gebhart/patrepeval huggingface dataset:
Tethering human immunodeficiency virus 1 integrase to a DNA site directs integration to nearby sequences. (1994)

Certain retrovirus and retrotransposons display strong biases in the selection of host DNA sites for integration. To probe the possibility that simple tethering of the retroelement integrase protein to a target DNA site is sufficient to direct integration, the activities of a hybrid composed of human immunodeficiency virus 1 integrase and lambda repressor were analyzed. In in vitro reactions containing several target DNAs, the lambda repressor-integrase hybrid was found to direct integration selectively to targets containing lambda operators. Addition of lambda repressor blocked selective integration, indicating that binding to the operators was required. The lambda repressor-integrase hybrid protein directed integration primarily to sites near the operators on the same face of the B-DNA helix, indicating that target DNA was probably captured by looping out the intervening sequences. Such hybrid integrase proteins may be useful for directing retroviral integration to specific sequences in vivo.
BCL‐2 family proteins: Regulators of cell death involved in the pathogenesis of cancer and resistance to therapy (1996)

The BCL-2 gene was first discovered because of its involvement in the t(14;18) chromosomal translocations commonly found in lymphomas, which result in deregulation of BCL-2 gene expression and cause inappropriately high levels of Bcl-2 protein production. Expression of the BCL-2 gene can also become altered in human cancers through other mechanisms, including loss of the p53 tumor suppressor which normally functions as a repressor of BCL-2 gene expression in some tissues. Bcl-2 is a blocker of programmed cell death and apoptosis that contributes to neoplastic cell expansion by preventing cell turnover caused by physiological cell death mechanisms, as opposed to accelerating rates of cell division. Overproduction of the Bcl-2 protein also prevents cell death induced by nearly all cytotoxic anticancer drugs and radiation, thus contributing to treatment failures in patients with some types of cancer. Several homologs of Bcl-2 have recently been discovered, some of which function as inhibitors of cell death and others as promoters of apoptosis that oppose the actions of the Bcl-2 protein. Many of these Bcl-2 family proteins can interact through formation of homo- and heterotypic dimers. In addition, several nonhomologous proteins have been identified that bind to Bcl-2 and that can modulate apoptosis. These protein-protein interactions may eventual serve as targets for pharmacologically manipulating the physiological cell death pathway for treatment of cancer and several other diseases. © 1996 Wiley-Liss, Inc.
Retinosomes (2004)

Lipid bodies form autonomous intracellular structures in many model cells and in some cells of specific tissue origin. They contain hydrophobic substances, a set of structural proteins such as perilipin or adipose differentiation-related protein, enzymes implicated in lipid metabolism, and proteins that participate in signaling and membrane trafficking. Retinosomes, particles reminiscent of lipid bodies, have been identified in retinal pigment epithelium as distinct structures compartmentalizing a metabolic intermediate involved in regeneration of the visual chromophore. These observations suggest that lipid bodies, including retinosomes, carry out specific functions that go beyond those of mere lipid storage organelles.
Activation of the proto-oncogene p60c-src by point mutations in the SH2 domain. (1990)

To investigate the importance of a conserved region spanning residues 137 to 241 in the noncatalytic domain of p60c-src (SH2 region), we used oligonucleotide-directed mutagenesis to change residues that are highly conserved in this region. Chicken embryo fibroblasts infected with a p60c-src variant containing arginine instead of tryptophan at residue 148 (W148R) appeared more rounded than cells overexpressing a normal c-src gene, and they formed colonies in soft agar. p60c-src variants containing serine instead of arginine at residue 155 (R155S) or isoleucine instead of glycine at residue 170 (G170I) also appeared transformed and were anchorage independent, but to a lesser extent than W148R. Mutation of residue 201 from histidine to leucine (H201L) had no observable effect. The in vitro kinase activity of cells infected with W148R or G170I was elevated twofold. Expression of p60W148R (or, to a lesser extent, of p60G170I) increased the number of proteins phosphorylated on tyrosine in infected cells. All of the mutants were phosphorylated in vivo on Tyr-527, instead of Tyr-416 as observed for p60v-src. Immunoprecipitated p60W148R and p60G170I were found to be associated with a phosphatidylinositol kinase activity, a factor which appears to be necessary for transformation by tyrosine-specific protein kinases. These results show that a single point mutation in the SH2 region of the cellular src gene can activate its transforming potential. This type of activation is in a new category of alterations at the amino terminus that activate but do not cause a shift in phosphorylation at the carboxy terminus.
Evaluation of the Protein Quality of Soya and Wheat Based Supplementary Food Mixes on Albino Rats (1993)

