gebhart/patrepeval huggingface dataset:
AKAP-Lbc Anchors Protein Kinase A and Nucleates Gα12-selective Rho-mediated Stress Fiber Formation (2001)

Guanine nucleotide exchange factors of the Dbl family relay signals from membrane receptors to Rho family GTPases. We now demonstrate that a longer transcript of the Lbc gene encodes a chimeric molecule, which we have called AKAP-Lbc, that functions as an A-kinase-anchoring protein (AKAP) and a Rho-selective guanine nucleotide exchange factor. Expression of AKAP-Lbc in fibroblasts favors the formation of stress fibers in a Rho-dependent manner. Application of lysophosphatidic acid or selective expression of Galpha(12) enhances cellular AKAP-Lbc activation. Furthermore, biochemical studies indicate that AKAP-Lbc functions as an adaptor protein to selectively couple Galpha(12) to Rho. Thus, AKAP-Lbc anchors PKA and nucleates the assembly of a Rho-mediated signaling pathway.
Semi-solid albumin solder improved mechanical properties for laser tissue welding (2000)

Acutely and at 7 days, semi-solid solder was stronger than 50% liquid albumin with better handling characteristics.
Gag-specific cytotoxic T lymphocytes from human immunodeficiency virus type 1-infected individuals: Gag epitopes are clustered in three regions of the p24gag protein (1993)

Virus-specific cytotoxic T lymphocytes (CTL) may be an important host defense mechanism in the control of virus replication in persons infected with human immunodeficiency virus type 1 (HIV-1). Cytotoxic T-cell lines generated by nonspecific stimulation with anti-CD3 monoclonal antibodies and interleukin 2 were used to identify regions within the HIV-1 Gag protein that are the most frequently recognized. Using autologous Epstein-Barr virus-transformed target cells infected with recombinant vaccinia viruses encoding p18gag, p24gag, and p55gag proteins of HIV-1/Lai or selected truncations of p24gag, we show that within a group of 29 infected subjects, the p24gag protein is the target of Gag-specific CTL in most donors. Using autologous Epstein-Barr virus-transformed target cells coated with different synthetic peptides spanning the Gag amino acid sequence, we found clusters of partially overlapping peptides in three conserved regions of the p24 protein (amino acids [aa] 169 to 192, aa 219 to 304, and aa 335 to 372) that are frequently recognized by CTL and presented by a variety of human leukocyte antigen class I molecules. Since there are experiments both in vitro and in vivo showing the role of CTL in the control of virus replication in HIV and simian immunodeficiency virus infections, these results may be particularly important for vaccine development.
Information Processing in the Primate Retina: Circuitry and Coding (2007)

The function of any neural circuit is governed by connectivity of neurons in the circuit and the computations performed by the neurons. Recent research on retinal function has substantially advanced understanding in both areas. First, visual information is transmitted to the brain by at least 17 distinct retinal ganglion cell types defined by characteristic morphology, light response properties, and central projections. These findings provide a much more accurate view of the parallel visual pathways emanating from the retina than do previous models, and they highlight the importance of identifying distinct cell types and their connectivity in other neural circuits. Second, encoding of visual information involves significant temporal structure and interactions in the spike trains of retinal neurons. The functional importance of this structure is revealed by computational analysis of encoding and decoding, an approach that may be applicable to understanding the function of other neural circuits.
Prediction of Aggregation Prone Regions of Therapeutic Proteins (2010)

