Journal articles: 'Paired interactions'

1

Cooke, D., D. Corp, J. Hsu, R. Perellón Alfonso, A. Pascual-Leone, and M. Fox. "Mapping interhemispheric interactions with paired-pulse TMS." Brain Stimulation 12, no. 2 (March 2019): 478. http://dx.doi.org/10.1016/j.brs.2018.12.560.

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Jun, S., and C. Desplan. "Cooperative interactions between paired domain and homeodomain." Development 122, no. 9 (September 1, 1996): 2639–50. http://dx.doi.org/10.1242/dev.122.9.2639.

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The Pax proteins are a family of transcriptional regulators involved in many developmental processes in all higher eukaryotes. They are characterized by the presence of a paired domain (PD), a bipartite DNA binding domain composed of two helix-turn-helix (HTH) motifs, the PAI and RED domains. The PD is also often associated with a homeodomain (HD) which is itself able to form homo- and hetero-dimers on DNA. Many of these proteins therefore contain three HTH motifs each able to recognize DNA. However, all PDs recognize highly related DNA sequences, and most HDs also recognize almost identical sites. We show here that different Pax proteins use multiple combinations of their HTHs to recognize several types of target sites. For instance, the Drosophila Paired protein can bind, in vitro, exclusively through its PAI domain, or through a dimer of its HD, or through cooperative interaction between PAI domain and HD. However, prd function in vivo requires the synergistic action of both the PAI domain and the HD. Pax proteins with only a PD appear to require both PAI and RED domains, while a Pax-6 isoform and a new Pax protein, Lune, may rely on the RED domain and HD. We propose a model by which Pax proteins recognize different target genes in vivo through various combinations of their DNA binding domains, thus expanding their recognition repertoire.

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Grasshoff*, Ulrike, Heiko Grossmann†, Heinz Holling‡, and Rainer Schwabe. "Optimal paired comparison designs for first-order interactions." Statistics 37, no. 5 (September 2003): 373–86. http://dx.doi.org/10.1080/0233188031000154812.

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GERLACH, ULRICH H. "PAIRED ACCELERATED FRAMES." International Journal of Modern Physics A 11, no. 20 (August 10, 1996): 3667–88. http://dx.doi.org/10.1142/s0217751x96001711.

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The geometrical and quantum-mechanical basis for Davies’ and Unruh’s acceleration temperature is traced to a type of quantum-mechanical (“achronal”) spin. Its existence and definition are based on pairs of causally disjoint accelerated frames. For bosons the expected spin vector of monochromatic particles is given by the “Planckian power” and the “r.m.s. thermal fluctuation” spectra. Under space–time translation the spin direction precesses around that “Planckian” vector. By exhibiting the conserved achronal spin four-current, we extend the identification of achronal spin from single quanta to multiparticle systems. Total achronal spin conservation is also shown to hold, even in the presence of quadratic interactions. In addition, the Lorentz invariance of the acceleration temperature is made explicit by the introduction of pairs of “spherical” Rindler frames.

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Lu, Wanli, Huajin Chen, Shiyang Liu, Jian Zi, and Zhifang Lin. "Extremely strong bipolar optical interactions in paired graphene nanoribbons." Physical Chemistry Chemical Physics 18, no. 12 (2016): 8561–69. http://dx.doi.org/10.1039/c5cp06581j.

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Extremely strong bipolar optical forces are demonstrated in a pair of coupled graphene nanoribbons, due to the remarkable confinement and enhancement of optical fields, and analytical formulae are derived.

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Yang, HA, K. Sivasithamparam, and PA Obrien. "Mycelial Interactions and the Potential Use of Tuft Formation in Characterizing Rhizoctonia solani Isolates Infecting Cereals." Australian Journal of Botany 41, no. 2 (1993): 253. http://dx.doi.org/10.1071/bt9930253.

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Field isolates of Rhizoctonia solani anastomosis group (AG) 8, the most important causal pathogen of cereal bare-patch disease, were paired with each other and with tester strains of other AGs on potato-dextrose agar amended with charcoal (PDCA) to investigate mycelial interactions. Pairings among AG 8 field isolates produced compatible interactions of either tuft or merging reactions. Tufts formed between all paired field isolates from different pectic zymogram groups (ZGs) within AG 8, but pairings between genetically identical isolates showed merging reactions. Pairings of AG 8 field isolates with the tester strains of the other AGs led to incompatible interactions varying from merging line to barrage reactions. As formation of a tuft indicates that the paired isolates are able to anastomose and to form viable heterokaryons, the testing of mycelial interaction types, highlighted by tuft formation, may be used as a rapid procedure to characterise field isolates of R. solani obtained from cereals.

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7

Guney, Emre. "Revisiting Cross-Validation of Drug Similarity Based Classifiers Using Paired Data." Genomics and Computational Biology 4, no. 1 (December 6, 2017): 100047. http://dx.doi.org/10.18547/gcb.2018.vol4.iss1.e100047.

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Following the recent availability of high-throughput data for drug discovery, computational methods, especially machine learning based approaches, have gained remarkable attention. A number of studies use chemical, target and side effect similarity between drugs to build knowledge-based models that predict drug indications and drug-drug interactions. In light of previous works demonstrating the perils of cross-validation using paired data, in this study, we employ a disjoint cross validation approach for similarity-based drug-drug interaction (DDI) prediction and we investigate the prediction accuracy of classifier under various settings. Our results point to the dependence on the cross validation strategy used to evaluate prediction accuracy of drug similarity-based classifiers operating on paired data such as pharmacokinetic interactions between drugs.

