gebhart/patrepeval huggingface dataset:
Engineering a nicking endonuclease N. Alw I by domain swapping (2001)

Changing enzymatic function through genetic engineering still presents a challenge to molecular biologists. Here we present an example in which changing the oligomerization state of an enzyme changes its function. Type IIs restriction endonucleases such as AlwI usually fold into two separate domains: a DNA-binding domain and a catalytic/dimerization domain. We have swapped the putative dimerization domain of AlwI with a nonfunctional dimerization domain from a nicking enzyme, N.BstNBI. The resulting chimeric enzyme, N.AlwI, no longer forms a dimer. Interestingly, the monomeric N.AlwI still recognizes the same sequence as AlwI but only cleaves the DNA strand containing the sequence 5'-GGATC-3' (top strand). In contrast, the wild-type AlwI exists as a dimer in solution and cleaves two DNA strands; the top strand is cleaved by an enzyme binding to that sequence, and its complementary bottom strand is cleaved by the second enzyme dimerized with the first enzyme. N.AlwI is unable to form a dimer and therefore nicks DNA as a monomer. In addition, the engineered nicking enzyme is at least as active as the wild-type AlwI and is thus a useful enzyme. To our knowledge, this is the first report of creating a nicking enzyme by domain swapping.
Tyrosine phosphorylation and dissociation of occludin–ZO-1 and E-cadherin–β-catenin complexes from the cytoskeleton by oxidative stress (2002)

The oxidative-stress-induced alteration in paracellular junctional complexes was analysed in Caco-2 cell monolayer. Oxidative stress induced a rapid increase in tyrosine phosphorylation of occludin, zonula occludens (ZO)-1, E-cadherin and beta-catenin. An oxidative-stress-induced decrease in transepithelial electrical resistance was associated with a redistribution of occludin-ZO-1 and E-cadherin-beta-catenin complexes from the intercellular junctions. Genistein, a tyrosine kinase inhibitor, prevented the oxidative-stress-induced decrease in resistance and redistribution of protein complexes. Occludin, ZO-1, E-cadherin and beta-catenin in the Triton-insoluble cytoskeletal fraction were reduced by oxidative stress, which was prevented by genistein. Oxidative stress also reduced the co-immunoprecipitation of ZO-1 with occludin, which was prevented by genistein. Co-immunoprecipitation of beta-catenin with E-cadherin was unaffected by oxidative stress or genistein. ZO-1, E-cadherin and beta-catenin in the plasma membrane or membrane-cytoskeleton were either slightly reduced or unaffected by oxidative stress or genistein. These results show that oxidative stress induces tyrosine phosphorylation and cellular redistribution of occludin-ZO-1 and E-cadherin-beta-catenin complexes by a tyrosine-kinase-dependent mechanism.
Current Concepts in Lactate Exchange (1991)

There are several goals to this introductory paper in the symposium proceedings, “Current Concepts in Lactate Exchange.” First, an attempt is made to set the historical context for the symposium and foreshadow how the paper of each participant contributes to our contemporary understanding of the field. As implied in the symposium title, an emphasis will be placed on the exchange of lactate for other metabolites and ions so that utilization can be temporally and spatially disassociated from formation. Thus, rather than a dead-end metabolite, which only accumulates during exercise, there appears to be great usefulness in the formation, exchange between cells, blood and organs, and utilization of lactic acid (lactate). Specific papers will deal with aspects of lactate release and uptake by skeletal muscle, hepatic lactate balance, the flux of dietary carbohydrate through various lactate pools in the synthesis of liver glycogen, lactate metabolism in the heart, properties of the sarcolemmal lactate transporter, and evolution of a model to predict lactate production from blood measurements. Second, in this review an attempt will be made to present and support a unifying hypothesis (the “lactate shuttle”) in which the various aspects of lactate exchange may be integrated and understood. Emphasis will be placed on showing several corollaries between muscle and whole-body lactate metabolism. These are: temporal dependence on lactate uptake and release, the effects of beta-adrenergic stimulation on lactate formation and release, the effect of prior endurance training on lactate metabolism, the effect of lactate on glucose uptake and utilization, and the role of low oxygen tension (hypoxia) in loosening the control of glycolysis. The formation, exchange, and utilization of lactate represents a central means by which the coordination of intermediary metabolism in diverse tissues and different cells within tissues can be accomplished.
Immunoinformatics and the prediction of immunogenicity. (2002)

