gebhart/patrepeval huggingface dataset:
Complete amino acid sequence of the catalytic subunit of bovine cardiac muscle cyclic AMP-dependent protein kinase. (1981)

The complete amino acid sequence of the 349-residue catalytic subunit of cyclic AMP-dependent protein kinase from bovine cardiac muscle is presented. The sequence of the subunit (Mr 40,580 including phosphate groups at threonine-196 and serine-337) was derived largely by automated Edman degradation of nine fragments generated from the carboxymethylated protein by cleavage of methionyl bonds with cyanogen bromide. These fragments were aligned along the polypeptide chain by analysis of methionine-containing tryptic peptides isolated from protein radiolabeled in vitro by [14C]methyl exchange at methionyl residues. The molecule contains only two cysteinyl residues, at positions 198 and 342. It is relatively polar, containing clusters of cationic residues toward the amino terminus and anionic residues towards the carboxyl terminus. Predictions of secondary structure suggest the presence of three major domains with approximately half of the residues occurring in alpha-helices and 12% in beta-strands.
Thin monocrystalline silicon solar cells (1999)

One of the most effective approaches for a cost reduction of crystalline silicon solar cells is the better utilization of the crystals by cutting thinner wafers. However, such thin silicon wafers must have sufficient mechanical strength to maintain a high mechanical yield in cell and module manufacturing. The electrical performance of thin cells drops strongly with decreasing cell thickness if solar cell manufacturing technologies without a backside passivation or a back-surface-field (BSF) are applied. However, with the application of a BSF, stable efficiencies of over 17%, even with decreasing cell thickness, have been reached. Thin solar cells show lower photodegradation, as is normally observed for Cz-silicon cells with today's standard thickness (about 300 /spl mu/m) because of a higher ratio of the diffusion length compared to the cell thickness. Cells of about 100-150 /spl mu/m thickness fabricated with the production Cz-silicon show almost no photodegradation. Furthermore, thin boron BSF cells have a pronounced efficiency response under backside illumination. The backside efficiency increases with decreasing cell thickness and reaches 60% of the frontside cell efficiency for 150 /spl mu/m solar cells and also for solar modules assembled of 36 cells of a thickness of 150 /spl mu/m. Assuming, for example, a rearside illumination of 150 W/m/sup 2/, this results in an increased module power output of about 10% relatively.
The membrane proteins of the vacuolar system. II. Bidirectional flow between secondary lysosomes and plasma membrane. (1980)

Lactoperoxidase covalently coupled to latex spheres (LPO-latex) has been used to selectively iodinate the phagolysome (PL) membrane within living macrophages, as discussed in the accompanying article. This procedure labeled approximately 24 polypeptides in the PL membrane; these were similar to those iodinatable on the external surface of the plasma membrane (PM). We now report on the translocation and fate of these proteins when the cells are returned to culture. TCA-precipitable radioactivity was lost from cells with biphasic kinetics. 20-50% of the cell-associated radiolabel was rapidly digested (t 1/2 approximately equal to 1 h) and recovered in the culture medium as monoiodotyrosine. 50-80% of the label was lost slowly from cells ( 1/2 approximately equal to 24-30 h). Quantitative analysis of gel autoradiograms showed that all radiolabeled proteins were lost at the same rate in both the rapid and slow phases of digestion. Within 15-30 min aftr labeling of the PL membrane, EM autoradiography revealed that the majority of the cell-associated grains, which at time 0 were associated with PL, were now randomly dispersed over the plasmalemma. At this time, analysis of PM captured by a second phagocytic load revealed the presence of all labeled species originally present in the PL membrane. This demonstrated the rapid, synchronous centrifugal flow of PL polypeptides to the cell surface. Evidence was also obtained for the continuous influx of representative samples of the PM into the PL compartment by way of pinocytic vesicles. This was based on the constant flow of fluid phase markers into latex-containing PL and on the internalization of all iodinatable PM polypeptides into this locus. These observations provide evidence for the continuous, bidirectional flow of membrane polypeptides between the PM and the secondary lysosome and represent an example of a membrane flow and recycling mechanism.
L1 Is Sequentially Processed by Two Differently Activated Metalloproteases and Presenilin/γ-Secretase and Regulates Neural Cell Adhesion, Cell Migration, and Neurite Outgrowth (2005)

