gebhart/patrepeval huggingface dataset:
Group III nitride semiconductor compounds : physics and applications (1998)

1. Beyond silicon: the rise of compound semiconductors 2. Deposition and properties of III-nitrides by molecular beam epitaxy 3. MOVPE growth of nitrides 4. Structural defects and materials performance of the III-V nitrides 5. Modulation spectroscopy of the group III nitrides 6. Optical properties and lasing in GaN 7. Defect spectroscopy in the nitrides 8. Electronic and optical properties of GaN based quantum wells 9. Transistors and detectors based on GaN related materials 10. III-V nitride based short-wavelength LEDs and LDs 11. Cubic group III nitrides
Inhibition of inflammatory liver injury by a monoclonal antibody against lymphocyte function-associated antigen-1. (1993)

When mice were given an i.v. injection of LPS 7 days after an i.v. injection of Propionibacterium acnes, liver injury and a rapid increase of serum alanine aminotransferase and asparagine acid aminotransferase occurred. The in vivo administration of mAb against LFA-1 on days 1, 2, and 3 after the i.v. injection of P. acnes resulted in a potent inhibition of all these dysfunctions. Using P. acnes and the LPS model, we found that anti-LFA-1 mAb protected the mice from P. acnes and LPS-induced lethal shock. During the course of P. acnes and LPS-induced liver injury, inflammatory cells infiltrated the liver and caused a massive hepatic cell necrosis. Flow cytometry revealed that the liver-infiltrating cells were mainly leukocytes expressing a higher level of LFA-1 antigen than that seen in the normal liver. These results suggested that the LFA-1 molecule on liver-infiltrating leukocytes may play an important role in the induction of inflammatory liver injury.
Role of the N-terminal Catalytic Domain of Angiotensin-converting Enzyme Investigated by Targeted Inactivation in Mice (2004)

Angiotensin-converting enzyme (ACE) produces the vasoconstrictor angiotensin II. The ACE protein is composed of two homologous domains, each binding zinc and each independently catalytic. To assess the physiologic significance of the two ACE catalytic domains, we used gene targeting in mice to introduce two point mutations (H395K and H399K) that selectively inactivated the ACE N-terminal catalytic site. This modification does not affect C-terminal enzymatic activity or ACE protein expression. In addition, the testis ACE isozyme is not affected by the mutations. Analysis of homozygous mutant mice (termed ACE 7/7) showed normal plasma levels of angiotensin II but an elevation of plasma and urine N-acetyl-Ser-Asp-Lys-Pro, a peptide suggested to inhibit bone marrow maturation. Despite this, ACE 7/7 mice had blood pressure, renal function, and hematocrit that were indistinguishable from wild-type mice. We also studied compound heterozygous mice in which one ACE allele was null (no ACE expression) and the second allele encoded the mutations selectively inactivating the N-terminal catalytic domain. These mice produced approximately half the normal levels of ACE, with the ACE protein lacking N-terminal catalytic activity. Despite this, the mice have a phenotype indistinguishable from wild-type animals. This study shows that, in vivo, the presence of the C-terminal ACE catalytic domain is sufficient to maintain a functional renin-angiotensin system. It also strongly suggests that the anemia present in ACE null mice is not due to the accumulation of the peptide N-acetyl-Ser-Asp-Lys-Pro.
A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site (1995)

We have observed a high correlation between the intermolecular interaction energy (Einter) calculated for HIV-1 protease inhibitor complexes and the observed in vitro enzyme inhibition. A training set of 33 inhibitors containing modifications in the P1' and P2' positions was used to develop a regression equation which relates Einter and pIC50. This correlation was subsequently employed to successfully predict the activity of proposed HIV-1 protease inhibitors in advance of synthesis in a structure-based design program. This included a precursor, 47, to the current phase II clinical candidate, L-735,524 (51). The development of the correlation, its applications, and its limitations are discussed, and the force field (MM2X) and host molecular mechanics program (OPTIMOL) used in this work are described.
Cascode voltage switch logic: A differential CMOS logic family (1984)

