gebhart/patrepeval huggingface dataset:
Optimization and Scale-Up of a Lipase-Catalyzed Enzymatic Resolution of an Indole Ester Intermediate for a Prostaglandin D2(DP) Receptor Antagonist Targeting Allergic Rhinitis (2006)

Pseudomonas fluorescens lipase was found to catalyze the asymmetric hydrolysis of racemic indole-ethyl ester 1.1 The lipase converted the undesired (S) enantiomer to its corresponding acid, while leaving the desired (R) enantiomer untouched, yielding optically enhanced (R)-ester with an ee of 95%1 at 48% conversion. The original process conditions for this resolution contained a second-phase immiscible organic solvent to solubilize the substrate, and required 128 g/L enzyme for a 100 g/L substrate charge (Shafiee, A.; Upadhyay, V.; Corley, E.; Biba, M.; Zhao, D.; Marcoux, J.-F.; Campos, K.; Journet, M.; King, A.; Larsen, R.; Grabowski, E.; Volante, R.; Tillyer, R. Tetrahedron Asymmetry 2005, 16, 3094). A study of substrate solubility and phase-partitioning behavior in a wide range of miscible and immiscible solvent concentrations demonstrated that the presence of the immiscible organic solvent caused the reaction to reach a mass transfer limited regime at conversions >40%. Process optimization led to the elimination of the second-phase immiscible organic solvent, a greater than 4-fold reduction in enzyme charge, and an increased product ee of >99%. The optimized process has been demonstrated at scale on two 40-kg batches and has resulted in product ester ee of 99.75% at 50% conversion.
An In Vitro Study to Assess Determinant Features Associated With Fluid Sealing in the Design of Endotracheal Tube Cuffs and Exerted Tracheal Pressures* (2012)

The high-volume low-pressure cuffs' outer diameter, length, material, and internal pressure are the main determinants of sealing efficacy. Despite internal pressure within the safe range, transmitted tracheal pressure is extremely heterogeneous and differs among cuffs, occasionally reaching localized, very high, unsafe levels.
Isolation and Identification of Actinobacteria from Surface-Sterilized Wheat Roots (2003)

This is the first report of filamentous actinobacteria isolated from surface-sterilized root tissues of healthy wheat plants (Triticum aestivum L.). Wheat roots from a range of sites across South Australia were used as the source material for the isolation of the endophytic actinobacteria. Roots were surface-sterilized by using ethanol and sodium hypochlorite prior to the isolation of the actinobacteria. Forty-nine of these isolates were identified by using 16S ribosomal DNA (rDNA) sequencing and found to belong to a small group of actinobacterial genera including Streptomyces, Microbispora, Micromonospora, and Nocardiodes spp. Many of the Streptomyces spp. were found to be similar, on the basis of their 16S rDNA gene sequence, to Streptomyces spp. that had been isolated from potato scabs. In particular, several isolates exhibited high 16S rDNA gene sequence homology to Streptomyces caviscabies and S. setonii. None of these isolates, nor the S. caviscabies and S. setonii type strains, were found to carry the nec1 pathogenicity-associated gene or to produce the toxin thaxtomin, indicating that they were nonpathogenic. These isolates were recovered from healthy plants over a range of geographically and temporally isolated sampling events and constitute an important plant-microbe interaction.
Sulindac for polyposis of the colon (1983)

Four members of a Gardner's syndrome family had rectal and colon polyposis treated with nonsteroid anti-inflammatory drugs. Three of these patients had had subtotal colectomy and ileoproctostomy and the residual polyps arose in the rectal mucosa. The polyps almost completely disappeared when sulindac was administered. Indomethacin therapy over the course of a preceding year was ineffective in one of these patients. One patient (case 4) had diffuse polyposis in an intact colon. After sulindac therapy for a year, only three small mucosal polyps could be identified by air contrast barium enema and colonoscopic examination. These observations confirm those of Pollard and Luckert [1,2] on rats with chemically induced polyposis of the intestinal tract.
Adeno-associated virus--an extreme state of viral defectiveness. (1979)

