gebhart/patrepeval huggingface dataset:
Tubulin tyrosination is a major factor affecting the recruitment of CAP-Gly proteins at microtubule plus ends (2006)

Tubulin-tyrosine ligase (TTL), the enzyme that catalyzes the addition of a C-terminal tyrosine residue to alpha-tubulin in the tubulin tyrosination cycle, is involved in tumor progression and has a vital role in neuronal organization. We show that in mammalian fibroblasts, cytoplasmic linker protein (CLIP) 170 and other microtubule plus-end tracking proteins comprising a cytoskeleton-associated protein glycine-rich (CAP-Gly) microtubule binding domain such as CLIP-115 and p150 Glued, localize to the ends of tyrosinated microtubules but not to the ends of detyrosinated microtubules. In vitro, the head domains of CLIP-170 and of p150 Glued bind more efficiently to tyrosinated microtubules than to detyrosinated polymers. In TTL-null fibroblasts, tubulin detyrosination and CAP-Gly protein mislocalization correlate with defects in both spindle positioning during mitosis and cell morphology during interphase. These results indicate that tubulin tyrosination regulates microtubule interactions with CAP-Gly microtubule plus-end tracking proteins and provide explanations for the involvement of TTL in tumor progression and in neuronal organization.
Polycarbonates with Potent and Selective Antimicrobial Activity toward Gram-Positive Bacteria (2016)

The resistance developed by life-threatening bacteria toward conventional antibiotics has become a major concern in public health. To combat antibiotic resistance, there has been a significant interest in the development of antimicrobial cationic polymers due to the ease of synthesis and low manufacturing cost compared to host-defense peptides (HDPs). Herein, we report the design and synthesis of amphiphilic polycarbonates containing primary amino groups. These polymers exhibit potent antimicrobial activity and excellent selectivity to Gram-positive bacteria, including multidrug resistant pathogens. Fluorescence and TEM studies suggest that these polymers are likely to kill bacteria by disrupting bacterial membranes. These polymers also show low tendency to elicit resistance in bacteria. Their further development may lead to new antimicrobial agents combating drug-resistance.
Sterilization using a microwave-induced argon plasma system at atmospheric pressure (2003)

The use of microwave plasma for sterilization is relatively new. The advantages of this method are the relatively low temperature, time-savings and its nontoxic nature, in contrast to traditional methods such as heat and gas treatment, and radiation. This study investigated the sterilization effects of microwave-induced argon plasma at atmospheric pressure on materials contaminated with various microorganisms, such as bacteria and fungi. A low-cost and reliable 2.45 GHz, waveguide-based applicator was designed to generate microwave plasma at atmospheric pressure. This system consisted of a 1 kW magnetron power supply, a WR-284 copper waveguide, an applicator including a tuning section, and a nozzle section. Six bacterial and fungal strains were used for the sterilization test. The results showed that regardless of the strain, all the bacteria used in this study were fully sterilized within 20 seconds and all the fungi were sterilized within 1 second. These results show that this sterilization method is easy to use, requires significantly less time than the other traditional methods and established plasma sterilization methods, and it is nontoxic. It can be used in the field of sterilization in medical and dental clinics as well as in laboratory settings.
The theory of variational hybrid quantum-classical algorithms (2016)

Many quantum algorithms have daunting resource requirements when compared to what is available today. To address this discrepancy, a quantum-classical hybrid optimization scheme known as 'the quantum variational eigensolver' was developed (Peruzzo et al 2014 Nat. Commun. 5 4213) with the philosophy that even minimal quantum resources could be made useful when used in conjunction with classical routines. In this work we extend the general theory of this algorithm and suggest algorithmic improvements for practical implementations. Specifically, we develop a variational adiabatic ansatz and explore unitary coupled cluster where we establish a connection from second order unitary coupled cluster to universal gate sets through a relaxation of exponential operator splitting. We introduce the concept of quantum variational error suppression that allows some errors to be suppressed naturally in this algorithm on a pre-threshold quantum device. Additionally, we analyze truncation and correlated sampling in Hamiltonian averaging as ways to reduce the cost of this procedure. Finally, we show how the use of modern derivative free optimization techniques can offer dramatic computational savings of up to three orders of magnitude over previously used optimization techniques.
Purification and properties of 6-methylsalicylic acid synthase from Penicillium patulum (1992)