A differential CMOS Logic family that is well suited to automated logic minimization and placement and routing techniques, yet has comparable performance to conventional CMOS, will be described. A CMOS circuit using 10,880 NMOS differential pairs has been developed using this approach.
Seminal Plasma Lipocalin-Type Prostaglandin D Synthase: A Potential New Marker for the Diagnosis of Obstructive Azoospermia (2008)

Our results suggest that seminal L-PGDS level can potentially be a biomarker for assessing patency in the seminal tract in men with azoospermia. In men with azoospermia and high seminal L-PGDS (more than 100 microg/l) the diagnosis of nonobstructive azoospermia can be potentially made without biopsy. Our study shows that using semen L-PGDS levels provides a diagnosis of nonobstructive azoospermia in almost 30% of these men.
Application of a superword array in genome assembly (2006)

We introduce a data structure called a superword array for finding quickly matches between DNA sequences. The superword array possesses some desirable features of the lookup table and suffix array. We describe simple algorithms for constructing and using a superword array to find pairs of sequences that share a unique superword. The algorithms are implemented in a genome assembly program called PCAP.REP for computation of overlaps between reads. Experimental results produced by PCAP.REP and PCAP on a whole-genome dataset show that PCAP.REP produced a more accurate and contiguous assembly than PCAP.
Development of cell lines stably expressing human immunodeficiency virus type 1 proteins for studies in encapsidation and gene transfer. (1998)

Experiments were done to test cell lines for their capacity to express human immunodeficiency virus type 1 (HIV-1) proteins in a stable manner. Marked differences were seen in the ability to stably express and export viral Gag and Pol proteins. Two cell lines, one suspension (MDS) and one monolayer (SW480), were established which exported these proteins at high level. Two other cell lines, HeLa and THP-1, showed poorer expression and very limited particle release. Single cell cloning was used to select the optimal producing clones from the lines. These produced large quantities of viral core particles pelletable from the supernatants. Cell lines were constructed from these clones which stably expressed in addition either the HIV-1 Envelope or a packageable HIV-based vector. The vector was shown to be packaged within the viral core particles. Transient transfection of envelope expressing constructs into a gag-pol plus vector cell line, or the vector into a gag-pol plus envelope expressing cell line resulted in gene transfer to CD4+ target cells. These cell lines provide useful tools with which to study the assembly and export of viral proteins and RNA, for assay of alternative envelope proteins to pseudotype HIV cores, for assessment of antiviral drugs and as a source of correctly processed proteins for immunological studies.
Mutagenesis-based definitions and probes of residue burial in proteins (2005)

Every residue of the 101-aa Escherichia coli toxin CcdB was substituted with Ala, Asp, Glu, Lys, and Arg by using site-directed mutagenesis. The activity of each mutant in vivo was characterized as a function of Controller of Cell Division or Death B protein (CcdB) transcriptional level. The mutation data suggest that an accessibility value of 5% is an appropriate cutoff for definition of buried residues. At all buried positions, introduction of Asp results in an inactive phenotype at all CcdB transcriptional levels. The average amount of destabilization upon substitution at buried positions decreases in the order Asp>Glu>Lys>Arg>Ala. Asp substitutions at buried sites in two other proteins, maltose-binding protein and thioredoxin, also were shown to be severely destabilizing. Ala and Asp scanning mutagenesis, in combination with dose-dependent expression phenotypes, was shown to yield important information on protein structure and activity. These results also suggest that such scanning mutagenesis data can be used to rank order sequence alignments and their corresponding homology models, as well as to distinguish between correct and incorrect structural alignments. With continuous reductions in oligonucleotide costs and increasingly efficient site-directed mutagenesis procedures, comprehensive scanning mutagenesis experiments for small proteins/domains are quite feasible.
Dialog concepts for learning retina encoders (2002)

This paper defines the biomedical and technological constraints for retina implants and describes our recent results and concepts regarding the function and training of learning retina encoder (RE) by means of neural networks. We show that: 1) system identification of a portable Mark I RE in analog hardware with tunable RF-filters can be achieved by means of supervised learning in connection with a neural net; and 2) the tunable RE-filters of a Mark II RE as DSP implementation can be tuned individually to typical RF properties of primate retinal ganglion cells in real time. These results demonstrate the feasibility of approximating the retinal information processing by means of tunable RF-filters in a RE system with a photosensor array at the input and simulated ganglion cells at the output. A concept is presented for training the learning RE with tunable RE-filters in a dialog with human subjects using their visual perception.
4-Substituted semicarbazones of mono- and dichlorobenzaldehydes as antihypertensive agents (1977)

