions of potassium aluminophosphate glasses, of the K&lt;sub&gt;2&lt;/sub&gt;O-Al&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt;-P&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;5&lt;/sub&gt; system, were prepared with O/P ranging from 2.8 to 3.1. Refractive indices, glass transition temperature (T&lt;sub&gt;g&lt;/sub&gt;), coefficient of thermal expansion (CTE) and thermo-optic coefficient (dn/dT) measured for the glasses are what is expected with the addition of aluminium : an increase in T&lt;sub&gt;g&lt;/sub&gt; and a reduction in CTE. Tg changes in the range of 272°C to 621°C while CTE decreases from 21x10&lt;sup&gt;-6&lt;/sup&gt;/°C to 7x10&lt;sup&gt;-6&lt;/sup&gt;/°C as the aluminium content increases. We are able to achieve dn/dT value as negative as -16x10&lt;sup&gt;-6&lt;/sup&gt;/°C. In addition, the glasses are thermally stable, judging by the large difference between T&lt;sub&gt;g&lt;/sub&gt; and the temperature of onset of crystallisation. Athermal glasses have been achieved at low aluminium content with high CTE, which in turn leads to negative dn/dT. These results are consistent with the polarisability effect in the glasses as low aluminium content lowers polarisability, which gives rise to negative dn/dT. The CTE of glasses must be more than 10x10&lt;sup&gt;-6&lt;/sup&gt;/°C to achieve negative dn/dT. Any deficit or excess P&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;5&lt;/sub&gt; does not seem to affect the CTE and dn/dT.
Autoantibodies to T Cell Costimulatory Molecules in Systemic Autoimmune Diseases (1999)

To determine whether antilymphocyte Abs to T cell costimulatory molecules are generated in patients with autoimmune diseases and, if they exist, to clarify the mechanism of their production and pathological roles, we investigated the presence of autoantibodies to CTLA-4 (CD152), CD28, B7-1 (CD80), and B7-2 (CD86) in serum samples obtained from patients with various autoimmune diseases and from normal subjects using recombinant fusion proteins. In ELISAs, anti-CD28, anti-B7-1, and anti-B7-2 Abs were rarely seen, whereas anti-CTLA-4 Abs were detected in 8.2% of the patients with systemic lupus erythematosus, 18.8% of those with rheumatoid arthritis, 3.1% of those with systemic sclerosis, 31.8% of those with Behçet's disease, 13.3% of those with Sjögren's syndrome, and 0% of healthy donors. This reactivity was confirmed by immunoblotting. More importantly, the purified anti-CTLA-4 Abs reacted with CTLA-4 expressed on P815 cells by flow cytometry. In addition, we found at least three epitopes on the CTLA-4 molecule. Furthermore, among the patients with Behçet's disease, uveitis was seen significantly less frequently in the anti-CTLA-4 Ab-positive patients. Taken collectively, these data indicate that anti-CTLA-4 autoantibodies are generated in systemic autoimmune diseases by an Ag-driven mechanism and may modulate the immune response in vivo by binding to CTLA-4 on T cells.
Nanometre-size tubes of carbon (1997)

We review the present state of understanding of the structure, growth and properties of nanometre-size tubes of carbon. Two different types of carbon nanotubes, namely single-shell nanotubes made of single layers of graphene cylinders and multishell nanotubes made of concentric cylinders of graphene layers have now become available. The subtle structure parameters such as helicity in the carbon network and the nanometre diameters give the nanotubes a rich variety in physical properties. Recent experimental progress on the measurements of properties using electron-energy loss spectroscopy, Raman spectroscopy, electron-spin resonance, electrical conductance, mechanical stiffness and theoretical predictions on electronic and mechanical properties of nanotubes will be discussed. In addition to synthesis techniques, methods to purify and make aligned arrays of nanotubes will be described. Different approaches for fabricating composite structures using nanotubes as moulds and templates and their future implications in materials science will be evaluated. Finally, promising areas of future applications, for example as tiny field-emitting devices, micro-electrodes, nanoprobes and hydrogen storage material will be outlined.
DNA Triplet Repeat Expansion and Mismatch Repair (2015)

