Estimation of Ratio Using Rank Set Sampling

Ranked set sampling (RSS) as suggested by McIntyre (1952) and developed by Takahasi and Wakimoto (1968) is used to estimate the ratio. It is proved that by using RSS method the efficiency of the estimator relative to the simple random sampling (SRS) method has increased. Computer simulated results are given. An example using real data is presented to illustrate the computations.     

Parameters Estimation in a Simple Linear Regression Using Rank Set Sampling

Ranked set sampling (RSS) as suggested by MCINTYRE (1952) and TAKAHASI and WAKIMOTO (1968) may be used to estimate the parameters of the simple regression line. The objective is to use the RSS method to increase the efficiency of the estimators relative to the simple random sampling (SRS) method. Estimators of the slope and intercept are considered. Computer simulated results are given, and an example using real data presented to illustrate the computations.     

Pair Rank Set Sampling

Ranked set sampling (RSS) as suggested by McIntyre (1952) may be modified to introduced a new sampling method called pair rank set sampling (PRSS), which might be used in some area of application instead of the RSS to increase the efficiency of the estimators relative to the simple random sampling (SRS) method. Estimators of the population mean are considered. An example using real data is presented to illustrate computations.     

Ranked set sampling: cost and optimal set size

McIntyre (1952, Australian Journal of Agricultural Research 3, 385-390) introduced ranked set sampling (RSS) as a method for improving estimation of a population mean in settings where sampling and ranking of units from the population are inexpensive when compared with actual measurement of the units. Two of the major factors in the usefulness of RSS are the set size and the relative costs of the various operations of sampling, ranking, and measurement. In this article, we consider ranking error models and cost models that enable us to assess the effect of different cost structures on the optimal set size for RSS. For reasonable cost structures, we find that the optimal RSS set sizes are generally larger than had been anticipated previously. These results will provide a useful tool for determining whether RSS is likely to lead to an improvement over simple random sampling in a given setting and, if so, what RSS set size is best to use in this case.     

Application of Numerical Classification to Study the Grazing Retrogressive Succession Stages of the Kobresia Vegetation on the Subalpine Meadow

Using the nearest-neighbour method in the course of numerical classification the four stages of the grazing retrogressive succession .of the Kobresia vegetation in Maqu Xian are divided: Ligularia virgaurea +Stipa aliena -Saussurea sp community and Leontopodium sp-Saussurea superba f. Pygmaea community belongs to the RSS (Retrogressive Succession Stages) of the grazing extremely; Anemone rivularis var fioreminore-Ligularia virgaurea-Kobresia spp community belongs to the RSS of the grazing seriously; Brachy-podium sylvaticum var gracile-Kobresia spp, Kobresia spp-Polygonum viviparum-Festuca rubra and Kobresia spp-Blysmus sinocompressus -Potentilla anserina communities belong to the RSS of the grazing moderately; Kobresia spp-Trollius farrei community belongs to the RSS of the grazing properly. Such classification method gives the same result as the traditional classificational methods of the RSS do. But it gives the numerical bases.     

Initiation of V(D)J recombination in vivo: role of recombination signal sequences in formation of single and paired double-strand breaks.

In V(D)J recombination, double-strand breaks (DSBs) are introduced at recombination signal sequences (RSSs) which consist of three distinct elements: a heptamer, a 12 or 23 nucleotide spacer and a nonamer. Efficient DSB formation requires a 12/23 RSS pair and occurs at both RSS in a temporally coupled fashion (coupled cleavage). It remains unknown which RSS elements are important for coupled cleavage. Furthermore, it has not been established whether some RSS components are critical only for cleavage in cis, with others mainly promoting cleavage in trans at the partner RSS. We investigated these questions by analyzing the effects of RSS mutations on the formation of DSBs in vivo. The abundance of DSBs in cis (at the mutant RSS) and in trans (at the consensus RSS) was determined using an established ligation-mediated PCR assay. We also developed a Southern blotting approach that allows the first direct measurement of dual and single RSS cleavage in vivo. Our results demonstrate that the heptamer, spacer and nonamer elements are all required for coupled cleavage in vivo. These studies also provide evidence for cleavage events involving a single RSS both in mutant substrates and in substrates containing a consensus 12/23 RSS pair.     