Therapeutic proteins such as antibodies are playing an increasingly prominent role in the treatment of numerous diseases including cancer and rheumatoid arthritis. However, these proteins tend to degrade due to aggregation during manufacture and storage. Aggregation decreases protein activity and raises concerns about an immunological response. We have recently developed a method based on full antibody atomistic simulations to predict antibody aggregation prone regions [Proc. Natl. Acac. Sci. 2009, 106, 11937]. This method is based on "spatial-aggregation-propensity (SAP)", a measure of the dynamic exposure of hydrophobic patches. In the present paper, we expand on this method to analyze the aggregation prone regions over a wide parameter range. We also explore the effect of different hydrophilic mutations on these predicted aggregation prone regions to engineer antibodies with enhanced stability. The mutation to lysine is more effective than serine but less effective than glutamic acid in enhancing antibody stability. Furthermore, we show that multiple simultaneous mutations on different SAP peaks can have a cumulative effect on enhancing protein stability. We also investigate the accuracy of various cheaper alternatives for SAP evaluation because the full antibody atomistic simulations are highly computationally expensive. These cheaper alternatives include antibody fragment (Fab, Fc) simulations, implicit solvent models, or direct computations from a static structure (i.e., a structure from X-ray or homology modeling). The SAP evaluation from the static structure is 200,000 times faster but less accurate compared to the SAP from explicit atom simulations. Nevertheless, the SAP from a static structure still predicts most of the major aggregation prone regions, making it a potential approach for use in high-throughput applications. Thus, the SAP technology described here could be employed either in high-throughput developability screening of therapeutic protein candidates or to improve their stability at later stages of manufacturing.
Crystal structure of stereocomplex of poly(L-lactide) and poly(D-lactide) (1991)

Abstract An equimolar mixture of poly(L-lactide) and poly(D-lactide) was crystallized into a stereocomplex whose crystal system is triclinic (P1) with cell dimensions: a = 0.916 nm, b = 0.916 nra, c (chain axis) = 0.870 nm, α = 109.2°, β - 109.2°, and γ = 109.8°. In the unit cell, a poly(L-lactide) segment and a poly (D-lactide) segment are contained as a pair and packed laterally in parallel fashion. The L- and D-poly(lactides) in the complex take a 31 helical conformation, which is a little extended from a 103 helix in the homopolymer crystal with the α-form. Homopolymers are also able to take the 31 helical conformation and form the β-form crystal. The 31 helix in the homopolymer crystal is less stable than the 103 one, and hence the β-form is easily transformed to the α-form by annealing.
A Ribonucleotide Reductase Homolog of Cytomegalovirus and Endothelial Cell Tropism (2001)

Human cytomegalovirus infects vascular tissues and has been associated with atherogenesis and coronary restenosis. Although established laboratory strains of human cytomegalovirus have lost the ability to grow on vascular endothelial cells, laboratory strains of murine cytomegalovirus retain this ability. With the use of a forward-genetic procedure involving random transposon mutagenesis and rapid phenotypic screening, we identified a murine cytomegalovirus gene governing endothelial cell tropism. This gene, M45, shares sequence homology to ribonucleotide reductase genes. Endothelial cells infected with M45-mutant viruses rapidly undergo apoptosis, suggesting that a viral strategy to evade destruction by cellular apoptosis is indispensable for viral growth in endothelial cells.
A new self-organisation strategy for floorplan design (2003)

Floorplanning of VLSI circuits is a complex combinatorial problem. A floorplanning approach based on space mapping is presented. The mapping is considered as a weighted projection between two spaces, input circuit description space and output floorplan space, with the projection between the two being carried out by a self-organizing process based on Kohonen's self-organizing networks. The technique was implemented and tested on difficult benchmarks floorplanning problem producing good results. Optimization and floorplan solution production is achieved by the means of weighted projection with the weights computed in a self-organizing manner.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cellular and Molecular Biology of the Aquaporin Water Channels (1999)

The high water permeability characteristic of mammalian red cell membranes is now known to be caused by the protein AQP1. This channel freely permits movement of water across the cell membrane, but it is not permeated by other small, uncharged molecules or charged solutes. AQP1 is a tetramer with each subunit containing an aqueous pore likened to an hourglass formed by obversely arranged tandem repeats. Cryoelectron microscopy of reconstituted AQP1 membrane crystals has revealed the three-dimensional structure at 3-6 A. AQP1 is distributed in apical and basolateral membranes of renal proximal tubules and descending thin limbs as well as capillary endothelia. Ten mammalian aquaporins have been identified in water-permeable tissues and fall into two groupings. Orthodox aquaporins are water-selective and include AQP2, a vasopressin-regulated water channel in renal collecting duct, in addition to AQP0, AQP4, and AQP5. Multifunctional aquaglyceroporins AQP3, AQP7, and AQP9 are permeated by water, glycerol, and some other solutes. Aquaporins are being defined in numerous other species including amphibia, insects, plants, and microbials. Members of the aquaporin family are implicated in numerous physiological processes as well as the pathophysiology of a wide range of clinical disorders.
Nano and microparticles as controlled drug delivery devices. (2000)

