Miracle-dz/UniFAR-FTUs huggingface dataset:
T Cell Recognition of Distinct Peptide:I-Au Conformers in Murine Experimental Autoimmune Encephalomyelitis 1

We have used T cells bearing TCRs that are closely related in sequence as probes to detect conformational variants of peptide-MHC complexes in murine experimental autoimmune encephalomyelitis in H-2u mice. The N-terminal epitope of myelin basic protein (MBP) is immunodominant in this model. Our studies have primarily focused on T cell recognition of a position 4 analog of this peptide (MBP1–9[4Y]) complexed with I-Au. Using site-directed mutagenesis, we have mapped the functionally important complementarity determining region residues of the 1934.4 TCR Vα domain. One of the resulting mutants (Tyr95 to alanine in CDR3α, Y95A) has interesting properties: relative to the parent wild-type TCR, this mutant poorly recognizes Ag complexes generated by pulsing professional APCs (PL-8 cells) with MBP1–9[4Y] while retaining recognition of MBP1–9[4Y]-pulsed unconventional APCs or insect cell-expressed complexes of I-Au containing tethered MBP1–9[4Y]. Insect cell expression of recombinant I-Au with covalently tethered class II-associated invariant chain peptide or other peptides which bind relatively weakly, followed by proteolytic cleavage of the peptide linker and replacement by MBP1–9[4Y] in vitro, results in complexes that resemble peptide-pulsed PL-8 cells. Therefore, the distinct conformers can be produced in recombinant form. T cells that can distinguish these two conformers can also be generated by the immunization of H-2u mice, indicating that differential recognition of the conformers is observed for responding T cells in vivo. These studies have relevance to understanding the molecular details of T cell recognition in murine experimental autoimmune encephalomyelitis. They are also of particular importance for the effective use of multimeric peptide-MHC complexes to characterize the properties of Ag-specific T cells.
Content-based retrieval in multimedia imaging

Content-based retrieval is founded on neural networks, this technology allows automatic filing of images and a wide range of possible queries of the resulting database. This is in contrast to methods such as entering SQL keys manually for each image as it is filed and later correctly re-entering those keys to retrieve the same image. An SQL-based approach does not take into account information that is hard to describe with text, such as sounds and images. Neural networks can be trained to translate `noisy' or chaotic image data into simpler, more reliable feature sets. By converting the images into the level of abstraction necessary for symbolic processing, standard database indexing methods can then be applied, or used in layers of associative database neural networks directly.
Genomic and Proteomic Analyses Indicate that Banchine and Campoplegine Polydnaviruses Have Similar, if Not Identical, Viral Ancestors

