gebhart/patrepeval huggingface dataset:
Medium‐chain dehydrogenases/reductases (MDR) (2002)

Completed eukaryotic genomes were screened for medium-chain dehydrogenases/reductases (MDR). In the human genome, 23 MDR forms were found, a number that probably will increase, because the genome is not yet fully interpreted. Partial sequences already indicate that at least three further members exist. Within the MDR superfamily, at least eight families were distinguished. Three families are formed by dimeric alcohol dehydrogenases (ADH; originally detected in animals/plants), cinnamyl alcohol dehydrogenases (originally detected in plants) and tetrameric alcohol dehydrogenases (originally detected in yeast). Three further families are centred around forms initially detected as mitochondrial respiratory function proteins, acetyl-CoA reductases of fatty acid synthases, and leukotriene B4 dehydrogenases. The two remaining families with polyol dehydrogenases (originally detected as sorbitol dehydrogenase) and quinone reductases (originally detected as zeta-crystallin) are also distinct but with variable sequences. The most abundant families in the human genome are the dimeric ADH forms and the quinone oxidoreductases. The eukaryotic patterns are different from those of Escherichia coli. The different families were further evaluated by molecular modelling of their active sites as to geometry, hydrophobicity and volume of substrate-binding pockets. Finally, sequence patterns were derived that are diagnostic for the different families and can be used in genome annotations.
Developmental expression of human cartilage matrix protein (1994)

Cartilage matrix protein (CMP) is a non-collagenous component of cartilage with a yet unknown function. In this study we used in situ hybridization to investigate the temporal and spatial distribution of CMP transcripts during human embryonic and early fetal development, and compared it to the pattern of expression observed for collagen types I, II, X, and decorin. The distribution of CMP and collagen type II transcripts followed a similar pattern in the embryonic bone anlage, the fetal growth plate, and the developing vertebral column. Expression was highest in the upper hypertrophic and lower proliferative zone, whereas calcified cartilage was negative throughout the different stages of bone development. Chondrocytes of calcified cartilage, however, were not quiescent but expressed collagen type X. The onset of collagen type X expression was linked to hypertrophy and occurred before calcification became apparent. In contrast, decorin and collagen type I were highly expressed in bone and perichondrium but not in growth plate cartilage. During the development of the synovial joints a different pattern of expression emerged. After formation of the joint cavity, there was a halt in expression of CMP but not of collagen type II in chondrocytes close to the articular surface. A band of CMP negative chondrocytes covering the joint surface was observed in all joints investigated. Decorin mRNA was demonstrated in the reserve zone adjacent to the joints, but not in articular cartilage. Extraskeletal expression of CMP was observed in the embryonic retina. The results demonstrate the differential expression of CMP during human skeletal development and chondrocyte differentiation. The distribution of CMP transcripts is unique and distinct from other known matrix genes.
Immunochemistry of purified polysaccharide type antigens of group B streptococcal types Ia, Ib, and Ic (1975)

The HCl-extracted purified polysaccharide type antigens of group B Streptococcus types Ia and Ib were composed of galactose and N-acetylglucosamine in a molar ratio of 3:1 for the Ia antigen and 2:1 for the Ib antigen. Immunochemical data were the same for the Ia antigens of type Ia, purified in this study, and type Ic, purified earlier. Glucosamine inhibited the Ib quantitative precipitin reactions more effectively than did N-acetylglucosamine, whereas the reverse was true of the Ia reaction. Ouchterlony studies were consistent with these observations and also revealed two type-specific precipitin bands with the HCl-extracted Ia antigens. All saline-extracted type antigens, however, formed single Ouchterlony bands that were only partially identical to the corresponding HCl antigens. Purification of the saline antigens was accomplished by treatment with cold trichloroacetic acid and by fractional ethanol precipitation. Immunoelectrophoresis experiments showed that the saline antigens were more negatively charged than the HCl antigens. The presence of sialic acid in the saline antigens probably accounted for their net negative charge and the fact that they were partially degraded by mild acid hydrolysis. The same serological specificities were observed with saline- and with HCl-extracted antigens.
Density of the Notch ligand Delta1 determines generation of B and T cell precursors from hematopoietic stem cells (2005)

