gebhart/patrepeval huggingface dataset:
Phosphorylation states of the (Na+ + K+)-transporting ATPase in preparations from lamb kidney and electric-eel (Electophorus electricus) electric organ (1984)

Phosphorylation states of the (Na+ + K+)-transporting ATPase were studied in highly purified preparations isolated from electric-eel electric organ and from lamb kidney. The steady-state level of phosphorylated lamb kidney enzyme, obtained by reaction with [gamma-32P]ATP, was not appreciably reduced in the presence of ADP unless oligomycin was present. The phosphorylated form of the electric-eel electric-organ enzyme was reduced by at least 95% under the same conditions, suggesting that the E1P state in the kidney enzyme is more transitory than that in electric organ. The level of phosphorylation from [32P]Pi was higher in the lamb kidney preparation than in the electric-organ preparation, and the difference in stimulation of phosphorylation by ouabain in the two preparations was striking. Ouabain increased the level of phosphorylation by 35% in the kidney preparation and 734% in the electric-organ preparation. The E2P state seems to be stabilized by ouabain in the latter preparation. These findings, as well as the different reactivities of the thiol groups to blocking reagents in these preparations, suggest that the tertiary structure in the enzyme isolated from these two sources is different.
Distance-2 Cyclic Chaining of Constant-Weight Codes (1973)

The cyclic distance-2 chaining of constant-weight codes has applications in A/ D conversions as well as in combinatorial problems involving the exhaustion of m-out-of-n combinations. It is shown in this paper that such a chaining can be obtained from the Gray code circuit and its transformations. Algorithms based on several theorems derived have been developed and programmed in APL.
Basic Linear Algebra Subprograms for Fortran Usage (1979)

A package of 38 low level subprograms for many of the basic operations of numerical linear algebra m presented. The package is intended to be used with Fortran. The operations m the package include dot product, elementary vector operation, Givens transformation, vector copy and swap, vector norm, vector scaling, and the determination of the index of the vector component of largest magnitude.
Synthesis of a chiral amino acid with bicyclo[1.1.1]pentane moiety and its incorporation into linear and cyclic antimicrobial peptides (2007)

The synthesis of the lipophilic chiral amino acid 1 bearing the bicyclo[1.1.1]pentane moiety is described. Linear and cyclic hexapeptides of the type Arg-Arg-Xaa-Yaa-Arg-Phe containing 1 instead of one or two tryptophan residues are prepared by solid phase peptide synthesis and the antimicrobial and hemolytic activity of the peptides obtained are discussed.
New insights into internal ribosome entry site elements relevant for viral gene expression (2008)

A distinctive feature of positive-strand RNA viruses is the presence of high-order structural elements at the untranslated regions (UTR) of the genome that are essential for viral RNA replication. The RNA of all members of the family Picornaviridae initiate translation internally, via an internal ribosome entry site (IRES) element present in the 5' UTR. IRES elements consist of cis-acting RNA structures that usually require specific RNA-binding proteins for translational machinery recruitment. This specialized mechanism of translation initiation is shared with other viral RNAs, e.g. from hepatitis C virus and pestivirus, and represents an alternative to the cap-dependent mechanism. In cells infected with many picornaviruses, proteolysis or changes in phosphorylation of key host factors induces shut off of cellular protein synthesis. This event occurs simultaneously with the synthesis of viral gene products since IRES activity is resistant to the modifications of the host factors. Viral gene expression and RNA replication in positive-strand viruses is further stimulated by viral RNA circularization, involving direct RNA-RNA contacts between the 5' and 3' ends as well as RNA-binding protein bridges. In this review, we discuss novel insights into the mechanisms that control picornavirus gene expression and compare them to those operating in other positive-strand RNA viruses.
High‐level transient expression of recombinant protein in lettuce (2005)