Immunoinformatics is the application of informatics techniques to molecules of the immune system. One of the key goals of immunoinformatics is the development of computer aided vaccine design (CAVD), or computational vaccinology, and its application to the search for new vaccines. Key to solving this challenge is the prediction of immunogenicity, be that at the level of epitope, subunit vaccine or attenuated pathogen. This paper reviews the current state of play in the prediction of immunogenicity and focuses on well developed methods for the prediction of peptide binding affinity to major histocompatibility complexes, which are the necessary preliminary to the in silico identification of T cell epitopes.
Evaluation of (S)-Verbenone Applications for Suppressing Southern Pine Beetle (Coleoptera: Scolytidae) Infestations (1989)

Field tests were conducted to evaluate the efficacy of various applications of the beetle-produced, inhibitory compound (S)-verbenone for suppressing infestations of the southern pine beetle, Dendroctonus frontalis Zimmermann. Twenty-four expanding infestations (spots), ranging in size from 22 to 140 active trees, and representing a variety of stand conditions, were treated with one of five different applications. Treatments included: (A) (S)-verbenone applied at the rate of 4 ml per tree, (B) (S)-verbenone applied at 8 ml per tree, (C) (S)-verbenone at 8 ml per tree in combination with felling all freshly-attacked trees, and the preliminary treatments; (D) (S)-verbenone in combination with the attractant frontalin, and (E) (S)-verbenone plus frontalin, plus felling all infested trees. In all treatments, (S)-verbenone was mixed with a sustained release liquid polymer and applied to a horseshoeshaped buffer of uninfested trees at the advancing head of the infestation. To draw emerging beetles away from the advancing head, in Treatments D and E, frontalin, a beetle-produced attractant, was applied in the center of the infestation to nonhost trees or to host trees previously infested by beetles. To measure treatment efficacy, rates of spot growth following treatment were compared with pretreatment infestation growth rates. Observed rates of spot growth before and after treatment were compared with spot growth projections generated by a southern pine beetle spot growth prediction model. Results showed that Treatment C was the most effective and practical treatment tested. Spot growth in all five infestations treated with this application was completely halted with few or no additional trees being attacked. Treatment B proved relatively effective in slowing rates of spot growth in small or moderate-sized spots. Treatment E was effective in completely halting spot growth in two large infestations in sawtimber stands, but the treatment required the use of two behavioral chemicals. Treatments A and D were less successful in disrupting spot growth than the other treatments.
Identification and cellular localization of unique interferon mRNA from human placenta. (1994)

Although constitutive expression of trophoblast or pregnancy-associated interferon (IFN) has long been recognized, their cDNA sequences have been determined for only ruminant ungulates. Here we show a human trophoblast IFN (htIFN) cDNA whose nucleotide sequence is very similar (85% identity) to that of ovine and bovine trophoblast IFNs, IFN tau s. Like ruminant IFN tau s, htIFN cDNAs contain an open reading frame of 195 codons including a signal sequence of 23 amino acids, resulting in a mature polypeptide of 172 amino acids. The deduced amino acid sequence of htIFN shares 73, 62, and 56% identities with ovine IFN tau, human IFN alpha II, and human IFN alpha I, respectively. However, the expression of htIFN is not limited to a specific period of pregnancy because transcripts of htIFN genes are detected in human lymphocytes, cells obtained by amniocentesis (amniocytes), first trimester, and term placentas. Human trophoblast IFN mRNA is localized mainly in extravillous trophoblasts cells of placental villi, particularly in the migrating cytotrophoblasts cells, which eventually replace maternal endothelial cells in spiral arteries of the decidua. Both sense and antisense mRNAs for human IFN alpha II are localized in the outer layer of villous structures. Coexistence of these mRNAs at the placental villi throughout pregnancy suggests that, in addition to a role in placental cell growth and differentiation, IFNs may play a role protecting the fetus in viral environments.
Selective Precipitation of Large RNAs (2012)