&lt;p&gt;The production of high-modulus and high-strength polymer nanofibers using centrifugal or rotary jet spinning (RJS) was explored. Co-polyimide nanofibers based on 3,3′,4,4′-biphenyl-tetracarboxylic dianhydride (BPDA)/p-phenylenediamine (PDA)/4,4′-oxydianiline (ODA) (BPO) were successfully spun by RJS from a polyamic acid precursor solution before conversion into highly oriented and chain extended BPO co-polyimide fibers via an imidization step. Fourier transform infrared (FTIR) characterization was used to evaluate the chemical conversion of the fibers. Nanocomposite laminates based on co-polyimide nonwoven fiber mats in epoxy were manufactured for mechanical testing. Analysis using the generalized rule of mixtures resulted in a back-calculated fiber modulus and strength of around 50 and 2 GPa, approaching that of high-performance fibers like Kevlar&lt;sup&gt;®&lt;/sup&gt; 29, and equaling those of co-polyimide fibers obtained via electrospinning, making them the strongest centrifugal spun fibers ever reported.&lt;/p&gt;
Controlling Proppant Flowback in High-Temperature, High-Production Wells (2003)

Abstract Curable resins have been used to coat onto proppant for controlling proppant flowback after hydraulic fracturing treatments as well as in screenless, frac-pack completions. As more wells are drilled into deeper reservoirs, severe conditions including high temperatures and high production flow rates impose more constraint requirements on the use of curable resin systems. This paper presents the results of an extensive study, including both laboratory and field testing, of a new liquid resin coating system that is particularly useful in controlling proppant flowback in high-temperature, high-flow rate wells. Additives included in the liquid resin system can eliminate fracturing fluid interference and permit good consolidation properties to be achieved without any formation closure stress. Results of this work demonstrate the difficulty in designing fracturing treatments such that the curing of resin does not occur too fast relative to fracture treatment time and the time for formation closure to achieve good consolidation, but fast enough to prevent flowback upon fluid recovery operations. The useful window for resin-coated proppants has been greatly expanded by the incorporation of simple chemical additives into the resin that react with fracturing fluids, rendering them noninterfering to the consolidation process. These additives permit resin-coated proppant to achieve good consolidation properties without closure stress. This study provides new answers as to why resin precoated proppant (RCP) consolidations sometimes fail in the field. Operators can use the information presented to help them select the appropriate curable resin systems for their applications where consolidations are expected to withstand production conditions of high temperatures, high flow rates, and stress loading.
A New Process for Synthesis of the Astrocyte Activation Suppressor, ONO-2506 (2005)

Development of a new process for the synthesis of ONO-2506, an agent that suppresses astrocyte activation, is described. Previous processes that involved asymmetric synthesis with a chiral auxiliary were unsatisfactory from a cost perspective because the relatively expensive chiral auxiliaries were not recyclable. To develop a more cost-effective process, we designed a new process starting from chiral 1,2-epoxyoctane, which was readily prepared catalytically by Prof. Jacobsen's method. The new five-step process was developed with the establishment of a modified cyanation condition, in which lithium cyanide was prepared in situ by combining lithium hydroxide with acetone cyanohydrin. Then the mechanisms for racemization and the side reaction until the cyanation step were clarified, and these problems were solved. The main features of this process are crystallization of the amide intermediate, since its optical purity is readily improved by recrystallization up to 100% ee in addition to formation of the dibenzylamine salt with ONO-2506 that leads to improved chemical and optical purity of the final product. The shorter synthesis, including a one-pot reaction was ruled out because of the hazardous nature of the Katriztky hydrolysis conditions for the conversion of nitrile to amide in the presence of sodium cyanide.
Quasi-Andreev reflection in inhomogeneous Luttinger liquids (1998)