Transient expression following agroinfiltration of plant tissue was investigated as a system for producing recombinant protein. As a model system, Agrobacterium tumefaciens containing the beta-glucuronidase (GUS) gene was vacuum infiltrated into lettuce leaf disks. Infiltration with a suspension of 10(9) colony forming units/mL followed by incubation for 72 h at 22 degrees C in continuous darkness produced a maximum of 0.16% GUS protein based on dry tissue or 1.1% GUS protein based on total soluble protein. This compares favorably to expression levels for commercially manufactured GUS protein from transgenic corn seeds. A. tumefaciens culture medium pH between 5.6 and 7.0 and surfactant concentrations < or = 100 ppm in the vacuum infiltration did not affect GUS expression, while infiltration with an A. tumefaciens density of 10(7) and 10(8) colony forming units/mL, incubation at 29 degrees C, and a surfactant concentration of 1,000 ppm significantly reduced expression. Incubation in continuous light caused lettuce to produce GUS protein more rapidly, but final levels did not exceed the GUS production in leaves incubated in continuous darkness after 72 h at 22 degrees C. The kinetics of GUS expression during incubation in continuous light and dark were represented well using a logistic model, with rate constants of 0.30 and 0.29/h, respectively. To semi-quantitatively measure the GUS expression in large numbers of leaf disks, a photometric enhancement of the standard histochemical staining method was developed. A linear relationship with an R2 value of 0.90 was determined between log10 (% leaf darkness) versus log10 (GUS activity). Although variability in expression level was observed, agroinfiltration appears to be a promising technology that could potentially be scaled up to produce high-value recombinant proteins in planta.
Analysis of Short-Channel Schottky Source/Drain Metal-Oxide-Semiconductor Field-Effect Transistor on Silicon-on-Insulator Substrate and Demonstration of Sub-50-nm n-type Devices with Metal Gate (1999)

The Schottky source/drain metal-oxide-semiconductor field-effect transistor (MOSFET) has potential for scaling to the nanometer regime, because low electrode resistances with very shallow extension can be realized using metal source/drain. In this study, very short channel n- and p-type Schottky source/drain MOSFETs with silicon-on-insulator (SOI) structure were analyzed theoretically, and n-type devices were demonstrated experimentally. It was shown theoretically that a drivability of the Schottky source/drain MOSFET comparable to that of conventional MOSFETs can be realized with a low Schottky barrier height. The short-channel effect can be suppressed even with a 15-nm-long channel at t OX = 1 nm and t SOI = 3 nm. The room-temperature operation of sub-50-nm n-type ErSi 2 Schottky source/drain MOSFETs on a separation by implanted oxygen (SIMOX) substrate was demonstrated.
The VLA-4/VCAM-1 pathway is involved in lymphocyte adhesion to endothelium in rheumatoid synovium (1991)

Lymphocyte migration to inflammatory sites is an essential factor in the pathogenesis of chronic inflammation. An ensemble of adhesion receptors mediating lymphocyte-endothelial cell recognition and binding are thought to play a crucial role in this process. In the present study, we have explored the molecular basis of lymphocyte adhesion to endothelium in the synovial membrane of patients with rheumatoid arthritis. We established that the very late antigen-4 [VLA-4 (CD49d)] and the vascular cell adhesion molecule-1 (VCAM-1) are important mediators of binding to synovial endothelium of resting and, to a greater extent, of activated T lymphocytes, whereas the leukocyte-function associated antigen-1 [LFA-1 (CD11a/18)]/intercellular adhesion molecule-1 [ICAM-1 (CD54)] pathway is less important in this interaction. In contrast to its prominent role in lymphocyte interaction with endothelium in rheumatoid synovium, the VLA-4/VCAM-1 pathway does not significantly contribute to lymphocyte adhesion to peripheral lymph node high endothelial venule. Thus, the VLA-4/VCAM-1 pathway may be of primary importance in mediating lymphocyte adhesion to inflamed endothelium and in lymphocyte homing to rheumatoid synovium.
Phenyl‐2,4,6‐trimethylbenzoylphosphinates as water‐soluble photoinitiators. Generation and reactivity of OṖ(C6H5)(O−) radical anions (1991)

Abstract Lithium‐ and magnesium phenyl‐2,4,6‐trimethylbenzoylphosphinates (TMPPL and TMPPM) are effective water‐soluble photoinitiators for the free‐radical polymerization of appropriate monomers such as acrylamide (AA) and methacrylamide (MAA) in aqueous solution. They are also capable of initiating the polymerization of other olefinic compounds such as styrene (St), methyl methacrylate (MMA) or acrylonitrile (AN) in water‐containing solvent mixtures such as 1:1 water‐acetonitrile mixtures. This is due to the fact that TMPPL and TMPPM undergo α‐scission with a rather high quantum yield (ϕ(α) ≈ 0,35) resulting in the formation of 2,4,6‐trimethylbenzoyl radicals and OṖ (C 6 H 5 )(O − ) radical anions. The latter are very reactive toward olefinic monomers. Bimolecular rate constants k R+M /(L/(mol · s)) were determined by flash photolysis at room temperature, e. g. in neat water: 3,8 · 10 8 (MAA), 2,2 · 10 8 (AA), and in H 2 O/CH 3 CN (1:1, v/v): 1,8 · 10 7 (St), 1,2 · 10 8 (MMA), 8,4 · 10 7 (AN).
Langerhans cells in the immunopathology of contact allergic dermatitis. (1994)