Notch signaling regulates multiple cell fate decisions by hematopoietic precursors. To address whether different amounts of Notch ligand influence lineage choices, we cultured murine bone marrow lin(-)Sca-1(+)c-kit+ cells with increasing densities of immobilized Delta1(ext-IgG) consisting of the extracellular domain of Delta1 fused to the Fc domain of human IgG1. We found that relatively lower densities of Delta1(ext-IgG) enhanced the generation of Sca-1(+)c-kit+ cells, Thy1(+)CD25+ early T cell precursors, and B220(+)CD43(-/lo) cells that, when cocultured with OP9 stroma cells, differentiated into CD19+ early B cell precursors. Higher densities of Delta1(ext-IgG) also enhanced the generation of Sca-1(+)c-kit+ precursor cells and promoted the development of Thy1(+)CD25+ cells, but inhibited the development of B220(+)CD43(-/lo) cells. Analyses of further isolated precursor populations suggested that the enhanced generation of T and B cell precursors resulted from the effects on multipotent rather than lymphoid-committed precursors. The results demonstrate the density-dependent effects of Delta1 on fate decisions of hematopoietic precursors at multiple maturational stages and substantiate the previously unrecognized ability of Delta1 to enhance the development of both early B and T precursor cells.
Critical appraisal of cabazitaxel in the management of advanced prostate cancer (2010)

Docetaxel remains a cornerstone of therapy for the patient with metastatic castration-resistant prostate cancer (CRPC). However, the landscape of CRPC therapy is changing rapidly - recently, data from the phase III TROPIC study revealed a survival advantage with the novel taxane cabazitaxel/prednisone (compared with mitoxantrone/prednisone) in a cohort of 755 men with docetaxel-refractory metastatic CRPC. Interestingly, cabazitaxel bears substantial structural similiarity to docetaxel but appears to be mechanistically distinct. In preclinical studies, the agent has antitumor activity in a variety of docetaxel-refractory in vitro and in vivo models. Subsequent to phase I testing in advanced solid tumors (where neutropenia was identified as a dose-limiting toxicity), the agent was assessed in a phase II trial in advanced, taxane-refractory breast cancer and in the aforementioned phase III TROPIC study. This review describes in detail the preclinical and clinical development of cabazitaxel.
The VuSystem: a programming system for compute-intensive multimedia (1996)

In compute-intensive multimedia applications, the computer not only manipulates media, but also digests it and performs independent actions based on media content. We present a design approach that applies the programming techniques of visualization systems to the development of compute-intensive multimedia applications. We describe an implementation based on this approach, and report performance measurements that demonstrate it is practical. We conclude with a description of some applications that have been implemented and a discussion of the implications for the design and engineering of operating systems.
Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,D (1985)

Thermodynamic parameters for double strand formation have been measured for the sixteen double helices of the sequence dCA3XA3G.dCT3YT3G, with each of the bases A, C, G and T at the positions labelled X and Y. The results are analyzed in terms of nearest-neighbors and are compared with thermodynamic parameters for RNA secondary structure. At room temperature the sequence (Formula: see text) is more stable than (Formula: see text) and is similar in stability to (Formula: see text) and (Formula: see text) are least stable. At higher temperatures the sequences containing a G.C base pair become more stable than those containing only A.T. All molecules containing mismatches are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. At room temperature the most stable mismatches are those containing guanine (G.T, G.G, G.A); the least stable contain cytosine (C.A, C.C). At higher temperatures pyrimidine-pyrimidine mismatches become the least stable.
High efficiency InGaP/InGaAs tandem solar cells on Ge substrates (2002)

