On maximum entropy and minimum KL-divergence optimization by Grobner basis methods

In this paper we study constrained maximum entropy and minimum divergence optimization problems, in the cases where integer valued sufficient statistics exists, using tools from computational commutative algebra. We show that the estimation of parametric statistical models in this case can be transformed to solving a system of polynomial equations. We give an implicit description of maximum entropy models by embedding them in algebraic varieties for which we give a Grobner basis method to compute it. In the cases of minimum KL-divergence models we show that implicitization preserves specialization of prior distribution. This result leads us to a Grobner basis method to embed minimum KL-divergence models in algebraic varieties. (C) 2012 Elsevier Inc. All rights reserved.

Simulating grasping behavior of people using the relational description scheme

This paper presents an enhanced relational description for the prescription of the grasp requirement and evolution of the posture of a digital human hand towards satisfaction of this requirement. Precise relational description needs anatomical segmentation of the hand geometry into palmar, dorsal and lateral patches using the palm-plane and joint locations information, and operational segmentation of the object geometry into pull,push and lateral patches with due consideration to the effect of friction. Relational description identifies appropriate patches for a desired grasp condition. Satisfaction of this requirement occurs in two discrete stages,namely,contact establishment and post-contact force exertion for object capturing. Contact establishment occurs in four potentially overlapping phases,namely,re-orientation,transfer,pre- shaping,and closing-in. The novel h and re-orientation phase,enables the palm to face the object in a task sequence scenario, transfer takes the wrist to the ball park ; pre-shaping and close-in finally achieves the contact. In this paper, an anatomically pertinent closed-form formulation is presented for the closing-in phase for identification of the point of contact on the patches ,prescribed by the relational description. Since mere contact does not ensure grasp and slip phenomenon at the point of contact on application of force is a common occurrence, the effect of slip in presence of friction has been studied for 2D and 3D object grasping endeavours and a computational generation of the slip locus is presented.A general slip locus is found to be a non-linear curve even on planar faces.Two varieties of slip phenomena,namely,stabilizing and non-stabilizing slips, and their local characteristics have been identified.Study of the evolution of this slip characteristic over the slip locus exhibited diverse grasping behaviour possibilities. Thus, the relational description paradigm not only makes the requirement specification easy and meaningful but also enables high fidelity hand object interaction studies possible.

High speed digital holographic interferometry for hypersonic flow visualization

Optical imaging techniques have played a major role in understanding the flow dynamics of varieties of fluid flows, particularly in the study of hypersonic flows. Schlieren and shadowgraph techniques have been the flow diagnostic tools for the investigation of compressible flows since more than a century. However these techniques provide only the qualitative information about the flow field. Other optical techniques such as holographic interferometry and laser induced fluorescence (LIF) have been used extensively for extracting quantitative information about the high speed flows. In this paper we present the application of digital holographic interferometry (DHI) technique integrated with short duration hypersonic shock tunnel facility having 1 ms test time, for quantitative flow visualization. Dynamics of the flow fields in hypersonic/supersonic speeds around different test models is visualized with DHI using a high-speed digital camera (0.2 million fps). These visualization results are compared with schlieren visualization and CFD simulation results. Fringe analysis is carried out to estimate the density of the flow field.

Rapid determination of main constituents of packed juices by reverse phase-high performance liquid chromatography: an insight in to commercial fruit drinks

The present work reports the compositional analysis of thirteen different packed fruit juices using high performance liquid chromatography (HPLC). Vitamin C, organic acids (citric and malic) and sugars (fructose, glucose and sucrose) were separated, analyzed and quantified using different reverse phase methods. A new rapid reverse phase HPLC method was developed for routine analysis of vitamin C in fruit juices. The precision results of the methods showed that the relative standard deviations of the repeatability and reproducibility were < 0.05 and < 0.1 respectively. Correlation coefficient of the calibration models developed was found to be higher than 0.99 in each case. It has been found that the content of Vitamin C was less variable amongst different varieties involved in the study. It is also observed that in comparison to fresh juices, the packed juices contain lesser amounts of vitamin C. Citric acid was found as the major organic acids present in packed juices while maximum portion of sugars was of sucrose. Comparison of the amount of vitamin C, organic acids and sugars in same fruit juice of different commercial brands is also reported.

Phenotypic characters of rice landraces reveal independent lineages of short-grain aromatic indica rice

Rice landraces are lineages developed by farmers through artificial selection during the long-term domestication process. Despite huge potential for crop improvement, they are largely understudied in India. Here, we analyse a suite of phenotypic characters from large numbers of Indian landraces comprised of both aromatic and non-aromatic varieties. Our primary aim was to investigate the major determinants of diversity, the strength of segregation among aromatic and non-aromatic landraces as well as that within aromatic landraces. Using principal component analysis, we found that grain length, width and weight, panicle weight and leaf length have the most substantial contribution. Discriminant analysis can effectively distinguish the majority of aromatic from non-aromatic landraces. More interestingly, within aromatic landraces long-grain traditional Basmati and short-grain non-Basmati aromatics remain morphologically well differentiated. The present research emphasizes the general patterns of phenotypic diversity and finds out the most important characters. It also confirms the existence of very unique short-grain aromatic landraces, perhaps carrying signatures of independent origin of an additional aroma quantitative trait locus in the indica group, unlike introgression of specific alleles of the BADH2 gene from the japonica group as in Basmati. We presume that this parallel origin and evolution of aroma in short-grain indica landraces are linked to the long history of rice domestication that involved inheritance of several traits from Oryza nivara, in addition to O. rufipogon. We conclude with a note that the insights from the phenotypic analysis essentially comprise the first part, which will likely be validated with subsequent molecular analysis.