The immunoglobulin superfamily recognition molecule L1 plays important functional roles in the developing and adult nervous system. Metalloprotease-mediated cleavage of this adhesion molecule has been shown to stimulate cellular migration and neurite outgrowth. We demonstrate here that L1 cleavage is mediated by two distinct members of the disintegrin and metalloprotease family, ADAM10 and ADAM17. This cleavage is differently regulated and leads to the generation of a membrane bound C-terminal fragment, which is further processed through gamma-secretase activity. Pharmacological approaches with two hydroxamate-based inhibitors with different preferences in blocking ADAM10 and ADAM17, as well as loss of function and gain of function studies in murine embryonic fibroblasts, showed that constitutive shedding of L1 is mediated by ADAM10 while phorbol ester stimulation or cholesterol depletion led to ADAM17-mediated L1 cleavage. In contrast, N-methyl-d-aspartate treatment of primary neurons stimulated ADAM10-mediated L1 shedding. Both proteases were able to affect L1-mediated adhesion and haptotactic migration of neuronal cells. In particular, both proteases were involved in L1-dependent neurite outgrowth of cerebellar neurons. Thus, our data identify ADAM10 and ADAM17 as differentially regulated L1 membrane sheddases, both critically affecting the physiological functions of this adhesion protein.
Regulatory T cells, especially ICOS+ FOXP3+ regulatory T cells, are increased in the hepatocellular carcinoma microenvironment and predict reduced survival (2016)

Hepatocellular carcinoma (HCC) is a common malignant tumour, especially in Asia. Its prognosis is poor, and there are limited methods for predicting patient survival. This study was carried out to analyse the prognostic value of tumour-infiltrating lymphocytes (TILs), especially regulatory T cells (Tregs), in HCC patients. TILs were analysed in 57 randomly selected HCC patients. The prognostic effects of groups with high and low numbers were evaluated by the Kaplan-Meier and Cox model analyses. Although higher densities of CD3<sup>+</sup>, CD4<sup>+</sup>, and CD8<sup>+</sup> cytotoxic lymphocytes (CTLs) as well as CD56<sup>+</sup> NK cells and CD68<sup>+</sup> macrophages were observed in peritumoural tissue, increased numbers of forkhead/winged helix transcription factor P3<sup>+</sup> (FOXP3<sup>+</sup>) Tregs were found in intratumoural tissue. Additionally, regarding ICOS<sup>+</sup> FOXP3<sup>+</sup> Tregs, an increased prevalence in carcinoma was not only associated with the absolute number but also with the percentage of FOXP3<sup>+</sup> cells. Higher Treg levels in tumour tissues indicated a worse prognosis, and the FOXP3<sup>+</sup> Tregs/CD4<sup>+</sup> T cells ratio was an independent prognostic factor for OS. Therefore, FOXP3<sup>+</sup> Tregs, especially ICOS<sup>+</sup> FOXP3<sup>+</sup> Tregs, contribute to the immunosuppressive HCC microenvironment. High tumour-infiltrating Tregs are thought to be an unfavourable prognostic indicator of HCC.
Control elements situated downstream of the major transcriptional start site are sufficient for highly efficient polyomavirus late transcription (1989)

In a transient expression assay in mouse fibroblasts in which neither replication nor T-antigen synthesis occurred, the polyomavirus late promoter functioned faithfully and even more efficiently than the simian virus 40 early promoter. Surprisingly, the DNA sequences upstream of the main transcriptional start sites were not required to obtain the high mRNA level observed. It appeared to result from the combined action of a basal promoter element within the A enhancer domain and of a more downstream element, located in the VP3 intron and abutting the late splice donor. We also show that although an enhancer region was required, enhancer function per se was not. Instead, it appeared that only a defined subset of the DNA-protein interactions necessary for enhancer function was involved in late promoter activity.
Synthesis of Large-Area Silicon Nanowire Arrays via Self-Assembling Nanoelectrochemistry (2002)

Large-area silicon nanowire arrays have been prepared on a silicon wafer without the use of a template. The simple method, which can be carried out near room temperature, involves the nanoelectrochemistry of silver nanowires in an aqueous HF solution containing silver nitrate. This technique may be generally applicable to other semiconductors and metals. The Figure shows nanodendritic silicon wires.
Shutdown of Class Switch Recombination by Deletion of a Switch Region Control Element (1993)

