Jones-matrix Formalism as a Representation of the Lorentz Group

It is shown that the two-by-two Jones-matrix formalism for polarization optics is a six-parameter two-by-two representation of the Lorentz group. The attenuation and phase-shift filters are represented respectively by the three-parameter rotation subgroup and the three-parameter Lorentz group for two spatial and one time dimensions. It is noted that the Lorentz group has another three-parameter subgroup which is like the two-dimensional Euclidean group. Possible optical filters having this Euclidean symmetry are discussed in detail. It is shown also that the Jones-matrix formalism can be extended to some of the non-orthogonal polarization coordinate systems within the framework of the Lorentz-group representation.Comment: RevTeX, 27 pages, no figures, to be published in J. Opt. Soc. Am.

Stokes Parameters as a Minkowskian Four-vector

It is noted that the Jones-matrix formalism for polarization optics is a six-parameter two-by-two representation of the Lorentz group. It is shown that the four independent Stokes parameters form a Minkowskian four-vector, just like the energy-momentum four-vector in special relativity. The optical filters are represented by four-by-four Lorentz-transformation matrices. This four-by-four formalism can deal with partial coherence described by the Stokes parameters. A four-by-four matrix formulation is given for decoherence effects on the Stokes parameters, and a possible experiment is proposed. It is shown also that this Lorentz-group formalism leads to optical filters with a symmetry property corresponding to that of two-dimensional Euclidean transformations.Comment: RevTeX, 22 pages, no figures, submitted to Phys. Rev.

Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness

While Simple Sequence Repeats (SSRs) are extremely useful genetic markers, recent advances in technology have produced a shift toward use of single nucleotide polymorphisms (SNPs). The different mutational properties of these two classes of markers result in differences in heterozygosities and allele frequencies that may have implications for their use in assessing relatedness and evaluation of genetic diversity. We compared analyses based on 89 SSRs (primarily dinucleotide repeats) to analyses based on 847 SNPs in individuals from the same 259 inbred maize lines, which had been chosen to represent the diversity available among current and historic lines used in breeding. The SSRs performed better at clustering germplasm into populations than did a set of 847 SNPs or 554 SNP haplotypes, and SSRs provided more resolution in measuring genetic distance based on allele-sharing. Except for closely related pairs of individuals, measures of distance based on SSRs were only weakly correlated with measures of distance based on SNPs. Our results suggest that 1) large numbers of SNP loci will be required to replace highly polymorphic SSRs in studies of diversity and relatedness and 2) relatedness among highly-diverged maize lines is difficult to measure accurately regardless of the marker system

Being user-oriented: convergences, divergences, and the potentials for systematic dialogue between disciplines and between researchers, designers, and providers