The estimation of event related potentials affected by random shifts and scalings

There is considerable evidence for trial to trial variability of the event related potentials (ERPs) within a given subject's recording. This variability influences the outcome of usual procedures in ERP analysis. Better results may be obtained if the sources of variability are explicitly taken into account in an appropriate model. This paper considers a probabilistic model, the random shift and scaling (RSS) model, where the response is modified by a random time shift and a random scale factor. In addition to this, an additional random scale factor which affects both the response and the background noise is taken into account. This time shift and these scale factors are handled as nuisance parameters. Maximum likelihood and least squares estimators of these parameters and the waveform of response are derived for the RSS model. It is shown that the Woody estimate of the ERP reported in earlier work can be derived by restricting the assumptions for the RSS model. Test statistics for hypotheses on means are obtained for the RSS model and a new type of discriminant function. The usefulness of the method is illustrated by means of simulation studies. Receiver operating characteristic (ROC) curves are used to demonstrate that the new type of discriminant performs better than the usual Fisher's Linear Discriminant.     

Assembly Pathway and Characterization of the RAG1/2-DNA Paired and Signal-end Complexes

Mammalian immune receptor diversity is established via a unique restricted set of site-specific DNA rearrangements in lymphoid cells, known as V(D)J recombination. The lymphoid-specific RAG1-RAG2 protein complex (RAG1/2) initiates this process by binding to two types of recombination signal sequences (RSS), 12RSS and 23RSS, and cleaving at the boundaries of RSS and V, D, or J gene segments, which are to be assembled into immunoglobulins and T-cell receptors. Here we dissect the ordered assembly of the RAG1/2 heterotetramer with 12RSS and 23RSS DNAs. We find that RAG1/2 binds only a single 12RSS or 23RSS and reserves the second DNA-binding site specifically for the complementary RSS, to form a paired complex that reflects the known 12/23 rule of V(D)J recombination. The assembled RAG1/2 paired complex is active in the presence of Mg²⁺, the physiologically relevant metal ion, in nicking and double-strand cleavage of both RSS DNAs to produce a signal-end complex. We report here the purification and initial crystallization of the RAG1/2 signal-end complex for atomic-resolution structure elucidation. Strict pairing of the 12RSS and 23RSS at the binding step, together with information from the crystal structure of RAG1/2, leads to a molecular explanation of the 12/23 rule.     

Population approaches to estimate minimal model indexes of insulin sensitivity and glucose effectiveness using full and reduced sampling schedules

The intravenous glucose tolerance test (IVGTT) interpreted with the minimal model provides individual indexes of insulin sensitivity (S(I)) and glucose effectiveness (S(G)). In population studies, the traditional approach, the standard two-stage (STS) method, fails to account for uncertainty in individual estimates, resulting in an overestimation of between-subject variability. Furthermore, in the presence of reduced sampling and/or insulin resistance, individual estimates may be unobtainable, biasing population information. Therefore, we investigated the use of two population approaches, the iterative two-stage (ITS) method and nonlinear mixed-effects modeling (NM), in a population (n = 235) of insulin-sensitive and insulin-resistant subjects under full (FSS, 33 samples) and reduced [RSS(240-min), 13 samples and RSS(180-min), 12 samples] IVGTT sampling schedules. All three population methods gave similar results with the FSS. Using RSS(240), the three methods gave similar results for S(I), but S(G) population means were overestimated. With RSS(180), S(I) and S(G) population means were higher for all three methods compared with their FSS counterparts. NM estimated similar between-subject variability (19% S(G), 53% S(I)) with RSS(180), whereas ITS showed regression to the mean for S(G) (0.01% S(G), 56% S(I)) and STS provided larger population variability in S(I) (29% S(G), 91% S(I)). NM provided individual estimates for all subjects, whereas the two-stage methods failed in 16-18% of the subjects using RSS(180) and 6-14% using RSS(240). We conclude that population approaches, specifically NM, are useful in studies with a sparsely sampled IVGTT ( approximately 12 samples) of short duration ( approximately 3 h) and when individual parameter estimates in all subjects are desired.     

