gebhart/patrepeval huggingface dataset:
Direct expression of Bordetella pertussis filamentous hemagglutinin in Escherichia coli and Salmonella typhimurium aroA (1991)

Nonfused (i.e., nonhybrid) filamentous hemagglutinin (FHA) of Bordetella pertussis was efficiently expressed in Escherichia coli K-12 and Salmonella typhimurium aroA at levels higher than those found in wild-type B. pertussis when the upstream signals of the gene were replaced and the translation initiation region was engineered to optimize translational efficiency. Inclusion of part of the C-terminal FHA open reading frame, whose translation product does not appear to be part of the major secreted species of FHA, was shown to be important in achieving protein expression in both E. coli and S. typhimurium aroA; removal of the downstream gene sequence abolished recombinant FHA production. The levels of expression observed varied widely according to the construct and host bacterium used.
High hole mobility in SiGe alloys for device applications (1994)

We report high hole mobility in modulation-doped SiGe alloys with Ge content up to 80%. The layers which are grown using ultrahigh-vacuum chemical vapor deposition are of high crystalline quality, have smooth surfaces, and have a low density of misfit dislocations. As a result of strain and high Ge content, we have measured hole mobilities in the range of 800–1050 cm2/V s at room temperature, and 3300–3500 cm2/V s at 77 K. The corresponding two-dimensional sheet hole density is about 3×1012 cm−2. Those numbers are, to our knowledge, the highest numbers ever reported for a SiGe alloy. The resistivity of this two-dimensional hole channel at room temperature is, to our knowledge, the lowest for any p-type semiconductor quantum well.
Termination of Ventricular Fibrillation in Man by Externally Applied Electric Countershock (1956)

VENTRICULAR fibrillation is usually a rapidly fatal arrhythmia that may occur in cardiac patients, in any patient under anesthesia and in drowning and electrocution. In cardiac patients it is a frequent cause of sudden death in the course of coronary-artery disease, a well recognized mechanism of Stokes–Adams attacks, an uncommon toxic reaction to digitalis, quinidine and procaine amide, an occasional terminating event in ventricular tachycardia and a rare, but dreaded, complication of cardiac catheterization. In the operating room ventricular standstill is the usual initial mechanism of cardiac arrest, but ventricular fibrillation occasionally occurs,1 particularly during hypothermia or during anesthesia with . . .
Detection of Mutations in Human Type I Collagen mRNA in Osteogenesis Imperfecta by Indirect RNase Protection (1989)

A method for detecting a wide variety of mutations within type I collagen has been developed and evaluated on a series of patients with osteogenesis imperfecta. RNA, extracted from the nuclear and cytoplasmic compartment of cultured fibroblasts from affected individuals, is hybridized with antisense single-stranded cDNA to the alpha 1(I) mRNA. The hybrid is digested with RNase A and T1 under varying degrees of stringency. The resistant RNA bands are separated by electrophoresis in agarose, transferred to nitrocellulose, and hybridized with antisense cRNA colinear with the protecting probe. This approach is capable of detecting previously defined mutations such as 252-base pair deletion and a 1-base pair mismatch within the alpha 1(I) mRNA. The method appears to be particularly useful in detecting abnormalities of RNA processing that behave as an insert or deletion within the mature mRNA. The procedure should be generally applicable for the identification and localization of any mutation within an entire gene if the gene is expressed as an RNA and a complete cDNA for the mRNA is available.
Caspases: A Molecular Switch Node in the Crosstalk between Autophagy and Apoptosis (2014)