Upon activation, B lymphocytes can change the class of the antibody they express by immunoglobulin class switch recombination. Cytokines can direct this recombination to distinct classes by the specific activation of repetitive recombinogenic DNA sequences, the switch regions. Recombination to a particular switch region (s gamma 1) was abolished in mice that were altered to lack sequences that are 5' to the s gamma 1 region. This result directly implicates the functional importance of 5' switch region flanking sequences in the control of class switch recombination. Mutant mice exhibit a selective agammaglobulinemia and may be useful in the assessment of the biological importance of immunoglobulin G1.
Lattice Surgery with a Twist: Simplifying Clifford Gates of Surface Codes (2018)

We present a planar surface-code-based scheme for fault-tolerant quantum computation which eliminates the time overhead of single-qubit Clifford gates, and implements long-range multi-target CNOT gates with a time overhead that scales only logarithmically with the control-target separation. This is done by replacing hardware operations for single-qubit Clifford gates with a classical tracking protocol. Inter-qubit communication is added via a modified lattice surgery protocol that employs twist defects of the surface code. The long-range multi-target CNOT gates facilitate magic state distillation, which renders our scheme fault-tolerant and universal.
Effects of Peritonsillar Injection of Tramadol and Adrenaline before Tonsillectomy. (2013)

Large randomized controlled studies are needed to compare tramadol plus adrenaline infiltration with other heamostatic and analgesics, but the current study indicated that Tramadol plus adrenaline infiltration could be an effective method to reduce the post operative pain , operative time and time to achieve heamostasis in tonsillectomy surgeries. Therefore the use of Tramadol plus adrenaline infiltration should be further promoted and implemented as routine use in tonsillectomy surgeries.
GLYCOPROTEINS IN MEMBRANES (1968)

Summary 1. Although the classical models of biomembranes have emphasized the lipid and protein nature of these structures, a small quantity of carbohydrate is present as glycoprotein and glycolipid in animal cell membranes. In this article an attempt has been made to indicate that such carbohydrate materials should be considered in any complete model of animal cell membranes. 2. Various techniques that have demonstrated the presence of glycoproteins in animal cell membranes have been discussed here. In particular, cell electrophoresis, especially when the measurements are combined with specific enzyme treatments of the cells, has indicated that the net negative surface charge on intact viable cells is mainly due to sialic acid‐containing glycoproteins and not as previously thought to ionizable phosphate groups associated with a complex phospholipid system. 3. Membrane‐bound antigens are complex carbohydrate‐containing macro‐molecules whose antigenic activity is principally associated with the configuration at terminal positions on the carbohydrate chains. Enzymic degradation of the glycoproteins of the intact plasma membrane of cells, especially erythrocytes, causes profound changes in the immunological behaviour of the cell. 4. Histology and electron microscopy have indicated the presence of carbohydrate at the periphery of many mammalian cells. Some workers consider that such materials are present in a ‘cell coat’ covering the plasma membrane, rather than in the membrane itself. 5. Studies on the isolation and characterization of membrane glycoproteins have indicated that small oligosaccharide units linked to O ‐seryl or glutamyl residues in proteins are important structural units in plasma membranes. 6. The glycosylation of proteins takes place within the membranes of the endo‐plasmic reticulum. Studies of glycoprotein biosynthesis suggest that the cell is able to synthesize a diversity of cell‐surface structures from a relatively small number of monosaccharides. 7. Modification of the sialic acid‐containing glycoproteins of the plasma membrane affects the transport of materials in and out of cells. Glycoproteins are present in membranes other than the plasma membrane, and are therefore considered to be integral components of membranes; hence the designation ‘cell coat’, whilst useful as a descriptive term, should not be taken to indicate that glycoproteins are constituents of a functional entity separate from that of the membrane. 8. Evidence that membrane glycoproteins may act as sites of interaction between cells is discussed. The involvement of glycoproteins in such a role would explain why the cell had developed a biosynthetic process capable of producing varied surface oligosaccharide structures from monosaccharides.
Crystalline morphology and thermal properties for random copolyesters of(R)-3-hydroxybutyric acid with different hydroxyalkanoic groups (2001)