6-Methylsalicylic acid synthase has been isolated in homogeneous form from Penicillium patulum grown in liquid culture from a spore inoculum. The enzyme is highly susceptible to proteolytic degradation in vivo and in vitro, but may be stabilized during purification by incorporating proteinase inhibitors in the buffers. The enzyme exists as a homotetramer of M(r) 750,000, with a subunit M(r) of 180,000. 6-Methylsalicyclic acid synthase also accepts acetoacetyl-CoA as an alternative starter molecule to acetyl-CoA. The enzyme also catalyses the formation of small amounts of triacetic acid lactone as an oligatory by-product of the reaction. In the absence of NADPH, triacetic acid lactone is the exclusive enzymic product, being formed at 10% of the rate of 6-methylsalicylic acid. The enzyme is inactivated by 1,3-dibromopropan-2-one, leading to the formation of cross-linked dimers similar to that observed with type I fatty acid synthases. Acetyl-CoA protects the enzyme against the inactivation and inhibits dimer formation. An adaptation of the purification method for 6-methylsalicylic acid synthase may be used for the isolation of fatty acid sythase from Penicillium patulum.
Insulin-Like Growth Factor Family and Combined Antisense Approach in Therapy of Lung Carcinoma (2002)

Our data suggest that lung cancer cells produce IGF-IR and IGF-II, which in turn stimulates their proliferation by autocrine mechanism. Cancer cell proliferation can be abrogated or alleviated by blocking the mRNA activity of these genes indicating that an antisense approach may represent an effective and practical cancer gene therapy strategy.
Cystatin C and cathepsin B in human colon carcinoma: Expression by cell lines and matrix degradation (1992)

Expression of the cysteine proteinase cathepsin B and its physiological inhibitor cystatin C was analyzed in vitro in 1 human fibrosarcoma and 4 human colon carcinoma cell lines. Cystatin C antigen as well as cathepsin B activity were detected in the conditioned media of the 5 cell lines. The corresponding cell extracts expressed high levels of cathepsin B activity, whereas only trace amounts of cystatin C antigen could be found. Northern-blot analysis revealed the presence in the 5 cell lines of a 0.8-kb cystatin C mRNA transcript and 2 cathepsin B transcripts of 2.3 and 4.3 kb. Pepsin treatment of tumor-cell-released cathepsin B induced an average 7.3-fold increase in activity, indicating that the enzyme was mainly present as a latent form in conditioned medium. The pepsin-activated cathepsin B from one colon carcinoma cell line was further characterized using the cysteine proteinase inhibitors E-64, recombinant cystatin C, a cystatin-C-derived peptidyl inhibitor (Z-LVG-CHN2), and cathepsin-B-specific diazomethyl ketone inhibitors (Z-FT(OBzl)-CHN2, Z-FS(OBzl)-CHN2). This activity was totally neutralized by recombinant cystatin C, suggesting a potential for interaction between released extracellular cathepsin B and cystatin C. In vitro assays of degradation of extracellular matrix showed that cysteine proteinase inhibitors could decrease matrix degradation induced by pepsin-activated conditioned media. With colon cells, this inhibition was not observed, indicating a requirement for an extracellular activation of latent cathepsin B. Our data provide evidence that cystatin C and latent cathepsin B are both released extracellularly by colon carcinoma cells in vitro. They suggest that cystatin C and cathepsin B interactions may participate, in an as yet unelucidated way, in the modulation of the invasive phenotype of human colonic tumors.
A scanning laser rangefinder for a robotic vehicle (1977)

A scanning Laser Rangefinder (LRF) which operates in conjunction with a minicomputer as part of a robotic vehicle is described. The description includes both hardware and software. Also included is a discussion of our functional requirements relative to the state-of-the-art; a detailing of the instrument and its performance; a summary of the robot system in which the LRF functions; the software organization, interfaces, and description; and some applications to which the LRF has been put.
Group I Self-Splicing Intron in the recA Gene of Bacillus anthracis (2002)

