gebhart/patrepeval huggingface dataset:
A Spiroplasma tRNA gene cluster. (1984)

Using molecular cloning techniques, a clone containing a 7-kb insert of Spiroplasma species BC3 DNA that hybridized strongly to total labeled Spiroplasma tRNA was identified. Sequence analysis of a portion of this recombinant plasmid identified a cluster of tRNA genes. The gene order was as follows: tRNACys-tRNAArg-tRNAPro-tRNAAla-tRNAMet-tRNAIle and a portion of tRNASer All the genes encode the 3'-terminal CCA and have very high A + T and relatively long intergenic regions. An RNA polymerase promoter site was found upstream of the tRNACys gene. The tRNA gene cluster found in Spiroplasma can be compared with a similar Bacillus subtilis gene cluster, which raises interesting questions concerning gene organization and transcription.
The cell-cell adhesion receptor Mel-CAM acts as a tumor suppressor in breast carcinoma. (1997)

Mel-CAM (MUC18 or CD146) is a cell adhesion molecule sharing sequence homology with members of the immunoglobulin gene superfamily. Mel-CAM was originally described as a marker associated with invasion and metastasis in melanoma. We determined here the distribution and biological significance of Mel-CAM in normal, benign proliferative, and neoplastic breast ductal epithelium. Using a Mel-CAM-specific monoclonal antibody, we, immunohistochemically demonstrate Mel-CAM expression in 14 of 14 (100%) normal breast epithelia and benign proliferative ductal epithelial lesions, whereas Mel-CAM expression can only be focally detected in 12 of 72 (17%) breast carcinomas. Solid-phase cell adhesion assay revealed that breast carcinoma cells in culture express the ligand for Mel-CAM. Transfection of Mel-CAM cDNA into breast carcinoma cells induces a more cohesive cell growth pattern and establishes smaller tumors in immunocompromised mice than mock transfectants. In conclusion, Mel-CAM is distributed throughout normal and benign proliferative mammary ductal epithelium, but it is frequently lost in carcinomas; it functions as a heterophilic cell-cell adhesion molecule in breast epithelium, and loss of Mel-CAM expression in breast carcinoma may be an important step for tumor progression.
Rapid separation and purification of oligonucleotides by high-performance capillary gel electrophoresis. (1988)

Picomole amounts of oligodeoxynucleotides [polydeoxyadenylic acids, (dA)40-60] were baseline resolved and analyzed in less than 8 min by high-performance capillary electrophoresis with polyacrylamide gels. In addition, fast analysis of a crude 70-mer oligodeoxynucleotide and a slab gel-purified 99-mer oligodeoxynucleotide was accomplished, demonstrating the ability of high-performance capillary electrophoresis to characterize rapidly synthesized oligonucleotides. Besides analytical separations, 800 ng of a primer (20-mer) was isolated in less than 20 min. The purified species was collected in water and subsequently used as a probe in a standard dot-blot analysis. The use of high-performance capillary electrophoresis for the analysis and purification of a variety of biopolymers is simple, rapid, and has the potential for automation.
Nuclear receptors, their coactivators and modulation of transcription. (1999)

Nuclear receptors are ligand-dependent transcription factors which can also be activated in the absence of their lipophilic ligands by signaling substances acting on cell membrane receptors. This ligand-independent activation indicates the importance of nuclear receptor phosphorylation for their function. Nuclear receptor-mediated transcription of target genes is further increased by interactions with recruited coactivators forming a novel family of nuclear proteins. CBP/p300, a coactivator of different classes of transcription factors, including the tumor suppressor protein p53, plays a special role acting as a bridging protein between inducible transcription factors and the basal transcription apparatus, and as an integrator of diverse signaling pathways. Coactivators of nuclear receptors and associated proteins forming a multicomponent complex have an intrinsic histone acetylase activity in contrast to nuclear receptor and heterodimer Mad-Max corepressors, which recruit histone deacetylase. Similarly the Rb protein interacts with histone deacetylase to repress transcription of cell cycle regulatory genes. Targeted histone acetylation/deacetylation results in remodeling of chromatin structure and correlates with activation/repression of transcription. Recent data point to the important role of coactivator proteins associated with inducible transcription factors in transcription regulation, and in the integration of multiple signal transduction pathways within the nucleus.
Inter- and Intramolecular Interactions of α-Lactalbumin. III. Spectral Changes at Acid pH* (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInter- and Intramolecular Interactions of α-Lactalbumin. III. Spectral Changes at Acid pH*M. J. Kronman, L. Cerankowski, and L. G. HolmesCite this: Biochemistry 1965, 4, 3, 518–525Publication Date (Print):March 1, 1965Publication History Published online1 May 2002Published inissue 1 March 1965https://pubs.acs.org/doi/10.1021/bi00879a022https://doi.org/10.1021/bi00879a022research-articleACS PublicationsRequest reuse permissionsArticle Views78Altmetric-Citations47LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Additional Conjugation Methods and Immunogenicity of Bacillus anthracis Poly-γ- d -Glutamic Acid-Protein Conjugates (2006)