The challenge this panel addresses is drawn from intersecting literature reviews and critical commentaries focusing on: 1) user studies in multiple fields; and 2) the difficulties of bringing different disciplines and perspectives to bear on user‐oriented research, design, and practice. 1 The challenge is that while we have made some progress in collaborative work, we have some distance to go to become user‐oriented in inter‐disciplinary and inter‐perspective ways. The varieties of our approaches and solutions are, as some observers suggest, an increasing cacophony. One major difficulty is that most discussions are solution‐oriented, offering arguments of this sort ‐‐ if only we addressed users in this way… Each solution becomes yet another addition to the cacophony. This panel implements a central approach documented for its utility by communication researchers and long used by communication mediators and negotiators ‐‐ that of focusing not on communication but rather on meta‐communication: communicating about communication. The intent in the context of this panel is to help us refocus attention from too frequent polarizations between alternative solutions to the possibility of coming to understand what is behind the alternatives and where they point to experientially‐based convergences and divergences, both of which might potentially contribute to synergies. The background project for this panel comes from a series of in‐depth interviews with expert researchers, designers, and providers in three field groupings ‐‐ library and information science; human computer interaction/information technology; and communication and media studies. One set of interviews involved 5‐hour focus groups with directors of academic and public libraries serving 44 colleges and universities in central Ohio; the second involved one‐on‐one interviews averaging 50 minutes with 81 nationally‐internationally known experts in the 3 fields, 25‐27 interviews per field. Using Dervin\u27s Sense‐Making Methodological approach to interviewing, the expert interviews of both kinds asked each interviewee: what he/she considered to be the big unanswered questions about users and what explained why the questions have not been answered; and, what he/she saw as hindering versus helping in attempts to communicate about users across disciplinary and perspective gaps. 2 The panel consists of six teams, two from each field. Prior to the panel presentation at ASIST, each team will have read the set of interviews and completed impressionistic essays of what patterns and themes they saw as emerging. At this stage, team members will purposively not homogenize their differences and most will write solo‐authored essays that will be placed on a web‐site accessible to ASIST members prior to the November meeting. In addition, at least one systematic analysis will be completed and available online. 3 At the ASIST panel, each team\u27s leader will present a brief and intentionally provocative impressionist account of what his/her team came to understand about our struggles communicating across fields and perspectives about users. Again, each team will purposively not homogenize its own differences in viewpoints, but rather highlight them as fodder for discussion. A major purpose will be to invite audience members to join the panel in discussion. At least 20 minutes will be left open for this purpose

Mapping quantitative trait loci (QTL) in sheep. I. A new male framework linkage map and QTL for growth rate and body weight

A male sheep linkage map comprising 191 microsatellites was generated from a single family of 510 Awassi-Merino backcross progeny. Except for ovine chromosomes 1, 2, 10 and 17, all other chromosomes yielded a LOD score difference greater than 3.0 between the best and second-best map order. The map is on average 11% longer than the Sheep Linkage Map v4.7 male-specific map. This map was employed in quantitative trait loci (QTL) analyses on body-weight and growth-rate traits between birth and 98 weeks of age. A custom maximum likelihood program was developed to map QTL in half-sib families for non-inbred strains (QTL-MLE) and is freely available on request. The new analysis package offers the advantage of enabling QTL × fixed effect interactions to be included in the model. Fifty-four putative QTL were identified on nine chromosomes. Significant QTL with sex-specific effects (i.e. QTL × sex interaction) in the range of 0.4 to 0.7 SD were found on ovine chromosomes 1, 3, 6, 11, 21, 23, 24 and 26

An 11-bp Insertion in Zea mays fatb Reduces the Palmitic Acid Content of Fatty Acids in Maize Grain

The ratio of saturated to unsaturated fatty acids in maize kernels strongly impacts human and livestock health, but is a complex trait that is difficult to select based on phenotype. Map-based cloning of quantitative trait loci (QTL) is a powerful but time-consuming method for the dissection of complex traits. Here, we combine linkage and association analyses to fine map QTL-Pal9, a QTL influencing levels of palmitic acid, an important class of saturated fatty acid. QTL-Pal9 was mapped to a 90-kb region, in which we identified a candidate gene, Zea mays fatb (Zmfatb), which encodes acyl-ACP thioesterase. An 11-bp insertion in the last exon of Zmfatb decreases palmitic acid content and concentration, leading to an optimization of the ratio of saturated to unsaturated fatty acids while having no effect on total oil content. We used three-dimensional structure analysis to explain the functional mechanism of the ZmFATB protein and confirmed the proposed model in vitro and in vivo. We measured the genetic effect of the functional site in 15 different genetic backgrounds and found a maximum change of 4.57 mg/g palmitic acid content, which accounts for ∼20–60% of the variation in the ratio of saturated to unsaturated fatty acids. A PCR-based marker for QTL-Pal9 was developed for marker-assisted selection of nutritionally healthier maize lines. The method presented here provides a new, efficient way to clone QTL, and the cloned palmitic acid QTL sheds lights on the genetic mechanism of oil biosynthesis and targeted maize molecular breeding