ABSTRACT Polydnaviruses form a group of unconventional double-stranded DNA (dsDNA) viruses transmitted by endoparasitic wasps during egg laying into caterpillar hosts, where viral gene expression is essential to immature wasp survival. A copy of the viral genome is present in wasp chromosomes, thus ensuring vertical transmission. Polydnaviruses comprise two taxa, Bracovirus and Ichnovirus, shown to have distinct viral ancestors whose genomes were “captured” by ancestral wasps. While evidence indicates that bracoviruses derive from a nudivirus ancestor, the identity of the ichnovirus progenitor remains unknown. In addition, ichnoviruses are found in two ichneumonid wasp subfamilies, Campopleginae and Banchinae, where they constitute morphologically and genomically different virus types. To address the question of whether these two ichnovirus subgroups have distinct ancestors, we used genomic, proteomic, and transcriptomic analyses to characterize particle proteins of the banchine Glypta fumiferanae ichnovirus and the genes encoding them. Several proteins were found to be homologous to those identified earlier for campoplegine ichnoviruses while the corresponding genes were located in clusters of the wasp genome similar to those observed previously in a campoplegine wasp. However, for the first time in a polydnavirus system, these clusters also revealed sequences encoding enzymes presumed to form the replicative machinery of the progenitor virus and observed to be overexpressed in the virogenic tissue. Homology searches pointed to nucleocytoplasmic large DNA viruses as the likely source of these genes. These data, along with an analysis of the chromosomal form of five viral genome segments, provide clear evidence for the relatedness of the banchine and campoplegine ichnovirus ancestors. IMPORTANCE Recent work indicates that the two recognized polydnavirus taxa, Bracovirus and Ichnovirus, are derived from distinct viruses whose genomes integrated into the genomes of ancestral wasps. However, the identity of the ichnovirus ancestor is unknown, and questions remain regarding the possibility that the two described ichnovirus subgroups, banchine and campoplegine ichnoviruses, have distinct origins. Our study provides unequivocal evidence that these two ichnovirus types are derived from related viral progenitors. This suggests that morphological and genomic differences observed between the ichnovirus lineages, including features unique to banchine ichnovirus genome segments, result from evolutionary divergence either before or after their endogenization. Strikingly, analysis of selected wasp genomic regions revealed genes presumed to be part of the replicative machinery of the progenitor virus, shedding new light on the likely identity of this virus. Finally, these genes could well play a role in ichnovirus replication as they were overexpressed in the virogenic tissue.
Homogeneity of 16S-23S Ribosomal Intergenic Spacer Regions of Tropheryma whippelii in Swiss Patients with Whipple’s Disease

ABSTRACT The current genetic strategies used to identify Tropheryma whippelii, the putative agent of Whipple’s disease, are based on PCR-mediated amplification of a part of its 16S rRNA gene (16S rDNA). Because there is very little intraspecies variation in these molecules, they are not suitable as targets for epidemiologic investigations. However, the intergenic spacer region between the 16S and 23S rDNAs is usually much more variable and has repeatedly been used for epidemiologic purposes. We have therefore amplified the spacer region of T. whippelii directly from clinical specimens from nine independent Swiss patients with Whipple’s disease by PCR with primers complementary to the 3′ and 5′ ends of the 16S and 23S rDNAs, respectively. The amplicons were directly sequenced and the sequences were compared to the T. whippelii reference sequence in GenBank/EMBL (accession no. X99636 ). Complete sequence homogeneity was found between the samples from our nine patients; the spacer sequence was also identical to the reference sequence. However, the sequences corresponding to the 3′ and 5′ ends of the 16S and the 23S rDNAs ofT. whippelii, respectively, differed from the respective sequences in GenBank/EMBL. The same sequence found in our patients was then found in a sample from the German patient from which the published sequence had been derived. We conclude that the 16S-23S rDNA spacer region seems to be very conserved in T. whippelii and that the respective reference entry in public databases should be revised.
Quantitative RT-PCR analyses of five evolutionary conserved genes in Alligator brains during development

Gene expression was investigated in the major brain subdivisions (telencephalon, diencephalon, midbrain and hindbrain) in a representative reptile, Alligator mississipiensis, during the later stages of embryonic development. The following genes were examined: voltage-gated sodium channel isoforms: NaV1.1 and NaV1.2; synaptic vesicle 2a (SV2a); synaptophysin; and calbindin 2. With the exception of synaptophysin, which was only expressed in the telencephalon, all genes were expressed in all brain regions sampled at the time periods examined. For NaV1.1, gene expression varied according to brain area sampled. When compared with NaV1.1, the pattern of NaV1.2 gene expression differed appreciably. The gene expression of SV2a was the most robust of any of the genes examined. Of the other genes examined, although differences were noted, no statistically significant changes were found either between brain part or time interval. Although limited, the present analysis is the first quantitative mRNA gene expression study in any reptile during development. Together with future experiments of a similar nature, the present gene expression results should determine which genes are expressed in major brain areas at which times during development in Alligator. When compared with other amniotes, these results will prove useful for determining how gene expression during development influences adult brain structure.
Application of Dynamic Contrast-Enhanced MRI Parameters for Differentiating Squamous Cell Carcinoma and Malignant Lymphoma of the Oropharynx.