The capsule of Bacillus anthracis, composed of poly-gamma-d-glutamic acid (gammaDPGA), is an essential virulence factor of B. anthracis. The capsule inhibits innate host defense through its antiphagocytic action. gammaDPGA is a poor immunogen, but when covalently bound to a carrier protein, it elicits serum antibodies. To identify the optimal construct for clinical use, synthetic gammaDPGAs of different lengths were bound to carrier proteins at different densities. The advantages of the synthetic over the natural polypeptide are the homogeneous chain length and end groups, allowing conjugates to be accurately characterized and standardized and their chemical compositions to be related to their immunogenicities. In the present study, we evaluated, in addition to methods reported by us, hydrazone, oxime, and thioether linkages between gammaDPGA and several proteins, including bovine serum albumin, recombinant Pseudomonas aeruginosa exotoxin A, recombinant B. anthracis protective antigen (rPA), and tetanus toxoid (TT). The effects of the dosage and formulation on the immunogenicities of the conjugates were evaluated in mice. All conjugates were immunogenic. The optimal gammaDPGA chain length of 10 to 15 amino acids and the density, an average of 15 mol gammaDPGA per mol of protein, were confirmed. The thioether bond was the optimal linkage type, and TT and rPA were the best carriers. The optimal dosage was 1.2 to 2.5 microg of gammaDPGA per mouse, and adsorption of the conjugates onto aluminum hydroxide significantly increased the antibody response to the protein with a lesser effect on anti-gammaDPGA levels.
Isothermal titration calorimetric studies of Saccharomyces cerevisiae myristoyl-CoA:protein N-myristoyltransferase. Determinants of binding energy and catalytic discrimination among acyl-CoA and peptide ligands (1994)

Saccharomyces cerevisiae myristoyl-CoA:protein N-myristoyltransferase (Nmt1p) is an essential, monomeric enzyme that catalyzes the transfer of myristate from CoA to the amino-terminal Gly residue of cellular proteins. Product inhibition studies indicate that Nmt1p has an ordered Bi Bi reaction mechanism with myristoyl-CoA binding to the apo-enzyme to form a high affinity binary complex followed by binding of peptide with subsequent release of CoA and then the myristoylpeptide product. We have used isothermal titration calorimetry to quantify the effects of varying acyl chain length and removing the 3'-phosphate group of CoA on the energetics of interaction between Nmt1p and acyl-CoA ligands. Myristoyl-CoA binds to apo-Nmt1p with an affinity of 15 nM, corresponding to a binding free energy of -10.9 kcal/mol. This free energy is composed of a large favorable enthalpy of -24 kcal/mol and a large unfavorable entropic term. This large negative delta H degrees is consistent with a conformational change in the enzyme upon ligation, allowing synthesis of a functional peptide binding site. Binding of palmitoyl-CoA and lauroyl-CoA is driven by an exothermic enthalpy change which is much smaller than the corresponding parameter for myristoyl-CoA binding. The large differences in binding enthalpy and entropy (delta delta H degrees and T delta delta S degrees = 8-9 kcal/mol) demonstrate that the "off-length" acyl-CoAs bind to Nmt1p in a significantly different energetic fashion from myristoyl-CoA, even though the enzyme does not have a great deal of specificity among these ligands in terms of binding free energy (delta delta G degrees < or = 1 kcal/mol). The effect of removing the CoA 3'-phosphate group from myristoyl-CoA is similar to the effect of a two-carbon change in acyl chain length: i.e. an enthalpy dominated reduction in binding affinity. However, kinetic studies reveal that removing the 3'-phosphate from myristoyl-CoA has little effect on Nmt1p's catalytic efficiency, indicating that the 3'-phosphate group contributes binding free energy but little catalytic destabilization. The greater delta delta G degrees, with smaller delta delta H degrees and delta delta S degrees components, produced by removing the 3'-phosphate compared to increasing chain length suggests that it is not primarily the interactions of the 3'-phosphate which are disrupted when palmitoyl-CoA is substituted for myristoyl-CoA. No detectable interactions were noted between apo-Nmt1p and the substrate peptide, GAAPSKIV-NH2, providing additional support for the preferred ordered reaction mechanism.(ABSTRACT TRUNCATED AT 400 WORDS)
ZERO-BIAS CONDUCTANCE PEAKS IN MAJORANA NANOWIRES: THE GOOD, THE BAD, AND THE UGLY (2022)