Although, the drug delivery system (DDS) concept is not new, great progress has recently been made in the treatment of a variety of diseases. Targeting delivery of drugs to the diseased lesions is one of the most important aspects of DDS. To convey a sufficient dose of drug to the lesion, suitable carriers of drugs are needed. Nano and microparticle carriers have important potential applications for the administration of therapeutic molecules. The research in this area is being carried out all over the world at a great pace. Research areas cover novel properties that have been developed increased efficiency of drug delivery, improved release profiles and drug targeting. The purpose of this review is to take a closer look at nano/microparticles as drug delivery devices.
An integrated grammar/bigram language model using path scores (2002)

This paper describes a language model in which context-free grammar rules are integrated into an n-gram framework, complementing it instead of attempting to replace it. This releases the grammar from the aim of parsing sentences overall (which is often undesirable as well as unrealistic), enabling it to be employed selectively in modelling phrases that are identifiable within a flow of speech. Algorithms for model training and for sentence scoring and interpretation are described. All are based on the principle of summing over paths that span the sentence, but implementation is node-based for efficiency. Perplexity results for this system (using a hierarchy of grammars from empty to full-coverage) are compared with those for n-gram models, and the system is used for re-scoring N-best sentence lists for a speaker-independent recogniser.
Nucleotide sequence of the LuxA and LuxB genes of the bioluminescent marine bacterium<i>Vibrio fischeri</i> (1988)

Luminescence in marine bacteria is catalyzed by the heterodimeric enzyme luciferase, whose alpha and beta suibunits are encoded by the lujxA and lljxB genes respectively (1). In Vibrio harveyi, these genes have been sequenced (2,3). We have determined the nucleotide (nt) sequence of both strands of a cloned DNA fragment that contains these genes from a second species, V. fischeri strain MJ-1 (4). Start and stop codons are uinderlined. LujxA (startE89) and lujxB (start=1392) are 1065 and 981 nt in length (355 and 327 aa), respectively, and are separated by 38 nt. The 3' end of an open reading
Rhizobium japonicum derivatives differing in nitrogen-fixing efficiency and carbohydrate utilization (1976)

Four derivatives of Rhizobium japonicum 110 were isolated on the basis of morphologically different colonies formed on yeast extract-mannitol-HM salts medium. All are able to nodulate Lee soybeans. The bacteria-plant associations formed by each clone have measurable acetylene-reducing activity, but those formed by two of these clones (designated L1-110 and L2-110) are 5- to 10-fold less efficient than those formed by the others (designated I-110 and S-110). These derivatives were not detectable with ordinary culture techniques since, because of cell adherence, genetically mixed colonies result. When a detergent (Tween 40 at 0.01%, vol/vol) was added to the dilution medium, separate clones resulted. The metabolic basis for the gross differences in colony morphology on yeast extract-mannitol-HM salts medium was found to be that L1-110 and L2-110 utilized p-mannitol for growth, whereas I-110 and S-110 did not. These clones differ analogously in ability to utilize D-arabitol. Clones I-110 and L1-110 were chosen for studies of growth rates on various carbohydrates. Although clone I-110 and clone L1-110 did not differ in growth rates on a number of sugars, such as gluconate, arabinose, glycerol, and mannose, they differed in growth rates on glucose and fructose. Although clone I-110 grew faster on glucose than did clone L1-110, clone L1-110 grew faster on fructose than did clone I-110. Clones I-110 and L1-110 showed identical responses to several antibiotics and deoxyribonucleic acid (DNA) synthesis inhibitors and identical susceptibility to some highly specific bacteriophages. Identical buoyant densities of their DNAs in isopycnic CsCl density gradients and identical thermal denaturation temperatures of their DNAs suggest that clones I-110 and L1-110 have the same DNA base composition. Preliminary DNA/DNA hybridization experiments show that strain I-110 DNA and strain L1-110 DNA have a high degree of common polynucleotide sequences.
A High Assurance Window System Prototype1 (1993)