Over 30% AM1.5G efficiency was achieved by adding a small quantity of indium into a GaAs bottom cell in the conventional tandem cell on a Ge substrate. Characteristics of InGaAs cells on Ge were investigated by varying In-composition. The maximum efficiency was obtained for the cell with 0.01 In-composition, which was lattice-matched to Ga and produced no misfit-dislocations. Relatively high efficiencies were obtained for the cells with In-compositions less than 0.1, which did not produce cracks but misfit-dislocations. InGaP/In/sub x/Ga/sub 1-x/As tandem cells with In-composition x between 0.01 and 0.07 demonstrated higher efficiency than the conventional InGaP/GaAs cells, that was attributed to an increase in photo-currents both in the top and bottom cells. Remarkably, an In/sub 0.49/Ga/sub 0.51/P/In/sub 0.01/Ga/sub 0.99/As tandem cell lattice-matched to Ga showed an improvement in Voc, which was attributed to an elimination of misfit-dislocations in thick GaAs layers. Also, those lnGaP/In/sub x/Ga/sub 1-x/As cells with low In-compositions were found to be favorable for improving efficiency of triple junction cells using Ga cells. Over 31% AM1.5G efficiency was demonstrated for the lnGaP/In/sub x/Ga/sub 1-x/As/Ge triple-junction cells with In-composition x of 0.01 and 0.06, at present.
Analogies in biology textbooks in zoology teaching (2011)

The biologic structures of living creatures are of difficult understanding for students, because they are usually unknown by those, in needs of strategic didactics in order to facilitate the student understanding. There are several strategies and methods for teaching, such as, analogies, metaphors, descriptions, among others. In this article we aim to identify, assess and classify the analogies used in the Higher School Biology textbooks, commonly used in Public State Schools of Manaus – AM, related to the zoology theme. The methodological procedure includes: a) analysis of the whole zoological content of the most used textbooks in the public state network of Amazonas throughout the year; b) three didactic textbooks have been specifically analyzed in order to specify the class taxon of “Fish” for the comparison of possible variations of types and quantities of analogies. The adopted classification of analogies was of Curtis & Reigeluth (1984) and the model of enriching analysis was according to the TWA Glynn model (Harrison & Treagust, 1993). It has been concluded that the use of analogies is greater in the content of invertebrates than that of vertebrates. Most Analogies are presented in a simple and direct manner, comparing structures, concrete to concrete, and of verbal mediation, almost nothing is presented in a diverse and heuristic manner of Zoology content on the LD. The development of limits of comparison and reflexion about the analogies was rare, only the presentation of the analogue and the target of analogy occurred.
Highly efficient germ-line transmission of proviral insertions in zebrafish. (1996)

An important technology in model organisms is the ability to make transgenic animals. In the past, transgenic technology in zebrafish has been limited by the relatively low efficiency with which transgenes could be generated using either DNA microinjection or retroviral infection. Previous efforts to generate transgenic zebrafish with retroviral vectors used a pseudotyped virus with a genome based on the Moloney murine leukemia virus and the envelope protein of the vesicular stomatitis virus. This virus was injected into blastula-stage zebrafish, and 16% of the injected embryos transmitted proviral insertions to their offspring, with most founders transmitting a single insertion to approximately 2% of their progeny. In an effort to improve this transgenic frequency, we have generated pseudotyped viral stocks of two new Moloney-based genomes. These viral stocks have titers up to two orders of magnitude higher than that used previously. Injection of these viruses resulted in a dramatic increase in transgenic efficiency; over three different experiments, 83% (110/133) of the injected embryos transmitted proviral insertions to 24% of their offspring. Furthermore, founders made with one of the viruses transmitted an average of 11 different insertions through their germ line. These results represent a 50- to 100-fold improvement in the efficiency of generating transgenic zebrafish, making it now feasible for a single lab to rapidly generate tens to hundreds of thousands of transgenes. Consequently, large-scale insertional mutagenesis strategies, previously limited to invertebrates, may now be possible in a vertebrate.
Gradient Elution Moving Boundary Electrophoresis for High-Throughput Multiplexed Microfluidic Devices (2006)