The challenge in the prevention of PEM is to ensure that preschool children get their habitual cereal legume vegetable, foods in amounts adequate to meet their calorie and protein needs. There is a need for developing weaning foods that would at least combine some of the desired characteristics of high nutrient density, low bulk property, low cost and locally available in nature. There are a number of reports available on protein supplements of high nutritive value prepared by suitable blending of two or more vegetable proteins.
Force Balance and Membrane Shedding at the Red-Blood-Cell Surface (2007)

During the aging of the red-blood cell, or under conditions of extreme echinocytosis, membrane is shed from the cell plasma membrane in the form of nanovesicles. We propose that this process is the result of the self-adaptation of the membrane surface area to the elastic stress imposed by the spectrin cytoskeleton, via the local buckling of membrane under increasing cytoskeleton stiffness. This model introduces the concept of force balance as a regulatory process at the cell membrane and quantitatively reproduces the rate of area loss in aging red-blood cells.
Cyclization-activated prodrugs. Basic esters of 5-bromo-2'-deoxyuridine (1990)

Some 3'- and 5'-[[(alkylamino)ethyl]glycyl] esters of 5-bromo-2'-deoxyuridine were prepared and evaluated in vitro as progenitors of the parent alcohol. The esters proved to be relatively stable at low pH but released 5-bromo-2'-deoxyuridine cleanly at rates which were pH and structure dependent. These basic esters are examples of cyclization-activated prodrugs in which generation of active drug is not linked to enzymatic cleavage but rather results from an intramolecular cyclization-elimination reaction.
Degradation of Myoglobin by Polymeric Artificial Metalloproteases Containing Catalytic Modules with Various Catalytic Group Densities:  Site Selectivity in Peptide Bond Cleavage (2003)

Mononuclear, dinuclear, and tetranuclear artificial metalloproteases were prepared by attaching respective catalytic modules containing the Cu(II) complex of cyclen (Cu(II)Cyc) to a derivative of cross-linked polystyrene. The polymeric artificial metalloproteases effectively cleaved peptide bonds of myoglobin (Mb) by hydrolysis. The proteolytic activity increased considerably as the catalytic group density was raised: the ratio of k(cat)/K(m) was 1:13:100 for the mono-, di-, and tetranuclear catalysts. In the degradation of Mb by the dinuclear catalyst, two pairs of intermediate proteins accumulated. One of the two initial cleavage sites leading to the formation of the protein fragments is identified as Gln(91)-Ser(92) and the other is suggested as Ala(94)-Thr(95). On the basis of a molecular modeling study by using the X-ray crystallographic structure of Mb, the site-selectivity is attributed to anchorage of one Cu(II)Cyc unit of the catalytic module to a heme carboxylate of Mb. The high site selectivity for the initial cleavage of a protein substrate and mechanistic analysis of the catalytic action are unprecedented for polymeric artificial enzymes.
Full deacylation of polyethylenimine dramatically boosts its gene delivery efficiency and specificity to mouse lung (2005)

