gebhart/patrepeval huggingface dataset:
Surface separation investigation of ultrafast pulsed laser welding (2016)

Techniques for joining materials, especially optical materials such as glass to structural materials such as metals, or to other optical materials, while maintaining their surface and optical properties are essential for a wide range of industrial applications. Adhesive bonding is commonly used but leads to many issues including optical surface contamination and outgassing. It is possible to generate welds using an ultra-short pulsed laser process, whereby two flat material surfaces are brought into close contact and the laser is focused through the optical material onto the interface. Highly localised melting and rapid resolidification form a strong bond between the two surfaces whilst avoiding significant heating of the surrounding material, which is important for joining materials with different thermal expansion coefficients. Previous reports on ultrafast laser welding have identified a requirement for the surface separation gap to be less than 500nm in order to avoid cracking or ablation at the interface. We have investigated techniques for increasing this gap (to reduce weld fit-up problems), and tested by bonding two surfaces with a weld-controlled gap. These gaps were generated either by a series of etched grooves on the surface of one of the substrates, or by using a cylindrical lens as a substrate. By careful optimisation of parameters such as laser power, process speed and focal position, we were able to demonstrate successful welding with a gap of up to 3μm.
Synthesis, Solution Structure, and Biological Evaluation of Urokinase Type Plasminogen Activator (uPA)-Derived Receptor Binding Domain Mimetics (2002)

Tumor cell migration and metastasis in cancer are facilitated by interaction of the serine protease urokinase type plasminogen activator (uPA) with its receptor uPAR (CD 87). Overexpression of uPA and uPAR in cancer tissues is associated with a high incidence of disease recurrence and early death. In agreement with these findings, disruption of the protein-protein interaction between uPAR present on tumor cells and its ligand uPA evolved as an attractive intervention strategy to impair tumor growth and metastasis. For this, the uPAR antagonist cyclo[19,31][D-Cys(19)]-uPA(19)(-)(31) was optimized to efficiently interrupt binding of uPA to cellular uPAR. First, the disulfide bridge of this lead compound was shifted and then the modified peptide was shortened from the amino and carboxy terminus to generate cyclo[21,29][Cys(21,29)]-uPA(21)(-)(30). Next, cyclo[21,29][D-Cys(21)Cys(29)]-uPA(21)(-)(30) was yielded by changing the chirality of Cys(21) to D-Cys(21). For analysis of uPAR binding activity, we employed competitive flow cytofluorometric receptor binding assays, using FITC-uPA as the ligand and U937 promyeloid leukemia cells as the cellular source of uPAR. As demonstrated for cyclo[21,29][D-Cys(21)Cys(29)]-uPA(21)(-)(30), the achieved peptide modifications maintained receptor binding activity (IC(50) = 0.04 microM), which is close in order to that of the parent protein ligand, uPA (IC(50) = 0.01 microM). A detailed NMR analysis with restrained and free molecular dynamics calculations in explicit H(2)O exhibits a well-defined structure with characteristic features such as an omega-loop with two betaI-turns about Lys(3), Tyr(4), Ser(6), and Asn(7). Hydrophobic clustering of the side chains of Tyr(4), Phe(5), Ile(8), and Trp(10) is observed. Side chain mobility is analyzed with time-dependent distance restraints. The NMR structure of cyclo[21,29][D-Cys(21)Cys(29)]-uPA(21)(-)(30) is very similar to the previously reported structure of the amino terminal fragment of uPA. Systematic point mutations led to cyclo[21,29][D-Cys(21)Nle(23)Cys(29)]-uPA(21)(-)(30), which still binds to uPAR but is resistant to proteolytic cleavage, e.g., by the tumor-associated serine proteases uPA and plasmin, and is stable in blood serum or plasma. In conclusion, small cyclic peptides were created, which mimic the structure and activity of the binding epitope of uPA to uPAR and which may serve as novel therapeutic agents in cancer metastasis.
Synopsis of Ophthalmology (1972)