Genetic diversity fuels gene discovery for tobacco and alcohol use

Tobacco and alcohol use are heritable behaviours associated with 15% and 5.3% of worldwide deaths, respectively, due largely to broad increased risk for disease and injury(1-4). These substances are used across the globe, yet genome-wide association studies have focused largely on individuals of European ancestries(5). Here we leveraged global genetic diversity across 3.4 million individuals from four major clines of global ancestry (approximately 21% non-European) to power the discovery and fine-mapping of genomic loci associated with tobacco and alcohol use, to inform function of these loci via ancestry-aware transcriptome-wide association studies, and to evaluate the genetic architecture and predictive power of polygenic risk within and across populations. We found that increases in sample size and genetic diversity improved locus identification and fine-mapping resolution, and that a large majority of the 3,823 associated variants (from 2,143 loci) showed consistent effect sizes across ancestry dimensions. However, polygenic risk scores developed in one ancestry performed poorly in others, highlighting the continued need to increase sample sizes of diverse ancestries to realize any potential benefit of polygenic prediction.Peer reviewe

Behavioural indicators of welfare in farmed fish

Behaviour represents a reaction to the environment as fish perceive it and is therefore a key element of fish welfare. This review summarises the main findings on how behavioural changes have been used to assess welfare in farmed fish, using both functional and feeling-based approaches. Changes in foraging behaviour, ventilatory activity, aggression, individual and group swimming behaviour, stereotypic and abnormal behaviour have been linked with acute and chronic stressors in aquaculture and can therefore be regarded as likely indicators of poor welfare. On the contrary, measurements of exploratory behaviour, feed anticipatory activity and reward-related operant behaviour are beginning to be considered as indicators of positive emotions and welfare in fish. Despite the lack of scientific agreement about the existence of sentience in fish, the possibility that they are capable of both positive and negative emotions may contribute to the development of new strategies (e. g. environmental enrichment) to promote good welfare. Numerous studies that use behavioural indicators of welfare show that behavioural changes can be interpreted as either good or poor welfare depending on the fish species. It is therefore essential to understand the species-specific biology before drawing any conclusions in relation to welfare. In addition, different individuals within the same species may exhibit divergent coping strategies towards stressors, and what is tolerated by some individuals may be detrimental to others. Therefore, the assessment of welfare in a few individuals may not represent the average welfare of a group and vice versa. This underlines the need to develop on-farm, operational behavioural welfare indicators that can be easily used to assess not only the individual welfare but also the welfare of the whole group (e. g. spatial distribution). With the ongoing development of video technology and image processing, the on-farm surveillance of behaviour may in the near future represent a low-cost, noninvasive tool to assess the welfare of farmed fish.Fundação para a Ciência e Tecnologia, Portugal [SFRH/BPD/42015/2007]info:eu-repo/semantics/publishedVersio

Refined histopathological predictors of BRCA1 and BRCA2 mutation status: A large-scale analysis of breast cancer characteristics from the BCAC, CIMBA, and ENIGMA consortia

Introduction: The distribution of histopathological features of invasive breast tumors in BRCA1 or BRCA2 germline mutation carriers differs from that of individuals with no known mutation. Histopathological features thus have utility for mutation prediction, including statistical modeling to assess pathogenicity of BRCA1 or BRCA2 variants of uncertain clinical significance. We analyzed large pathology datasets accrued by the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) and the Breast Cancer Association Consortium (BCAC) to reassess histopathological predictors of BRCA1 and BRCA2 mutation status, and provide robust likelihood ratio (LR) estimates for statistical modeling. Methods: Selection criteria for study/center inclusion were estrogen receptor (ER) status or grade data available for invasive breast cancer diagnosed younger than 70 years. The dataset included 4,477 BRCA1 mutation carriers, 2,565 BRCA2 mutation carriers, and 47,565 BCAC breast cancer cases. Country-stratified estimates of the