The detection of a spleen focus-forming virus neoantigen by lymphocyte- mediated cytolysis

The existence of a nonvirion tumor-associated cell surface antigen (TASA) on cells transformed with Friend (FLV) on Rauscher (RLV) leukemia virus has been difficult to demonstrate. Antisera raised against classically defined Friend- Moloney-Rauscher antigenic determinants have been shown to react with virus structural proteins coded for by genetic information contained in the lymphatic leukemia or helper (LLV) virus genome. The recent development of nontrans-formed fibroblast cell lines which contain the replication-defective spleen focus-forming virus (SFFV) genome, free of replicating LLV, has allowed investigation of an SFFV-specific antigen. We have applied the techniques of mixed tumor-lymphocyte culture stimulation followed by lymphocyte-mediated cytolysis assays to search for the cell surface expression of an antigen coded expressly by SFFV genetic information. SFFV nonproducer-immune, in vitro activated spleen cells were capable of effecting the lysis of SFFV-containing BALB/c 3T3 and Fischer rat epithelial, cloned cell lines. Normal BALB/c 3T3 and BALB/c 3T3 cells infected with three types of ecotropic LLV were unaffected. Syngeneic FLV and RLV-induced murine leukemia cells were also killed by SFFV nonproducer-immune lymphocytes. In addition, Kirsten sarcoma virus-transformed, replication-defective and replication-rescued BALB/c 3T3 fibroblasts were not susceptible to SFFV antigen-directed cytolysis. Antibody-dependent complement-mediated cytolysis assays using monospecific goat antisera confirmed that SFFV nonproducers lacked cell surface expression of virion structural proteins. These observations suggest that the antigen detected in LMC experiments was not coded for by genetic information contained in the helper component of FLV, and that it represents a true SFFV-specific cell surface antigen. Based upon the recent molecular evaluation of the SFFV genome as consisting of both xenotropic and ecotropic virus sequences, it appears reasonable that xenotropic genetic information may be responsible for expression of the SFFV- specific antigen. Since the replication-defective SFFV genome is also responsible for the malignant transformation associated with FLV-induced erythroleukemia, one might postulate that gene sequences capable of programming transformation may also code for the TASA detected in these studies

Shell Repair in Geukensia demissa and Predation Preferences of Callinectes sapidus: Do Crabs Target Mussels with Weakened Shells?

Atlantic blue crabs, Callinectes sapidus, are voracious predators that often leave damage on the shells of unconsumed ribbed marsh mussels, Geukensia demissa. The extent of shell damage and size-dependent tradeoffs in marsh mussel growth and repair, as well as the effects of shell damage on crab predation preferences, were determined in this thesis. A preliminary experiment investigated characteristics of damaged mussels in the field. Mussels (n = 30) were collected in the fall of 2011 within two ocean-dominated inlets along the South Carolina coast and were measured for size (length, width, height), area of damage, shell thickness, mass, and strength (crushing resistance). Shell damage was significantly different between inlets and shell repair was evident in damaged mussels. During the summer of 2012 three sizes of field-collected mussels (small: 20-30 mm, medium: 50-60 mm, large: \u3e60 mm) were damaged (undamaged 0%, moderate 33%, extensive 66% shell surface removed), caged in the mid-marsh, and sampled monthly. Changes in mussel characteristics (e.g., shell length, strength), were measured. In most cases, increased damage suppressed growth, however, only medium, moderately-damaged mussels repaired shells. Medium, moderately-damaged mussels also experienced a greater mortality rate, suggesting mussels enter a critical stage around 55 mm with increased energy demands for both growth and repair. Small mussels eschewed repair and focused entirely on growth, as larger sizes create a refuge from predation. Large mussels did not exhibit any signs of shell repair and had minimal growth, possibly instead prioritizing reproduction. A series of wet lab mesocosm experiments and field trials were conducted to determine if blue crabs target damaged mussels. In the wet lab mesocosms, crabs showed a significant preference for damaged and first-touched mussels. Crab consumed damaged mussels in 68% of all successful predation attempts and mussels touched-first in 73% of successful predation attempts. Unsuccessful crabs targeted undamaged mussels first more frequently than successful crabs (55% vs 33%). However, a preference for damaged mussels was not observed consistently in the field and may have been masked by various mitigating factors. Undamaged mussels survived significantly longer than damaged mussels in the mid-marsh but were consumed at equal rates on mudflats, oyster reefs, and in the low-marsh. Mussel survival was greater overall in the mid-marsh with large mussels (\u3e 60 mm) surviving significantly longer than medium (50-60 mm) and small (20-30 mm) mussels. Limited tidally-influenced inundation and densely distributed Spartina alterniflora stems likely increased survival by impeding access of large predators (e.g., blue crabs). The generally thicker shells of larger mussels also will increase predator time and effort required to breach shells successfully and should increase survival rates for large mussels. Both mussels and crabs play a vital role in maintaining healthy salt marsh systems and reductions in either population have dramatic consequences. Salt marshes are structured in part by the top-down control of blue crabs and recent die-offs of Spartina is suspected to be caused by declining blue crab numbers while salt marsh loss due to sea level rise is suspected to be exacerbated by declining mussel numbers. Pollution, overfishing, habitat destruction, and the various effects of climate change (e.g., temperature rise, ocean acidification, sea level rise, etc.) threaten crab and mussel populations. Mussel response to shell damage and the ability of crabs to detect weakened mussels may be increasingly important as environmental conditions deteriorate. Further research should investigate the effect of shell damage on mussel pumping and if changes in pumping influences crab predation. The latitudinal differences in crab and mussel growth and behavior should also be examined, as additional insight into mussel-crab dynamics would be useful for salt marsh conservation

AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression

In addition to detecting novel transcripts and higher dynamic range, a principal claim for RNA-sequencing has been greater replicability, typically measured in sample-sample correlations of gene expression levels. Through a re-analysis of ENCODE data, we show that replicability of transcript abundances will provide misleading estimates of the replicability of conditional variation in transcript abundances (i.e., most expression experiments). Heuristics which implicitly address this problem have emerged in quality control measures to obtain 'good' differential expression results. However, these methods involve strict filters such as discarding low expressing genes or using technical replicates to remove discordant transcripts, and are costly or simply ad hoc. As an alternative, we model gene-level replicability of differential activity using co-expressing genes. We find that sets of housekeeping interactions provide a sensitive means of estimating the replicability of expression changes, where the co-expressing pair can be regarded as pseudo-replicates of one another. We model the effects of noise that perturbs a gene's expression within its usual distribution of values and show that perturbing expression by only 5% within that range is readily detectable (AUROC~0.73). We have made our method available as a set of easily implemented R scripts

In vitro generation of tumor-specific cytotoxic lymphocytes. Secondary allogeneic mixed tumor lymphocyte culture of normal murine spleen cells

In vivo or in vitro immunity to murine leukemia virus (MuLV)-induced leukemia cells which do not effectively produce virus, has been difficult to demonstrate. Because immunizations with allogeneic murine leukemia cells have been used to confer syngeneic tumor immunity to virus- producing cells, we attempted to generate lymphocytes, cytotoxic to syngeneic nonproducer leukemia cells, by stimulating normal murine spleen cells with allogeneic nonproducer leukemia cells in mixed tumor lymphocyte culture (MTLC) reactions in vitro. Secondary allogeneic MTLC of normal C57BL/6 or DBA/2 spleen cells effectively produced syngeneic tumor-specific cytotoxic lymphocytes. Target cells lysed in lymphocyte- mediated cytolysis (LMC) assays, included both Friend and Rauscher virus- induced syngeneic murine leukemia cells and chemically-induced hematopoietic tumor cells. Syngeneic tumor cells were lysed regardless of whether they produced infectious MuLV or expressed viral antigens gp-71, p-30, or p-12 at the cell surface. Syngeneic normal cells (thymus, lymph node, or Concanavalin A-stimulated spleen cells) used as targets in LMC assays were uneffected by lymphocytes harvested from secondary allogeneic MTLC. Several other in vitro culture treatments including secondary syngeneic MTLC and repetitive mixed lymphocyte culture stimulations were incapable of generating tumor-specific cytotoxic lymphocytes. Based upon these results, we propose that secondary MTLC stimulation of normal spleen cells with allogeneic nonproducer leukemia cells selects for the proliferation of two subpopulations of antigen-specific cytotoxic lymphocytes. The population capable of effecting syngeneic tumor cell lysis is directed against tumor-associated cell surface antigens which may be distinct from viral structural proteins or glycoproteins. The growth of these tumor-specific cytotoxic lymphocytes may be enhanced by a soluble allogeneic effect factor produced by the proliferation of the second subpopulation of lymphocytes generated in repetitive allogeneic MTLC, namely those lymphocytes with specificities directed against differing histocompatibility antigens

Algorithms and Comparisons of Non-negative Matrix Factorization with Volume Regularization for Hyperspectral Unmixing