Self-splicing introns are rarely found in bacteria and bacteriophages. They are classified into group I and II according to their structural features and splicing mechanisms. While the group I introns are occasionally found in protein-coding regions of phage genomes and in several tRNA genes of cyanobacteria and proteobacteria, they had not been found in protein-coding regions of bacterial genomes. Here we report a group I intron in the recA gene of Bacillus anthracis which was initially found by DNA sequencing as an intervening sequence (IVS). By using reverse transcriptase PCR, the IVS was shown to be removable from the recA precursor mRNA for RecA that was being translated in E. coli. The splicing was visualized in vitro with labeled free GTP, indicating that it is a group I intron, which is also implied by its predicted secondary structure. The RecA protein of B. anthracis expressed in E. coli was functional in its ability to complement a recA defect. When recA-negative E. coli cells were irradiated with UV, the Bacillus RecA reduced the UV susceptibility of the recA mutant, regardless of the presence of intron.
A Functionally Improved Locked Nucleic Acid Antisense Oligonucleotide Inhibits Bcl-2 and Bcl-xL Expression and Facilitates Tumor Cell Apoptosis (2004)

We previously reported the Bcl-2/Bcl-xL-bispecific activity of the 2'-O-(2-methoxy)ethyl (2'-MOE)-modified gapmer antisense oligonucleotide 4625. This oligonucleotide has 100% complementarity to Bcl-2 and three mismatches to Bcl-xL. In the present study, the isosequential locked nucleic acid (LNA)-modified oligonucleotide 5005 was generated, and its ability to further improve the downregulation of the two antiapoptotic targets in tumor cells was examined. We demonstrate that compared with 4625, 5005 more effectively decreased the expression of the mismatching Bcl-xL target gene in MDA-MB-231 breast and H125 lung cancer cells. In both cell lines, antisense activity caused decreased cell viability by induction of apoptosis. Moreover, in combination with various anticancer agents, 5005 reduced tumor cell viability more effectively than 4625. We describe for the first time the functional comparison of isosequential Bcl-2/Bcl-xL-bispecific 2'-MOE and LNA-modified antisense oligonucleotides and report that the LNA analog more effectively downregulated the two apoptosis inhibitors overexpressed in human tumors. Our data underscore the ability of LNA modifications to enhance the efficacy and favorably modulate the target specificity of antisense oligonucleotides.
Pharmacological characterization of a 1,4‐dihydropyridine analogue, 9‐(3,4‐dichlorophenyl)‐3,3,6,6‐tetramethyl‐3,4,6,7,9,10‐hexahydro‐1,8(2H,5H)‐acridinedione (A‐184209) as a novel KATP channel inhibitor (2003)

1. This study reports on the identification and characterization of a 1,4-dihydropyridine analogue, 9-(3,4-dichlorophenyl)-3,3,6,6-tetramethyl-3,4,6,7,9,10-hexahydro-1,8(2H,5H)-acridinedione (A-184209) as a novel inhibitor of ATP-sensitive K(+) channels. 2. A-184209 inhibited membrane potential changes evoked by the prototypical cyanoguanidine ATP-sensitive K(+) channel opener (KCO) P1075 in both vascular (A10) and urinary bladder smooth muscle cells with IC(50) values of 1.44 and 2.24 micro M respectively. 3. P1075-evoked relaxation of 25 mM K(+) stimulated aortic strips was inhibited by A-184209 in an apparently competitive fashion with a pA(2) value of 6.34. 4. The potencies of A-184209 to inhibit P1075-evoked decreases in membrane potential responses in cardiac myocytes (IC(50)=0.53 micro M) and to inhibit 2-deoxyglucose-evoked cation efflux pancreatic RINm5F cells (IC(50)=0.52 micro M) were comparable to the values for inhibition of smooth muscle K(ATP) channels. 5. On the other hand, a structural analogue of A-184209 that lacked the gem-dimethyl substituent, 9-(3,4-dichlorophenyl)-3,4,6,7,9,10-hexahydro-1,8(2H,5H)-acridinedione (A-184208), was found to be a K(ATP) channel opener, evoking membrane potential responses in A10 smooth muscle cells (EC(50)=385 nM) and relaxing aortic smooth muscle strips (IC(50)=101 nM) in a glyburide-sensitive manner. 6. Radioligand binding studies demonstrated that A-184209 displaced SUR1 binding defined by [(3)H]glyburide binding to RINm5F cell membranes with a K(i) value of 0.11 micro M whereas A-184208 was ineffective. On the other hand, both A-184209 (K(i)=1.34 micro M) and A-184208 (K(i)=1.14 micro M) displaced binding of the KCO radioligand, [(125)I]A-312110 in guinea-pig bladder membranes with similar affinities. 7. These studies demonstrate that A-184209 is a novel and structurally distinct compound that inhibits K(ATP) channels in smooth muscle with potencies comparable to glyburide. The structural overlap between DHP openers and blockers, together with their differential interaction with ligand binding sites, support the notion that both openers and blockers bind to similar or very closely coupled sites on the sulfonylurea receptor and that subtle changes in the pharmacophore itself could switch functional properties from K(ATP) channel activation to inhibition.
Nucleotide sequence variation of chitin synthase genes among ectomycorrhizal fungi and its potential use in taxonomy (1994)