Majorana zero modes are neutral zero-energy localized excitations emerging in the low-dimensional condensed matter systems, which are their own antiparticles. These excitations are topological with an intrinsic ground-state degeneracy, belonging to the (SU$_2$)$_2$ algebra and obeying the non-Abelian anyonic braiding statistics, which provides a possibility to implement the fault-tolerant topological quantum computing. As a result, enormous experimental efforts have focused on the realization of the Majorana zero modes, especially in the one-dimensional semiconductor-superconductor Majorana nanowires during the past decade. Although experiments have observed the zero-bias conductance peaks, these experimentally observed peaks are not robustly quantized as theoretically predicted for the signature of Majorana zero modes, and many other hallmarks of Majorana zero modes are yet to be unambiguously confirmed in experiments, which makes the experimentally observed zero-bias conductance peaks being interpreted as the Majorana zero modes questionable. Therefore, in this dissertation, we carry out a detailed theoretical analysis of the experimental results, and classify the experimentally observed zero-bias conductance peaks into three types: the good (i.e., the actual topological Majorana zero modes), the bad (i.e., which is the partially-separated quasi-Majorana modes induced by the inhomogeneous potential and quantum dot in the nanowire), and the ugly (i.e., which is the trivial low energy fermionic state induced by random disorder). Our study concludes that almost all the current experimentally observed zero-bias conductance peaks in the publications are the ugly zero-bias conductance peaks, and future experiments should focus on the improvement of the material quality to reduce disorder.
Optical Pumping of NeonP23Metastable Atoms (1969)

The $^{3}P_{2}$ metastable atoms of neon have been optically oriented. This represents the first case of the optical pumping of non-$S$ state atoms. The optical-pumping process is described, and depolarization cross sections for collisions with ground-state neon and ground-state helium atoms measured. The cross section for collisional depolarization with helium is 4.30 \ifmmode\pm\else\textpm\fi{} 0.22 \ifmmode\times\else\texttimes\fi{} ${10}^{\ensuremath{-}17}$ ${\mathrm{cm}}^{2}$, and with neon is 166 \ifmmode\pm\else\textpm\fi{} 8 \ifmmode\times\else\texttimes\fi{} ${10}^{\ensuremath{-}17}$ ${\mathrm{cm}}^{2}$ at 300\ifmmode^\circ\else\textdegree\fi{}K. The metastable $^{3}P_{2}$ atoms of Ar and Xe have also been optically pumped. As the polarizability of the noble-gas buffer increases, the collisional depolarization cross section approaches the diffusion cross section.
A NEW APPROACH TO THE BIOLOGICAL DETERMINATION OF THE LUTEINIZING HORMONE (1968)

ABSTRACT The response of the uterine weight of immature mice to FSH and LH preparations with low contamination by each other was studied. The new approach to the biological assay of LH, which could be designated the »uterine-augmentation« test, was based on injecting intact immature mice with a constant dose (4.44 IU) of a biologically pure FSH preparation plus increasing amounts of extracts containing LH. A dose as little as 0.068 IU of LH is capable to increase the uterine weight when injected together with 4.44 IU of biologically pure FSH. A significant uterine response can be obtained when animals are injected with 29.4 μg of 2nd IRP-HMG (equivalent to 0.128 IU-LH and 0.128 IU-FSH). When a constant dose of 4.44 IU of biologically pure FSH is added to each dose level of the 2nd IRP-HMG, a significant uterine response is obtained with 14.7 μg of this reference preparation. The end point was the mouse uterine weight. Some determinations of the LH activity in urinary extracts have been performed according to this new method and from the results it seems that the LH activities, as determined by the ovarian ascorbic acid depletion method, agree with those determined by the uterine-augmentation test. It also seems that the uterine weight response is proportional to the LH activity and not dependent on the FSH-LH ratio of the samples assayed.
p53: Guardian of ploidy (2011)