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PELLIZZARI, Lucia, Dora FABBRO, Renata LONIGRO, Roberto DI LAURO, and Guiseppe DAMANTE. "A network of specific minor-groove contacts is a common characteristic of paired-domain-DNA interactions." Biochemical Journal 315, no. 2 (April 15, 1996): 363–67. http://dx.doi.org/10.1042/bj3150363.

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Pax proteins are a family of transcription factors conserved during evolution and able to bind specific DNA sequences through a domain called a ‘paired domain’. The DNA-binding specificity of the Pax-8 paired domain was investigated. Site-selection experiments indicate that Pax-8 binds to a consensus sequence similar to those bound by Pax-2 and Pax-5. When consensus sequences of various paired domains are observed in light of recent structural studies describing paired-domain–DNA interaction [Xu, Rould, Jun, Desplan and Pabo (1995) Cell 80, 639–650], it appears that base-pairs contacted in the minor groove are conserved, while most of the base-pairs contacted in the major groove are not. Therefore a network of specific minor groove contacts is a common characteristic of paired-domain–DNA interactions. The functional importance of such a network was successfully tested by analysing the effect of consensus-based mutations on the Pax-8 binding site of the thyroglobulin promoter.

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Devine, Warren D., and Timothy B. Harrington. "Aboveground growth interactions of paired conifer seedlings in close proximity." New Forests 41, no. 2 (August 11, 2010): 163–78. http://dx.doi.org/10.1007/s11056-010-9218-8.

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10

Hanakahi, L. A., Hui Sun, and Nancy Maizels. "High Affinity Interactions of Nucleolin with G-G-paired rDNA." Journal of Biological Chemistry 274, no. 22 (May 28, 1999): 15908–12. http://dx.doi.org/10.1074/jbc.274.22.15908.

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11

Fujimoto, Hiroshi. "Paired interacting orbitals: a way of looking at chemical interactions." Accounts of Chemical Research 20, no. 12 (December 1987): 448–53. http://dx.doi.org/10.1021/ar00144a004.

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12

Butler, Yuko Goto, and Wei Zeng. "Young Foreign Language Learners’ Interactions During Task-Based Paired Assessments." Language Assessment Quarterly 11, no. 1 (January 2, 2014): 45–75. http://dx.doi.org/10.1080/15434303.2013.869814.

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13

Goos, Merrilyn. "Metacognitive decision making and social interactions during paired problem solving." Mathematics Education Research Journal 6, no. 2 (December 1994): 144–65. http://dx.doi.org/10.1007/bf03217269.

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14

Huang, Feihe, Jason W. Jones, and Harry W. Gibson. "Competitive Interactions of Two Ion-Paired Salts with a Neutral Host To Form Two Non-Ion-Paired Complexes." Journal of Organic Chemistry 72, no. 17 (August 2007): 6573–76. http://dx.doi.org/10.1021/jo070792g.

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15

Pandolfino, John E., Guoxiang Shi, Qing Zhang, and Peter J. Kahrilas. "Absence of a deglutitive inhibition equivalent with secondary peristalsis." American Journal of Physiology-Gastrointestinal and Liver Physiology 288, no. 4 (April 2005): G671—G676. http://dx.doi.org/10.1152/ajpgi.00388.2004.

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This study aimed to determine the interactions between closely paired swallow-induced primary peristalsis (PP) and air injection-induced secondary peristalsis (SP). Ten subjects (7 men, 18–42 yr) were studied using a catheter, including two sleeves (upper and lower esophageal sphincters), a midesophageal infusion port, and seven esophageal and two pharyngeal recording sites. Ten iterations of PP and SP were induced by 5-ml water swallows and 20-ml intraesophageal air injections, respectively. Thereafter, the interactions between PP and SP, separated by 1- to 12-s intervals, were studied in all four possible sequences: paired swallows, swallow preceded by air injection, air injection preceded by swallow, and paired air injections. Tracings were analyzed for lower esophageal sphincter relaxation, presence and integrity of peristalsis, and event interaction. Eight subjects with success rates of both ≥90% PP and ≥80% SP were analyzed (PP 97 ± 2%, SP 90 ± 3%). During paired PP interactions and SP followed by PP, the first sequence was inhibited by the second with intervals < 4–6 s. However, no inhibition of the first peristaltic sequence was found in either PP followed by SP trials or SP followed by air injection. In contrast to swallowing or proximal esophageal distention, air injection into the lumen of the midesophagus does not inhibit an ongoing peristaltic event. Being that the elicitation of SP in the smooth muscle esophagus is intramurally mediated, this suggests that deglutitive inhibition is a centrally mediated phenomenon rather than an intrinsic property of peristalsis.

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Klibaite, Ugne, and Joshua W. Shaevitz. "Paired fruit flies synchronize behavior: Uncovering social interactions in Drosophila melanogaster." PLOS Computational Biology 16, no. 10 (October 6, 2020): e1008230. http://dx.doi.org/10.1371/journal.pcbi.1008230.

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17

Horsager, Alan, Geoffrey M. Boynton, Robert J. Greenberg, and Ione Fine. "Temporal Interactions during Paired-Electrode Stimulation in Two Retinal Prosthesis Subjects." Investigative Opthalmology & Visual Science 52, no. 1 (January 31, 2011): 549. http://dx.doi.org/10.1167/iovs.10-5282.

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18

Norman, Colin A. "Paired and Interacting Galaxies: Conference Summary." International Astronomical Union Colloquium 124 (1990): 765–70. http://dx.doi.org/10.1017/s0252921100005959.