High-molecular-mass polyethylenimines (PEIs) are widely used vectors for nucleic acid delivery. We found that removal of the residual N-acyl moieties from commercial linear 25-kDa PEI enhanced its plasmid DNA delivery efficiency 21 times in vitro, as well as 10,000 times in mice with a concomitant 1,500-fold enhancement in lung specificity. Several additional linear PEIs were synthesized by acid-catalyzed hydrolysis of poly(2-ethyl-2-oxazoline), yielding the pure polycations. PEI87 and PEI217 exhibited the highest efficiency in vitro: 115-fold and 6-fold above those of the commercial and deacylated PEI25s, respectively; moreover, PEI87 delivered DNA to mouse lung as efficiently as the pure PEI25 but at a lower concentration and with a 200-fold lung specificity. These improvements stem from an increase in the number of protonatable nitrogens, which presumably results in a tighter condensation of plasmid DNA and a better endosomal escape of the PEI/DNA complexes. As a validation of the potential of such linear, fully deacylated PEIs in gene therapy for lung diseases, systemic delivery in mice of the complexes of a short interfering RNA (siRNA) against a model gene, firefly luciferase, and PEI25 or PEI87 afforded a 77% and 93% suppression of the gene expression in the lungs, respectively. Furthermore, a polyplex of a siRNA against the influenza viral nucleocapsid protein gene and PEI87 resulted in a 94% drop of virus titers in the lungs of influenza-infected animals.
Asymmetrical Fc Engineering Greatly Enhances Antibody-dependent Cellular Cytotoxicity (ADCC) Effector Function and Stability of the Modified Antibodies (2013)

Antibody-dependent cellular cytotoxicity (ADCC) is mediated through the engagement of the Fc segment of antibodies with Fcγ receptors (FcγRs) on immune cells upon binding of tumor or viral antigen. The co-crystal structure of FcγRIII in complex with Fc revealed that Fc binds to FcγRIII asymmetrically with two Fc chains contacting separate regions of the FcγRIII by utilizing different residues. To fully explore this asymmetrical nature of the Fc-FcγR interaction, we screened more than 9,000 individual clones in Fc heterodimer format in which different mutations were introduced at the same position of two Fc chains using a high throughput competition AlphaLISA® assay. To this end, we have identified a panel of novel Fc variants with significant binding improvement to FcγRIIIA (both Phe-158 and Val-158 allotypes), increased ADCC activity in vitro, and strong tumor growth inhibition in mice xenograft human tumor models. Compared with previously identified Fc variants in conventional IgG format, Fc heterodimers with asymmetrical mutations can achieve similar or superior potency in ADCC-mediated tumor cell killing and demonstrate improved stability in the CH2 domain. Fc heterodimers also allow more selectivity toward activating FcγRIIA than inhibitory FcγRIIB. Afucosylation of Fc variants further increases the affinity of Fc to FcγRIIIA, leading to much higher ADCC activity. The discovery of these Fc variants will potentially open up new opportunities of building the next generation of therapeutic antibodies with enhanced ADCC effector function for the treatment of cancers and infectious diseases.
Bacteriuria in the Catheterized Patient (1984)

We studied 110 catheterized patients to determine the concentration of microorganisms that would indicate infection in urine aspirated from an indwelling urethral catheter. High-level bacteriuria or candiduria (greater than 10(5) colony-forming units per milliliter) developed in 34 patients. However, low-level bacteriuria or candiduria (less than 10(5) organisms per milliliter), which developed in 41 patients, progressed to concentrations above 10(5) organisms per milliliter 96 per cent of the time (P less than 0.001), usually within three days of the initial culture showing growth, unless the patient received intercurrent suppressive antimicrobial therapy. We conclude that the urinary tract of catheterized patients is highly susceptible to infection once small numbers of microorganisms gain access and that a concentration considerably below 10(5) organisms per milliliter may be clinically and epidemiologically important in this setting.
Editorial: CSF1R, CSF-1, and IL-34, a “ménage à trois” conserved across vertebrates (2010)

Abstract Editorial discusses the perspectives opened by the recently discovered IL-34, its conservation across species in the biology of the cytokine CSF-1, and identification of a new CSF-1R ligand that could together account for the well-known heterogeneity of monocytes.
Surface fatigue crack identification in steel box girder of bridges by a deep fusion convolutional neural network based on consumer-grade camera images (2018)