Autophagy and apoptosis are two important catabolic processes contributing to the maintenance of cellular and tissue homeostasis. Autophagy controls the turnover of protein aggregates and damaged organelles within cells, while apoptosis is the principal mechanism by which unwanted cells are dismantled and eliminated from organisms. Despite marked differences between these two pathways, they are highly interconnected in determining the fate of cells. Intriguingly, caspases, the primary drivers of apoptotic cell death, play a critical role in mediating the complex crosstalk between autophagy and apoptosis. Pro-apoptotic signals can converge to activate caspases to execute apoptotic cell death. In addition, activated caspases can degrade autophagy proteins (i.e., Beclin-1, Atg5, and Atg7) to shut down the autophagic response. Moreover, caspases can convert pro-autophagic proteins into pro-apoptotic proteints to trigger apoptotic cell death instead. It is clear that caspases are important in both apoptosis and autophagy, thus a detailed deciphering of the role of caspases in these two processes is still required to clarify the functional relationship between them. In this article, we provide a current overview of caspases in its interplay between autophagy and apoptosis. We emphasized that defining the role of caspases in autophagy-apoptosis crosstalk will provide a framework for more precise manipulation of these two processes during cell death.
Molecular Cloning and Functional Expression of the Human Golgi UDP-N-Acetylglucosamine Transporter (1999)

We have cloned the human UDP-N-acetylglucosamine (UDP-GlcNAc) transporter cDNA, which was recognized through a homology search in the expressed sequence tags database (dbEST) based on its similarity to the human UDP-galactose transporter. The chromosomal location of the UDP-GlcNAc transporter gene was assigned to chromosome 1p21 by fluorescence in situ hybridization (FISH). The transporter was expressed ubiquitously in every tissue so far examined. Expression of the transporter cDNA in CHO-K1 cells in its native and in a C-terminally HA-tagged form indicated that the human UDP-GlcNAc transporter was localized in the Golgi apparatus. The membrane vesicles prepared from yeast cells expressing the cDNA product exhibited UDP-GlcNAc-specific transporting activity. Comparison among UDP-galactose, CMP-sialic acid, and UDP-GlcNAc transporters from several organisms enabled us to identify residues highly conserved among the transporters and residues specific for each group of transporters.
Human acute leukemia cell line with the t(4;11) chromosomal rearrangement exhibits B lineage and monocytic characteristics (1985)

A cell line, designated RS4;11, was established from the bone marrow of a patient in relapse with an acute leukemia that was characterized by the t(4;11) chromosomal abnormality. The cell line and the patient's fresh leukemic cells both had the t(4;11)(q21;q23) and an isochromosome for the long arm of No. 7. Morphologically, all cells were lymphoid in appearance. Ultrastructurally and cytochemically, approximately 30% of the cells possessed myeloid features. The cells were strongly positive for terminal deoxynucleotidyl transferase. They were HLA-DR positive and expressed surface antigens characteristic for B lineage cells, including those detected by anti-B4, BA-1, BA-2, and PI153/3. Immunoglobulin gene analysis revealed rearrangements of the heavy chain and kappa chain genes. The cells lacked the common acute lymphoblastic leukemia antigen and antigenic markers characteristic of T lineage cells. The cells reacted with the myeloid antibody 1G10 but not with other myeloid monoclonal antibodies. Treatment with 12-O-tetradecanoyl- phorbol-13-acetate induced a monocyte-like phenotype demonstrated by cytochemical, functional, immunologic, and electron microscopic studies. The expression of markers of both early lymphoid and early myeloid cells represents an unusual phenotype and suggests that RS4;11 represents a cell with dual lineage capabilities. To our knowledge, RS4;11 is the first cell line established from t(4;11)-associated acute leukemia.
Databases and cell-selection algorithms for VLSI cell libraries (1990)

The issues that must be addressed before commercial database management systems can be used to manage VLSI CAD data are defined. A survey is presented of approaches addressing four of the defined issues: design hierarchies and multilevel representations, design alternatives and version control, common interface between cell libraries and efficient cell selection based on given design constraints. A frame-based model is considered as a case study of the special-purpose design database management system approach. This framework for capturing design data is based on semantic networks. It is well suited for application-specific ICs, yet general enough for other CAD/CAM environments. Benchmark results for the selection algorithms that run on top of the frame-based database system are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Optical Constants of Silicon in the Region 1 to 10 ev (1960)

