Assessing stationary distributions derived from chromatin contact maps.

BACKGROUND:The spatial configuration of chromosomes is essential to various cellular processes, notably gene regulation, while architecture related alterations, such as translocations and gene fusions, are often cancer drivers. Thus, eliciting chromatin conformation is important, yet challenging due to compaction, dynamics and scale. However, a variety of recent assays, in particular Hi-C, have generated new details of chromatin structure, spawning a number of novel biological findings. Many findings have resulted from analyses on the level of native contact data as generated by the assays. Alternatively, reconstruction based approaches often proceed by first converting contact frequencies into distances, then generating a three dimensional (3D) chromatin configuration that best recapitulates these distances. Subsequent analyses can enrich contact level analyses via superposition of genomic attributes on the reconstruction. But, such advantages depend on the accuracy of the reconstruction which, absent gold standards, is inherently difficult to assess. Attempts at accuracy evaluation have relied on simulation and/or FISH imaging that typically features a handful of low resolution probes. While newly advanced multiplexed FISH imaging offers possibilities for refined 3D reconstruction accuracy evaluation, availability of such data is limited due to assay complexity and the resolution thereof is appreciably lower than the reconstructions being assessed. Accordingly, there is demand for new methods of reconstruction accuracy appraisal. RESULTS:Here we explore the potential of recently proposed stationary distributions, hereafter StatDns, derived from Hi-C contact matrices, to serve as a basis for reconstruction accuracy assessment. Current usage of such StatDns has focussed on the identification of highly interactive regions (HIRs): computationally defined regions of the genome purportedly involved in numerous long-range intra-chromosomal contacts. Consistent identification of HIRs would be informative with respect to inferred 3D architecture since the corresponding regions of the reconstruction would have an elevated number of k nearest neighbors (kNNs). More generally, we anticipate a monotone decreasing relationship between StatDn values and kNN distances. After initially evaluating the reproducibility of StatDns across replicate Hi-C data sets, we use this implied StatDn - kNN relationship to gauge the utility of StatDns for reconstruction validation, making recourse to both real and simulated examples. CONCLUSIONS:Our analyses demonstrate that, as constructed, StatDns do not provide a suitable measure for assessing the accuracy of 3D genome reconstructions. Whether this is attributable to specific choices surrounding normalization in defining StatDns or to the logic underlying their very formulation remains to be determined

Abacus models for parabolic quotients of affine Weyl groups

We introduce abacus diagrams that describe minimal length coset representatives in affine Weyl groups of types B, C, and D. These abacus diagrams use a realization of the affine Weyl group of type C due to Eriksson to generalize a construction of James for the symmetric group. We also describe several combinatorial models for these parabolic quotients that generalize classical results in affine type A related to core partitions.Comment: 28 pages, To appear, Journal of Algebra. Version 2: Updated with referee's comment

The enumeration of fully commutative affine permutations

We give a generating function for the fully commutative affine permutations enumerated by rank and Coxeter length, extending formulas due to Stembridge and Barcucci--Del Lungo--Pergola--Pinzani. For fixed rank, the length generating functions have coefficients that are periodic with period dividing the rank. In the course of proving these formulas, we obtain results that elucidate the structure of the fully commutative affine permutations.Comment: 18 pages; final versio

Results and conjectures on simultaneous core partitions

An n-core partition is an integer partition whose Young diagram contains no hook lengths equal to n. We consider partitions that are simultaneously a-core and b-core for two relatively prime integers a and b. These are related to abacus diagrams and the combinatorics of the affine symmetric group (type A). We observe that self-conjugate simultaneous core partitions correspond to the combinatorics of type C, and use abacus diagrams to unite the discussion of these two sets of objects. In particular, we prove that (2n)- and (2mn+1)-core partitions correspond naturally to dominant alcoves in the m-Shi arrangement of type C_n, generalizing a result of Fishel--Vazirani for type A. We also introduce a major statistic on simultaneous n- and (n+1)-core partitions and on self-conjugate simultaneous (2n)- and (2n+1)-core partitions that yield q-analogues of the Coxeter-Catalan numbers of type A and type C. We present related conjectures and open questions on the average size of a simultaneous core partition, q-analogs of generalized Catalan numbers, and generalizations to other Coxeter groups. We also discuss connections with the cyclic sieving phenomenon and q,t-Catalan numbers.Comment: 17 pages; to appear in the European Journal of Combinatoric