OBJECTIVE The purpose of this study was to investigate the usefulness of histogram analysis of dynamic contrast-enhanced MRI (DCE-MRI) parameters for the differentiation of squamous cell carcinoma (SCC) and malignant lymphoma of the oropharynx. MATERIALS AND METHODS Pretreatment DCE-MRI was performed in 21 patients with pathologically confirmed oropharyngeal SCC and six patients with malignant lymphoma. DCE-MRI parameter maps including the volume transfer constant (K(trans)), flux rate constant (kep), and extravascular extracellular volume fraction (ve) based on the Tofts model were obtained. Enhancing tumors were manually segmented on each slice of the parameter maps, and the data were collected to obtain a histogram for the entire tumor volume. The Wilcoxon rank sum test was used to compare the histogram parameters of each DCE-MRI-derived variable of oropharyngeal SCC and lymphoma. RESULTS Histogram analysis of K(trans) and ve maps revealed that the median and mode of K(trans) were significantly higher in SCC than in lymphoma (p = 0.039 and 0.032, respectively), and the mode, skewness, and kurtosis of ve were significantly different in SCC than in lymphoma (p = 0.046, 0.039, and 0.032, respectively). On ROC analysis, the kurtosis of ve had the best discriminative value for distinguishing between oropharyngeal SCC and lymphoma (AUC, 0.865; cutoff value, 2.60; sensitivity, 83.3%; specificity, 90.5%). CONCLUSION Our preliminary evidence using histogram analysis of DCE-MRI parameters based on the whole tumor volume suggests that it might be useful for differentiating SCC from malignant lymphoma of the oropharynx.
Syllabic pseudohomophone priming in tip-of-the-tongue states resolution: The role of syllabic position and number of syllables

The tip-of-the-tongue (TOT) state is a common experience, usually coupled with a frustrating feeling caused by the incapability of retrieving a familiar word. It is thought that TOTs occur when the semantic and syntactic information of the word is retrieved but not its phonology. This study aims to further understand the role of phonology in TOT resolution. Specifically, using a syllabic pseudohomophone priming paradigm, we aim to analyse the role of the phonological syllabic position (first vs. last) and the number of syllables in TOT states resolution. TOT was elicited by a picture naming task, after which a lexical decision task was presented. Here, first, last, or none of the phonological syllables of the target word were embedded in pseudohomophone primes. Results showed a significant syllabic pseudohomophone priming effect facilitating TOT resolution. The effect was stronger for four-syllable words, especially when the last syllable was used as prime. These results seem to reinforce the importance of phonology in TOT states resolution, particularly the role of the syllable as an important sublexical unit in speech processing.
Hepatic and thymic alterations in newborn offspring of malnourished rat dams.

BACKGROUND Protein-energy malnutrition encompasses a group of conditions resulting from a lack of both protein and calories. It affects immune function and the gastrointestinal tract. Animal model studies of the effect of malnutrition during pregnancy and lactation have shown changes in the body weight of dams, with consequences for the pups. METHODS Sixty healthy adult Wistar rats were mated for breeding. Pregnant dams (n = 19) were separated and randomly divided into 2 groups: normally nourished (NG; n = 10) and malnourished (MG; n = 9). The authors measured the average amount of feed eaten by the dams in the NG group in 24 hours and offered half this amount to the MG dams until delivery, after which both groups had an adequate amount of feed. Offspring were killed after birth and after lactation. Morphometric liver parameters were measured, and the tissue microarray method was performed manually to carry out histopathological and immunohistochemical analysis of thymuses from the offspring. RESULTS Body weight, body length, and intestine length measured after birth were statistically lower (P < .05) in the MG group offspring than in the NG group offspring but recovered after lactation. Histological comparison of pups' livers revealed minimal differences. However, morphometric evaluation showed significant differences. Slides exposed to antivimentin and anti-CD45 RO stained positively in both groups, but the samples from the NG group were more heavily stained. CONCLUSIONS Malnutrition in dams causes alterations in the liver, thymus, and other internal organs of newborn offspring. Significant changes in thymuses were found using human monoclonal antibodies that cross-react with rat proteins, a novel finding in the literature.
The voluntary contribution mechanism with complementarity