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This has been an excellent conference with a very international component and a rich and wide ranging diversity of views on the topical subject of paired and interacting galaxies. The southern hospitality shown to us by our hosts Jack Sulentic and Bill Keel has been most gracious and the general growth of the astronomy group at the University of Alabama is most impressive.The conference began with the presentation of the basic data sets on pairs, groups, and interacting galaxies with the latter being further discussed with respect to both global properties and properties of the galactic nuclei. Then followed the theory, modelling and interpretation using analytic techniques, simulations and general modelling for spirals and ellipticals, starbursts and active galactic nuclei. Before the conference I had written down the three questions concerning pairs, groups and interacting galaxies that I hoped would be answered at the meeting: (1) How do they form? including the role of initial conditions, the importance of subclustering, the evolution of groups to compact groups, and the fate of compact groups; (2) How do they evolve? including issues such as relevant timescales, the role of halos and the problem of overmerging, the triggering and enhancement of star formation and activity in the galactic nuclei, and the relative importance of dwarf versus giant encounters; and (3) Are they important? including the frequency of pairs and interactions, whether merging and interactions are very important aspects of the life of a normal galaxy at formation, during its evolution, in forming bars, shells, rings, bulges etc., and in the formation and evolution of active galaxies. In what follows I shall summarize the meeting and where possible focus on these three central issues. Since this is a conference summary my references are all to papers presented at this meeting.

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19

MATTIS, DANIEL C. "ANOMALOUS INTERACTIONS AND EXACT Tc IN SUPERCONDUCTIVITY." Modern Physics Letters B 22, no. 28 (November 10, 2008): 2715–25. http://dx.doi.org/10.1142/s0217984908017242.

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This theoretical study of superconductivity examines repulsive forces that, surprisingly, favor the BCS paired state. The value of Tc and the pairing symmetry (s-, p-, d-wave) are obtained exactly as eigenvalues in a given sector of a Fredholm integral equation of the second kind.

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20

Ferkin, Michael. "Effects of previous interactions and sex on over-marking in meadow voles." Behaviour 144, no. 10 (2007): 1297–313. http://dx.doi.org/10.1163/156853907781890913.

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AbstractThe effects of winning and losing on over-marking behaviour of mammals, a behaviour associated with competition, are not known. The current study tests the hypothesis that after having a staged dyadic encounter with a same-sex conspecific, individuals adjust the proportion of scent marks they use to over-mark the marks of same-sex conspecifics. Female meadow voles that won their encounter used a higher proportion of their marks to over-mark the marks of female conspecifics than did females that either lost their encounter, were evenly matched, unfamiliar, or had no previous paired encounter. Females that lost their encounter used a lower proportion of their marks to over-mark those of female conspecifics than did females that either won their encounter or females that were evenly matched, unfamiliar, or had no previous paired encounter. Females that were evenly matched, unfamiliar, or had no previous paired encounter used a similar percentage of marks to over-mark those of another female. Male meadow voles, however, independent of whether they won, lost, were evenly matched, unfamiliar, or had no previous paired encounter used a similar proportion of marks to over-mark those of male conspecifics. The role of over-marking and the effects of previous social experience are discussed.

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21

Zhang, K., Q. Wang, Y. Xie, G. Mor, E. Sega, P. S. Low, and Y. Huang. "Receptor-mediated delivery of siRNAs by tethered nucleic acid base-paired interactions." RNA 14, no. 3 (January 18, 2008): 577–83. http://dx.doi.org/10.1261/rna.739308.

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22

Usrey, W. Martin, John B. Reppas, and R. Clay Reid. "Paired-spike interactions and synaptic efficacy of retinal inputs to the thalamus." Nature 395, no. 6700 (September 1998): 384–87. http://dx.doi.org/10.1038/26487.

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23

Lv, Xianzi, Fei Sun, Jinyan Tong, Qiang Feng, and Jianxin Zhang. "Paired Dislocations and Their Interactions with γ′ Particles in Polycrystalline Superalloy GH4037." Journal of Materials Engineering and Performance 24, no. 1 (November 15, 2014): 143–48. http://dx.doi.org/10.1007/s11665-014-1307-y.

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24

Davis, Larry. "The influence of interlocutor proficiency in a paired oral assessment." Language Testing 26, no. 3 (June 24, 2009): 367–96. http://dx.doi.org/10.1177/0265532209104667.

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The use of pair work in speaking assessment may encourage collaboration in the classroom and has other advantages (Saville & Hargreaves, 1999; Taylor, 2000) but from a measurement perspective, the paired oral format may be problematic because a partner may unfairly influence an examinee's performance or otherwise bias scores. In this study, the influence of interlocutor proficiency on speaking performance was examined in a group of 20 first-year students at a Chinese university. The students were divided into groups of relatively high and low English proficiency and tested once with a partner of similar proficiency and once with a partner of higher or lower proficiency. Interlocutor proficiency level had no observable effect on Rasch analysis ability measures, but lower-level examinees produced more language (words) when working with a higher-level partner. The majority of dyads produced collaborative interactions (Galaczi, 2008), unless an examinee was paired with a much lower-level partner, in which case the interaction tended to be asymmetric. Overall, these data suggest that proficiency differences among examinees need not preclude use of the paired oral test format.

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Wolfe, Katie, S. Shanun Kunnavatana, and Adrianna M. Shoemaker. "An Investigation of a Video-Based Preference Assessment of Social Interactions." Behavior Modification 42, no. 5 (September 14, 2017): 729–46. http://dx.doi.org/10.1177/0145445517731062.