Improving Surrogate Monitoring Techniques for Suspended Sediment

The quality of water of our nation’s rivers and streams is important to many vital uses including drinking water treatment, recreation, and the natural environment. Water quality can be severely impacted by the quantity and type of suspended sediment found therein. Because suspended sediment can be associated with many other contaminants that degrade water quality, it is noted as the most common impairment to water quality in the United States. Suspended sediment can cause significant ecological impacts to the chemical and biological characteristics of surface waters. The ability to accurately quantify suspended sediment concentrations at the appropriate time(s) and location(s) is critical in assessing whether streams are meeting their designated beneficial uses and in implementing and evaluating watershed management and mitigation plans and restoration efforts. Currently, new methods for quantifying suspended sediment concentrations use mathematical and statistical techniques to relate turbidity and suspended sediment and have been shown to be affected by several factors, including the size and characteristics of suspended sediment particles. In this research we used turbidity as a surrogate (substitute) for suspended sediment at six locations in the Little Bear River, Utah, U.S.A. We also examined the differences between single-point and width and depth integrated suspended sediment sampling at two sites. This was used to develop a method to account for the differences and improve the resulting estimates of suspended sediment concentrations. Statistical techniques were used to assess—in probabilistic terms—the duration and magnitude of potential water quality criteria exceedance. Findings highlight that among some monitoring locations with wide geographic distances, turbiditysuspended sediment relationships are not site-specific for the more frequent (90th percentile) but lower (\u3c50 \u3eNTU) turbidity values. Comparisons of point measures of turbidity and width and depth integrated suspended sediment samples revealed that suspended sediment is homogenous at their respective stream cross sections for 90% and 99% of the time at sites 2 and 6, respectively. The results are applicable to water managers who are charged with the determination of attainment or exceedance of water quality standards

EDUCATIONAL PROGRAMS FOR COMMERCIAL AGRICULTURE AND AGRIBUSINESS

Agribusiness,

Structure of the doublet bands in doubly odd nuclei: The case of 128Cs^{128}Cs

The structure of the $\Delta J = 1$ doublet bands in $^{128}Cs$ is investigated within the framework of the Interacting Vector Boson Fermion Model (IVBFM). A new, purely collective interpretation of these bands is given on the basis of the used boson-fermion dynamical symmetry of the model. The energy levels of the doublet bands as well as the absolute $B(E2)$ and $B(M1)$ transition probabilities between the states of both yrast and yrare bands are described quite well. The observed odd-even staggering of both $B(M1)$ and $B(E2)$ values is reproduced by the introduction of an appropriate interaction term of quadrupole type, which produces such a staggering effect in the transition strengths. The calculations show that the appearance of doublet bands in certain odd-odd nuclei could be a consequence of the realization of a larger dynamical symmetry based on the non-compact supersymmetry group $OSp(2\Omega /12, R)$.Comment: 12 pages, 8 figure

Assessing explanations for sex differences in emotional support: A test of the different cultures and skill specialization accounts

Abstract OnlyResearch documents sex differences in interpersonal behaviors, such as comforting and emotional support, with women consistently being more likely than men to engage in comforting behavior, to produce sophisticated comforting messages, to value comforting skills, and to select friends based on comforting skills. Explanations for these gender differences include the “different cultures account” and the “skill specialization account.” This research was designed to test these explanations by assessing contrasting predictions derived from each account. Participants completed questionnaires assessing the types of comforting messages perceived as most sensitive and effective, preferences for the sex of comfort providers, and priorities assigned to affective and instrumental goals in comforting contexts. The results indicated that men and women evaluated comforting messages similarly, preferred receiving emotional support from female providers, and had similar priorities in comforting contexts. These results are most consistent with the skill specialization account and provide virtually no support for the different cultures account

Estudio conceptual de un buque modular configurable por misión

This work illustrates how modern high speed craft design tools may be effectively used to evaluate innovative concepts for which empirical data may be limited. The example presented here was motivated by the US Navy’s interest in a finding a replacement for, or complement to, the USN Special Operations Forces’ Mark V high speed craft. Given the conflicting demands of restricted size and weight imposed by air transportability and broad mission requirements, a modular, multi-hull configuration is proposed and studied. The boat parameter space that influences calm water performance, sea keeping accelerations, and structural loads is explored. A proposed trimaran concept shows how intelligent placement of outer, or wing hulls can, in principle, mitigate shock loads and lower resistance, but with the cost of increased structural complexity and potentially a heavier craft.Este trabajo muestra cómo las herramientas modernas de diseño de buques de alta velocidad pueden ser usadas para evaluar conceptos innovadores para los que los datos empíricos pueden ser limitados. El ejemplo presentado fue motivado por el interés de la Marina de los EE.UU. en reemplazar o complementar el buque de alta velocidad Mark V. Dados los requerimientos contradictorios de tamaño y peso reducido impuestos para poder ser transportados por aire frente a la capacidad de realizar un amplio rango de misiones, se propone y analiza una configuración modular multicasco. Se realiza la exploración del espacio de diseño de las variables que influencian el desempeño en aguas tranquilas, el comportamiento en el mar y las cargas estructurales. El diseño conceptual tipo trimarán muestra como la disposición adecuada de los cascos externos puede reducir las cargas de impacto y la resistencia del buque a cambio de un aumento en la complejidad estructural y potencialmente el peso de la embarcación

Relational implications of communication skill evaluations and love styles.

Abstract OnlyAs values placed by individuals on communication skills may associate with experiences of romantic love, this study explores relationships between communication values and the adoption of six major love styles (Lee, 1973). Two hundred and seventy‐two participants (119 males and 153 females) completed an expanded version of Burleson and Samter's (1990) Communication Functions Questionnaire, which generates judgments about the importance of several communication skills, and Hendrick and Hendrick's (1986) Love Attitudes Scale, which provides assessments of love styles. Results indicated numerous significant associations between communication values and love styles, sex differences in the evaluation of some communication values and in the adoption of some love styles, and that sex moderates relationships between some of the communication values and love styles