Theodore Roosevelt cannot accept Walter B. Bullen's kind offer. His secretary suggests that if Bullen wants to help with the campaign, he should contact Senator Dixon in Chicago.
Dynamical Signature of the Mott-Hubbard Transition in Ni(S,Se) 2 (1996)

The transition metal chalcogenide Ni(S,Se)2 is one of the few highly correlated, Mott-Hubbard systems without a strong first-order structural distortion that normally cuts off the critical behavior at the metal-insulator transition. The zero-temperature (T) transition was tuned with pressure, and significant deviations were found near the quantum critical point from the usual T1/2 behavior of the conductivity characteristic of electron-electron interactions in the presence of disorder. The transport data for pressure and temperature below 1 kelvin could be collapsed onto a universal scaling curve.
New Spatial-Gradient-Features for Video Script Identification (2012)

In this paper, we present new features based on Spatial-Gradient-Features (SGF) at block level for identifying six video scripts namely, Arabic, Chinese, English, Japanese, Korean and Tamil. This works helps in enhancing the capability of the current OCR on video text recognition by choosing an appropriate OCR engine when video contains multi-script frames. The input for script identification is the text blocks obtained by our text frame classification method. For each text block, we obtain horizontal and vertical gradient information to enhance the contrast of the text pixels. We divide the horizontal gradient block into two equal parts as upper and lower at the centroid in the horizontal direction. Histogram on the horizontal gradient values of the upper and the lower part is performed to select dominant text pixels. In the same way, the method selects dominant pixels from the right and the left parts obtained by dividing the vertical gradient block vertically. The method combines the horizontal and the vertical dominant pixels to obtain text components. Skeleton concept is used to reduce pixel width to a single pixel to extract spatial features. We extract four features based on proximity between end points, junction points, intersection points and pixels. The method is evaluated on 770 frames of six scripts in terms of classification rate and is compared with an existing method. We have achieved 82.1% average classification rate.
NF-κB activation as a pathological mechanism of septic shock and inflammation (2006)

The pathophysiology of sepsis and septic shock involves complex cytokine and inflammatory mediator networks. NF-kappaB activation is a central event leading to the activation of these networks. The role of NF-kappaB in septic pathophysiology and the signal transduction pathways leading to NF-kappaB activation during sepsis have been an area of intensive investigation. NF-kappaB is activated by a variety of pathogens known to cause septic shock syndrome. NF-kappaB activity is markedly increased in every organ studied, both in animal models of septic shock and in human subjects with sepsis. Greater levels of NF-kappaB activity are associated with a higher rate of mortality and worse clinical outcome. NF-kappaB mediates the transcription of exceptional large number of genes, the products of which are known to play important roles in septic pathophysiology. Mice deficient in those NF-kappaB-dependent genes are resistant to the development of septic shock and to septic lethality. More importantly, blockade of NF-kappaB pathway corrects septic abnormalities. Inhibition of NF-kappaB activation restores systemic hypotension, ameliorates septic myocardial dysfunction and vascular derangement, inhibits multiple proinflammatory gene expression, diminishes intravascular coagulation, reduces tissue neutrophil influx, and prevents microvascular endothelial leakage. Inhibition of NF-kappaB activation prevents multiple organ injury and improves survival in rodent models of septic shock. Thus NF-kappaB activation plays a central role in the pathophysiology of septic shock.
Isolierung und Konstitutionsermittlung von Chrysodin (1973)

Abstract The constitution of Chrysodin ( 2 ), a metabolite of Sepedonium chrysospermum , is proposed on the basis of chemical transformations and physical measurements.
Dacarbazine-based chemotherapy for metastatic melanoma: thirty-year experience overview. (2000)