This study conducts crack identification from real-world images containing complicated disturbance information (cracks, handwriting scripts, and background) inside steel box girders of bridges. Considering the multilevel and multi-scale features of the input images, a modified fusion convolutional neural network architecture is proposed. As input, 350 raw images are taken with a consumer-grade camera and divided into sub-images with resolution of 64 × 64 pixels (67,200 in total). A regular convolutional neural network structure is employed as baseline to demonstrate the accuracy benefits from the proposed fusion convolutional neural network structure. The confusion matrix is defined for prediction performance evaluation on the test set. A total of six additional entire raw images are used to investigate the robustness and feasibility of the proposed approach. A binary conversion process based on the optimal entropy threshold method is applied and closely followed to identify the crack pixels in the sub-images. The effect of the super-resolution inputs on accuracy is investigated. Results show that the trained modified fusion convolutional neural network can automatically detect the cracks, handwriting, and background from the raw images. The recognition errors of the fusion convolutional neural network in both the training and validation processes are smaller than those of the regular convolutional neural network. The super-resolution process hurts the general identification accuracy.
Studies of Polymerization and Ring Formation. XIX.1 Many-Membered Cyclic Anhydrides (1933)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies of Polymerization and Ring Formation. XIX.1 Many-Membered Cyclic AnhydridesJulian W. Hill and Wallace H. CarothersCite this: J. Am. Chem. Soc. 1933, 55, 12, 5023–5031Publication Date (Print):December 1, 1933Publication History Published online1 May 2002Published inissue 1 December 1933https://pubs.acs.org/doi/10.1021/ja01339a054https://doi.org/10.1021/ja01339a054research-articleACS PublicationsRequest reuse permissionsArticle Views405Altmetric-Citations56LEARN 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
Current strategies towards hemocompatible coatings (2007)

A wide range of biomedical devices is applied clinically in contact with blood. Tailoring the surface properties of the involved biomaterials is a common approach to enhance performance and to limit adverse reactions. This review summarizes current trends in coating technologies developed for that purpose. Inorganic coatings were shown to substantially improve the durability and inertness of biomaterials while a number of advanced polymer coatings were demonstrated to be very effective by targeting specific biochemical pathways. However, to fully utilize the power of these bioactive coatings safety issues need to be thoroughly addressed in future studies.
CHEMILUMINESCENCE INVOLVING PEROXIDE DECOMPOSITIONS (1965)

Abstract— It is a reasonable assumption that many of the known cherniluminescent organic compounds react to give a carbonyl group in an excited state. By extension of this hypothesis we were led to test several substituted acridinium salts. Oxidation of these with hydrogen peroxide in the presence of base resulted in the formation of N‐methylacridone in high yield, and the emission of light from an excited state of this ketone. Mechanisms for this process are discussed. Interest in indole derivatives aroused by the finding of a tryptamine residue in the luminescent cypridina luciferin, in conjunction with the hypothesis mentioned above, has led to an investigation of some indoles, and in particular, the important isolable peroxide of tetrahydrocarbazole. A preliminary account of this work is given.
Botulinum Neurotoxin Type A in the Preventive Treatment of Refractory Headache: A Review of 100 Consecutive Cases (2004)

BoNT-A may play a role in the preventive treatment of refractory headache. A significant number of patients showed decrease in clinically important measurements of their headaches as well as reduced headache-related disability with this treatment. Prospective, controlled studies must be considered for severely disabled, refractory patients.
Intercoder Agreement in Analysis of Responses to Open-Ended Interview Questions: Examples from Tuberculosis Research (1996)

Social scientists commonly conduct surveys to learn about beliefs, attitudes, reported behaviors, or experiences prevalent in a population. These interviews often involve the use of structured questions with closed-ended responses (e.g., true/false, agree/disagree, or multiple choice). Open-ended questions can also yield useful information, especially when researchers need to explore complex issues that do not have a finite or predetermined set of responses.
Steric activation of chelate catalysts: efficient polyketone catalysts based on four-membered palladium(ii) diphosphine chelates (2001)

Palladium(II) complexes of ligands of the type Ar2PCH2- PAr2 and Ar2PN(Me)PAr2 (Ar = ortho-substituted phenyl group) are very efficient catalysts for copolymerisation of CO and C2H4.
Phosphorylation of Ser-241 is essential for the activity of 3-phosphoinositide-dependent protein kinase-1: identification of five sites of phosphorylation in vivo (1999)