This paper describes the architecture of a prototype multilevel secure windowing system based on the X Window System. The prototype, known as TX, is designed to meet the class B3 architectural requirements of the Trusted Computer System Evaluation Cr
Targeting SV2A for Discovery of Antiepileptic Drugs (2012)

Abstract Synaptic vesicle 2A constitutes the unique binding site for LEV and plays an important role in synaptic vesicle function. Affinity–potency correlations in several models of partial and generalized epilepsy indicate that SV2A is a broad-spectrum anticonvulsant target. The anticonvulsant activity of LEV is closely linked with occupancy and availability of SV2A, whereas SV2A deficiency leads to increased seizure vulnerability and accelerated epileptogenesis. Taken together, existing experimental data prove that SV2A plays a crucial role in mediating the anticonvulsant action of LEV in vivo and indicate that the SV2A protein represents an important and well-validated target for the discovery of novel AEDs. Finally, the finding that SV2A protein is a clinically validated target for epilepsy has triggered further discovery programs exploring the therapeutic potential for SV2A ligands with different binding properties.
Primary structure of a glycosylated DNA-binding domain in human plasma fibronectin. (1985)

The complete amino acid sequence of a DNA-binding domain isolated from human plasma fibronectin after limited trypsin digestion has been obtained. It contains 132 amino acids and one biantennary glycosyl unit at residue 104, for an estimated Mr of 16,931. The fragment can be purified by a two-step procedure consisting of DNA-affinity chromatography and reverse-phase high performance liquid chromatography. It can also be purified by heparin-affinity chromatography. The domain is unusual in its susceptibility to tryptic-like cleavages even by neutral or aromatic residue-specific proteases. It has no cysteine residues and is predicted to favor a beta-sheet structure by Chou and Fasman analysis. Based on this analysis we have proposed a model which exhibits a clustering of aromatic and basic residues, consistent with similar involvement of basic and aromatic residues in other DNA-binding proteins. The net charge of the domain at neutral pH (+1, without sialic acid) argues against a nonspecific charge interaction with polyanionic macromolecules such as DNA and heparin. Internal sequence repeats occur at intervals of 30, 60, and 90 residues, thus suggesting a maximum size for a repetitive building block which gave rise to this domain.
Accuracy of automatic couch corrections with on‐line volumetric imaging<sup>*</sup> (2009)

The purpose of this study was to characterize automatic remote couch adjustment and to assess the accuracy of automatic couch corrections following localization with cone-beam CT (CBCT). Automatic couch movement was evaluated through passive reflector markers placed on a phantom, tracked with an optical tracking system (OTS). Repeated couch movements in the lateral, cranial/caudal, and vertical directions were monitored through the OTS to assess velocity and response time. In conjunction with CBCT, remote table movement for patient displacements following initial setup was available on four linear accelerators (Elekta Synergy). After the initial CBCT scan assessment, patients with isocenter displacements that exceeded clinical protocol tolerances were corrected using remote automatic couch movement. A verification CBCT scan was acquired after any remote movements. These verification CBCT datasets were assessed for the following time periods: one month post clinical installation, and six months later to monitor remote couch correction stability. Residual error analysis was evaluated using the verification scans. The mean +/- standard deviations (mu +/- sigma) of couch movement based on phantom measurements with the OTS were 0.16 +/- 0.48 mm, 0.32 +/- 0.30 mm, 0.11 +/- 0.12 mm in the L/R, A/P, and S/I couch directions, respectively. The fastest maximum velocity was observed in the inferior direction at 10.5 mm/s, and the slowest maximum velocity in the left direction at 3.6 mm/s. From 1134 verification CBCT registrations for 207 patients, the residual error for each translational direction from each month evaluated are reported. The mu was less than 0.3 mm in all directions, and sigma was in the order of 1 mm. At a 3 mm threshold, 21 of the 1134 fractions (2%) exceeded tolerance, attributed to patient intrafraction movement. Remote automatic couch movement is reliable and effective for adjusting patient position with a precision of approximately 1mm. Patient residual error observed in this study demonstrates that displacement is minimal after remote couch adjustment.
Interfering with interferons in inflammatory bowel disease (2006)