For reasons that are somewhat mysterious, "large" RNAs ≥100 nucleotides long can be selectively separated from small RNAs <100 nucleotides long by precipitation with either LiCl or PEG/NaCl. These methods are very straightforward, and are valuable for enriching for very small RNAs (i.e., miRNAs) in unprecipitated material while retaining all other RNAs in the precipitate.
Optimizing the affinity and specificity of proteins with molecular display (2005)

Affinity maturation of receptor-ligand interactions represents an important area of academic and pharmaceutical research. Improving affinity and specificity of proteins can tailor potency for both in vivo and in vitro applications. A number of different display platforms including phage display, bacterial and yeast display, ribosome display, and mRNA display can optimize protein affinity and specificity. Here, we will review the advantages and disadvantages of these molecular display methods with a focus on their suitability for protein affinity maturation.
Optimized TAL effector nucleases (TALENs) for use in treatment of sickle cell disease (2012)

TAL effector nucleases (TALENs) represent a new class of artificial nucleases capable of cleaving long, specific target DNA sequences in vivo and are powerful tools for genome editing with potential therapeutic applications. Here we report a pair of custom-designed TALENs for targeted genetic correction of the sickle cell disease mutation in human cells, which represents an example of engineered TALENs capable of recognizing and cleaving a human disease-associated gene. By using a yeast reporter system, a systematic study was carried out to optimize TALEN architecture for maximal in vivo cleavage efficiency. In contrast to the previous reports, the engineered TALENs were capable of recognizing and cleaving target binding sites preceded by A, C or G. More importantly, the optimized TALENs efficiently cleaved a target sequence within the human β-globin (HBB) gene associated with sickle cell disease and increased the efficiency of targeted gene repair by >1000-fold in human cells. In addition, these TALENs showed no detectable cytotoxicity. These results demonstrate the potential of optimized TALENs as a powerful genome editing tool for therapeutic applications.
Organic reactions in aqueous media (1998)

Pericyclic Reactions. Nucleophilic Additions and Substitutions. Metal-- Mediated Reactions. Transition--Metal--Catalyzed Reactions. Oxidations and Reductions. Industrial Applications. Index.
The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository (2013)

The National Institutes of Health have placed significant emphasis on sharing of research data to support secondary research. Investigators have been encouraged to publish their clinical and imaging data as part of fulfilling their grant obligations. Realizing it was not sufficient to merely ask investigators to publish their collection of imaging and clinical data, the National Cancer Institute (NCI) created the open source National Biomedical Image Archive software package as a mechanism for centralized hosting of cancer related imaging. NCI has contracted with Washington University in Saint Louis to create The Cancer Imaging Archive (TCIA)-an open-source, open-access information resource to support research, development, and educational initiatives utilizing advanced medical imaging of cancer. In its first year of operation, TCIA accumulated 23 collections (3.3 million images). Operating and maintaining a high-availability image archive is a complex challenge involving varied archive-specific resources and driven by the needs of both image submitters and image consumers. Quality archives of any type (traditional library, PubMed, refereed journals) require management and customer service. This paper describes the management tasks and user support model for TCIA.
A Multi-Level and Multi-Band Class-D CMOS Power Amplifier for the LINC System in the Cognitive Radio Application (2010)

In this letter, a multi-level and multi-band Class-D CMOS power amplifier (PA) in a standard 0.18 ¿m CMOS process is presented. Using multiple PMOS devices with control switches, the proposed PA improves efficiency with the multi-level operation. In order to enable the multi-band operation, the proposed PA employs a tunable series resonator. The measured maximum drain efficiencies were 72% and 70% for the low power mode and high power mode, respectively. The 3 dB bandwidth of the proposed system was from 450 MHz to 730 MHz, which covers the cognitive radio white spectrum standard. The measured EVM using a commercial 16QAM OFDM signal was -34 dB with a LINC system.
Nurturing curiosity and creativity through mathematical exploration (2013)