In this work, we consider nonnegative matrix factorization (NMF) with a regularization that promotes small volume of the convex hull spanned by the basis matrix. We present highly efficient algorithms for three different volume regularizers, and compare them on endmember recovery in hyperspectral unmixing. The NMF algorithms developed in this work are shown to outperform the state-of-the-art volume-regularized NMF methods, and produce meaningful decompositions on real-world hyperspectral images in situations where endmembers are highly mixed (no pure pixels). Furthermore, our extensive numerical experiments show that when the data is highly separable, meaning that there are data points close to the true endmembers, and there are a few endmembers, the regularizer based on the determinant of the Gramian produces the best results in most cases. For data that is less separable and/or contains more endmembers, the regularizer based on the logarithm of the determinant of the Gramian performs best in general.Comment: 11 pages, 10 figure

Dynamics of coreless vortices and rotation-induced dissipation peak in superfluid films on rotating porous substrates

We analyze dynamics of 3D coreless vortices in superfluid films covering porous substrates. The 3D vortex dynamics is derived from the 2D dynamics of the film. The motion of a 3D vortex is a sequence of jumps between neighboring substrate cells, which can be described, nevertheless, in terms of quasi-continuous motion with average vortex velocity. The vortex velocity is derived from the dissociation rate of vortex-antivortex pairs in a 2D film, which was developed in the past on the basis of the Kosterlitz-Thouless theory. The theory explains the rotation-induced dissipation peak in torsion-oscillator experiments on $^4$He films on rotating porous substrates and can be used in the analysis of other phenomena related to vortex motion in films on porous substrates.Comment: 8 pages, 3 figures submitted to Phys. Rev.

Using predictive specificity to determine when gene set analysis is biologically meaningful

Gene set analysis, which translates gene lists into enriched functions, is among the most common bioinformatic methods. Yet few would advocate taking the results at face value. Not only is there no agreement on the algorithms themselves, there is no agreement on how to benchmark them. In this paper, we evaluate the robustness and uniqueness of enrichment results as a means of assessing methods even where correctness is unknown. We show that heavily annotated ('multifunctional') genes are likely to appear in genomics study results and drive the generation of biologically non-specific enrichment results as well as highly fragile significances. By providing a means of determining where enrichment analyses report non-specific and non-robust findings, we are able to assess where we can be confident in their use. We find significant progress in recent bias correction methods for enrichment and provide our own software implementation. Our approach can be readily adapted to any pre-existing package

Over vlugge spraak en vluchtige sjwa’s De relatie tussen spreektempo en de duur van Nederlandse svarabhaktivocalen

This study investigates the relationship between speech tempo and the duration of epentheticschwa in Dutch. The speech materials consisted of the spontaneous speech of 160 teachers of Dutch: these speakers were equally distributed over four different regions in Belgium and the Netherlands. There were an equal number of men and women. The research focus was on 750words which contained a consonant cluster with ras the first element and a non-alveolar consonant or nas the second element. These words consisted of two or three syllables after schwa insertion (e.g., werk‘work’ > [wɛrək], werken‘to work’ > [wɛrəkən]). The speech rate of these words was calculated and the duration of any inserted schwa was measured. As predicted, the results show a clear relationship between speech rate and the duration of schwa: faster speech yields shorter schwas. Besides this general trend a statistically significant effect was found of geographical region, the number of syllables, the place of articulation of rand the second element of the consonant cluster. In addition, there was a significant interaction between speech tempo and the schwa duration in men and women: women produce shorter schwas in faster speech, while their shwas in slower speech are longer thanthose in men. As such the durational differences in schwa are more outspoken in women thanin men. This can be accounted for by the general trend that vowels are generally longer in women’s speech. The shorter schwa durations in women’s fast speech may have to do with the fact that it is easier for women to bridge articulatory distances as a result of smaller oral cavity volume

Meta-Learning for Phonemic Annotation of Corpora

We apply rule induction, classifier combination and meta-learning (stacked classifiers) to the problem of bootstrapping high accuracy automatic annotation of corpora with pronunciation information. The task we address in this paper consists of generating phonemic representations reflecting the Flemish and Dutch pronunciations of a word on the basis of its orthographic representation (which in turn is based on the actual speech recordings). We compare several possible approaches to achieve the text-to-pronunciation mapping task: memory-based learning, transformation-based learning, rule induction, maximum entropy modeling, combination of classifiers in stacked learning, and stacking of meta-learners. We are interested both in optimal accuracy and in obtaining insight into the linguistic regularities involved. As far as accuracy is concerned, an already high accuracy level (93% for Celex and 86% for Fonilex at word level) for single classifiers is boosted significantly with additional error reductions of 31% and 38% respectively using combination of classifiers, and a further 5% using combination of meta-learners, bringing overall word level accuracy to 96% for the Dutch variant and 92% for the Flemish variant. We also show that the application of machine learning methods indeed leads to increased insight into the linguistic regularities determining the variation between the two pronunciation variants studied.Comment: 8 page