Early experience of fontolizumab, a humanised anti‐interferon γ antibody, in active Crohn's disease has shown that the drug caused a significant decrease in endoscopic severity scores and CRP and was reasonably well tolerated. Fontolizumab may be worthy of further clinical trials
Zinc Finger Nuclease-Expressing Baculoviral Vectors Mediate Targeted Genome Integration of Reprogramming Factor Genes to Facilitate the Generation of Human Induced Pluripotent Stem Cells (2013)

Integrative gene transfer using retroviruses to express reprogramming factors displays high efficiency in generating induced pluripotent stem cells (iPSCs), but the value of the method is limited because of the concern over mutagenesis associated with random insertion of transgenes. Site-specific integration into a preselected locus by engineered zinc-finger nuclease (ZFN) technology provides a potential way to overcome the problem. Here, we report the successful reprogramming of human fibroblasts into a state of pluripotency by baculoviral transduction-mediated, site-specific integration of OKSM (Oct3/4, Klf4, Sox2, and c-myc) transcription factor genes into the AAVS1 locus in human chromosome 19. Two nonintegrative baculoviral vectors were used for cotransduction, one expressing ZFNs and another as a donor vector encoding the four transcription factors. iPSC colonies were obtained at a high efficiency of 12% (the mean value of eight individual experiments). All characterized iPSC clones carried the transgenic cassette only at the ZFN-specified AAVS1 locus. We further demonstrated that when the donor cassette was flanked by heterospecific loxP sequences, the reprogramming genes in iPSCs could be replaced by another transgene using a baculoviral vector-based Cre recombinase-mediated cassette exchange system, thereby producing iPSCs free of exogenous reprogramming factors. Although the use of nonintegrating methods to generate iPSCs is rapidly becoming a standard approach, methods based on site-specific integration of reprogramming factor genes as reported here hold the potential for efficient generation of genetically amenable iPSCs suitable for future gene therapy applications.
Effects of Biofinishing on Cotton /Wool Blended Fabrics (1995)

Enzymatic degradation, which improves surface properties by digesting protruding loose fibers, is gaining popularity because of its beneficial effects on the environment. In this study, two cotton / wool fabrics of different blend composition are treated with both cellulase and protease enzymes, applied at two different concentrations and con ditions. In general, the enzyme treatments have significant effects on the physical and aesthetic properties of the blended fabrics, which is statistically evident from a one- way analysis of variance. Subjective means of evaluations are also used to assess fabric hand and pilling resistance. The enzyme treatment reduces protruding fibers, and more direct evidence of their absence is provided by SEM examination.
Primary structure of a human IgA1 immunoglobulin. IV. Streptococcal IgA1 protease, digestion, Fab and Fc fragments, and the complete amino acid sequence of the alpha 1 heavy chain. (1979)

In order to establish the complete amino acid sequence of the human IgA alpha1 chain Bur, IgA1 protease from Streptococcus sanguis was employed to generate Fabalpha and Fcalpha fragments in the final stage of this investigation. Cyanogen bromide cleavage of the Fabalpha fragment followed by reduction and aminoethylation produced the Fd' fragment (residues 84 to 227); this contains part of the variable region (VR), the whole first constant domain (Calpha1), and part of the hinge region of this heavy chain. The tryptic peptides of the Fd' fragment were isolated, characterized, and sequenced. The results together with the data in the preceding papers on chymotryptic, tryptic, and thermolysin peptides permitted the complete amino acid sequence of the human IgA alpha1 chain to be established.
Fabrication and Electrical Characterization of Pt/(Ba,Sr)TiO<sub>3</sub>/Pt Capacitors for Ultralarge-Scale Integrated Dynamic Random Access Memory Applications (1996)

Pt/(Ba, Sr)TiO 3 /Pt capacitors are fabricated using DC and RF magnetron sputtering processes on thermally oxidized silicon wafers for ultralarge scale integrated dynamic random access memory (ULSI DRAM) applications. (Ba,Sr)TiO 3 (BST) thin film deposited at 640°C to 20 nm thickness shows an equivalent SiO 2 thickness ( t oxeq ) of 0.35 nm and a leakage current density, measured at an applied voltage of 1.5 V, of about 100 nA/cm 2 . t oxeq of the BST film and leakage current density are further decreased to 0.24 nm and 40 nA/cm 2 , respectively, by postannealing at 750°C after fabrication of the top electrode.