The solid-state structures and thermal properties of melt-crystallized films of random copolymers of (R)-3-hydroxybutyric acid (3HB) with different hydroxyalkanoic acids such as (R)-3-hydroxypentanoic acid (3HV), (R)-3-hydroxyhexanoic acid (3HH), medium-chain-length (R)-3-hydroxyalkanoic acids (mcl-3HA; C8-C12), 4-hydroxybutyric acid (4HB), and 6-hydroxyhexanoic acid (6HH) were characterized by means of small-angle X-ray scattering, differential scanning calorimetry, and optical microscopy. The randomly distributed second monomer units except for 3HV in copolyesters act as defects of P(3HB) crystal and are excluded from the P(3HB) crystalline lamellae. The lamellar thickness of copolymers decreased with an increase in either the main-chain or the side-chain carbon numbers of second monomer units. In addition, the growth rate of spherulites decreased with an increase in the carbon numbers of second monomer units for copolymers with an identical comonomer composition. These results indicate that the steric bulkiness of second monomer unit affects on the crystallization of 3HB segments in random copolyesters.
Is the Site of Action of Ketamine Anesthesia the N-Methyl-D-Aspartate Receptor? (1990)

Synaptic mechanisms underlying ketamine anesthesia were studied using in vitro preparations of the lamprey CNS. Although lampreys are one of the most primitive vertebrates, the synaptic physiology and pharmacology are similar to those in the higher vertebrates. Axonal conduction, transmitter release from the presynaptic terminal, postsynaptic response to the putative neurotransmitters, and resting and activated membrane properties were studied in the absence and the presence of various concentrations of ketamine. Ketamine markedly reduced N-methyl-D-aspartate (NMDA)-activated responses, such as depolarizations to bath-applied NMDA and bursting rhythm during "fictive locomotion." The 50% block of the responses took place in the presence of 10-20 microM ketamine, whereas those induced by kainate and quisqualate (the other two subclasses of L-glutamate/L-aspartate agonists) were spared at concentrations higher than 600-800 microM. None of the other neuronal events tested were suppressed in the presence of still higher concentrations of ketamine. The results support the hypothesis that ketamine might exert its anesthetic effect by a pharmacologically specific interaction with the NMDA receptor.
Prostaglandins as ocular hypotensive agents; development of an analogue for glaucoma treatment. (1995)

Prostaglandins as ocular hypotensive agents; Development of an analogue for glaucoma treatment.
Noise-Induced Entrainment and Stochastic Resonance in Human Brain Waves (2002)

We present the first observation of stochastic resonance (SR) in the human brain's visual processing area. The novel experimental protocol is to stimulate the right eye with a subthreshold periodic optical signal and the left eye with a noisy one. The stimuli bypass sensory organs and are mixed in the visual cortex. With many noise sources present in the brain, higher brain functions, e.g., perception and cognition, may exploit SR.
Therapeutic applications and specificity of action of designer nucleases for precision genome engineering (2015)

Designer nucleases allow for the precise modification of a given DNA sequence by the introduction of a sequence-specific double strand break. This targeted genetic engineering confers the ability to modify genomes of complex organisms, and has far-reaching applications in human medicine, agriculture, and biotechnology. As these nucleases act in a sequence specific manner, understanding their specificity is of paramount importance to prevent potentially genotoxic side effects. In this thesis, I assessed the ability of a class of designer nucleases (ZFNs)--zinc finger nucleases--to simultaneously inactivate two genes encoding entry factors required for HIV infection in human CD4 T cells. Additionally, I sought to develop a high-throughput means of identifying sites of designer nuclease off-target activity across the genome, in an effort to better understand the factors governing designer nuclease specificity. This work demonstrates the ability of ZFNs to simultaneously modify two distinct genetic loci in primary human CD4 T cells--the main target of HIV infection. These gene-modified cells are protected from HIV infection and represent a novel means of treating--and potentially curing HIV infection. This work also demonstrates that DNA double-strand breaks introduced by a single designer nuclease at on- and off-target loci can result in the formation of genomic rearrangements. Taken together, this work advances in the field of genome engineering on two fronts--a novel therapeutic application of designer nucleases and a novel means of detecting off-target genomic modification.
Interactions Between Histidine Kinase NblS and the Response Regulators RpaB and SrrA are Involved in the Bleaching Process of the Cyanobacterium Synechococcus elongatus PCC 7942 (2011)