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We examined the use of a paired-stimulus, video-based preference assessment (VPA) to identify high- and low-preference social interactions for three children with autism spectrum disorder. We conducted two VPAs with each participant: one with access to the interaction contingent on each selection and one without access. We also conducted a concurrent-operant reinforcer assessment to evaluate the accuracy of the VPAs in identifying reinforcers. For two participants, the VPAs corresponded strongly and the results of the reinforcer assessment suggest that the high-preference interaction produced more of the target response than the low-preference interaction. For the other participant, the VPAs identified different high- and low-preference interactions, and the results of the reinforcer assessment suggest that the VPA without access may have been more accurate in identifying a reinforcer.

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Kennicutt, Robert C. "Global Effects of Interactions on Galaxy Evolution." International Astronomical Union Colloquium 124 (1990): 269–84. http://dx.doi.org/10.1017/s0252921100005224.

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AbstractRecent observations of the evolutionary properties of paired and interacting galaxies are reviewed, with special emphasis on their global emission properties and star formation rates. Data at several wavelengths provide strong confirmation of the hypothesis, proposed originally by Larson and Tinsley, that interactions trigger global bursts of star formation in galaxies. The nature and properties of the starbursts, and their overall role in galactic evolution will also be discussed.

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Florenza, Javier, Manu Tamminen, and Stefan Bertilsson. "Uncovering microbial inter-domain interactions in complex communities." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1786 (October 7, 2019): 20190087. http://dx.doi.org/10.1098/rstb.2019.0087.

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Interactions between unicellular eukaryotes and bacteria are difficult to characterize in the environment owing to their large number and inherently microscopic scale. Although particular co-occurrences can be recovered through targeted approaches, e.g. single-cell sequencing or fluorescence in situ hybridization, the vast majority of the interactions remain unseen. Here, we discuss Emulsion, Paired Isolation and Concatenation polymerase chain reaction (epicPCR) as a tool to uncover these interactions in very high throughput. Originally developed for taxonomy-to-function linkage in bacterial communities, epicPCR has the potential to recover the complete interaction network in a given environment at single-cell resolution. This approach relies on the encapsulation of protistan single cells in emulsion droplets that can subsequently be gelified into beads. In this way, encapsulated cells can be exposed to lysis reagents and further phylogenetic paired marker amplification. A bacterium that physically co-occurs with the eukaryote will be jointly trapped, and the amplification will generate a concatenated PCR product containing physically coupled taxonomic markers from both partners, creating a link. Further amplification and sequencing enable the construction of an association pattern with statistically verified physical co-occurrences. Here, we discuss the potential, challenges and limitations of epicPCR. We argue that the microscopic scale at which epicPCR operates, the high throughput it delivers and its exploratory nature make it an unparalleled approach to unravel associations between microbes directly from environmental samples. This article is part of a discussion meeting issue ‘Single cell ecology’.

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Golden, Michael, Benjamin Murrell, Darren Martin, Oliver G. Pybus, and Jotun Hein. "Evolutionary Analyses of Base-Pairing Interactions in DNA and RNA Secondary Structures." Molecular Biology and Evolution 37, no. 2 (October 30, 2019): 576–92. http://dx.doi.org/10.1093/molbev/msz243.

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Abstract Pairs of nucleotides within functional nucleic acid secondary structures often display evidence of coevolution that is consistent with the maintenance of base-pairing. Here, we introduce a sequence evolution model, MESSI (Modeling the Evolution of Secondary Structure Interactions), that infers coevolution associated with base-paired sites in DNA or RNA sequence alignments. MESSI can estimate coevolution while accounting for an unknown secondary structure. MESSI can also use graphics processing unit parallelism to increase computational speed. We used MESSI to infer coevolution associated with GC, AU (AT in DNA), GU (GT in DNA) pairs in noncoding RNA alignments, and in single-stranded RNA and DNA virus alignments. Estimates of GU pair coevolution were found to be higher at base-paired sites in single-stranded RNA viruses and noncoding RNAs than estimates of GT pair coevolution in single-stranded DNA viruses. A potential biophysical explanation is that GT pairs do not stabilize DNA secondary structures to the same extent that GU pairs do in RNA. Additionally, MESSI estimates the degrees of coevolution at individual base-paired sites in an alignment. These estimates were computed for a SHAPE-MaP-determined HIV-1 NL4-3 RNA secondary structure. We found that estimates of coevolution were more strongly correlated with experimentally determined SHAPE-MaP pairing scores than three nonevolutionary measures of base-pairing covariation. To assist researchers in prioritizing substructures with potential functionality, MESSI automatically ranks substructures by degrees of coevolution at base-paired sites within them. Such a ranking was created for an HIV-1 subtype B alignment, revealing an excess of top-ranking substructures that have been previously identified as having structure-related functional importance, among several uncharacterized top-ranking substructures.

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Page, Heather N., Clay Hewett, Hayden Tompkins, and Emily R. Hall. "Ocean Acidification and Direct Interactions Affect Coral, Macroalga, and Sponge Growth in the Florida Keys." Journal of Marine Science and Engineering 9, no. 7 (July 4, 2021): 739. http://dx.doi.org/10.3390/jmse9070739.