The functional morphology, topography and frequency of Langerhans cells (LCs), which are significant factors in the pathogenesis of contact allergic dermatitis (CAD), were studied by histoenzymatic methods (adenosine triphosphatase (ATP-ase), acid phosphatase (AF) and alpha naphtylacetate esterase (ANAE), immunohistochemical methods (indirect immunoperoxidase (IPO) with the monoclonal antibody OKT 6), and the peroxidase-antiperoxidase (PAP) method with the polyclonal S-100 antibody in skin biopsies of 24 patients with CAD, as well in skin biopsies in experimental models in guinea pigs. The results confirmed the significant role of LCs in the pathogenesis of contact allergic dermatitis.
End-to-End Learning of Driving Models from Large-Scale Video Datasets (2017)

Robust perception-action models should be learned from training data with diverse visual appearances and realistic behaviors, yet current approaches to deep visuomotor policy learning have been generally limited to in-situ models learned from a single vehicle or simulation environment. We advocate learning a generic vehicle motion model from large scale crowd-sourced video data, and develop an end-to-end trainable architecture for learning to predict a distribution over future vehicle egomotion from instantaneous monocular camera observations and previous vehicle state. Our model incorporates a novel FCN-LSTM architecture, which can be learned from large-scale crowd-sourced vehicle action data, and leverages available scene segmentation side tasks to improve performance under a privileged learning paradigm. We provide a novel large-scale dataset of crowd-sourced driving behavior suitable for training our model, and report results predicting the driver action on held out sequences across diverse conditions.
Syntheses of Ru−S Clusters with Kinetically Labile Ligands via the Photolysis of [(cymene)3Ru3S2](PF6)2 (2001)

Three ruthenium sulfide clusters with labile CH3CN ligands have been photochemically synthesized. Irradiation of [(cymene)3Ru3S2](PF6)2 ([1](PF6)2) in CH3CN gives [(cymene)2(CH3CN)3Ru3S2](PF6)2 ([2](PF6)2), which has been characterized by 1H NMR spectroscopy, ESI mass spectrometry, and chemical reactivity. Treatment of [2](PF6)2 with PPh3 gives [(cymene)2(CH3CN)2(PPh3)Ru3S2](PF6)2 ([3](PF6)2) and [(cymene)2(CH3CN)(PPh3)2Ru3S2](PF6)2 ([4](PF6)2), while treatment with 1,4,7-trithiacyclononane (9S3) gives [(cymene)2(9S3)Ru3S2](PF6)2 ([5](PF6)2). A crystallographic study demonstrated that the Ru3 core in [3](PF6)2, [4](PF6)2, and [5](PF6)2 is distorted with a pair of elongated Ru-Ru bonds. Cyclic voltammetry shows that [3](PF6)2 and [4](PF6)2 undergo two closely spaced reversible one-electron reductions whereas [5](PF6)2 undergoes one irreversible one-electron reduction and one reversible one-electron reduction. Prolonged irradiation of [1](PF6)2 in CH3CN causes decomposition, resulting in the pentanuclear cluster [(cymene)4Ru5S4](PF6)2 ([6](PF6)2).
PLGA nanoparticle-mediated delivery of tumor antigenic peptides elicits effective immune responses (2012)

The peptide vaccine clinical trials encountered limited success because of difficulties associated with stability and delivery, resulting in inefficient antigen presentation and low response rates in patients with cancer. The purpose of this study was to develop a novel delivery approach for tumor antigenic peptides in order to elicit enhanced immune responses using poly(DL-lactide-co-glycolide) nanoparticles (PLGA-NPs) encapsulating tumor antigenic peptides. PLGA-NPs were made using the double emulsion-solvent evaporation method. Artificial antigen-presenting cells were generated by human dendritic cells (DCs) loaded with PLGA-NPs encapsulating tumor antigenic peptide(s). The efficiency of the antigen presentation was measured by interferon-γ ELISpot assay (Vector Laboratories, Burlingame, CA). Antigen-specific cytotoxic T lymphocytes (CTLs) were generated and evaluated by CytoTox 96(®) Non-Radioactive Cytotoxicity Assay (Promega, Fitchburg, WI). The efficiency of the peptide delivery was compared between the methods of emulsification in incomplete Freund's adjuvant and encapsulation in PLGA-NPs. Our results showed that most of the PLGA-NPs were from 150 nm to 500 nm in diameter, and were negatively charged at pH 7.4 with a mean zeta potential of -15.53 ± 0.71 mV; the PLGA-NPs could be colocalized in human DCs in 30 minutes of incubation. Human DCs loaded with PLGA-NPs encapsulating peptide induced significantly stronger CTL cytotoxicity than those pulsed with free peptide, while human DCs loaded with PLGA-NPs encapsulating a three-peptide cocktail induced a significantly greater CTL response than those encapsulating a two-peptide cocktail. Most importantly, the peptide dose encapsulated in PLGA-NPs was 63 times less than that emulsified in incomplete Freund's adjuvant, but it induced a more powerful CTL response in vivo. These results demonstrate that the delivery of peptides encapsulated in PLGA-NPs is a promising approach to induce effective antitumor CTL responses in vivo.
An expanded role for heterozygous mutations of ABCB4, ABCB11, ATP8B1, ABCC2 and TJP2 in intrahepatic cholestasis of pregnancy (2017)