Reflection of charge excitations at the step in the interaction strength in a Luttinger liquid can be of the Andreev type, even the interactions are purely repulsive. The region with stronger repulsion plays the role of a normal metal in a normal-metal/superconductor junction, whereas the region with weaker repulsion plays the role of a superconductor. It is shown that this quasi-Andreev reflection leads to a number of proximitylike effects, including the local enhancement (suppression) of superconducting fluctuations on the quasinormal (quasisuperconducting) side of the step and significant modification of the local density of states, as well as others. The observable consequences of these proximity effects are analyzed for the case of single- and two-particle tunneling from a normal-metal or superconducting tip into an inhomogeneous Luttinger-liquid wire.
Analysis of the Promoter of the ninaE Opsin Gene in Drosophila melanogaster (1987)

We have analyzed the cis-acting regulatory sequences of the ninaE gene. This gene encodes the major Drosophila melanogaster opsin, the protein component of the primary chromophore of photo-receptor cells R1-R6 of the adult eye. DNA fragments containing the start point of transcription of the ninaE gene were fused to either the Escherichia coli chloramphenicol acetyltransferase or lacZ (beta-galactosidase) gene and introduced into the Drosophila germline by P-element-mediated transformation. Expression of the E. coli genes was then used to assay the ability of various sequences from the ninaE gene to confer the ninaE pattern of expression. Fragments containing between 2.8 kb and 215 bp of the sequences upstream of the start of transcription plus the first 67 bp of the untranslated leader were able to direct nearly wild-type expression. We have identified three separable control regions in the ninaE promoter. The first, which has the properties of an enhancer element, is located between nucleotides -501 and -219. The removal of this sequence had little effect on promoter function; this sequence appears to be redundant. However, it appears to be able to substitute for the second control region which is located between nucleotides -215 and -162, and which also affects the level of output from this promoter. Removal of these two control regions resulted in a 30-fold decrease in expression; however tissue specificity was not affected. The third control region, located downstream from nucleotide -120, appears to be absolutely necessary for promoter function in the absence of the first two regulatory sequences. Examination of larvae containing fusion genes expressing beta-galactosidase suggests that the ninaE gene is also expressed in a subset of cells in the larval photoreceptor organ.
Asymmetric receptor contact is required for tyrosine autophosphorylation of fibroblast growth factor receptor in living cells (2010)

Tyrosine autophosphorylation of receptor tyrosine kinases plays a critical role in regulation of kinase activity and in recruitment and activation of intracellular signaling pathways. Autophosphorylation is mediated by a sequential and precisely ordered intermolecular (trans) reaction. In this report we present structural and biochemical experiments demonstrating that formation of an asymmetric dimer between activated FGFR1 kinase domains is required for transphosphorylation of FGFR1 in FGF-stimulated cells. Transphosphorylation is mediated by specific asymmetric contacts between the N-lobe of one kinase molecule, which serves as an active enzyme, and specific docking sites on the C-lobe of a second kinase molecule, which serves a substrate. Pathological loss-of-function mutations or oncogenic activating mutations in this interface may hinder or facilitate asymmetric dimer formation and transphosphorylation, respectively. The experiments presented in this report provide the molecular basis underlying the control of transphosphorylation of FGF receptors and other receptor tyrosine kinases.
Clonal analysis of epiblast fate during germ layer formation in the mouse embryo (1991)