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Coral reef community composition, function, and resilience have been altered by natural and anthropogenic stressors. Future anthropogenic ocean and coastal acidification (together termed “acidification”) may exacerbate this reef degradation. Accurately predicting reef resilience requires an understanding of not only direct impacts of acidification on marine organisms but also indirect effects on species interactions that influence community composition and reef ecosystem functions. In this 28-day experiment, we assessed the effect of acidification on coral–algal, coral–sponge, and algal–sponge interactions. We quantified growth of corals (Siderastrea radians), fleshy macroalgae (Dictyota spp.), and sponges (Pione lampa) that were exposed to local summer ambient (603 μatm) or elevated (1105 μatm) pCO2 seawater. These species are common to hard-bottom communities, including shallow reefs, in the Florida Keys. Each individual was maintained in isolation or paired with another organism. Coral growth (net calcification) was similar across seawater pCO2 and interaction treatments. Fleshy macroalgae had increased biomass when paired with a sponge but lost biomass when growing in isolation or paired with coral. Sponges grew more volumetrically in the elevated seawater pCO2 treatment (i.e., under acidification conditions). Although these results are limited in temporal and spatial scales due to the experimental design, they do lend support to the hypothesis that acidification may facilitate a shift towards increased sponge and macroalgae abundance by directly benefiting sponge growth which in turn may provide more dissolved inorganic nitrogen to macroalgae in the Florida Keys.

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Whitmire, Clarissa J., Daniel C. Millard, and Garrett B. Stanley. "Thalamic state control of cortical paired-pulse dynamics." Journal of Neurophysiology 117, no. 1 (January 1, 2017): 163–77. http://dx.doi.org/10.1152/jn.00415.2016.

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Sensory stimulation drives complex interactions across neural circuits as information is encoded and then transmitted from one brain region to the next. In the highly interconnected thalamocortical circuit, these complex interactions elicit repeatable neural dynamics in response to temporal patterns of stimuli that provide insight into the circuit properties that generated them. Here, using a combination of in vivo voltage-sensitive dye (VSD) imaging of cortex, single-unit recording in thalamus, and optogenetics to manipulate thalamic state in the rodent vibrissa pathway, we probed the thalamocortical circuit with simple temporal patterns of stimuli delivered either to the whiskers on the face (sensory stimulation) or to the thalamus directly via electrical or optogenetic inputs (artificial stimulation). VSD imaging of cortex in response to whisker stimulation revealed classical suppressive dynamics, while artificial stimulation of thalamus produced an additional facilitation dynamic in cortex not observed with sensory stimulation. Thalamic neurons showed enhanced bursting activity in response to artificial stimulation, suggesting that bursting dynamics may underlie the facilitation mechanism we observed in cortex. To test this experimentally, we directly depolarized the thalamus, using optogenetic modulation of the firing activity to shift from a burst to a tonic mode. In the optogenetically depolarized thalamic state, the cortical facilitation dynamic was completely abolished. Together, the results obtained here from simple probes suggest that thalamic state, and ultimately thalamic bursting, may play a key role in shaping more complex stimulus-evoked dynamics in the thalamocortical pathway. NEW & NOTEWORTHY For the first time, we have been able to utilize optogenetic modulation of thalamic firing modes combined with optical imaging of cortex in the rat vibrissa system to directly test the role of thalamic state in shaping cortical response properties.

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Taylor, I. C., and R. E. Kingston. "Factor substitution in a human HSP70 gene promoter: TATA-dependent and TATA-independent interactions." Molecular and Cellular Biology 10, no. 1 (January 1990): 165–75. http://dx.doi.org/10.1128/mcb.10.1.165.

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To investigate interactions between transcription factors on mammalian promoters, we constructed a set of 24 variations of the human HSP70 gene promoter in which six upstream sequence motifs are paired in every possible combination with four TATA motifs. These promoters were analyzed for in vivo expression, and selected constructs were examined by in vitro template commitment studies. Activation transcription factor (ATF) and CP1 showed dramatically different interactions with the factor(s) bound to the TATA region. CP1 functioned in vivo regardless of the TATA motif that it was paired with and was not capable of sequestering the core promoter complex in a template commitment assay. ATF activity was dramatically altered by changing the TATA motif, and ATF was able to sequester the core promoter complex. These data suggest that CP1 and ATF function by distinct mechanisms that differ with respect to interaction with the factor(s) at the TATA box. Factor Sp1 also appeared to function by a TATA-independent mechanism. These data imply that the ability of a factor to function is determined not only by the intrinsic properties of the factor but also by promoter context.

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Taylor, I. C., and R. E. Kingston. "Factor substitution in a human HSP70 gene promoter: TATA-dependent and TATA-independent interactions." Molecular and Cellular Biology 10, no. 1 (January 1990): 165–75. http://dx.doi.org/10.1128/mcb.10.1.165-175.1990.

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To investigate interactions between transcription factors on mammalian promoters, we constructed a set of 24 variations of the human HSP70 gene promoter in which six upstream sequence motifs are paired in every possible combination with four TATA motifs. These promoters were analyzed for in vivo expression, and selected constructs were examined by in vitro template commitment studies. Activation transcription factor (ATF) and CP1 showed dramatically different interactions with the factor(s) bound to the TATA region. CP1 functioned in vivo regardless of the TATA motif that it was paired with and was not capable of sequestering the core promoter complex in a template commitment assay. ATF activity was dramatically altered by changing the TATA motif, and ATF was able to sequester the core promoter complex. These data suggest that CP1 and ATF function by distinct mechanisms that differ with respect to interaction with the factor(s) at the TATA box. Factor Sp1 also appeared to function by a TATA-independent mechanism. These data imply that the ability of a factor to function is determined not only by the intrinsic properties of the factor but also by promoter context.

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Großmann, Heiko, Rainer Schwabe, and Steven G. Gilmour. "Designs for first-order interactions in paired comparison experiments with two-level factors." Journal of Statistical Planning and Inference 142, no. 8 (August 2012): 2395–401. http://dx.doi.org/10.1016/j.jspi.2012.02.033.