A minimalist's reactive potential for efficient molecular modelling of chemistry

We review a minimalist's reactive force field, reactive state summation (RSS) potential. The essence of RSS potential scheme is to model each reactive state by individual non-reactive force fields, then modulate each term by a reaction-coordinate-dependent weight function, finally sum together to obtain the reactive potential. Compared with existing reactive potentials, RSS potential is easier to formulate and parameterise and is computationally efficient, at the expense of lesser accuracy. Thus, RSS potential can be regarded as a ‘reactive Lennard-Jones’ potential. Three exemplary RSS potentials are described in the context of their respective chemical systems: RSS-nitrogen for modelling detonation, RSS-carbon for modelling pyrolysis of activated carbon and RSS-fuel-catalyst for modelling catalytic chemical reaction.     

Full-length RAG1 promotes contact with coding and intersignal sequences in RAG protein complexes bound to recombination signals paired in cis

The RAG proteins initiate V(D)J recombination by mediating synapsis and cleavage of two different antigen receptor gene segments through interactions with their flanking recombination signal sequences (RSS). The protein–DNA complexes that support this process have mainly been studied using RAG–RSS complexes assembled using oligonucleotide substrates containing a single RSS that are paired in trans to promote synapsis. How closely these complexes model those formed on longer, more physiologically relevant substrates containing RSSs on the same DNA molecule (in cis) remains unclear. To address this issue, we characterized discrete core and full-length RAG protein complexes bound to RSSs paired in cis. We find these complexes support cleavage activity regulated by V(D)J recombination's ‘12/23 rule’ and exhibit plasticity in RSS usage dependent on partner RSS composition. DNA footprinting studies suggest that the RAG proteins in these complexes mediate more extensive contact with sequences flanking the RSS than previously observed, some of which are enhanced by full-length RAG1, and associated with synapsis and efficient RSS cleavage. Finally, we demonstrate that the RAG1 C-terminus facilitates hairpin formation on long DNA substrates, and full-length RAG1 promotes hairpin retention in the postcleavage RAG complex. These results provide new insights into the mechanism of physiological V(D)J recombination.     

The central domain of core RAG1 preferentially recognizes single-stranded recombination signal sequence heptamer

RAG1 and RAG2 initiate V(D)J recombination by introducing DNA double strand breaks between each selected gene segment and its bordering recombination signal sequence (RSS) in a two-step mechanism in which the DNA is first nicked, followed by hairpin formation. The RSS consists of a conserved nonamer and heptamer sequence, in which the latter borders the site of DNA cleavage. A region within RAG1, referred to as the central domain (residues 528-760 of 1040 in the full-length protein), has been shown previously to bind specifically to the double-stranded (ds) RSS heptamer, but with both weak specificity and affinity. However, additional investigations into the RAG1-RSS heptamer interaction are required because the DNA substrate forms intermediate conformations during the V(D)J recombination reaction. These include the nicked and hairpin products, as well as likely base unpairing to produce single-stranded (ss) DNA near the cleavage site. Here, it was determined that although the central domain showed substantially higher binding affinity for ss and nicked versus ds substrate, the interaction with ss RSS was particularly robust. In addition, the central domain bound with greater sequence specificity to the ss RSS heptamer than to the ds form. This study provides important insight into the V(D)J recombination reaction, specifically that significant interaction of the RSS heptamer with RAG1 occurs only after the induction of conformational changes at the RSS heptamer.     

Functional organization of single and paired V(D)J cleavage complexes

RAG-1 and RAG-2 initiate V(D)J recombination by binding to specific recognition sequences (RSS) and then cleave the DNA in two steps: nicking and hairpin formation. Recent work has established that a dimer of RAG-1 and either one or two monomers of RAG-2 bind to a single RSS, but the enzymatic contributions of the RAG molecules within this nucleoprotein complex and its functional organization have not been elucidated. Using heterodimeric protein preparations containing both wild-type and catalytically deficient RAG-1 molecules, we found that one active monomer is sufficient for both nicking and hairpin formation at a single RSS, demonstrating that a single active site can carry out both cleavage steps. Furthermore, the mutant heterodimers efficiently cleaved both RSS in a synaptic complex. These results strongly suggest that two RAG-1 dimers are responsible for RSS cleavage in a synaptic complex, with one monomer of each dimer catalyzing both nicking and hairpin formation at each RSS.     