Intrahepatic cholestasis of pregnancy (ICP) affects 1/140 UK pregnancies; with pruritus, hepatic impairment and elevated serum bile acids. Severe disease is complicated by spontaneous preterm delivery and stillbirth. Previous studies have reported mutations in hepatocellular transporters (ABCB4, ABCB11). High throughput sequencing in 147 patients was performed in the transporters ABCB4, ABCB11, ATP8B1, ABCC2 and tight junction protein 2 (TJP2). Twenty-six potentially damaging variants were identified with the following predicted protein changes: Twelve ABCB4 mutations - Arg47Gln, Met113Val, Glu161Gly, Thr175Ala, Glu528Glyfs*6, Arg590Gln, Ala601Ser, Glu884Ter, Gly722Ala, Tyr775Met (x2), Trp854Ter. Four potential ABCB11 mutations - Glu297Gly (x3) and a donor splice site mutation (intron 19). Five potential ATP8B1 mutations - Asn45Thr (x3), and two others, Glu114Gln and Lys203Glu. Two ABCC2 mutations - Glu1352Ala and a duplication (exons 24 and 25). Three potential mutations were identified in TJP2; Thr62Met (x2) and Thr626Ser. No patient harboured more than one mutation. All were heterozygous. An additional 545 cases were screened for the potential recurrent mutations of ATP8B1 (Asn45Thr) and TJP2 (Thr62Met) identifying three further occurrences of Asn45Thr. This study has expanded known mutations in ABCB4 and ABCB11 and identified roles in ICP for mutations in ATP8B1 and ABCC2. Possible novel mutations in TJP2 were also discovered.
Physicochemical aspects of the enzymatic hydrolysis of carboxylic esters. (2002)

Considering the important role played by enzymatic hydrolysis in the metabolism of therapeutic agents designed by retrometabolic approaches (soft drugs and chemical delivery systems), the present article offers a review of a number of issues related to the enzymatic hydrolysis of carboxylic esters. Current knowledge regarding interorgan- and interspecies variability, stereospecificity, activation energy, proposed mechanism, and quantitative structure-metabolism relationship is summarized. The effects of chain-length and branching in the alcohol or acyl substituent on the rate of hydrolysis in congener series are also summarized. Available in vitro human blood data suggest that shortest half-lives are achieved with sterically non-hindered chains that are neither too short nor too long and are of around four carbon-atom long.
Granulocyte-macrophage colony-stimulating factor requires interaction with accessory cells or granulocyte-colony stimulating factor for full stimulation of human myeloid progenitors (1989)

Human recombinant GM-CSF (rGM-CSF) was tested on highly purified and fractionated CFU-GM subsets. The fractionation was performed with the DS1–1 monoclonal antibody (MoAb), which distinguishes early and late CFU-GM. On whole bone marrow cells, rGM-CSF had a colony-stimulating activity comparable to that of known sources of CSFs, ie, the supernatant (SN) of TPA 30–1 or 5637 cell lines, used as control. A greatly reduced activity was observed when CFU-GM were depleted of phagocytizing and E rosetting cells (colony growth of 27% as compared with control). On fractionated CFU-GM, the rGM-CSF activity was even more reduced on both early and late progenitors (18% and 6% of colony growth, respectively). However, when rGM-CSF was used together with rG- CSF at suboptimal concentrations, the colony growth reached values analogous to that of control cultures. A synergistic interaction between rGM-CSF and rG-CSF in stimulating either early or late myeloid progenitors was observed. The results suggest that the activity of rGM- CSF on CFU-GM is mainly exerted through cooperation with accessory cells. r-G-CSF is one of the factors that can synergistically cooperate with r-GM-CSF in the myelopoietic stimulation.
Estrogen‐dependent expression of the tissue kallikrein gene (Klk1) in the mouse uterus and its implications for endometrial tissue growth (2007)