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Cicione, R., J. B. Fallon, G. D. Rathbone, C. E. Williams, and M. N. Shivdasani. "Spatiotemporal Interactions in the Visual Cortex Following Paired Electrical Stimulation of the Retina." Investigative Ophthalmology & Visual Science 55, no. 12 (November 4, 2014): 7726–38. http://dx.doi.org/10.1167/iovs.14-14754.

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Begg, Gillian E., Sandra L. Harper, Michael B. Morris, and David W. Speicher. "Initiation of Spectrin Dimerization Involves Complementary Electrostatic Interactions between Paired Triple-helical Bundles." Journal of Biological Chemistry 275, no. 5 (February 4, 2000): 3279–87. http://dx.doi.org/10.1074/jbc.275.5.3279.

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Shurgalina, E. G. "Features of the Paired Soliton Interactions Within the Framework of the Gardner Equation." Radiophysics and Quantum Electronics 60, no. 9 (February 2018): 703–8. http://dx.doi.org/10.1007/s11141-018-9839-x.

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Summers, Cliff H., and Thomas J. Andrews. "Aggression, and the Acquisition and Function of Social Dominance in Female Anolis Carolinensis." Behaviour 133, no. 15-16 (1996): 1265–79. http://dx.doi.org/10.1163/156853996x00396.

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AbstractFemale green anoles, Anolis carolinensis, were paired in terraria to investigate behavioral components of social interaction. Resources (perching sites, prey, and males as potential mates) were limited to assess their importance to cohabiting females. During interaction, paired females exhibited aggressive social behavior which contributed to the development of dominant-subordinate relationships. Dominant status and its relationship to differential resource acquisition was defined primarily by frequency of displacement of another female. Along with displacement, dominant females also had increased frequency of assertion displays, challenge displays, attacks and biting (Figs 1 & 2). Subordinate females were displaced more often and assumed submissive postures. No differences were found between dominant and subordinate females for perch site selection, body color or in prey capturing latency or success (Figs 3 & 4). Perch site elevation was not different between dominant and subordinate females, but was significantly lower than males. The color of paired females was not different unless males were present, in which case dominant females were darker. Paired females also respond differently to courtship display (Fig. 5). Dominant females responded with displays significantly more often than subordinate females to male courtship, indicating receptivity. The role of dominant-subordinate relationships among female A. carolinensis may include courtship and reproductive success as an important component, with consequences for the outcome of aggressive and reproductive social interactions with males.

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Grinzato, Alessandro, Pascal Albanese, Roberto Marotta, Paolo Swuec, Guido Saracco, Martino Bolognesi, Giuseppe Zanotti, and Cristina Pagliano. "High-Light versus Low-Light: Effects on Paired Photosystem II Supercomplex Structural Rearrangement in Pea Plants." International Journal of Molecular Sciences 21, no. 22 (November 16, 2020): 8643. http://dx.doi.org/10.3390/ijms21228643.

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In plant grana thylakoid membranes Photosystem II (PSII) associates with a variable number of antenna proteins (LHCII) to form different types of supercomplexes (PSII-LHCII), whose organization is dynamically adjusted in response to light cues, with the C2S2 more abundant in high-light and the C2S2M2 in low-light. Paired PSII-LHCII supercomplexes interacting at their stromal surface from adjacent thylakoid membranes were previously suggested to mediate grana stacking. Here, we present the cryo-electron microscopy maps of paired C2S2 and C2S2M2 supercomplexes isolated from pea plants grown in high-light and low-light, respectively. These maps show a different rotational offset between the two supercomplexes in the pair, responsible for modifying their reciprocal interaction and energetic connectivity. This evidence reveals a different way by which paired PSII-LHCII supercomplexes can mediate grana stacking at diverse irradiances. Electrostatic stromal interactions between LHCII trimers almost completely overlapping in the paired C2S2 can be the main determinant by which PSII-LHCII supercomplexes mediate grana stacking in plants grown in high-light, whereas the mutual interaction of stromal N-terminal loops of two facing Lhcb4 subunits in the paired C2S2M2 can fulfil this task in plants grown in low-light. The high-light induced accumulation of the Lhcb4.3 protein in PSII-LHCII supercomplexes has been previously reported. Our cryo-electron microscopy map at 3.8 Å resolution of the C2S2 supercomplex isolated from plants grown in high-light suggests the presence of the Lhcb4.3 protein revealing peculiar structural features of this high-light-specific antenna important for photoprotection.

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Ibrahim, Adriana N. A. F., Ilan Karplus, and Wagner C. Valenti. "Social interaction in males of the Amazon river prawn Macrobrachium amazonicum (Heller, 1862) (Decapoda, Palaemonidae)." Crustaceana 94, no. 3 (March 2, 2021): 325–41. http://dx.doi.org/10.1163/15685403-bja10081.

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Abstract The large size variation of Macrobrachium amazonicum reflects a complex population structure that consists of four morphotypes, called TC (Translucent Claw), CC (Cinnamon Claw), GC1 (Green Claw 1), and GC2 (Green Claw 2). The effect of the largest morphotype (GC2) claws on development and behaviour of the smallest male morphotype (TC) was analysed through manipulations of the large prawn’s second pair of claws. TC males were paired for 75 days in aquaria with (a) an intact GC2, (b) a GC2 with immobilized dactyls, and (c) a GC2 without chelipeds. Isolated TC males served as a control. The maintenance activities of TC males and social interactions with the GC2 morphotype were monitored. Survival and growth of TC males was lower in relation to the control when they were paired with intact GC2 males. Aggressive interactions were carried out almost exclusively by GC2 and strongly affected the behaviour of the small prawns. The absence of chelipeds and immobilization of dactyls in GC2 prawns reduced the negative effect on the development of TC males and agonistic behaviour. The social interactions between GC2 and TC prawns reflect a stable dominance hierarchy. The large claw of the GC2 morphotype plays a major role in the social interaction.