Investigations afford a wonderful opportunity for learners to explore a diverse array of mathematical ideas in a meaningful and engaging manner. Not only do investigations often lead to unexpected or serendipitous moments of mathematical discovery, but they also provide an opportunity to nurture curiosity and creativity, both of which are important components of a healthy mathematical disposition.
The investigation discussed in this article was presented to a group of secondary school teachers in the context of a teacher enrichment workshop. Teachers worked in groups of three or four and were tasked with generating as many different solutions as they could to the posed problem. The number and variety of solution strategies arising from what at first seemed like a simple starting point surprised many of the participants. In this article I synthesize the different solution methods that were generated in the workshop along with one or two additional solutions.
Algorithm for image reconstruction in multi-slice helical CT (1998)

Efforts are being made to develop a new type of CT system that can scan volumes over a large range within a short time with thin slice images. One of the most promising approaches is the combination of helical scanning with multi-slice CT, which involves several detector arrays stacked in the z direction. However, the algorithm for image reconstruction remains one of the biggest problems in multi-slice CT. Two helical interpolation methods for single-slice CT, 360LI and 180LI, were used a starting points and extended to multi-slice CT. The extended methods, however, had a serious image quality problem due to the following three reasons: (1) excessively close slice positions of the complementary and direct data, resulting in a larger sampling interval; (2) the existence of several discontinuous changeovers in pairs of data samples for interpolation; and (3) the existence of cone angles. Therefore we have proposed a new algorithm to overcome the problem. It consists of the following three parts: (1) optimized sampling scan; (2) filter interpolation; and (3) fan-beam reconstruction. Optimized sampling scan refers to a special type of multi-slice helical scan developed to shift the slice position of complementary data and to acquire data with a much smaller sampling interval in the z direction. Filter interpolation refers to a filtering process performed in the z direction using several data. The normal fan-beam reconstruction technique is used. The section sensitivity profile (SSP) and image quality for four-array multi-slice CT were investigated by computer simulations. Combinations of three types of optimized sampling scan and various filter widths were used. The algorithm enables us to achieve acceptable image quality and spatial resolution at a scanning speed that is about three times faster than that for single-slice CT. The noise characteristics show that the proposed algorithm efficiently utilizes the data collected with optimized sampling scan. The new algorithm allows suitable combinations of scan and filter parameters to be selected to meet the purpose of each examination.
Prevalence of Symptomatic Androgen Deficiency in Men (2007)

Prevalence of symptomatic androgen deficiency in men 30 and 79 yr of age is 5.6% and increases substantially with age. The aging of the U.S. male population will cause a large increase in the burden of symptomatic androgen deficiency. Future work should address the clinical significance of low testosterone levels in asymptomatic men.
The participation of the sympathetic innervation of the gastrointestinal tract in disease states (2009)

Knowledge of neural circuits, neurotransmitters and receptors involved in the sympathetic regulation of gastrointestinal (GI) function is well established. However, it is only recently that the interaction of sympathetic neurons, and of sympathetic transmitters, with the GI immune system and with gut flora has begun to be explored. Changes in the behaviour of sympathetic nerves when gut function is compromised, for example in ileus and in inflammation, have been observed, but the roles of the sympathetic innervation in these and other pathologies are not adequately understood. In this article, we first review the principal roles of the sympathetic innervation of the GI tract in controlling motility, fluid exchange and gut blood flow in healthy individuals. We then discuss the evidence that there are important interactions of sympathetic transmitters with the gut immune system and enteric glia, and evidence that inflammation has substantial effects on sympathetic neurons. These reciprocal interactions contribute to pathological changes in ways that are not yet clarified. Finally, we focus on inflammation, diabetes and postoperative ileus as conditions in which there is sympathetic involvement in compromised gut function.
The elastic constants of the human lens (1971)