Tissue kallikrein mK1 is a serine protease involved in the generation of bioactive kinins for normal cardiac and arterial function in the mouse. In the present study, the tissue kallikrein gene Klk1, which codes for mK1, was shown to be one of the most prevalent of the Klk gene species in the uteri of adult mice, and its mRNA level was significantly higher at estrus than at diestrus. Klk1 mRNA expression was enhanced in the uteri of ovariectomized mice receiving estradiol-17beta treatment. Both endometrial epithelial and stromal cells isolated from the mice exhibited Klk1 expression at detectable levels when cultured in the presence of estradiol-17beta. mK1 was characterized using the recombinant active enzyme. mK1 had trypsin-like activity with a strong preference for Arg over Lys in the P1 position, and its activity was inhibited by typical serine protease inhibitors. Casein, gelatin, fibronectin, collagen type IV, and high-molecular-weight kininogen were degraded by mK1. The single-chain tissue-type plasminogen activator was converted to the two-chain form by mK1. In addition, mK1 degraded insulin-like growth factor binding protein-3. The present data suggest that mK1 may be implicated in the growth of uterine endometrial tissues during the proliferative phase.
Purinergic responses in the feline pulmonary vascular bed (1993)

Abstract Adenosine and ATP produce dose‐dependent, tone‐dependent response in the pulmonary vascular (PV) bed, under conditions of controlled pulmonary blood flow and constant left atrial pressure in vivo in intact‐chest, spontaneously breathing cats. At low, resting PV tone, adenosine produces dose‐dependent vasoconstrictor responses by acting on “A 1 ‐like” adenosine receptors which activate a phospholipase and thromboxane release. ATP Produces dose‐dependent vasoconstrictor responses, in part, following its metabolism to adenosine, by acting on “A 1 ‐like” adenosine receptors and by acting on P 2x receptors. At elevated PV tone, data to date support that adenosine and ATP produce dose‐dependent vasodilator responses by acting on A 2 and P 2Y receptors, respectively. Mechanisms to explain how a change in vascular tone alters the response of the vascular bed to a substance are not known. Moreover, the role of purinoceptors in pulmonary vascular disease is not known. Identification of selective pharmacological probes for purinoceptors in the pulmonary vascular bed is necessary to investigate their role in the development of pulmonary hypertension of acute and chronic lung disease. © 1993 Wiley‐Liss, Inc.
Piezoelectric PZT Cantilever Array Integrated with Piezoresistor for High Speed Operation and Calibration of Atomic Force Microscopy (2002)

Two kinds of PZT cantilevers integrated with a piezoresistor have been newly designed, fabricated, and characterized for high speed AFM. In first cantilever, a piezoresistor is used to sense atomic force acting on tip, while in second cantilever, a piezoresistor is integrated to calibrate hysteresis and creep phenomena of the PZT cantilever. The fabricated PZT cantilevers provide high tip displacement of 0.55µm/V and high resonant frequency of 73 kHz. A new cantilever structure has been designed to prevent electrical coupling between sensor and PZT actuator and the proposed cantilever shows 5 times lower coupling voltage than that of the previous cantilever. The fabricated PZT cantilever shows a crisp scanned image at 1mm/sec, while the conventional piezo-tube scanner shows blurred image even at 180µm/sec. The non-linear properties of the PZT actuator are also well calibrated using the piezoresistive sensor for calibration.
Cyclopolymerizable Monomers for Use in Dental Resin Composites (1990)

The simple reaction of conventional monofunctional acrylate monomers with paraformaldehyde has yielded a new class of difunctional monomers. The unique proximity of the double bonds within these compounds allows a facile cyclopolymerization to incorporate a cyclic ether structure into the polymer backbone. The external position of the acrylate esters means that these pendant groups can be varied for alteration of the physical properties of the monomers and the corresponding polymers. A series of the new monomers has been prepared and polymerized under dilute solution and bulk conditions to yield non-crosslinked and crosslinked polymers, respectively. The polymers exhibited high degrees of conversion and significantly reduced polymerization shrinkage, compared with polymers obtained from conventional diacrylate or dimethacrylate monomers. These properties appear to be a direct result of an efficient cyclopolymerization process. The combination of improved conversion to polymer with less contraction makes these monomers ideal candidates for use in dental resin composites. A preliminary evaluation of their potential in this application has shown that with suitable ester functionality, they can be formulated to provide composites with excellent mechanical strength properties.
A User-Friendly Method of Pin Site Management for External Fixators (2011)

Therapeutic, Level V.