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Sclafani, Anthony, and John I. Glendinning. "Sugar and fat conditioned flavor preferences in C57BL/6J and 129 mice: oral and postoral interactions." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 289, no. 3 (September 2005): R712—R720. http://dx.doi.org/10.1152/ajpregu.00176.2005.

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C57BL/6J (B6) mice consume more sugar and fat solutions than do 129 mice in 24-h preference tests. Previous studies have attributed this observation to strain differences in taste responsiveness to these nutrients. We tested the hypothesis that differences in postingestive responsiveness contribute to the strain differences. In experiment 1, B6 and 129 mice were trained to associate consumption of a flavored solution (CS+) with intragastric (IG) infusions of 16% sucrose and a different flavored solution (CS−) with IG water infusions (22 h/day). They were then retrained with new flavors paired with IG infusions of 5.6% soybean oil and water. Although both strains developed preferences for the nutrient-paired CS+ solutions, the B6 mice displayed significantly stronger preferences. The B6 mice consumed more CS+ during training, which may have contributed to their enhanced preference. In a second experiment, training intakes were equated by giving B6 and 129 mice “isosweet” CS solutions prepared with different amounts of sucrose and saccharin. The B6 and 129 mice consumed more of the sugar- or fat-paired CS+ than the water-paired CS− during training. The two strains also displayed equally strong preferences for the CS+ over CS− in choice tests, indicating that they had similar postingestive responsiveness to the sucrose and soybean oil. We propose that B6 mice consume more sugar and fat than 129 mice because their stronger orosensory response stimulates greater intake, which leads to greater stimulation of postingestive nutrient detectors and further enhancement of consumption.

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Lundkvist, Pär, Sara Jupiter, Åsa Segerstolpe, Yvonne N. Osheim, Ann L. Beyer, and Lars Wieslander. "Mrd1p Is Required for Release of Base-Paired U3 snoRNA within the Preribosomal Complex." Molecular and Cellular Biology 29, no. 21 (August 24, 2009): 5763–74. http://dx.doi.org/10.1128/mcb.00428-09.

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ABSTRACT In eukaryotes, ribosomes are made from precursor rRNA (pre-rRNA) and ribosomal proteins in a maturation process that requires a large number of snoRNPs and processing factors. A fundamental problem is how the coordinated and productive folding of the pre-rRNA and assembly of successive pre-rRNA-protein complexes is achieved cotranscriptionally. The conserved protein Mrd1p, which contains five RNA binding domains (RBDs), is essential for processing events leading to small ribosomal subunit synthesis. We show that full function of Mrd1p requires all five RBDs and that the RBDs are functionally distinct and needed during different steps in processing. Mrd1p mutations trap U3 snoRNA in pre-rRNP complexes both in base-paired and non-base-paired interactions. A single essential RBD, RBD5, is involved in both types of interactions, but its conserved RNP1 motif is not needed for releasing the base-paired interactions. RBD5 is also required for the late pre-rRNP compaction preceding A2 cleavage. Our results suggest that Mrd1p modulates successive conformational rearrangements within the pre-rRNP that influence snoRNA-pre-rRNA contacts and couple U3 snoRNA-pre-rRNA remodeling and late steps in pre-rRNP compaction that are essential for cleavage at A0 to A2. Mrd1p therefore coordinates key events in biosynthesis of small ribosome subunits.

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Nunez, Eleuda, Soichiro Matsuda, Masakazu Hirokawa, Junichi Yamamoto, and Kenji Suzuki. "Effect of Sensory Feedback on Turn-Taking Using Paired Devices for Children with ASD." Multimodal Technologies and Interaction 2, no. 4 (September 20, 2018): 61. http://dx.doi.org/10.3390/mti2040061.

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Most children can naturally engage in play and by this, develop skills while interacting with their peers and toys. However, children with Autism Spectrum Disorder (ASD) often show impairments in play skills which result in limited opportunities for interaction with others and the learning of social skills. In this regard, robotic devices/toys that can provide simple and attractive indications are advantageous to engage children with ASD in play activities that require social and interaction skills. This project proposes a new interaction method using paired robotic devices called COLOLO to facilitate a fundamental exchange of intention in communication so-called turn-taking. These tangible devices are designed to sense the user’s manipulation, send a message to the paired device, and display visual cues for assisting children to achieve turn-taking through play. On the sessions with COLOLO there are two devices, one held by the therapist and one by the child, and they take turns to manipulate the toys and change their colors. In this article, two experimental conditions or interaction rules: the “two-sided lighting rule” and the “one-sided lighting rule" were introduced. The two interactions rules differ from each on the way the devices used the visual cues to indicate the turn-holder. The effect of each interaction rule on children’s turn-taking behaviors was investigated through an experimental study with four children with ASD. From the results, we found that with the one-sided lighting rule participants tended to shift their gaze more and to decrease the failed attempts of turn-taking. The discussion covers the possibilities of using paired devices to describe participants’ behaviors related to turn-taking quantitatively.

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Selig, Suzanne M., and Harry Perlstadt. "An Instructional Method for Mixed Medical Sociology Classes: Paired Observations of Practitioner-Patient Interactions." Teaching Sociology 12, no. 4 (July 1985): 463. http://dx.doi.org/10.2307/1318067.