DNA sequences of single-copy genes coding for chitin synthases (UDP-N-acetyl-D-glucosamine:chitin 4-beta-N-acetylglucosaminyltransferase; EC 2.4.1.16) were used to characterize ectomycorrhizal fungi. Degenerate primers deduced from short, completely conserved amino acid stretches flanking a region of about 200 amino acids of zymogenic chitin synthases allowed the amplification of DNA fragments of several members of this gene family. Different DNA band patterns were obtained from basidiomycetes because of variation in the number and length of amplified fragments. Cloning and sequencing of the most prominent DNA fragments revealed that these differences were due to various introns at conserved positions. The presence of introns in basidiomycetous fungi therefore has a potential use in identification of genera by analyzing PCR-generated DNA fragment patterns. Analyses of the nucleotide sequences of cloned fragments revealed variations in nucleotide sequences from 4 to 45%. By comparison of the deduced amino acid sequences, the majority of the DNA fragments were identified as members of genes for chitin synthase class II. The deduced amino acid sequences from species of the same genus differed only in one amino acid residue, whereas identity between the amino acid sequences of ascomycetous and basidiomycetous fungi within the same taxonomic class was found to be approximately 43 to 66%. Phylogenetic analysis of the amino acid sequence of class II chitin synthase-encoding gene fragments by using parsimony confirmed the current taxonomic groupings. In addition, our data revealed a fourth class of putative zymogenic chitin synthesis.
Synthesis of functional polymers bearing pendant mono‐and oligo‐saccharide residues (1995)

Abstract The present paper focuses on (i) a new synthetic methodology to prepare vinyl ether‐based synthetic glycoconjugates (glycopolymers) with well‐controlled structure, and on (ii) the application of glycopolymers bearing modified disaccharide residue as thermotropic liquid crystalline (LC) materials. Two vinyl ethers (VEs) having pendant glucose residues with their hydroxyl functions protected by acetyl and isopropylidene groups, respectively, were found to undergo living cationic polymerization initiated by a HI/ZnI2‐initiating system. Deprotection of the resultant monodisperse polymers led to water‐soluble polymers bearing a pendant glucose residue. Sequential living block copolymerization of glucose‐containing VE and alkyl VE, and subsequent deprotection afforded an amphiphilic block copolymer of well‐controlled structure. Transmission electron microscopic observation of its cast thin film revealed microphase‐separated surface morphologies that varied with varying segment composition ratio. A VE substituted with a heptadecanoated cellobiose pendant was independently prepared, and was cationically polymerized to give a thermotropic LC polymer. From X‐ray analysis, the mesophase was assigned to a discotic columnar in type, in which each main chain, extended due to the steric repulsion between the neighboring bulky pendants, was surrounded by three discotic columns.
Molecular relationships between 21 human rhinovirus serotypes (1995)

We have analysed, by PCR using consensus primers followed by sequencing, 12 human rhinoviruses (HRVs) in a genomic region including that corresponding to the immunogenic site NIm-II. Together with published information, 21 sequences are available for comparison. In the region analysed, which encodes 112 amino acids, the majority (18) of the serotypes exhibited at least 70% amino acid identity to one another and some serotypes are very closely related. These include HRV-36, -58 and -89, known to exhibit antigenic cross reactivity, which were shown to differ at only three amino acid positions. Three serotypes, HRV-3, -14 and -72, share at least 84% identity with one another but are less than 66% identical to the majority group. Interestingly, membership of these two molecular clusters correlates with the groupings determined by sensitivity to antivirus drugs, suggesting that they reflect a fundamental division of HRVs. In contrast, there is no correlation with receptor grouping, since the majority group contains members belonging to both HRV receptor groups.
Detecting and reducing the denial of Service attacks in WLANs (2011)