This dissertation investigates the effect of complementarity in the private provision of public goods. The inclusion of complementarity in contributions transforms the classic voluntary contribution mechanism into a coordination game, in which we are able to study how different behavioral types interact. The first chapter generalizes the linear voluntary contribution mechanism case by allowing agents’ contributions to be complements in production. When complementarity is sufficiently high, an additional full-contribution equilibrium emerges. We experimentally investigate subjects’ behavior using a between-subject design that varies complementarity. When two equilibria exist, subjects tend to coordinate on contributions close to the efficient equilibrium. When complementarity is sizable but only a zero-contribution selfish-equilibrium exists, subjects persistently contribute above it. Observed choices and other nonchoice data indicate heterogeneity among subjects and two distinct types. Homo pecuniarius maximizes profits by best responding to beliefs, while Homo behavioralis identifies this strategy but chooses to deviate from it, sacrificing pecuniary rewards to support altruism or competitiveness. The second chapter studies the effect of introducing thresholds on equilibrium selection in the voluntary contribution mechanism with complementarity (VCMC). The introduction of thresholds expands the basin of attraction of the socially inefficient equilibrium by raising the minimum group output necessary for a positive return from cooperation. If contributions are not sufficient to generate the minimum output, the social return is zero. The data suggest that the introduction of thresholds does not alter the equilibrium selection or the pattern of contribution dynamics. Individuals are still able to coordinate on the socially preferable outcome. The third chapter examines experimentally the effect of displaying feedback about the income of other group members on the evolution of contributions in the VCMC. The results show that the degree of coordination responds to the way information about outcomes is made available to subjects. Emphasis on income differences can be detrimental from a social perspective and may result in the unraveling of cooperation.
Instance Map Based Image Synthesis With a Denoising Generative Adversarial Network

Semantic layout-based image synthesizing, which has benefited from the success of generative adversarial networks (GANs), has received a substantial amount of attention recently. How to enhance the synthesis image equality while maintaining the stochasticity of the GAN remains a challenge. We propose a novel denoising framework to handle this problem. The generation of overlapping objects is another challenging task when synthesizing images from a semantic layout to a realistic RGB photograph. To overcome this deficiency, we include a one-hot semantic label map to force the generator to pay more attention to the generation of overlapping objects. Furthermore, we improve the loss function of the discriminator by considering the perturbed loss and cascade layer loss to guide the generation process. We applied our methods to the Cityscapes, photo-sketch, day–night, facades, and NYU datasets to demonstrate the image generation ability of our model.
Resolving Australian analogs for an Eocene Patagonian paleorainforest using leaf size and floristics.

UNLABELLED • PREMISE OF THE STUDY The diverse early Eocene flora from Laguna del Hunco (LH) in Patagonia, Argentina has many nearest living relatives (NLRs) in Australasia but few in South America, indicating the differential survival of an ancient, trans-Antarctic rainforest biome. To better understand this significant biogeographic pattern, we used detailed comparisons of leaf size and floristics to quantify the legacy of LH across a large network of Australian rainforest-plot assemblages. • METHODS We applied vein scaling, a new method for estimating the original areas of fragmented leaves. We then compared leaf size and floristics at LH with living Australian assemblages and tabulated the climates of those where NLRs occur, along with additional data on climatic ranges of "ex-Australian" NLRs that survive outside of Australia. • KEY RESULTS Vein scaling estimated areas as accurately as leaf-size classes. Applying vein scaling to fossil fragments increased the grand mean area of LH by 450 mm(2), recovering more originally large leaves. The paleoflora has a majority of microphyll leaves, comparable to leaf litter in subtropical Australian forests, which also have the greatest floristic similarity to LH. Tropical Australian assemblages also share many taxa with LH, and ex-Australian NLRs mostly inhabit cool, wet montane habitats no longer present in Australia. • CONCLUSIONS Vein scaling is valuable for improving the resolution of fossil leaf-size distributions by including fragmented specimens. The legacy of LH is evident not only in subtropical and tropical Australia but also in tropical montane Australasia and Southeast Asia, reflecting the disparate histories of surviving Gondwanan lineages.
The Use of Miniature Supersonic Nozzles for Microparticle Acceleration: A Numerical Study