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Barghorn, S., Q. Zheng-Fischhöfer, M. Ackmann, J. Biernat, M. von Bergen, E. M. Mandelkow, and E. Mandelkow. "Structure, Microtubule Interactions, and Paired Helical Filament Aggregation by Tau Mutants of Frontotemporal Dementias†." Biochemistry 39, no. 38 (September 2000): 11714–21. http://dx.doi.org/10.1021/bi000850r.

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Lakaev, S. N., and Zhanikul I. Abdullaev. "Spectrum of the four-particle Schrödinger operator with paired contact interactions on a lattice." Russian Mathematical Surveys 53, no. 3 (June 30, 1998): 630–32. http://dx.doi.org/10.1070/rm1998v053n03abeh000050.

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Volgushe, Maxim, Leon L. Voronin, Marina Chistiakova, and Wolf Singer. "Relations Between Long-term Synaptic Modifications and Paired-pulse Interactions in the Rat Neocortex." European Journal of Neuroscience 9, no. 8 (August 1997): 1656–65. http://dx.doi.org/10.1111/j.1460-9568.1997.tb01523.x.

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Carter, Glenda, and M. Gail Jones. "Relationship between ability-paired interactions and the development of fifth graders' concepts of balance." Journal of Research in Science Teaching 31, no. 8 (October 1994): 847–56. http://dx.doi.org/10.1002/tea.3660310807.

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Basílio Janke, Eline M., and Klaus Weisz. "Hydrogen Bond Mediated Association of Dinucleotide Analogs." Zeitschrift für Physikalische Chemie 217, no. 12 (December 1, 2003): 1463–72. http://dx.doi.org/10.1524/zpch.217.12.1463.20475.

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AbstractSeveral dinucleotide analogs, in which two of the nucleobases adenine, thymine and uracil are connected by a hexadecamethylene linker have been synthesized and studied for their base-base interaction in a chloroform solution. Using 1H NMR spectroscopic techniques intramolecular base pair formation through hydrogen bonding is observed at ambient temperatures but found to strongly depend on the identity of paired bases. Thus, whereas cyclization through intramolecular base-base interactions predominate for adenine–(CH2)16–thymine and adenine–(CH2)16–uracil, no intramolecular adenine-adenine pairing was observed. Upon addition of acetic acid to adenine–(CH2)16–thymine, strong adenine-acetic acid interactions result in the disruption of preformed intramolecular adenine-thymine base pairs.

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De Barro, P. J., and P. J. Hart. "Mating interactions between two biotypes of the whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae) in Australia." Bulletin of Entomological Research 90, no. 2 (April 2000): 103–12. http://dx.doi.org/10.1017/s0007485300000201.

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AbstractThe biological consequences of mating interactions between indigenous and exotic biotypes of Bemisia tabaci (Gennadius) in Australia were studied using a combination of field and laboratory experiments. The key results of the interaction between the B and eastern Australian biotypes were reduced population increase, a marked increase in the proportion of male progeny, fewer eggs produced by females paired with males of different biotype and no difference in the numbers of eggs per unmated female and females paired with males of the same biotype. In addition, there was no change in the proportion of eggs hatching, mixed biotype pairs spent more time courting than single biotype pairs and a low level of hybridization in field cages and small containers was observed. These observations suggest three possibilities. The first is the ‘distracting male hypothesis’ in which mating pairs made up of different biotypes apportion more time to courtship and less time to egg laying than single biotype pairs. The second invokes the ‘single-locus complementary sex determination model’ in which the production of non-viable diploid male zygotes may explain the reduction in eggs laid. The third is cytoplasmic incompatibility between biotypes caused by Wolbachia. The results also suggest that the geographical distribution of clusters of related biotypes both overseas and in Australia may be explained by between-biotype interactions leading to the formation of parapatric populations.

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Mitchell, G. S., M. A. Douse, and K. T. Foley. "Receptor interactions in modulating ventilatory activity." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 259, no. 5 (November 1, 1990): R911—R920. http://dx.doi.org/10.1152/ajpregu.1990.259.5.r911.

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The ventilatory control system utilizes a variety of sensory receptor groups, including chemoreceptors and mechanoreceptors, to provide feedback concerning the status of controlled variables. Most ventilatory responses to altered receptor inputs generally involve a complex interaction between several receptor groups, central integrative mechanisms, and other modulatory inputs (e.g., “state,” hormonal, or neurotransmitter status). Because the control system is complex, nonlinear, and dynamic, the ultimate ventilatory response elicited by a given stimulus is not easy to predict based on the reflex effects of individual receptor groups studied in isolation. A full understanding of the role that sensory receptors play in ventilatory control requires information concerning interactions among receptor groups and with other elements of the control system. The complexity of the problem and the lack of a uniform definition of the term “interaction” has hindered research in this area. An interaction is defined as a nonadditive relationship between independent inputs to the system. Within this definition, five domains of interaction are described. 1) Algebraic interactions occur in ventilation and/or its components because of their multiplicative and nonlinear relationship. 2) Closed-loop interactions occur because of the prevalence of feedback loops within the respiratory control system. 3) Neural interactions reflect central nervous system integration of simultaneous receptor inputs and are demonstrated when feedback loops are opened. Three subdomains of neural interactions are defined: modulatory, dynamic, and range-specific neural interactions. 4) Mechanical interactions result from nonlinear transformations of motoneuron output into mechanical actions. 5) Adaptive interactions occur when paired receptor or modulatory inputs alter future responses. To understand the role of any sensory receptor group in ventilatory control, it is necessary to define its interactions with other control system elements in each of these domains. Understanding the mechanisms of these interactions requires detailed information about the physical system subserving ventilatory control (mechanics and gas exchange) and the relevant properties of the neural network coordinating their actions.

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Journal articles on the topic 'Paired interactions'

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