The reflectance, ${|r(\ensuremath{\lambda})|}^{2}$, of single crystal silicon was measured in the range 1 to 11.3 ev. The phase, $\ensuremath{\theta}(\ensuremath{\lambda})$, was computed from these data using the Kramers-Kronig relation between the real and imaginary parts of the complex function $\mathrm{ln}r=\mathrm{ln}|r|+i\ensuremath{\theta}$. The optical constants, $n$ and $k$, were then determined from the Fresnel reflectivity equation. The real part of the refractive index, $n$, shows a sharp maximum of magnitude 6.9 at 3.3 ev. The extinction coefficient, $k$, shows maxima of magnitude 3.1 at 3.5 ev and 5.1 at 4.3 ev; optical absorption above 3 ev is associated with the onset of strong direct transitions. The results indicate that much useful information, applicable to band structure calculations for both silicon and germanium, could be obtained from limited reflectance studies (2 to 5 ev) on Ge-Si alloys.
Nanolithography and Nanochemistry: Probe‐Related Patterning Techniques and Chemical Modification for Nanometer‐Sized Devices (2004)

The size regime for devices produced by photolithographic techniques is limited. Therefore, other patterning techniques have been intensively studied to create smaller structures. Scanning-probe-based patterning techniques, such as dip-pen lithography, local force-induced patterning, and local-probe oxidation-based techniques are highly promising because of their relative ease and widespread availability. The latter of these is especially interesting because of the possibility of producing nanopatterns for a broad range of chemical and physical modification and functionalization processes; both the production of nanometer-sized electronic devices and the formation of devices involving (bio)molecular recognition and sensor applications is possible. This Review highlights the development of various scanning probe systems and the possibilities of local oxidation methods, as well as giving an overview of state-of-the-art nanometer-sized devices, and a view of future development.
Nebivolol Reduces Nitroxidative Stress and Restores Nitric Oxide Bioavailability in Endothelium of Black Americans (2005)

Reduced endothelial NO bioavailability in American blacks is mainly due to excessive O2- and ONOO- generation by NAD(P)H and uncoupled endothelial NO synthase. Nebivolol decreased O2- and ONOO- concentrations and restored NO bioavailability in blacks to the level recorded in cells from whites, independently of beta1-selective blockade.
Enhanced Microwave Absorption Properties of Intrinsically Core/shell Structured La0.6Sr0.4MnO3Nanoparticles (2009)

The intrinsically core/shell structured La(0.6)Sr(0.4)MnO(3) nanoparticles with amorphous shells and ferromagnetic cores have been prepared. The magnetic, dielectric and microwave absorption properties are investigated in the frequency range from 1 to 12 GHz. An optimal reflection loss of -41.1 dB is reached at 8.2 GHz with a matching thickness of 2.2 mm, the bandwidth with a reflection loss less than -10 dB is obtained in the 5.5-11.3 GHz range for absorber thicknesses of 1.5-2.5 mm. The excellent microwave absorption properties are a consequence of the better electromagnetic matching due to the existence of the protective amorphous shells, the ferromagnetic cores, as well as the particular core/shell microstructure. As a result, the La(0.6)Sr(0.4)MnO(3) nanoparticles with amorphous shells and ferromagnetic cores may become attractive candidates for the new types of electromagnetic wave absorption materials. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11671-009-9374-y) contains supplementary material, which is available to authorized users.
CONTROL OF TRANSLATION INITIATION IN ANIMALS (1998)

Regulation of translation initiation is a central control point in animal cells. We review our current understanding of the mechanisms of regulation, drawing particularly on examples in which the biological consequences of the regulation are clear. Specific mRNAs can be controlled via sequences in their 5' and 3' untranslated regions (UTRs) and by alterations in the translation machinery. The 5'UTR sequence can determine which initiation pathway is used to bring the ribosome to the initiation codon, how efficiently initiation occurs, and which initiation site is selected. 5'UTR-mediated control can also be accomplished via sequence-specific mRNA-binding proteins. Sequences in the 3' untranslated region and the poly(A) tail can have dramatic effects on initiation frequency, with particularly profound effects in oogenesis and early development. The mechanism by which 3'UTRs and poly(A) regulate initiation may involve contacts between proteins bound to these regions and the basal translation apparatus. mRNA localization signals in the 3'UTR can also dramatically influence translational activation and repression. Modulations of the initiation machinery, including phosphorylation of initiation factors and their regulated association with other proteins, can regulate both specific mRNAs and overall translation rates and thereby affect cell growth and phenotype.
Synthesis and characterization of poly‐β‐hydroxybutyrate. I. Synthesis of crystalline DL‐poly‐β‐hydroxybutyrate from DL‐β‐butyrolactone (1971)