The RAG1 Homeodomain Recruits HMG1 and HMG2 To Facilitate Recombination Signal Sequence Binding and To Enhance the Intrinsic DNA-Bending Activity of RAG1-RAG2

V(D)J recombination is initiated by the specific binding of the RAG1-RAG2 (RAG1/2) complex to the heptamer-nonamer recombination signal sequences (RSS). Several steps of the V(D)J recombination reaction can be reconstituted in vitro with only RAG1/2 plus the high-mobility-group protein HMG1 or HMG2. Here we show that the RAG1 homeodomain directly interacts with both HMG boxes of HMG1 and HMG2 (HMG1,2). This interaction facilitates the binding of RAG1/2 to the RSS, mainly by promoting high-affinity binding to the nonamer motif. Using circular-permutation assays, we found that the RAG1/2 complex bends the RSS DNA between the heptamer and nonamer motifs. HMG1,2 significantly enhance the binding and bending of the 23RSS but are not essential for the formation of a bent DNA intermediate on the 12RSS. A transient increase of HMG1,2 concentration in transfected cells increases the production of the final V(D)J recombinants in vivo.     

The respective roles of polar/nonpolar binary patterns and amino acid composition in protein regular secondary structures explored exhaustively using hydrophobic cluster analysis

Several studies have highlighted the leading role of the sequence periodicity of polar and nonpolar amino acids (binary patterns) in the formation of regular secondary structures (RSS). However, these were based on the analysis of only a few simple cases, with no direct mean to correlate binary patterns with the limits of RSS. Here, HCA‐derived hydrophobic clusters (HC) which are conditioned binary patterns whose positions fit well those of RSS, were considered. All the HC types, defined by unique binary patterns, which were commonly observed in three‐dimensional (3D) structures of globular domains, were analyzed. The 180 HC types with preferences for either α‐helices or β‐strands distinctly contain basic binary units typical of these RSS. Therefore a general trend supporting the “binary pattern preference” assumption was observed. HC for which observed RSS are in disagreement with their expected behavior (discordant HC) were also examined. They were separated in HC types with moderate preferences for RSS, having “weak” binary patterns and versatile RSS and HC types with high preferences for RSS, having “strong” binary patterns and then displaying nonpolar amino acids at the protein surface. It was shown that in both cases, discordant HC could be distinguished from concordant ones by well‐differentiated amino acid compositions. The obtained results could, thus, help to complement the currently available methods for the accurate prediction of secondary structures in proteins from the only information of a single amino acid sequence. This can be especially useful for characterizing orphan sequences and for assisting protein engineering and design. Proteins 2016; 84:624–638. © 2016 Wiley Periodicals, Inc.     

Renal sexual segment of the ground skink, Scincella laterale (Reptilia, Squamata, Scincidae)

Mature squamates possess hypertrophied regions of the distal urinary ducts, the renal sexual segment (RSS). The RSS is believed to provide seminal fluid that mixes with sperm and is released into the female cloaca during coitus. This study is the first to describe ultrastructure of the RSS in a lizard collected throughout the active season. The species examined, Scincella laterale, represents the largest family (Scincidae: 1,200 species) of lizards. Although sperm are present in the posterior ductus deferens of male S. laterale throughout the year, an annual spermatogenic cycle occurs that results in spermiation in spring, coinciding with maximum development of the RSS. Female S. laterale may possess stored sperm in vaginal crypts from March-May and large oviductal eggs April-June. Thus, the correlation between mating and RSS activity observed in other squamates is also found in S. laterale. Cytologically, the active RSS consists of columnar cells with numerous apical, electron-dense secretory vacuoles which are released by an apocrine process. The granules stain positively for proteins with bromphenol blue and react with PAS for neutral carbohydrates. After the mating season the RSS undergoes recrudescence and the electron-dense granules are replaced by a mucoid secretion that characterizes more proximal portions of the nephric tubules throughout the year. Little variation in ultrastructure of the RSS occurs between S. laterale and Cnemidophorus lemniscatus (Teiidae), the only other lizard in which seasonal variation of the RSS has been studied using similar methods. Females exhibit differentiation similar to that of males in the distal urinary tubules, but to a lesser degree. This is only the second such report for female squamates, and the differentiation of the region in females is proposed to result from adrenal androgens.     