Cyanobacteria have developed a light-harvesting antenna complex known as the phycobilisome. When cells are starved for nutrients or exposed to high light, the phycobilisome is rapidly degraded (bleaching). It has been suggested that in the cyanobacterium Synechococcus elongatus PCC 7942, the bleaching process is regulated by a two-component histidine kinase, NblS. To clarify the signaling pathway involving NblS, we identified the NblS-interacting response regulators RpaB and SrrA. In vitro assays using recombinant proteins showed that both RpaB and SrrA can receive phosphoryl groups from autophosphorylated NblS; the NblS-interacting protein SipA clearly enhances the phosphotransfer activity from NblS to RpaB and SrrA. In addition, NblS prefers SrrA over RpaB as the phosphotransfer target with or without SipA. Gel mobility shift assay revealed that both RpaB and SrrA can bind to the upstream region of nblA, a major regulatory factor in the bleaching process. nblA transcript accumulates in nblS or rpaB mutants even under normal growth conditions, while in the srrA disruptant the nblA transcripts are slightly up-regulated under stress conditions. These observations suggest that the bleaching signal transduction pathway via NblS is regulated by RpaB and that SrrA is partially involved.
Molecular cloning and physical mapping of the DNA of human adenovirus type 35. (1989)

The prototype strain of the human adenovirus type 35 (AV35) was examined. BamHI, EcoRI, HindIII, KpnI, PstI, and SalI restriction endonucleases were used for the mapping of DNA fragments. Three original maps were constructed, and previously published maps were somewhat modified. A PstI-specific fragment library was also prepared and characterized using the pBR322/E. coli system. Some of the recombinants seem to be applicable for rapid DNA diagnostics, and for the comparative mapping of type- and subgroup-specific DNA sequences. The comparative presentation of physical maps of subgroup B human adenoviruses might improve the efficiency of genotyping of adenoviruses using restriction endonucleases.
Converting a Protease Assay to a Caliper® Format LabChip System (2002)

The push for higher throughput screening coupled with the desire to use smaller volumes of material has sparked the development of new technologies. Caliper Technologies, Corp. (Mountain View, CA) has designed a microfluidics chip with unique properties yet to be fully exploited. The translation from a traditional plate-based assay to a microfluidic chip format has provided insights into assay development, screening data requirements, and the technology itself. Running a screen with this new technology presented challenges in throughput, signal acquisition from slow-conversion enzymes, the provision for a negative control, the translation of a time series into a single data point per compound, reagent adhesion in the channels, and fluid property mismatches. Overcoming these obstacles has resulted in a simple, robust system with significant savings in reagent use. Measures to improve throughput and generalize the system will be discussed.
Deregulated Akt3 Activity Promotes Development of Malignant Melanoma (2004)

Malignant melanoma is the skin cancer with the most significant impact on man, carrying the highest risk of death from metastasis. Both incidence and mortality rates continue to rise each year, with no effective long-term treatment on the horizon. In part, this reflects lack of identification of critical genes involved and specific therapies targeted to correct these defects. We report that selective activation of the Akt3 protein promotes cell survival and tumor development in 43 to 60% of nonfamilial melanomas. The predominant Akt isoform active in melanomas was identified by showing that small interfering RNA (siRNA) against only Akt3, and not Akt1 or Akt2, lowered the amount of phosphorylated (active) Akt in melanoma cells. The amount of active Akt3 increased progressively during melanoma tumor progression with highest levels present in advanced-stage metastatic melanomas. Mechanisms of Akt3 deregulation occurred through a combination of overexpression of Akt3 accompanying copy number increases of the gene and decreased PTEN protein function occurring through loss or haploinsufficiency of the PTEN gene. Targeted reduction of Akt3 activity with siRNA or by expressing active PTEN protein stimulated apoptotic signaling, which reduced cell survival by increasing apoptosis rates thereby inhibiting melanoma tumor development. Identifying Akt3 as a selective target in melanoma cells provides new therapeutic opportunities for patients in the advanced stages of this disease.