Aneuploidy, often preceded by tetraploidy, is one of the hallmarks of solid tumors. Indeed, both aneuploidy and tetraploidy are oncogenic occurrences that are sufficient to drive neoplastic transformation and cancer progression. True to form, the tumor suppressor p53 obstructs propagation of these dangerous chromosomal events by either instigating irreversible cell cycle arrest or apoptosis. The tumor suppressor Lats2, along with other tumor inhibitory proteins such as BRCA1/2 and BubR1, are central to p53-dependent elimination of tetraploid cells. Not surprisingly, these proteins are frequently inactivated or downregulated in tumors, synergizing with p53 inactivation to establish an atmosphere of "tolerance" for a non-diploid state.
Differential effects of extracellular vesicles secreted by mesenchymal stem cells from different sources on glioblastoma cells (2014)

Different effects of MSC-EVs on cancer cells were observed depending on their tissue of origin. Moreover, MSC-EVs can deliver antiblastic drugs to glioblastoma cells.
Organometallic chemistry on silicon surfaces: formation of functional monolayers bound through Si–C bonds (1999)

Silicon chips form the backbone of modern computing and yet until recently, the surface chemistry of this technologically essential material has remained relatively unexplored. As the size of devices on silicon wafers shrink (towards gigascale integration), the surface characteristics play increasingly crucial roles in the proper functioning of the device since the ratio of surface atoms/bulk escalates. While surface oxide has served thus far as the main passivation route, there is strong interest in precisely tailoring the interface properties, not only for microelectronics, but other applications including sensors, MEMS and biologically active surfaces. As a result, organometallic and organic chemistry has become essential for the synthesis of functional, modifiable monolayers, bound to non-oxidized silicon surfaces through silicon–carbon bonds. The latest approaches towards preparation of monolayers through Si–C bonds on both flat and photoluminescent porous silicon are described. Wet chemical techniques, accessible to most organometallic/organic chemists are highlighted, but recent developments using UHV conditions also receive attention.
Molecular targets for cannabidiol and its synthetic analogues: effect on vanilloid VR1 receptors and on the cellular uptake and enzymatic hydrolysis of anandamide (2001)

1. (-)-Cannabidiol (CBD) is a non-psychotropic component of Cannabis with possible therapeutic use as an anti-inflammatory drug. Little is known on the possible molecular targets of this compound. We investigated whether CBD and some of its derivatives interact with vanilloid receptor type 1 (VR1), the receptor for capsaicin, or with proteins that inactivate the endogenous cannabinoid, anandamide (AEA). 2. CBD and its enantiomer, (+)-CBD, together with seven analogues, obtained by exchanging the C-7 methyl group of CBD with a hydroxy-methyl or a carboxyl function and/or the C-5' pentyl group with a di-methyl-heptyl (DMH) group, were tested on: (a) VR1-mediated increase in cytosolic Ca(2+) concentrations in cells over-expressing human VR1; (b) [(14)C]-AEA uptake by RBL-2H3 cells, which is facilitated by a selective membrane transporter; and (c) [(14)C]-AEA hydrolysis by rat brain membranes, which is catalysed by the fatty acid amide hydrolase. 3. Both CBD and (+)-CBD, but not the other analogues, stimulated VR1 with EC(50)=3.2 - 3.5 microM, and with a maximal effect similar in efficacy to that of capsaicin, i.e. 67 - 70% of the effect obtained with ionomycin (4 microM). CBD (10 microM) desensitized VR1 to the action of capsaicin. The effects of maximal doses of the two compounds were not additive. 4. (+)-5'-DMH-CBD and (+)-7-hydroxy-5'-DMH-CBD inhibited [(14)C]-AEA uptake (IC(50)=10.0 and 7.0 microM); the (-)-enantiomers were slightly less active (IC(50)=14.0 and 12.5 microM). 5. CBD and (+)-CBD were also active (IC(50)=22.0 and 17.0 microM). CBD (IC(50)=27.5 microM), (+)-CBD (IC(50)=63.5 microM) and (-)-7-hydroxy-CBD (IC(50)=34 microM), but not the other analogues (IC(50)>100 microM), weakly inhibited [(14)C]-AEA hydrolysis. 6. Only the (+)-isomers exhibited high affinity for CB(1) and/or CB(2) cannabinoid receptors. 7. These findings suggest that VR1 receptors, or increased levels of endogenous AEA, might mediate some of the pharmacological effects of CBD and its analogues. In view of the facile high yield synthesis, and the weak affinity for CB(1) and CB(2) receptors, (-)-5'-DMH-CBD represents a valuable candidate for further investigation as inhibitor of AEA uptake and a possible new therapeutic agent.
A Charging Acceleration Technique for Highly Efficient Cascode Class-E CMOS Power Amplifiers (2010)