The fate of cells in the epiblast at prestreak and early primitive streak stages has been studied by injecting horseradish peroxidase (HRP) into single cells in situ of 6.7-day mouse embryos and identifying the labelled descendants at midstreak to neural plate stages after one day of culture. Ectoderm was composed of descendants of epiblast progenitors that had been located in the embryonic axis anterior to the primitive streak. Embryonic mesoderm was derived from all areas of the epiblast except the distal tip and the adjacent region anterior to it: the most anterior mesoderm cells originated posteriorly, traversing the primitive streak early; labelled cells in the posterior part of the streak at the neural plate stage were derived from extreme anterior axial and paraxial epiblast progenitors; head process cells were derived from epiblast at or near the anterior end of the primitive streak. Endoderm descendants were most frequently derived from a region that included, but extended beyond, the region producing the head process: descendants of epiblast were present in endoderm by the midstreak stage, as well as at later stages. Yolk sac and amnion mesoderm developed from posterolateral and posterior epiblast. The resulting fate map is essentially the same as those of the chick and urodele and indicates that, despite geometrical differences, topological fate relationships are conserved among these vertebrates. Clonal descendants were not necessarily confined to a single germ layer or to extraembryonic mesoderm, indicating that these lineages are not separated at the beginning of gastrulation. The embryonic axis lengthened up to the neural plate stage by (1) elongation of the primitive streak through progressive incorporation of the expanding lateral and initially more anterior regions of epiblast and, (2) expansion of the region of epiblast immediately cranial to the anterior end of the primitive streak. The population doubling time of labelled cells was 7.5 h; a calculated 43% were in, or had completed, a 4th cell cycle, and no statistically significant regional differences in the number of descendants were found. This clonal analysis also showed that (1) growth in the epiblast was noncoherent and in most regions anisotropic and directed towards the primitive streak and (2) the midline did not act as a barrier to clonal spread, either in the epiblast in the anterior half of the axis or in the primitive streak. These results taken together with the fate map indicate that, while individual cells in the epiblast sheet behave independently with respect to their neighbours, morphogenetic movement during germ layer formation is coordinated in the population as a whole.
Imaging through a scattering wall using absorption (1991)

An object hidden behind a cloudy wall is shown to become visible when the wall is made absorbing. The underlying principle is that the absorption in a random medium preferentially reduces the intensity of the multiple scattered light (noise) over the ballistic signal (image). The intensity of the noise can be reduced below the ballistic signal intensity when the medium is made sufficiently absorbing, thus allowing us to see through an otherwise opaque random scattering wall.
SF4 as the Fluorination Reactant for Al2O3 and VO2 Thermal Atomic Layer Etching (2019)

Thermal atomic layer etching (ALE) is an important technique for the precise isotropic etching of nanostructures. Thermal ALE of many materials can be achieved using a two-step fluorination and ligand-exchange reaction mechanism. Most previous thermal ALE processes have used HF as the fluorination reactant. Alternative fluorination reactants may be needed because HF is a weak nucleophilic fluorination reactant. Stronger fluorination agents may be required for the fluorination of some materials. To demonstrate the usefulness of SF4 as an alternative to HF, thermal Al2O3 ALE was compared using SF4 or HF together with Sn(acac)2 as the metal precursor for ligand exchange. SF4 and HF were observed to behave similarly as fluorination reactants during Al2O3 ALE. The mass gains during the initial SF4 and HF exposures on Al2O3 atomic layer deposition (ALD) films at 200 °C were comparable at 35 and 38 ng/cm2, respectively, using quartz crystal microbalance measurements. In addition, the etch rates were similar at 0.20 and 0.28 Å/cycle for Al2O3 ALE using SF4 and HF, respectively, at 200 °C. Thermal VO2 ALE was also performed for the first time using SF4 or HF and Sn(acac)2 as the reactants. There was evidence that SF4 is a stronger fluorination reactant than HF for VO2 fluorination. The mass gains during the initial SF4 and HF exposures on VO2 ALD films were 38 and 20 ng/cm2, respectively, at 200 °C. Thermal VO2 ALE also had a higher etch rate when fluorinating with SF4 compared with HF. Etch rates of 0.30 and 0.11 Å/cycle were measured for VO2 ALE using SF4 and HF, respectively, together with Sn(acac)2 at 200 °C. Fourier transform infrared experiments were also used to monitor fluorination of the Al2O3 and VO2 ALD films by SF4 or HF. FTIR difference spectroscopy was used to observe the increase of Al–F and V–F stretching vibrations and the loss of the Al–O and V—O/V═O stretching vibrations for Al2O3 and VO2, respectively, versus SF4 or HF exposure at 200 °C. Additional absorbance features after fluorination of the Al2O3 ALD films by SF4 were consistent with SFx surface species. SF4 is a useful fluorination agent for thermal ALE processes and can be used as an alternative to HF. In addition, SF4 may be necessary when fluorination requires a stronger fluorination reactant than HF.