The knight of sugar industry: T. S. Venkatraman (1884-1963)

Tiruvadi Sambasiva Venkatraman (TSV) was a plant breeder. In response to a call from Pundit Madan Mohan Malaviya, he made it his mission to develop high-yielding varieties of sugarcane for manufacturing sugar and making it available as a sweetening agent and an energy source for the malnourished children of India. Using Saccharum officinarum, then under cultivation in India, as the female parent, he artificially fertilized it with pollen from S. barberi, which grew wild in Coimbatore. After 4-5 recurrent backcrossings of S. officinarum Chi wild Sorghum spontaneum with S. officinarum as the female parent, TSV selected the `rare' interspecies hybrid cane varieties that resembled sugarcane and had approximately 2.5 cm thick juicy stems containing 16-18% sucrose - nearly 35 times more than what occurred in parent stocks. The hybrid canes matured quickly, were resistant to waterlogging, drought, and to the red-rot disease caused by Glomerella tucumanensis (Sordariomycetes: Glomerellaceae), and to the sereh-virus disease. Most importantly, they were amenable for propagation using stem cuttings. In recognition of the development of high-yielding sugarcane varieties, TSV was conferred the titles Rao Bahadur, Rao Sahib, and Sir by the British Government, and Padma Bhushan by the Republic of India. In the next few decades, consequent to TSV's work, India turned into the second largest sugar producer in the world, after Brazil. The hybrid sugarcane varieties developed are the foundational stocks for new sugarcane x bamboo hybrids, and for possible resistance to Puccinia megalocephala (Pucciniomycetes: Pucciniaceae) and Ustilago scitaminea (Ustilaginomycetes: Ustilaginaceae) using molecular techniques.

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.

Halogen Bonds in Crystal Engineering: Like Hydrogen Bonds yet Different

CONSPECTUS: The halogen bond is an attractive interaction in which an electrophilic halogen atom approaches a negatively polarized species. Short halogen atom contacts in crystals have been known for around 50 years. Such contacts are found in two varieties: type I, which is symmetrical, and type II, which is bent. Both are influenced by geometric and chemical considerations. Our research group has been using halogen atom interactions as design elements in crystal engineering, for nearly 30 years. These interactions include halogen center dot center dot center dot halogen interactions (X center dot center dot center dot X) and halogen center dot center dot center dot heteroatom interactions (X center dot center dot center dot B). Many X center dot center dot center dot X and almost all X center dot center dot center dot B contacts can be classified as halogen bonds. In this Account, we illustrate examples of crystal engineering where one can build up from previous knowledge with a focus that is provided by the modern definition of the halogen bond. We also comment on the similarities and differences between halogen bonds and hydrogen bonds. These interactions are similar because the protagonist atoms halogen and hydrogen are both electrophilic in nature. The interactions are distinctive because the size of a halogen atom is of consequence when compared with the atomic sizes of, for example, C, N, and O, unlike that of a hydrogen atom. Conclusions may be drawn pertaining to the nature of X center dot center dot center dot X interactions from the Cambridge Structural Database (CSD). There is a clear geometric and chemical distinction between type I and type II, with only type II being halogen bonds. Cl/Br isostructurality is explained based on a geometric model. In parallel, experimental studies on 3,4-dichlorophenol and its congeners shed light on the nature of halogen center dot center dot center dot halogen interactions and reveal the chemical difference between Cl and Br. Variable temperature studies also show differences between type I and type II contacts. In terms of crystal design, halogen bonds offer a unique opportunity in the strength, atom size and interaction gradation; this may be used in the design of ternary cocrystals. Structural modularity in which an entire crystal structure is defined as a combination of modules is rationalized on the basis of the intermediate strength of a halogen bond. The specific directionality of the halogen bond makes it a good tool to achieve orthogonality in molecular crystals. Mechanical properties can be tuned systematically by varying these orthogonally oriented halogen center dot center dot center dot halogen interactions. In a further development, halogen bonds are shown to play a systematic role in organization of LSAMs (long range synthon aufbau module), which are bigger structural units containing multiple synthons. With a formal definition in place, this may be the right time to look at differences between halogen bonds and hydrogen bonds and exploit them in more subtle ways in crystal engineering.

Graded IR Filters: Distinguishing Between Single and Multipoint NO2 center dot center dot center dot I Halogen Bonded Supramolecular Synthons (P, Q, and R Synthons)

The NO2 center dot center dot center dot I supramolecular synthon is a halogen bonded recognition pattern that is present in the crystal structures of many compounds that contain these functional groups. These synthons have been previously distinguished as P, Q, and R types using topological and geometrical criteria. A five step IR spectroscopic sequence is proposed here to distinguish between these synthon types in solid samples. Sets of known compounds that contain the P, Q, and R synthons are first taken to develop IR spectroscopic identifiers for them. The identifiers are then used to create graded IR filters that sieve the synthons. These filters contain signatures of the individual NO2 center dot center dot center dot I synthons and may be applied to distinguish between P, Q, and R synthon varieties. They are also useful to identify synthons that are of a borderline character, synthons in disordered structures wherein the crystal structure in itself is not sufficient to distinguish synthon types, and in the identification of the NO2 center dot center dot center dot I synthons in compounds with unknown crystal structures. This study establishes clear differences for the three different geometries P, Q, and Rand in the chemical differences in the intermolecular interactions contained in the synthons. Our IR method can be conveniently employed when single crystals are not readily available also in high throughput analysis. It is possible that such identification may also be adopted as an input for crystal structure prediction analysis of compounds with unknown crystal structures.