Employing the premise that most blindness is preventable, Dr. Havener challenges the medical profession in his introductory chapters to learn about the most "important square inch of the body." The author lucidly demonstrates that a careful ophthalmologic examination can aid and confirm many systemic medical problems. The instrumentation of the modern ophthalmologist often intimidates the general physician and forces him to refer any and all eye problems. His experience in eye disease is usually the few weeks, if that long, spent during medical school. Thus, Dr. Havener has not written just another review book, but has tackled the much larger problem of education. The book bridges the distance between the ophthalmologist and other physicians. Using mechanisms of action and basic physiology, he explains logically which problems the physician should treat and which he should refer. The physician can gain confidence in learning about the secrets of the black box
Interaction of graphene-related materials with human intestinal cells: an in vitro approach (2016)

Graphene-related materials (GRM) inherit unique combinations of physicochemical properties which offer a high potential for technological as well as biomedical applications. It is not clear which physicochemical properties are the most relevant factors influencing the behavior of GRM in complex biological environments. In this study we have focused on the interaction of GRM, especially graphene oxide (GO), and Caco-2 cells in vitro. We mimiked stomach transition by acid-treatment of two representative GRM followed by analysis of their physicochemical properties. No significant changes in the material properties or cell viability of exposed Caco-2 cells in respect to untreated GRM could be detected. Furthermore, we explored the interaction of four different GO and Caco-2 cells to identify relevant physicochemical properties for the establishment of a material property-biological response relationship. Despite close interaction with the cell surface and the formation of reactive oxygen species (ROS), no acute toxicity was found for any of the applied GO (concentration range 0-80 μg ml(-1)) after 24 h and 48 h exposure. Graphene nanoplatelet aggregates led to low acute toxicity at high concentrations, indicating that aggregation, the number of layers or the C/O ratio have a more pronounced effect on the cell viability than the lateral size alone.
A Rapid Verification Framework for Developing Multi-core Processor (2016)

A multi-core processor is widely used to achieve both high performance and low energy consumption. However, verification of a multi-core processor is more difficult than that of single-core processor. Because multi-core processor has large and complex circuits, and special mechanisms such as a cache coherency mechanism also increases complexity. In general, design flow of a processor include such as the following steps; functional verification by high level language, cycle accurate verification by RTL simulation and timing analysis considered gate delay, wiring delay and others. In particular, co-simulation framework for single-core processor has been proposed to reduce time of cycle accurate verification with RTL simulation. However, if the conventional framework is applied to verify a multi-core processor, it causes three problems; failure of the co-simulation framework by a mismatch of load and store operation, failure of the system call emulation by cache coherency mechanism and requirement of task scheduling by execution multi-threaded program. These problems makes verification of a multi-core processor difficult seriously and increases simulation time dramatically. Therefore, this paper proposes a rapid verification framework to support execution of a multi-threaded program for multi-core processors. The proposed method makes it possible to verify both a homogeneous and heterogeneous multi-core processors with the cache coherency mechanism, and to execute multithreaded programs without full system simulation. The proposed framework extends conventional co-simulation framework for a single-core processor. The proposed framework is composed of the following three extensions; bypassing loaded value from the verified processor to virtual processor, a cache access mechanism for system call emulation, and an internal task scheduler. As evaluation results, our framework verifies two-core processor correctly. Furthermore, the proposed method achieves to reduce the number of execution cycles by 71% in maximum and 46% in average compared with full system simulation.
Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase (2017)

Nuclear RNA exosomes catalyze a range of RNA processing and decay activities that are coordinated in part by cofactors, including Mpp6, Rrp47, and the Mtr4 RNA helicase. Mpp6 interacts with the nine-subunit exosome core, while Rrp47 stabilizes the exoribonuclease Rrp6 and recruits Mtr4, but it is less clear if these cofactors work together. Using biochemistry with <i>Saccharomyces cerevisiae</i> proteins, we show that Rrp47 and Mpp6 stimulate exosome-mediated RNA decay, albeit with unique dependencies on elements within the nuclear exosome. Mpp6-exosomes can recruit Mtr4, while Mpp6 and Rrp47 each contribute to Mtr4-dependent RNA decay, with maximal Mtr4-dependent decay observed with both cofactors. The 3.3 Å structure of a twelve-subunit nuclear Mpp6 exosome bound to RNA shows the central region of Mpp6 bound to the exosome core, positioning its Mtr4 recruitment domain next to Rrp6 and the exosome central channel. Genetic analysis reveals interactions that are largely consistent with our model.
Injectable hybrid hydrogels for tumor resection and cell-responsive degradation (2018)

Videos and photos of hydrogel injection for ESD
Amylin replacement with pramlintide as an adjunct to insulin therapy improves long‐term glycaemic and weight control in Type 1 diabetes mellitus: a 1‐year, randomized controlled trial (2004)

These results show that mealtime amylin replacement with pramlintide, as an adjunct to insulin therapy, improves long-term glycaemic and weight control in patients with Type 1 diabetes.
Rupture of rubber. X. The change in stored energy on making a small cut in a test piece held in simple extension (1963)

Abstract Application of the tearing energy criterion (Part I of this work) to the problem of the tearing of a rubber strip that contains a small cut or tear of length c in one edge and is stretched in simple extension is based on the relation W i – W = K (λ) c 2 hE , where W i and W are the total stored energies of the strip in the absence and presence of the cut, respectively, h is the thickness λ 0 of the strip, E is the stored‐energy density in the central region of simple extension, and K (λ) is a numerical factor that varies with the extension ratio λ in this region. An experimental method is described for measuring ( W i – W ), which enables the factor K (λ) to be evaluated. The results indicate that K (λ) decreases from a value of about 3 at low extensions to a value somewhat below 2 at λ = 3. The experiments also provide a more stringent test of the accuracy of the above relation than has been possible hitherto.
Godel, Escher, Bach: An Eternal Golden Braid. (1980)

By exploring common themes in the lives and works of logician Kurt Gödel , artist M. C. Escher and composer Johann Sebastian Bach , GEB expounds concepts fundamental to mathematics , symmetry, and intelligence. Through illustration and analysis, the book discusses how self-reference and formal rules allow systems to acquire meaning despite being made of "meaningless" elements. It also discusses what it means to communicate, how knowledge can be represented and stored, the methods and limitations of symbolic representation, and even the fundamental notion of "meaning" itself.
Phylogenetic Analysis of Dengue Viruses Isolated From Imported Dengue Patients: Possible Aid for Determining the Countries Where Infections Occurred (2007)

The study demonstrates that many dengue virus strains are introduced into Japan and that phylogenic analysis of isolated dengue viruses is a unique technique to determine the countries where infection occurred. Travelers carry viruses and provide important and unique information for clarifying dengue virus trait and its dissemination.
Microfluidic droplet liquid reactors for active pharmaceutical ingredient crystallization by diffusion controlled solvent extraction (2019)

A novel method for crystallization utilizing solvent/antisolvent extraction in microfluidic droplet liquid reactors has been developed for rapid and low-cost screening of crystal polymorphism (i.e. molecular crystallographic arrangement or internal structure) and habit (i.e. crystallographic shape or external structure). The method involves a ternary solvent system consisting of a dispersed phase of two miscible fluids, one in which the active pharmaceutical ingredient (API) is soluble (solvent) and one in which the API is insoluble (antisolvent). The solvent/antisolvent dispersed phase is immiscible with a third continuous phase. Crystallization of an API, GSK1, was controlled within droplets by altering the rate of solvent extraction from droplets into the continuous phase, thereby decreasing API solubility. Crystal size, habit, and population per droplet were directly impacted by the solvent's rate of extraction. Single crystals were grown in individual droplets by slow extraction of solvent into the surrounding continuous phase, which occurs when crystal growth gradually reduces API concentration such that it is maintained within the metastable zone throughout extraction. Rapid extraction of solvent from droplets results in API concentration significantly exceeding its metastable limit, producing a greater number of crystal nuclei compared to slow extraction conditions. When holding constant solubilized API mass per droplet, crystal sizes were larger for slow extraction rates (l = 96.3, w = 16.6 μm) compared to fast extraction rates (l = 48.8, w = 9.5 μm) as a result of crystal growth occurring on fewer crystal nuclei per droplet. Crystal habit can be controlled by adjusting the solvent extraction rate and consequently the saturation, where minimal saturation resulted in a rhombohedral habit and comparatively higher saturation resulted in an acicular habit with a higher aspect ratio. Antisolvents were tested using two hydrophobic APIs demonstrating the method's capability for rapidly identifying favorable crystal morphologies for downstream manufacturability using miniscule amounts of API.
Independent prognostic significance of a nuclear proliferation antigen in diffuse large cell lymphomas as determined by the monoclonal antibody Ki-67 (1988)

To assess the prognostic significance of the growth fraction in diffuse large cell lymphoma (DLCL), we studied 105 DLCL patients with the monoclonal antibody Ki-67 applied to frozen tissue sections. Ki-67 detects a nuclear antigen associated with cell proliferation not found in resting cells. Ki-67 findings and other clinical prognostic factors were correlated with outcome using univariate and multivariate analyses in the proportional hazards model. High proliferative activity, defined as nuclear Ki-67 expression in greater than 60% of malignant cells (Ki-67 greater than 60), was found to be a strong predictor of poor survival among these patients (P = .003, log-rank). The 19 patients with Ki-67 greater than 60% had a median survival of 8 months compared with a median survival of 39 months for the 86 patients with Ki-67 less than or equal to 60%. Examination of pretreatment clinical variables indicated the patient groups were similar with regard to age, sex, stage, B symptoms, tumor bulk, and lactate dehydrogenase (LDH). Both patient groups received comparable curative intent therapy and showed comparable complete response rate precluding treatment differences as modifying outcome. Multivariate analysis indicated Ki-67 is an independent predictor of survival (multivariate P = .006). Further statistical analysis using only B-cell DLCL patients treated with CHOP (63 patients) indicated that Ki-67 greater than 60 retained strong prediction of poor outcome (P = .002, log-rank) among this homogeneous group. We conclude that high proliferative activity (Ki-67 greater than 60) is an independent factor allowing laboratory prediction of probable poor outcome of DLCL.
Label-Free Optical Detection of Protein Antibody–Antigen Interaction on Au Capped Porous Anodic Alumina Layer Chip (2008)

The interaction of protein antibody and antigen will lead to change in the mass, electrical charge, or optical properties of the immobilized protein layer, which can be detected by microgrativimetric, potentiometric, amperometric or optical transducers. For this reason, we developed a new localized surface plasmon resonance (LSPR) coupled with interferometry based label-free optical biosensor in connection with a Au capped porous anodic alumina (PAA) layer chip. We could observe the formations of the self-assembled monolayer (SAM)/protein A/C-reactive protein (CRP) antibody/CRP antigen on the Au capped PAA layer chip surface by means of LSPR and interferometric characteristics. In the presence of CRP antigen, the change of the relative reflected intensity (RRI) in the interferometric pattern and a significant bathochromic shift were observed. The fabrication of uniformed Au capped oxide nanostructure is the primary advantage of our chip. It is known that biomolecular interaction which contributed to the change in the refractive index depends on the absorbance intensity change and wavelength shift. Using our Au capped PAA layer chip, one can measure both the information in one single event using a single optical fiber, which is the great additional advantage over SPR.
Single-crystal H2V3O8nanowires: a competitive anode with large capacity for aqueous lithium-ion batteries (2010)

Single-crystal H2V3O8 nanowires with a width of ∼50 nm were fabricated by a facile one-step hydrothermal method and SEM, TEM, TGA, XRD, XPS were used to characterize their morphology and structure details. The possibility of using this material as an anode candidate for aqueous lithium-ion batteries was investigated for the first time. CV and galvanostatic charge/discharge measurements indicated that the intercalation/deintercalation of Li+ in this material in aqueous electrolyte is highly reversible. A discharge capacity of 234 mAh g−1 can be obtained for the synthesized H2V3O8 nanowires at the current density of 0.1 A g−1 in aqueous solution of 5 M LiNO3 and 0.001 M LiOH, much larger than the available capacities (less than 110 mAh g−1) of other vanadium oxides in aqueous electrolyte. Furthermore, the H2V3O8 nanowires can be charge/discharged upon 50 cycles with nearly no capacity loss in organic electrolyte and a capacity retention over 70% in aqueous electrolyte, showing better cycle stability than other vanadium oxide predecessors for aqueous lithium-ion batteries.
Alkoxycarbonylation of Industrially Relevant Anilines Using Zn4O(O2CCH3)6 as Catalyst (2012)

An efficient procedure is presented for the alkoxycarbonylation of industrially important amines using environmentally friendly alkyl carbonates as reagents and Zn4O(OAc)6 as catalyst. Aromatic amines in particular (thirteen examples) consistently give high yields (up to 98%), regardless of the electronic properties of the substituents or the ring substitution pattern.
Transport in Caco-2 cell monolayers of cucurbitane triterpenoids from Momordica charantia (2012)

Bitter melon, Momordica charantia, is a widely-used treatment for diabetes in traditional medicine systems throughout the world. The compounds responsible for this biological activity are still under investigation, but curcurbitane triterpenoids are thought to be paramount. We investigated the gastrointestinal transport of a saponin-enriched n-BuOH fraction of M. charantia using a two-compartment transwell human intestinal epithelial cell Caco-2 monolayer system, simulating the intestinal barrier. Eleven triterpenoids in this extract were transported from the apical to basolateral direction across Caco-2 cell monolayers and were identified or tentatively identified by HPLC-TOF-MS. Cucurbitane-type triterpenoids permeated to the basolateral side with apparent permeability coefficient (Papp) values for 3-β-7-β,25-trihydroxycucurbita-5,23(E)-dien-19-al, momordicines I and II at 15.8 ×10- 6, 7.03 ×10- 6 and 4.34 ×10- 6 cm/s, respectively. Also, small amounts of these triterpenoids were absorbed inside the epithelial cells themselves, suggesting additional bioactivity for these compounds. To our knowledge, this is the first report of the transport of the reputed anti-diabetes cucurbitane-type triterpenoids in human intestinal epithelial cell monolayers; these results therefore point to a novel mechanism for the possible bioavailability of these bitter melon compounds in vivo.
Ocimum sanctum Linn--a study on gastric ulceration and gastric secretion in rats. (1993)

The antiulcerogenic property of Ocimum sanctum Linn (Tulsi) was studied in pyloric ligated and pyloric ligated & aspirin treated rats. The extract of OSL reduced the ulcer index, free & total acidity on acute and chronic administration. Seven days pretreatment with the drug increased the mucous secretion also. It may be concluded that OSL extract has antiulcerogenic property against experimental ulcers, and it is due to its ability to reduce acid secretion and increase mucous secretion.
Subsite Mapping of Aspergillus nigerEndopolygalacturonase II by Site-directed Mutagenesis (2000)

To assess the subsites involved in substrate binding in Aspergillus niger endopolygalacturonase II, residues located in the potential substrate binding cleft stretching along the enzyme from the N to the C terminus were subjected to site-directed mutagenesis. Mutant enzymes were characterized with respect to their kinetic parameters using polygalacturonate as a substrate and with respect to their mode of action using oligogalacturonates of defined length (n = 3-6). In addition, the effect of the mutations on the hydrolysis of pectins with various degrees of esterification was studied. Based on the results obtained with enzymes N186E and D282K it was established that the substrate binds with the nonreducing end toward the N terminus of the enzyme. Asn(186) is located at subsite -4, and Asp(282) is located at subsite +2. The mutations D183N and M150Q, both located at subsite -2, affected catalysis, probably mediated via the sugar residue bound at subsite -1. Tyr(291), located at subsite +1 and strictly conserved among endopolygalacturonases appeared indispensable for effective catalysis. The mutations E252A and Q288E, both located at subsite +2, showed only slight effects on catalysis and mode of action. Tyr(326) is probably located at the imaginary subsite +3. The mutation Y326L affected the stability of the enzyme. For mutant E252A, an increased affinity for partially methylesterified substrates was recorded. Enzyme N186E displayed the opposite behavior; the specificity for completely demethylesterified regions of substrate, already high for the native enzyme, was increased. The origin of the effects of the mutations is discussed.