By means of a high-speed gas flow generated by a miniature supersonic nozzle, we proposed a unique biolistic method to accelerate microparticle formulation of drugs to sufficient momentum, to penetrate the outer layer of human skin or mucosal tissue for the treatment of a range of diseases. One of the main concerns for designing and evaluating this system is ensuring mi- croparticles delivery into human skin with a controllable velocity range and spatial distribution. The initial experimental work suggested that the performance of the transdermal delivery strongly depends on aerodynamics of the supersonic nozzles employed. In this paper, computational fluid dynamics (CFD) is utilized to characterize existing prototype biolistic delivery systems, the device with a converging-diverging supersonic nozzle (CDSN) and the device based on the contoured-shock-tube (CST) design, with the aim at investigating the transient gas and particle dynamics in the supersonic nozzles. Whenever possible, predicted pressure and Mach number histories, 2D flow structures, and particle velocity distributions are made to compare with the corresponding experimental measurements to validate the implemented numerical approach. The gas-particle interaction and performance of two biolistic devices are interrogated and distinguished. Subsequently, the particle impact conditions are presented and discussed. It is demonstrated that the CST can deliver microparticles with a narrow and more controllable velocity range and spatial distribution.
Biofilm Formation and Disinfectant Susceptibility of Persistent and Nonpersistent Listeria monocytogenes Isolates from Gorgonzola Cheese Processing Plants.

The aim of this study was to investigate whether the biofilm-forming ability and/or the disinfectant susceptibility accounted for the persistence of Listeria monocytogenes in Gorgonzola cheese processing plants. For this purpose, a set of 16 L. monocytogenes isolates collected in the 2004-2007 period was analyzed, including 11 persistent isolates collected in different years, within the collection period, and displaying identical or highly correlated pulsotypes. The evaluation of biofilm-forming ability was assessed using crystal violet (CV) staining and the enumeration of viable cells on stainless steel coupons (SSC). Absorbance values obtained with CV staining for persistent and nonpersistent isolates were not significantly different (rm-ANOVA p > 0.05) and the cell counts from nonpersistent isolates showed to be higher compared with persistent isolates (rm-ANOVA p < 0.05). A simulation of disinfectant treatments was performed on spot inoculated coupons in clean and dirty conditions, according to EN 13697, and on biofilms on SSC, grown in nutrient-rich (dirty) and limiting (clean) conditions using acid acetic-hydrogen peroxide (P3) and acid citric-hydrogen peroxide (MS) commercial disinfectants. The treatment was considered effective when a 4 Log reduction in viable cell count was observed. The Log reductions of persistent and nonpersistent isolates, obtained with both the assays in clean and dirty conditions, were compared and no significant differences were detected (rm-ANOVA p > 0.05). A greater influence of organic matter on MS could explain why P3 was efficient in reducing to effective levels the majority of the isolates at the lowest concentration suggested by the manufacturer (0.2% [v/v]), while the same purpose required a higher concentration (1% [v/v]) of MS. In conclusion, our results demonstrate that the persistence of these isolates in Gorgonzola cheese processing plants was linked neither to the biofilm-forming ability nor to their susceptibility to hydrogen peroxide-based disinfectants; therefore, other factors should contribute to the persistent colonization of the dairies.