A novel method for performing electrophoretic separations is described-gradient elution moving boundary electrophoresis (GEMBE). The technique utilizes the electrophoretic migration of chemical species in combination with variable hydrodynamic bulk counterflow of the solution through a separation capillary or microfluidic channel. Continuous sample introduction is used, eliminating the need for a sample injection mechanism. Only analytes with an electrophoretic velocity greater than the counterflow velocity enter the separation channel. The counterflow velocity is varied over time so that each analyte is brought into the separation column at different times, allowing for high-resolution separations in very short channels. The new variable of bulk flow acceleration affords a new selectivity parameter to electrophoresis analogous to gradient elution compositions in chromatography. Because it does not require extra channels or access ports to form an injection zone and because separations can be performed in very short channels, GEMBE separations can be implemented in much smaller areas on a micro-fluidic chip as compared to conventional capillary electrophoresis. Demonstrations of GEMBE separations of small dye molecules, amino acids, DNA, and immunoassay products are presented. A low-cost, polymeric, eight-channel multiplexed microfluidic device was fabricated to demonstrate the reduced area requirements of GEMBE; the device was less than 1 in.2 in area and required only n + 1 fluidic access ports per n analyses (in this instance, nine ports for eight analyses). Parallel separations of fluorescein and carboxyfluorescein yielded less than 3% relative standard deviation (RSD) in interchannel migration times and less than 5% RSD in both peak and height measurements. The device was also used to generate a calibration curve for a homogeneous insulin immunoassay using each of the eight channels as a calibration point with less than 5% RSD at each point with replicate analyses.
Investigation of the properties of plasma-enhanced chemical vapor deposited silicon nitride and its effect on silicon surface passivation (1998)

Silicon nitride films grown by plasma-enhanced chemical vapor deposition (PECVD) are used for a variety of applications in integrated circuit and solar cell industries, such as surface passivation and insulation. The objective of this article is to investigate and understand the impact of the PECVD deposition parameters on the silicon surface passivation and establish the correlation between the properties of the silicon nitride and the ensuing silicon surface recombination velocity. All the films were annealed at 350 °C for 20 min in a rapid thermal annealer after the deposition. It is shown that bonded hydrogen and positive charge in the annealed PECVD silicon nitride films have the opposite effect on the surface passivation. The surface recombination velocity decreases with the increase in the positive charge density and the decrease in the bonded hydrogen content. It is found that the deposition temperature has the most influence on achieving low surface recombination velocity. Higher deposition temperature in the range of 200–300 °C produces lower surface recombination velocity. Optimal silicon nitride deposition conditions resulted in a surface recombination velocity of 119 cm/s on 2 Ω cm p-type silicon.
Interleukin-6 Induces Gr-1+CD11b+ Myeloid Cells to Suppress CD8+ T Cell-Mediated Liver Injury in Mice (2011)

We concluded that IL-6 induced Gr-1+CD11b+ MDSCs in the liver to inhibit T cell-mediated liver injury. The findings have defined a novel mechanism of IL-6 in protecting liver from CD8+ T cell-mediated injury.
Potent and Selective Inhibitors of MTH1 Probe Its Role in Cancer Cell Survival (2016)

Recent literature has claimed that inhibition of the enzyme MTH1 can eradicate cancer. MTH1 is one of the "housekeeping" enzymes that are responsible for hydrolyzing damaged nucleotides in cells and thus prevent them from being incorporated into DNA. We have developed orthogonal and chemically distinct tool compounds to those published in the literature to allow us to test the hypothesis that inhibition of MTH1 has wide applicability in the treatment of cancer. Here we present the work that led to the discovery of three structurally different series of MTH1 inhibitors with excellent potency, selectivity, and proven target engagement in cells. None of these compounds elicited the reported cellular phenotype, and additional siRNA and CRISPR experiments further support these observations. Critically, the difference between the responses of our highly selective inhibitors and published tool compounds suggests that the effect reported for the latter may be due to off-target cytotoxic effects. As a result, we conclude that the role of MTH1 in carcinogenesis and utility of its inhibition is yet to be established.
Transgenic modification of cows milk for value-added processing (1999)