3-phosphoinositide-dependent protein kinase-1 (PDK1) expressed in unstimulated 293 cells was phosphorylated at Ser-25, Ser-241, Ser-393, Ser-396 and Ser-410 and the level of phosphorylation of each site was unaffected by stimulation with insulin-like growth factor-1. Mutation of Ser-241 to Ala abolished PDK1 activity, whereas mutation of the other phosphorylation sites individually to Ala did not affect PDK1 activity. Ser-241, unlike the other phosphorylation sites on PDK1, was resistant to dephosphorylation by protein phosphatase 2A(1). Ser-241 lies in the activation loop of the PDK1 kinase domain between subdomains VII and VIII in the equivalent position to the site that PDK1 phosphorylates on its protein kinase substrates. PDK1 expressed in bacteria was active and phosphorylated at Ser-241, suggesting that PDK1 can phosphorylate itself at this site, leading to its own activation.
A novel dual specificity phosphatase induced by serum stimulation and heat shock. (1994)

To identify new members of a family of protein-tyrosine phosphatases (PTPs), of which VH1 is prototype, we screened a B5/589 human mammary epithelial cell cDNA library by low stringency hybridization with probes for the catalytic domains of the human VHR and mouse 3CH134 phosphatases. Two overlapping clones of 1.8 and 2.5 kilobase pairs were detected by 3CH134 but not VHR probes. Sequence analysis of the largest clone, B23, revealed a 2470-nucleotide open reading frame encoding a novel protein. Within the 397 amino acid sequence, the HCXAGXXR signature sequence for PTPs was located at positions 261-268. The closest similarities were to 3CH134, its human homolog CL100, and PAC-1, PTPs induced as early response genes to mitogen stimulation. Less relatedness was observed with VHR and VH1 dual specificity phosphatases of human and vaccinia virus, respectively. A bacterially expressed recombinant protein containing the catalytic domain of B23 showed significant but consistently lower activity than VHR in vitro. Among the substrates tested, B23 displayed the highest relative activity toward phosphorylated extracellular signal regulated kinase-1, suggesting that it may be a target for B23 activity in vivo. The B23 transcript was detected in a wide variety of normal human tissues, with relatively high expression in pancreas and brain. B23 was induced by serum stimulation of human fibroblasts as well as by heat shock with similar kinetics to those observed with CL100. Thus, B23 is a new human protein phosphatase which appears to be regulated in response to mitogenic signaling and at least some forms of stress.
ZntB Is a Novel Zn 2+ Transporter in Salmonella enterica Serovar Typhimurium (2002)

A Zn2+ transport system encoded by the zntB locus of Salmonella enterica serovar Typhimurium has been identified. The protein encoded by this locus is homologous to the CorA family of Mg2+ transport proteins and is widely distributed among the eubacteria. Mutations at zntB confer an increased sensitivity to the cytotoxic effects of Zn2+ and Cd2+, a phenotype that suggests that the encoded protein mediates the efflux of both cations. A direct analysis of transport activity identified a capacity for Zn2+ efflux. These data identify ZntB as a zinc efflux pathway in the enteric bacteria and assign a new function to the CorA family of cation transporters.
Vaccinia virus in postvaccinal encephalitis. (1983)

Results of virological examination of 239 samples taken from 84 children with neurological complications after smallpox vaccination are described. In postvaccinal encephalitis, vaccinia virus was isolated from blood, cerebrospinal fluid and pharyngeal secretions of 23 out of 40 children (57.5%) as well as from autopsy specimens sampled between 10-35 days after vaccination. During the acute period of disease, virus was detected in 17 out of 31 (54.2%) cerebrospinal fluid specimens. In 3 postvaccinal encephalitis cases the virus was present in brain and in a case of encephalomyelitis--in the spinal cord. These results confirmed the participation of vaccinia virus in the pathogenesis of postvaccinal encephalitis. The pathogenicity of vaccinia virus may be manifested only under a changed reactivity of the vaccinated host.