Large-scale prediction of function shift in protein families with a focus on enzymatic function

Protein function shift can be predicted from sequence comparisons, either using positive selection signals or evolutionary rate estimation. None of the methods have been validated on large datasets, however. Here we investigate existing and novel methods for protein function shift prediction, and benchmark the accuracy against a large dataset of proteins with known enzymatic functions. Function change was predicted between subfamilies by identifying two kinds of sites in a multiple sequence alignment: Conservation-Shifting Sites (CSS), which are conserved in two subfamilies using two different amino acid types, and Rate-Shifting Sites (RSS), which have different evolutionary rates in two subfamilies. CSS were predicted by a new entropy-based method, and RSS using the Rate-Shift program. In principle, the more CSS and RSS between two subfamilies, the more likely a function shift between them. A test dataset was built by extracting subfamilies from Pfam with different EC numbers that belong to the same domain family. Subfamilies were generated automatically using a phylogenetic tree-based program, BETE. The dataset comprised 997 subfamily pairs with four or more members per subfamily. We observed a significant increase in CSS and RSS for subfamily comparisons with different EC numbers compared to cases with same EC numbers. The discrimination was better using RSS than CSS, and was more pronounced for larger families. Combining RSS and CSS by discriminant analysis improved classification accuracy to 71%. The method was applied to the Pfam database and the results are available at http://FunShift.cgb.ki.se. A closer examination of some superfamily comparisons showed that single EC numbers sometimes embody distinct functional classes. Hence, the measured accuracy of function shift is underestimated.     

Possible role of positive reinforcement zones in the mechanisms of pain regulation and their relation to the endogenous opiate system

The consequences of self-stimulation reaction (RSS) to pain threshold in tail withdrawal test (55 degrees C) and naloxone effect have been investigated in tests, using male rats with chronically implanted electrodes into the hypothalamus (AP = 1.5, L = 1.5, H = 8.5) and suture dorsal nucleus (AP = 7.0, L = 0, H = 7.0) (coordinates according to Fifková atlas). It was established that right after RSS, pain threshold in both zones increased 2-2.5-fold and 30 min later reached the initial level. Naloxone injected before RSS increased pain thresholds and decreased RSS frequency from hypothalamus but failed to change these RSS parameters from suture dorsal nucleus. However, naloxone did not affect the increase in pain thresholds caused by RSS from both zones. Taking into account the fact that analgesia appearing after RSS from the anterior hypothalamus as well as from suture dorsal nucleus is not reversed by naloxone, it is suggested that positive reward zones activation partially realized by opioidergic mechanisms or having no connection with them may lead to the development of non-opiate type analgesia.     

DNA cleavage of a cryptic recombination signal sequence by RAG1 and RAG2. Implications for partial V(H) gene replacement

Antibody and T cell receptor genes are assembled from gene segments by V(D)J recombination to produce an almost infinitely diverse repertoire of antigen specificities. Recombination is initiated by cleavage of conserved recombination signal sequences (RSS) by RAG1 and RAG2 during lymphocyte development. Recent evidence demonstrates that recombination can occur at noncanonical RSS sites within Ig genes or at other loci, outside the context of normal lymphocyte receptor gene rearrangement. We have characterized the ability of the RAG proteins to bind and cleave a cryptic RSS (cRSS) located within an Ig V(H) gene segment. The RAG proteins bound with sequence specificity to either the consensus RSS or the cRSS. The RAG proteins nick the cRSS on both the top and bottom strands, thereby bypassing the formation of the DNA hairpin intermediate observed in RAG cleavage of canonical RSS substrates. We propose that the RAG proteins may utilize an alternative mechanism for double-stranded DNA cleavage, depending on the substrate sequence. These results have implications for further diversification of the antigen receptor repertoire as well as the role of the RAG proteins in genomic instability.     

The NS3 protein of rice hoja blanca virus complements the RNAi suppressor function of HIV‐1 Tat

The question of whether RNA interference (RNAi) acts as an antiviral mechanism in mammalian cells remains controversial. The antiviral interferon (IFN) response cannot easily be distinguished from a possible antiviral RNAi pathway owing to the involvement of double‐stranded RNA (dsRNA) as a common inducer molecule. The non‐structural protein 3 (NS3) protein of rice hoja blanca virus (RHBV) is an RNA silencing suppressor (RSS) that exclusively binds to small dsRNA molecules. Here, we show that this plant viral RSS lacks IFN antagonistic activity, yet it is able to substitute the RSS function of the Tat protein of human immunodeficiency virus type 1. An NS3 mutant that is deficient in RNA binding and its associated RSS activity is inactive in this complementation assay. This cross‐kingdom suppression of RNAi in mammalian cells by a plant viral RSS indicates the significance of the antiviral RNAi response in mammalian cells and the usefulness of well‐defined RSS proteins.