The application of transgenic technologies in dairy cattle has been restricted largely to producing potential pharmaceutical or nutriceutical products in the mammary gland. Broader application of transgenesis in dairy cattle production will require identifying target traits that are both amenable to transgenic modification and economically important to the dairy industry. The casein proteins are the most valuable component of cows milk destined for value-added processing. The four bovine casein genes lie within a single, multi-gene locus of approximately 200 kb in length. The working hypothesis is that this multi-gene locus contains all of the DNA sequences required to regulate the coordinated expression of all four individual casein genes (i.e. a locus control region or LCR). The initial research aim is to clone the entire casein locus into a bacterial artificial chromosome (BAC) vector, thus preserving the extended 5'and 3' regions that flank the locus, as well as maintaining the spatial integrity of the four individual casein genes that comprise the locus. The author's laboratory has prepared a bacterial artificial chromosome (BAC) library of genomic DNA from elite dairy cattle. Partial, non-elite BAC clones of the casein gene locus are being tested in transgenic mice to establish proof of concept. Advances in nuclear transfer of transfected somatic cells should improve the efficiency of producing transgenic calves that possess a BAC casein construct introduced into an elite genetic background.
A guide to binary vectors and strategies for targeted genome modification in fungi using Agrobacterium tumefaciens-mediated transformation (2011)

Agrobacterium tumefaciens-mediated transformation (ATMT) of fungi has become a common technique for the study of a wide variety of different fungal species over the past 12 years. The discovery that the host range of A. tumefaciens could be extended to include fungi provided an efficient transformation tool for species in which it was previously impossible to conduct molecular genetics experiments. ATMT experiments can be divided into three groups: i) Forward genetics (i.e., random mutagenesis), ii) Reverse genetics (i.e., targeted genome modification and random integration) and iii) the introduction of reporter genes (e.g., GFP, RFP and GUS) that allow in situ monitoring of the fungus. The use of ATMT for forward genetics experiments has primarily included classic random insertional inactivation strategies to obtain loss-of-function mutants. For reverse genetics experiments, ATMT has been used to introduce targeted genome modifications (e.g., disruptions, replacements, overexpression and complementation) and to generate random integrations for complementation, heterologous expression, expression of transcriptional and translational fusion reporters and RNAi-mediated down-regulation of gene expression. This review summarizes the technical advances within the field from 1998 to the summer of 2011, focusing on the development of binary vectors that are compatible with fungal transformation (over 180 general vectors) and methods for constructing binary vectors for targeted integration of T-DNA into fungal genomes.
Attempts To Improve the Overall Stereoselectivity of the Ireland−Claisen Rearrangement (2008)

With focus on the steric effects present in the transition states for the [3,3]-sigmatropic rearrangement, the substrate 5 has been designed to improve the overall stereoselectivity of the Ireland-Claisen rearrangement. Experimentally, it has been found that (1) only Z-6 rearranges to 7 at 80 degrees C and (2) E-6 isomerizes to Z-6 at 80 degrees C, thereby allowing the transformation of 5 into 7 in an almost quantitative yield. To illustrate the usefulness of this approach, two additional examples are given.
SON (silicon on nothing)-a new device architecture for the ULSI era (1999)

A novel device architecture called SON (silicon on nothing) is proposed, allowing extremely thin buried oxides and silicon films to be fabricated and thereby provide better resistance to short channel effects (SCE) and DIBL than any other device architecture. SON devices are shown to present excellent I/sub on//I/sub off/ trade-off, V/sub th/ roll-off suppression down to 15 nm channel length, and to be free from the shortcomings of conventional SOI, such as self-heating, high S/D series resistances, and expensive SOI substrates since SON devices are fabricated on bulk silicon.