Dacarbazine (DTIC) is the only single-agent approved by the Food and Drug Administration for treating metastatic melanoma. With DTIC as single agent, an approximately 20% objective response rate can be achieved with median response duration of 5 to 6 months and complete response rates of 5%. Current status of DTIC single agent and DTIC-based combination chemotherapy has been extensively reviewed in this article. Moreover, future directions including new combination chemotherapies and/or new therapeutical approaches have been considered. The addition to DTIC of agents such as cisplatin, nitrosoureas and tubular toxins has been reported to yield high response rates, up to 40%, in single-institution phase II trials. Historically, promising combination regimens like BOLD (bleomycin, vincristine, lomustine and DTIC) and CVD (cisplatin, vinblastine and DTIC) have induced responses on metastatic lesions to the liver, bone and brain, commonly unresponsive to DTIC alone, even though have failed to produce impact on patient survival. Several other studies have suggested a significant enhancement of antitumor effect associated with the addition of tamoxifen to various cytotoxic regimens. The four-drug combination CBDT (cisplatin, carmustine, DTIC and tamoxifen) or "Dartmouth regimen" has yielded high response rates, up to 55%, with continuous, maintained, complete responses, up to 82 months, in a subset of patients, that is considerably longer than observed with other combinations. Some authors recommend CBDT as reference therapy, even though recently presented results of a randomized phase III trial of CBDT versus DTIC alone, show no statistical difference in survival between the two groups. While a survival benefit from DTIC-based chemotherapy or DTIC alone has never been shown in metastatic melanoma patients and, therefore, the survival has remained unchanged over the past 30 years, some long term survivors have been reported with the "Dartmouth regimen" and/or with high dose interleukin-2 (IL-2) based regimens whose role is going to be defined in prospective randomized phase III trials. On the other hand, the better understanding of the mechanisms responsible for melanoma chemoresistance and the development of new therapeutical strategies could change the scenario in the next future.
Attachment of Histidine Tags to Recombinant Tumor Necrosis Factor-Alpha Drastically Changes Its Properties (2002)

When studying two different histidine tags attached to the N-termini of the trimeric cytokine tumor necrosis factor alpha (TNF), the biological activity--measured as cytotoxicity on the L-929 cell line--of both tagged proteins was drastically reduced. The longer His10 tag reduced cytotoxicity to approximately 16% and the shorter His7 tag to 6% of the activity of their nontagged counterparts. After removal of the tags, biological activities reverted to the expected normal values, which clearly shows the key role of the attached histidine tags in diminishing biological activity. Studies on the mechanism of these effects revealed no specific interactions and showed that even the natural flexible N-terminus of TNF presents a steric hindrance for receptor binding, while any extension of the N-terminus increases this hindrance and consequently reduces biological activity. Also, in other proteins, the ligand or substrate binding sites may be hindered by histidine tags, leading to wrong conclusions about biological activity or other properties of the proteins. Thus caution is advised when using His-tagged proteins directly in screening procedures or in research.
16.4: A New Projection System with Scrolling Illumination for Motion Picture (2003)

Abstract A projection system was developed to reduce blurred images caused by fast motion pictures on hold‐type display such as LCD panels. The system incorporates an optical scrolling system using a spiral aperture wheel (SAW) made of glass and aluminum to transmit and reflect light.
A Role for SlyD in the Escherichia coli Hydrogenase Biosynthetic Pathway (2004)

The [NiFe] centers at the active sites of the Escherichia coli hydrogenase enzymes are assembled by a team of accessory proteins that includes the products of the hyp genes. To determine whether any other proteins are involved in this process, the sequential peptide affinity system was used. The analysis of the proteins in a complex with HypB revealed the peptidyl-prolyl cis/trans-isomerase SlyD, a metal-binding protein that has not been previously linked to the hydrogenase biosynthetic pathway. The association between HypB and SlyD was confirmed by chemical cross-linking of purified proteins. Deletion of the slyD gene resulted in a marked reduction of the hydrogenase activity in cell extracts prepared from anaerobic cultures, and an in-gel assay was used to demonstrate diminished activities of both hydrogenase 1 and 2. Western analysis revealed a decrease in the final proteolytic processing of the hydrogenase 3 HycE protein, indicating that the metal center was not assembled properly. These deficiencies were all rescued by growth in medium containing excess nickel, but zinc did not have any phenotypic effect. Experiments with radioactive nickel demonstrated that less nickel accumulated in DeltaslyD cells compared with wild type, and overexpression of SlyD from an inducible promoter doubled the level of cellular nickel. These experiments demonstrate that SlyD has a role in the nickel insertion step of the hydrogenase maturation pathway, and the possible functions of SlyD are discussed.
Single-molecule analysis of ultradilute solutions with guided streams of 1-µm water droplets (1999)