Abstract The polymerization of β‐butyrolactone was investigated as a possible monomer for a proposed synthesis of the naturally occurring polyester, D ‐poly‐β‐hydroxybutyrate ( D ‐PHB). The racemic DL ‐monomer was used in this initial study to determine the best conditions and catalyst system for use in a subsequent study of the polymerization of optically active β‐butyrolactone. In so doing it was found that certain organometallic catalysts (Et 2 Zn and Et 3 Al) plus a cocatalyst of water produced highly crystalline samples of polyester from the racemic monomer. This paper describes the synthesis and characterization of the racemic polymer obtained using these catalyst systems, and compares the results obtained with certain other catalysts that were also investigated for this purpose. Examination of the DL ‐PHB by infrared, NMR, x‐ray, and electron microscopy shows that it is possible to synthesize a crystalline racemic polymer that is virtually identical (excepting optical activity) to the naturally occurring polymer, D ‐PHB.
Nitrofurantoin: Mechanism of action and implications for resistance development in common uropathogens (1994)

Nitrofurantoin is an effective urinary tract antibacterial to which no clinically significant resistance development has occurred. We have previously shown that nitrofurantoin susceptibility in bacteria correlates with the presence of bacterial nitroreductases which convert nitrofurantoin to highly reactive electrophilic intermediates. These intermediates were shown to attack bacterial ribosomal proteins non-specifically, causing complete inhibition of protein synthesis. In the present study, we confirm previous reports that low concentrations of nitrofurantoin specifically inhibit inducible enzyme synthesis in bacteria, and show that this inhibition occurs at levels equivalent to the MICs of nitrofurantoin for several bacterial species. Our previous studies had shown that nitrofurantoin at different concentrations interacts with bacterial ribosomal proteins in qualitatively the same fashion; we now report that quantitative differences are seen in the labelling observed at different nitrofurantoin concentrations and discuss these differences as they may relate to the inhibition of inducible enzyme synthesis. In addition, we have now demonstrated the existence of a novel mechanism of action for nitrofurantoin which does not require the production of reactive nitrofurantoin metabolites by bacterial reductases. The lack of clinically significant bacterial resistance development to nitrofurantoin is likely due to the combination of nitrofurantoin's multiple sites of attack and multiple mechanisms of action.
Mixed DNA/RNA polymers are cleaved by the hammerhead ribozyme (1990)

A series of chemically synthesized oligodeoxyribonucleotides containing one or two ribonucleotides (DNA/RNA mixed polymers) at and/or adjacent to the cleavage site of the substrate can be cleaved by the "hammerhead" ribozyme. In comparison with the all-RNA substrate, the predominantly deoxyribonucleotide substrates have (1) lower optimal temperatures of cleavage, (2) approximately 6-fold higher Km's and 7-fold lower kcat's at 30 degrees C, and (3) 15-fold higher Km's and 8-fold lower kcat's at 37 degrees C. The extent to which the RNA substrate cleavage is inhibited in the presence of an all-DNA (KI = 13 microM) and an RNA substrate analogue with a dC at the cleavage site (KI = 0.96 microM) supports the contention that the formation of the ribozyme-substrate complex with the predominantly deoxyribonucleotide substrates (D substrates) is impaired. The weaker binding of D substrates was confirmed by thermal denaturation and determination of the Tm of the complex. Analysis of the kinetic data also suggests that the conformation of the catalytic core of the ribozyme-substrate complex differs from that of the all-RNA complex, a change that results from the presence of a DNA/RNA heteroduplex in the complex.
Expression of CD28 by Bone Marrow Stromal Cells and Its Involvement in B Lymphopoiesis (2002)