1. When the lens is spun around its antero-posterior polar axis in an apparatus designed for the purpose, high speed photography can be used to record its changing profile. By this method a variable radial centrifugal force can be applied to the lens which mimics the pull of the zonule.2. If the lens is not stressed at its centre beyond 100 Nm(-2) it behaves as a truly elastic body. When stressed beyond this limit visco-elastic strain is produced at its poles.3. The human lens has isotropic elastic properties at the extremes of life, but at the other times Young's Modulus of Elasticity varies with the direction in which it is measured.4. Young's Modulus of Elasticity of the lens varies with age, polar elasticity and equatorial elasticity, at birth being 0.75 x 10(3) and 0.85 x 10(3) Nm(-2) respectively, while at 63 years of age both are equal to 3 x 10(3) Nm(-2).5. A comparison of Young's Modulus of the young human lens with that of the rabbit and cat shows that the polar elasticity of the lenses of these animals was 5 times greater in the young rabbit, and 21 times greater in the adult cat. Equatorial elasticities of the rabbit and human lens were equal, while in the cat the equatorial elasticity was four times greater.6. A mathematical model showing the lens substance possessing a nucleus of lower isotropic elasticity than that of the isotropic elastic cortex surrounding it, accounts for the difference between polar and equatorial elasticity of the intact adult lens.7. The implications of these findings are discussed in relation to:(i) accommodation and the rheological properties of the lens;(ii) possible differences in the physical state of the lenticular proteins in the cortex and nucleus which may account for the senile variations in Young's Modulus of Elasticity in these regions of the lens;(iii) the loss of accommodation due solely to an increase in Young's Modulus of Elasticity of the lens between the ages of 15 and 60. This would amount to 44% of the total observed in vivo.
The Arabidopsis AHK4 Histidine Kinase is a Cytokinin-Binding Receptor that Transduces Cytokinin Signals Across the Membrane (2001)

Common histidine-to-aspartate (His-->Asp) phosphorelay is a paradigm of signal transduction in both prokaryotes and eukaryotes for the propagation of certain environmental stimuli, in which histidine (His)-kinases play central roles as sensors for environmental signals. For the higher plant, Arabidopsis thaliana, it was recently suggested that the His-kinase (AHK4 / CRE1 / WOL) is a sensor for cytokinins, which are a class of plant hormones important for the regulation of cell division and differentiation. Interestingly, AHK4 is capable of functioning as a cytokinin sensor in the eubacterium, Escherichia coli (Suzuki et al. 2001, Plant Cell Physiol. 42: 107). Here we further show that AHK4 is a primary receptor that directly binds a variety of natural and synthetic cytokinins (e.g. not only N(6)-substituted aminopurines such as isopentenyl-adenine, trans-zeatin, benzyl-adenine, but also diphenylurea derivatives such as thidiazuron), in a highly specific manner (K(d) = 4.55+/-0.48x10(-9) M). AHK4 has a presumed extracellular domain, within which a single amino acid substitution (Thr-301 to Ile) was shown to result in loss of its ability to bind cytokinins. This particular mutation corresponds to the previously reported wol allele (wooden leg) that causes a striking phenotype defective in vascular morphogenesis. Collectively, evidence is presented that AHK4 and its homologues (AHK3 and possibly AHK2) are receptor kinases that can transduce cytokinin signals across the plasma membrane of A. thaliana.
An early block type decision method for intra prediction in H.264/AVC (2009)

In this paper, we propose an early block type decision method to reduce the complexity of rate-distortion (R-D) cost computation in intra prediction. Our method decides the block size early among luma 4 times 4, 8 times 8 and 16 times 16 with simple decision scheme. R-D cost for mode decision is used for R-D cost of a subblock ( 8 times 16 block ) instead of that of macroblock (MB) with the proposed encoding order for the intra prediction of 4 times 4 and 8 times 8 block. The R-D cost of a subblock consists of luma components only. Chroma components have a smaller potion of the R-D cost because they use subsampling (4:2:0) and there is relatively small variance among chroma pixels. Our method provides the reduction of computational complexity with average 0.04 dB PSNR degradation and rate increase of less than 1% in comparison with the full search method.