DNA mismatch repair is a conserved antimutagenic pathway that maintains genomic stability through rectification of DNA replication errors and attenuation of chromosomal rearrangements. Paradoxically, mutagenic action of mismatch repair has been implicated as a cause of triplet repeat expansions that cause neurological diseases such as Huntington disease and myotonic dystrophy. This mutagenic process requires the mismatch recognition factor MutSβ and the MutLα (and/or possibly MutLγ) endonuclease, and is thought to be triggered by the transient formation of unusual DNA structures within the expanded triplet repeat element. This review summarizes the current knowledge of DNA mismatch repair involvement in triplet repeat expansion, which encompasses in vitro biochemical findings, cellular studies, and various in vivo transgenic animal model experiments. We present current mechanistic hypotheses regarding mismatch repair protein function in mediating triplet repeat expansions and discuss potential therapeutic approaches targeting the mismatch repair pathway.
Microbial production of surfactants and their commercial potential (1997)

Many microorganisms, especially bacteria, produce biosurfactants when grown on water-immiscible substrates. Biosurfactants are more effective, selective, environmentally friendly, and stable than many synthetic surfactants. Most common biosurfactants are glycolipids in which carbohydrates are attached to a long-chain aliphatic acid, while others, like lipopeptides, lipoproteins, and heteropolysaccharides, are more complex. Rapid and reliable methods for screening and selection of biosurfactant-producing microorganisms and evaluation of their activity have been developed. Genes involved in rhamnolipid synthesis (rhlAB) and regulation (rhlI and rhlR) in Pseudomonas aeruginosa are characterized, and expression of rhlAB in heterologous hosts is discussed. Genes for surfactin production (sfp, srfA, and comA) in Bacillus spp. are also characterized. Fermentative production of biosurfactants depends primarily on the microbial strain, source of carbon and nitrogen, pH, temperature, and concentration of oxygen and metal ions. Addition of water-immiscible substrates to media and nitrogen and iron limitations in the media result in an overproduction of some biosurfactants. Other important advances are the use of water-soluble substrates and agroindustrial wastes for production, development of continuous recovery processes, and production through biotransformation. Commercialization of biosurfactants in the cosmetic, food, health care, pulp- and paper-processing, coal, ceramic, and metal industries has been proposed. However, the most promising applications are cleaning of oil-contaminated tankers, oil spill management, transportation of heavy crude oil, enhanced oil recovery, recovery of crude oil from sludge, and bioremediation of sites contaminated with hydrocarbons, heavy metals, and other pollutants. Perspectives for future research and applications are also discussed.
Evolutionary engineering of mixed-sugar utilization by a xylose-fermenting strain (2005)

We have recently reported about a Saccharomyces cerevisiae strain that, in addition to the Piromyces XylA xylose isomerase gene, overexpresses the native genes for the conversion of xylulose to glycolytic intermediates. This engineered strain (RWB 217) exhibited unprecedentedly high specific growth rates and ethanol production rates under anaerobic conditions with xylose as the sole carbon source. However, when RWB 217 was grown on glucose-xylose mixtures, a diauxic growth pattern was observed with a relatively slow consumption of xylose in the second growth phase. After prolonged cultivation in an anaerobic, xylose-limited chemostat, a culture with improved xylose uptake kinetics was obtained. This culture also exhibited improved xylose consumption in glucose-xylose mixtures. A further improvement in mixed-sugar utilization was obtained by prolonged anaerobic cultivation in automated sequencing-batch reactors on glucose-xylose mixtures. A final single-strain isolate (RWB 218) rapidly consumed glucose-xylose mixtures anaerobically, in synthetic medium, with a specific rate of xylose consumption exceeding 0.9 gg(-1)h(-1). When the kinetics of zero trans-influx of glucose and xylose of RWB 218 were compared to that of the initial strain, a twofold higher capacity (V(max)) as well as an improved K(m) for xylose was apparent in the selected strain. It is concluded that the kinetics of xylose fermentation are no longer a bottleneck in the industrial production of bioethanol with yeast.