Young mice lacking CD28 have normal numbers of peripheral B cells; however, abnormalities exist in the humoral immune response that may result from an intrinsic defect in the B cells. The goal of this study was to assess whether CD28 could be involved in the development of B cells. CD28 mRNA was detected preferentially in the fraction of bone marrow enriched for stromal cells. Flow cytometry and RT-PCR analysis demonstrated that CD28 was also expressed by primary-cultured stromal cells that supported B lymphopoiesis. Confocal microscopy revealed that in the presence of B-lineage cells, CD28 was localized at the contact interface between B cell precursors and stromal cells. In addition, CD80 was detected on 2-6% of freshly isolated pro- and pre-B cells, and IL-7 stimulation led to induction of CD86 on 15-20% of pro- and pre-B cells. We also observed that stromal cell-dependent production of B-lineage cells in vitro was greater on stromal cells that lacked CD28. Finally, the frequencies of B-lineage precursors in the marrow from young (4- to 8-wk-old) CD28(-/-) mice were similar to those in wild-type mice; however, older CD28(-/-) mice (15-19 mo old) exhibited a 30% decrease in pro-B cells and a 50% decrease in pre-B cells vs age-matched controls. Our results suggest that CD28 on bone marrow stromal cells participates in stromal-dependent regulation of B-lineage cells in the bone marrow. The localization of CD28 at the stromal cell:B cell precursor interface suggests that molecules important for T cell:B cell interactions in the periphery may also participate in stromal cell:B cell precursor interactions in the bone marrow.
Engagement of the Mannose Receptor by Tumoral Mucins Activates an Immune Suppressive Phenotype in Human Tumor‐Associated Macrophages (2010)

Tumor-Associated Macrophages (TAMs) are abundantly present in the stroma of solid tumors and modulate several important biological processes, such as neoangiogenesis, cancer cell proliferation and invasion, and suppression of adaptive immune responses. Myeloid C-type lectin receptors (CLRs) constitute a large family of transmembrane carbohydrate-binding receptors that recognize pathogens as well as endogenous glycoproteins. Several lines of evidence demonstrate that some CLRs can inhibit the immune response. In this study we investigated TAM-associated molecules potentially involved in their immune suppressive activity. We found that TAMs isolated from human ovarian carcinoma samples predominantly express the CLRs Dectin-1, MDL-1, MGL, DCIR, and most abundantly the Mannose Receptor (MR). Components of carcinomatous ascites and purified tumoral mucins (CA125 and TAG-72) bound the MR and induced its internalization. MR engagement by tumoral mucins and by an agonist anti-MR antibody modulated cytokine production by TAM toward an immune-suppressive profile: increase of IL-10, absence of IL-12, and decrease of the Th1-attracting chemokine CCL3. This study highlights that tumoral mucin-mediated ligation of the MR on infiltrating TAM may contribute to their immune suppressive phenotype.
A six-degree-of-freedom magnetically levitated variable compliance fine-motion wrist: design, modeling, and control (1991)

A high-performance six-degree-of-freedom magnetically levitated fine-motion wrist with programmable compliance is described. Design considerations, a discussion of the major elements of the device, and issues of modeling, kinematics, dynamics, and control are presented. A prototype wrist which has been built and controlled successfully is discussed. Experimental results, including high bandwidth position control, compliant control, and the emulation of several mechanisms through software gain setting which establish the use of magnetically levitated robot wrists as an option for manipulation tasks requiring high precision and fine compliant motions, are included.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure of proteins with single-site mutations: a minimum perturbation approach. (1985)

A large number of mutant proteins with single amino acid substitutions are now being produced. The ability to predict the structural changes expected from such mutations would aid greatly in the efficient utilization of the mutagenic techniques and in the interpretation of the changes in stability and function that result. A minimum perturbation approach is suggested as a first step in such structural predictions and is tested by application to a recently isolated variant of the hemagglutinin glycoprotein. The agreement between the predicted structure and that inferred from the x-ray refinement is encouraging and provides support for the proposed modeling procedure.