Wireless LANs are susceptible to Denial of Service (DoS) attacks. None of the existing wireless security protocols considers protection against them. We propose a novel scheme that detects and reduce DoS attacks in the WLANs. The scheme is based on random number rate control mechanism. It utilizes delegation concept for authentication at the Access Point (AP). Under flooding DoS, AP is unable to verify large number of client authentication requests. It hence, forwards optional message containing hash to the Authentication Server (AS). AS verifies the hash and sends response back to AP, thereby detecting DoS attack. The attack impact at the AP is reduced by dropping the attack packets while selecting the legitimate one. The scheme protects AS from DoS as hash calculations for detection of DoS are done once only. Scheme also prevents against legacy authentication/association and deauthentication/disassociation flooding DoS attacks.
Antibodies to the HIV-1 Tat protein correlated with nonprogression to AIDS: a rationale for the use of Tat toxoid as an HIV-1 vaccine. (1999)

Antibodies toward HIV-1 Tat, which are inversely correlated to p24 antigenemia, appear as a critical marker for a lack of disease progression. This study strongly suggests that rising anti-Tat antibodies through active immunization may be beneficial in AIDS vaccine development to control viral replication.
Cancer vaccines: Targeting KRAS-driven cancers (2020)

<b>Introduction</b>: Mutant KRAS is a genetic driver of multiple cancers that has challenged clinical anti-cancer therapeutics in the last 3 decades. Neo-antigens encoded by KRAS mutations have been identified as tumor-specific with high immunogenicity and can be used to deliver precision cancer vaccines to promote anti-tumor immune responses. KRAS mutation-based cancer vaccines have produced encouraging preclinical and clinical results. Cancer vaccines represent a promising approach to treat KRAS-driven cancers.<b>Areas covered</b>: In this review, we summarize the development and progress of vaccines targeting KRAS and evaluate their potential benefits and obstacles in the current landscape of therapy for KRAS-driven cancers.<b>Expert opinion</b>: KRAS mutation-based cancer vaccines can induce immunogenicity in patients with KRAS-driven cancers. However, the mechanisms of tumor suppression including cellular and molecular factors within the tumor microenvironment may limit vaccine efficacy. Combining KRAS-driven therapeutic cancer vaccines with other methods and adjuvants can circumvent immunosuppression and promote therapeutic successes.
Pyrosequencing<sup>®</sup> Applications (2007)

Genetics research has benefited tremendously from the release of the human genome sequence. Subsequent technology has been developed and adapted to accommodate the need for faster, easier throughput of genetic assays. Pyrosequencing is a unique system that allows the analysis of genetic variations including single-nucleotide polymorphisms, indels and short repeats, as well as assessing RNA allelic imbalance, DNA methylation status, and gene copy number. Advances in methodology, including multiplex and universal primer applications, have reduced assay cost and improved throughput. This chapter briefly reviews some of the many applications for Pyrosequencing technology.
Metal–organic container molecules through subcomponent self-assembly (2012)

A variety of different three-dimensional metal-organic container molecules have recently been prepared using subcomponent self-assembly, which relies upon metal template effects to generate complex structures from simple molecular precursors and metal salts. Many of these structures have well defined internal pockets, allowing guest species to be bound and the chemical reactivity of these guests to be modified. Such host molecules have potential applications ranging from the protection of sensitive chemical species to the separation and purification of substrates as diverse as gases, gold compounds, and fullerenes.
Studies of a novel human thrombomodulin immobilized substrate: surface characterization and anticoagulation activity evaluation (2001)

Immobilization of the anticoagulative or antithrombogenic biomolecule has been considered as one of the important methods to improve the blood compatibility of artificial biomaterials. In this study, a novel immobilization reaction scheme was utilized to incorporate the human thrombomodulin, an endothelial cell associated glycoprotein, onto the cover glass surface with an aim to develop an anticoagulative substrate. Trichlorotriazine and amino-terminated silane were employed as the coupling agents, while the polyethylene glycol with a molecular weight of 1500 was used as the spacer in this reaction scheme. Protein C activation assay indicated the immobilized human thrombomodulin still has this coenzymatic activity but is lower, possibly due to the conformation variation by the coupling agents. In vitro platelet adhesion assay has demonstrated the surface with immobilized human thrombomodulin is much less platelet-activating than others. Therefore, the novel reaction scheme proposed here is very promising for future development of an anticoagulative silicon or cover glass substrate (e.g. implantable sensor or biochip) by the immobilization of antithrombogenic protein, such as the human thrombomodulin in this study.