We describe instrumentation for real-time detection of single-molecule fluorescence in guided streams of 1-microm (nominal) water droplets. In this technique, target molecules were confined to droplets whose volumes were comparable with illumination volumes in diffraction-limited fluorescence microscopy and guided to the waist of a cw probe laser with an electrostatic potential. Concentration detection limits for Rhodamine 6G in water were determined to be approximately 1 fM, roughly 3 orders of magnitude lower than corresponding limits determined recently with diffraction-limited microscopy techniques for a chemical separation of similar dyes. In addition to its utility as a vehicle for probing single molecules, instrumentation for producing and focusing stable streams of 1-2-microm-diameter droplets may have other important analytical applications as well.
Topochemical Reaction Control in Solution (1995)

The controlling function of the crystal lattice in many reactions in the solid state can be exercised by the rigid [2.2]paracyclophane spacer in photochemical processes in solution. For example, irradiation of the bisvinylogous cinnamophane 1 affords [5]ladderane 2 in good yield.
Feedforward semantic segmentation with zoom-out features (2014)

We introduce a purely feed-forward architecture for semantic segmentation. We map small image elements (superpixels) to rich feature representations extracted from a sequence of nested regions of increasing extent. These regions are obtained by "zooming out" from the superpixel all the way to scene-level resolution. This approach exploits statistical structure in the image and in the label space without setting up explicit structured prediction mechanisms, and thus avoids complex and expensive inference. Instead superpixels are classified by a feedforward multilayer network. Our architecture achieves new state of the art performance in semantic segmentation, obtaining 64.4% average accuracy on the PASCAL VOC 2012 test set.
A review of materials, fabrication methods, and strategies used to enhance bone regeneration in engineered bone tissues (2007)

Over the last decade, bone engineered tissues have been developed as alternatives to autografts and allografts to repair and reconstruct bone defects. This article provides a review of the current technologies in bone tissue engineering. Factors used for fabrication of three-dimensional bone scaffolds such as materials, cells, and biomolecular signals, as well as required properties for ideal bone scaffolds, are reviewed. In addition, current fabrication techniques including rapid prototyping are elaborated upon. Finally, this review article further discusses some effective strategies to enhance cell ingrowth in bone engineered tissues; for example, nanotopography, biomimetic materials, embedded growth factors, mineralization, and bioreactors. In doing so, it suggests that there is a possibility to develop bone substitutes that can repair bone defects and promote new bone formation for orthopedic applications.
Intracellular Retention of the NKG2D Ligand MHC Class I Chain-Related Gene A in Human Melanomas Confers Immune Privilege and Prevents NK Cell-Mediated Cytotoxicity (2008)

Abstract Most tumors grow in immunocompetent hosts despite expressing NKG2D ligands (NKG2DLs) such as the MHC class I chain-related genes A and B (MICA/B). However, their participation in tumor cell evasion is still not completely understood. Here we demonstrate that several human melanomas (cell lines and freshly isolated metastases) do not express MICA on the cell surface but have intracellular deposits of this NKG2DL. Susceptibility to NK cell-mediated cytotoxicity correlated with the ratio of NKG2DLs to HLA class I molecules but not with the amounts of MICA on the cell surface of tumor cells. Transfection-mediated overexpression of MICA restored cell surface expression and resulted in an increased in vitro cytotoxicity and IFN-γ secretion by human NK cells. In xenografted nude mice, these melanomas exhibited a delayed growth and extensive in vivo apoptosis. Retardation of tumor growth was due to NK cell-mediated antitumor activity against MICA-transfected tumors, given that this effect was not observed in NK cell-depleted mice. Also, mouse NK cells killed MICA-overexpressing melanomas in vitro. A mechanistic analysis revealed the retention of MICA in the endoplasmic reticulum, an effect that was associated with accumulation of endoH-sensitive (immature) forms of MICA, retrograde transport to the cytoplasm, and degradation by the proteasome. Our study identifies a novel strategy developed by melanoma cells to evade NK cell-mediated immune surveillance based on the intracellular sequestration of immature forms of MICA in the endoplasmic reticulum. Furthermore, this tumor immune escape strategy can be overcome by gene therapy approaches aimed at overexpressing MICA on tumor cells.
The Number of Glutamate Transporter Subtype Molecules at Glutamatergic Synapses: Chemical and Stereological Quantification in Young Adult Rat Brain (1998)

The role of transporters in shaping the glutamate concentration in the extracellular space after synaptic release is controversial because of their slow cycling and because diffusion alone gives a rapid removal. The transporter densities have been measured electrophysiologically, but these data are from immature brains and do not give precise information on the concentrations of the individual transporter subtypes. Here we show by quantitative immunoblotting that the numbers of the astroglial glutamate transporters GLAST (EAAT1) and GLT (EAAT2) are 3200 and 12,000 per micrometer3 tissue in the stratum radiatum of adult rat hippocampus (CA1) and 18,000 and 2800 in the cerebellar molecular layer, respectively. The total astroglial cell surface is 1.4 and 3.8 m2/cm3 in the two regions, respectively, implying average densities of GLAST and GLT molecules in the membranes around 2300 and 8500 micrometer-2 in the former and 4700 and 740 micrometer-2 in the latter region. The total concentration of glial glutamate transporters in both regions corresponds to three to five times the estimated number of glutamate molecules in one synaptic vesicle from each of all glutamatergic synapses. However, the role of glial glutamate transporters in limiting synaptic spillover is likely to vary between the two regions because of differences in the distribution of astroglia. Synapses are completely ensheathed and separated from each other by astroglia in the cerebellar molecular layer. In contrast, synapses in hippocampus (stratum radiatum) are only contacted by astroglia and are often found side by side without intervening glial processes.
A Genome-Wide Functional Investigation into the Roles of Receptor-Like Proteins in Arabidopsis (2008)

Receptor-like proteins (RLPs) are cell surface receptors that typically consist of an extracellular leucine-rich repeat domain, a transmembrane domain, and a short cytoplasmatic tail. In several plant species, RLPs have been found to play a role in disease resistance, such as the tomato (Solanum lycopersicum) Cf and Ve proteins and the apple (Malus domestica) HcrVf2 protein that mediate resistance against the fungal pathogens Cladosporium fulvum, Verticillium spp., and Venturia inaequalis, respectively. In addition, RLPs play a role in plant development; Arabidopsis (Arabidopsis thaliana) TOO MANY MOUTHS (TMM) regulates stomatal distribution, while Arabidopsis CLAVATA2 (CLV2) and its functional maize (Zea mays) ortholog FASCINATED EAR2 regulate meristem maintenance. In total, 57 RLP genes have been identified in the Arabidopsis genome and a genome-wide collection of T-DNA insertion lines was assembled. This collection was functionally analyzed with respect to plant growth and development and sensitivity to various stress responses, including susceptibility toward pathogens. A number of novel developmental phenotypes were revealed for our CLV2 and TMM insertion mutants. In addition, one AtRLP gene was found to mediate abscisic acid sensitivity and another AtRLP gene was found to influence nonhost resistance toward Pseudomonas syringae pv phaseolicola. This genome-wide collection of Arabidopsis RLP gene T-DNA insertion mutants provides a tool for future investigations into the biological roles of RLPs.
The tunnelling field effect transistors (TFET): the temperature dependence, the simulation model, and its application (2004)

The TFET is an alternative device for deep sub-micron CMOS with very good short channel and leakage characteristics. The paper presents investigations on properties important for circuit implementation: measurements are performed to verify the working principle and the temperature dependence of the TFET. A simulation model is developed and fitted to the silicon results to be able to do circuit design. Using the simulation models for the n-channel and p-channel device, the complementary inverter is analyzed and compared to the standard CMOS implementation.