A cascode configuration in class-E CMOS power amplifiers (PAs) provides high reliability with respect to breakdown considerations. However, it causes a power loss due to the slow transition of a common-gate device from the triode region to the cut-off region. To minimize the power loss of cascode class-E CMOS PAs, we propose a charging acceleration technique, CAT. This method incorporates a capacitive element between the drain and the source of a common-gate device in a cascode configuration, accelerating the charging speed responsible for turning off a common-gate device instantly after a common-source device is turned off and thus minimizing power loss from the device. We compared the performance of the proposed cascode class-E PA to that of the conventional cascode class-E PA using a 0.18- CMOS process. With a 3.3-V power supply, the proposed fully-integrated CMOS PA achieves 30.7 dBm of maximum output power and 45.6% of power-added efficiency (PAE) with a dynamic range of 40 dB at 1.6 GHz. According to measurements, the proposed cascode class-E PA shows improvement in PAE over the conventional class-E PA of between 5% and 9% in a 1.5 to 2.0 GHz range.
A Comparative Study of the Radioprotective Effects of Cysteamine, WR-2721, and WR-1065 in Cultured Human Cells (1979)

The compounds, 2-mercaptoethylamine (cysteamine), S-2-(3-aminopropylamino)ethylphosphorothioic acid (WR-2721), and N-(2-mercaptoethyl)-1,3-diaminopropane (WR-1065) were tested for toxicity and radioprotective effect in cultured human cells using viability (reproductive death) as an indicator. WR-2721 and WR-1065 had no harmful effect at concentrations of 4 and 10 mM for periods up to 3 hr whereas cysteamine was toxic if left in contact with the cells for more than 30 min. The response of the cells to radiation was measured after a 30-min treatment with 4 mM of each protective agent. Survival curves were constructed and the following dose reduction factors (DRFs) were calculated: WR-2721, 1.3; cysteamine, 2.3; WR-1065, 2.9. Increasing the concentration of protective agent did not increase the DRF under these conditions except in the case of cysteamine. Extending the period of treatment with drug before irradiation increased the DRF for WR-2721 and WR-1065; values up to 1.8 and 3.4 were obtained with 10 mM WR-2721 and WR-1065, respectively. With these two compounds, the rate of development of protection with time is almost independent of concentration until the maximum is attained; it is probably controlled by the rate of transport across the cell membrane, in the case of WR-1065, and by
Micromachined arrayed dip pen nanolithography probes for sub-100 nm direct chemistry patterning (2003)

We report the development of micromachined passive and active probe arrays for parallel dip pen nanolithography (DPN). DPN is a soft lithography method that allows direct, mask-less deposition of chemicals onto substrates with sub 100-nm resolution. An active DPN probe with thermal bimetallic actuation has been developed and tested. Lithographic results and an analytical tool for optimizing active probe designs with respect to a number of performance criteria are also demonstrated.
Training agents to recognize text by example (1999)

Article Free Access Share on Training agents to recognize text by example Authors: Henry Lieberman Massachusetts Institute of Technology, Cambridge Massachusetts Institute of Technology, CambridgeView Profile , Bonnie A. Nardi AT&T Labs West, Menlo Park, CA AT&T Labs West, Menlo Park, CAView Profile , David Wright Apple Computer, Cupertino, CA Apple Computer, Cupertino, CAView Profile Authors Info & Claims AGENTS '99: Proceedings of the third annual conference on Autonomous AgentsApril 1999 Pages 116–122https://doi.org/10.1145/301136.301176Published:01 April 1999Publication History 13citation385DownloadsMetricsTotal Citations13Total Downloads385Last 12 Months8Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF