gebhart/patrepeval huggingface dataset:
Simultaneous visualization of spatial and chromatic aberrations by two-dimensional Fourier transform spectral interferometry (2006)

We demonstrate the use of a simple tool to simultaneously visualize and characterize chromatic and spherical aberrations that are present in multiphoton microscopy. Using two-dimensional Fourier transform spectral interferometry, we measured these aberrations, deducing in a single shot spatiotemporal effects in high-numerical-aperture objectives.
Combining Microarray‐based Genomic Selection (MGS) with the Illumina Genome Analyzer Platform to Sequence Diploid Target Regions (2009)

Novel methods of targeted sequencing of unique regions from complex eukaryotic genomes have generated a great deal of excitement, but critical demonstrations of these methods efficacy with respect to diploid genotype calling and experimental variation are lacking. To address this issue, we optimized microarray-based genomic selection (MGS) for use with the Illumina Genome Analyzer (IGA). A set of 202 fragments (304 kb total) contained within a 1.7 Mb genomic region on human chromosome X were MGS/IGA sequenced in ten female HapMap samples generating a total of 2.4 GB of DNA sequence. At a minimum coverage threshold of 5X, 93.9% of all bases and 94.9% of segregating sites were called, while 57.7% of bases (57.4% of segregating sites) were called at a 50X threshold. Data accuracy at known segregating sites was 98.9% at 5X coverage, rising to 99.6% at 50X coverage. Accuracy at homozygous sites was 98.7% at 5X sequence coverage and 99.5% at 50X coverage. Although accuracy at heterozygous sites was modestly lower, it was still over 92% at 5X coverage and increased to nearly 97% at 50X coverage. These data provide the first demonstration that MGS/IGA sequencing can generate the very high quality sequence data necessary for human genetics research. All sequences generated in this study have been deposited in NCBI Short Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra, Accession # SRA007913).
Roles of Plant Small RNAs in Biotic Stress Responses (2009)

A multitude of small RNAs (sRNAs, 18-25 nt in length) accumulate in plant tissues. Although heterogeneous in size, sequence, genomic distribution, biogenesis, and action, most of these molecules mediate repressive gene regulation through RNA silencing. Besides their roles in developmental patterning and maintenance of genome integrity, sRNAs are also integral components of plant responses to adverse environmental conditions, including biotic stress. Until recently, antiviral RNA silencing was considered a paradigm of the interactions linking RNA silencing to pathogens: Virus-derived sRNAs silence viral gene expression and, accordingly, viruses produce suppressor proteins that target the silencing mechanism. However, increasing evidence shows that endogenous, rather than pathogen-derived, sRNAs also have broad functions in regulating plant responses to various microbes. In turn, microbes have evolved ways to inhibit, avoid, or usurp cellular silencing pathways, thereby prompting the deployment of counter-defensive measures by plants, a compelling illustration of the never-ending molecular arms race between hosts and parasites.
Effects of cytochalasin D on occluding junctions of intestinal absorptive cells: further evidence that the cytoskeleton may influence paracellular permeability and junctional charge selectivity. (1986)

Intestinal absorptive cells may modulate both the structure and function of occluding junctions by a cytoskeleton dependent mechanism (Madara, J. L., 1983, J. Cell Biol., 97:125-136). To further examine the putative relationship between absorptive cell occluding junctions and the cytoskeleton, we assessed the effects of cytochalasin D (CD) on occluding junction function and structure in guinea pig ileum using ultrastructural and Ussing chamber techniques. Maximal decrements in transepithelial resistance and junctional charge selectivity were obtained with 10 micrograms/ml CD and the dose-response curves for these two functional parameters were highly similar. Analysis of simultaneous flux studies of sodium and the nonabsorbable extracellular tracer mannitol suggested that CD opened a transjunctional shunt and that this shunt could fully account for the increase in sodium permeability and thus the decrease in resistance. Structural studies including electron microscopy of detergent-extracted cytoskeletal preparations revealed that 10 micrograms/ml CD produced condensation of filamentous elements of the peri-junctional contractile ring and that this was associated with brush border contraction as assessed by scanning electron microscopy. Quantitative freeze-fracture studies revealed marked aberrations in absorptive cell occluding junction structure including diminished strand number, reduced strand-strand cross-linking, and failure of strands to impede the movement of intramembrane particles across them. In aggregate these studies show that CD-induced perturbation of the absorptive cell cytoskeleton results in production of a transepithelial shunt which is fully explained by a defect in the transjunctional pathway. Furthermore, substantial structural abnormalities in occluding junction structure accompany this response. Lastly, the abnormalities in occluding junction structure and function coincide with structural changes in and contraction of the peri-junctional actin-myosin ring. These data suggest that a functionally relevant association may exist between the cytoskeleton and the occluding junction of absorptive cells. We speculate that such an association may serve as a mechanism by which absorptive cells regulate paracellular transport.
On Doping CdS/ZnS Core/Shell Nanocrystals with Mn (2008)

This paper presents a mechanistic study on the doping of CdS/ZnS core/shell semiconductor nanocrystals with Mn based on a three-step synthesis, which includes host-particle synthesis, Mn-dopant growth, and ZnS-shell growth. We used a combination of electron paramagnetic resonance spectroscopy (EPR) and inductively coupled plasma atomic emission spectroscopy (ICP) to monitor Mn-doping level and growth yield during doping synthesis at both the dopant-growth and ZnS-shell-growth steps. First, our kinetic study shows that Mn adsorption onto the nanocrystal surface includes the formation of weakly and strongly bound Mn. The formation of weakly bound Mn is associated with a chemical equilibrium between adsorbed Mn species on the nanocrystal surface and free Mn species in growth solution, while the formation of strongly bound Mn exhibits first-order kinetics with an activation-energy barrier of 211 +/- 13 kJ/mol. Second, our results demonstrate that both weakly and strongly bound Mn can be removed from the surface of nanocrystals during ZnS-shell growth. The replacement of strongly bound Mn requires a higher temperature than that of weakly bound Mn. The yield of the replacement of strongly bound Mn is strongly dependent on the temperature of ZnS-shell growth. Third, our results show that the Mn-growth yield is not dependent on the size and crystal structure of nanocrystals. All together, these results suggest a mechanism in which nanocrystal doping is determined by the chemical kinetics of three activation-controlled processes: dopant adsorption, replacement, and ZnS-shell growth.
UbasM: An effective balanced optical clearing method for intact biomedical imaging (2017)

Optical clearing methods can facilitate deep optical imaging in biological tissue by reducing light scattering and this has enabled accurate three-dimensional signal visualization and quantification of complex biological structures. Unfortunately, existing optical clearing approaches present a compromise between maximizing clearing capability, the preservation of fluorescent protein emission and membrane integrity and the speed of sample processing - with the latter typically requiring weeks for cm scale tissue samples. To address this challenge, we present a new, convenient, aqueous optical clearing agent, termed UbasM: Urea-Based Amino-Sugar Mixture, that rapidly renders fixed tissue samples highly transparent and reliably preserves emission from fluorescent proteins and lipophilic dyes in membrane integrity preserved tissues. UbasM is simple, inexpensive, reproducible and compatible with all labeling methods that we have encountered. It can enable convenient, volumetric imaging of tissue up to the scale of whole adult mouse organs and should be useful for a wide range of light microscopy and tomography techniques applied to biomedical research, especially the study on organism-level systems biology at multiple levels.
Simple quantum computer (1995)

We propose an implementation of a quantum computer to solve Deutsch's problem, which requires exponential time on a classical computer but only linear time with quantum parallelism. By using a dual-rail quantum-bit representation as a simple form of error correction, our machine can tolerate some amount of decoherence and still give the correct result with high probability. The design that we employ also demonstrates a signature for quantum parallelism which unambiguously distinguishes the desired quantum behavior from the merely classical. The experimental demonstration of our proposal using quantum optical components calls for the development of several key technologies common to single photonics.
Characterization of Bacteria in Ballast Water Using MALDI-TOF Mass Spectrometry (2012)

To evaluate a rapid and cost-effective method for monitoring bacteria in ballast water, several marine bacterial isolates were characterized by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Since International Maritime Organization (IMO) regulations are concerned with the unintended transportation of pathogenic bacteria through ballast water, emphasis was placed on detecting species of Vibrio, enterococci and coliforms. Seawater samples collected from the North Sea were incubated in steel ballast tanks and the presence of potentially harmful species of Pseudomonas was also investigated. At the genus-level, the identification of thirty six isolates using MALDI-TOF MS produced similar results to those obtained by 16S rRNA gene sequencing. No pathogenic species were detected either by 16S rRNA gene analysis or by MALDI-TOF MS except for the opportunistically pathogenic bacterium Pseudomonas aeruginosa. In addition, in house software that calculated the correlation coefficient values (CCV) of the mass spectral raw data and their variation was developed and used to allow the rapid and efficient identification of marine bacteria in ballast water for the first time.
Lenticular stereoscopic imaging and displaying techniques with no special glasses (2002)

Autostereoscopic 3-D imaging and display system is implemented on the notebook 486 DxII PC with TFT active matrix LCD display module and accompanying lenticular sheet lens. An image processing board (e.g. Targa Plus which is commercially available) is used to capture and display the image. Display experiments for still images and animating graphics images were very promising and satisfactory. Measured depth perception is about 100 mm on a notebook PC LCD display unit. The compact design of lens-plate and TFT LCD display module would be appropriate for 3-D game machines, stereoscopic TV system on multimedia PC.
Light-Induced Nuclear Translocation of Endogenous Pea Phytochrome A Visualized by Immunocytochemical Procedures (2000)

Akiko Hisada, Hiroko Hanzawa, James L. Weller, Akira Nagatani, James B. Reid, Masaki Furuya, Light-Induced Nuclear Translocation of Endogenous Pea Phytochrome A Visualized by Immunocytochemical Procedures, The Plant Cell, Vol. 12, No. 7 (Jul., 2000), pp. 1063-1078
Structural and functional analysis of pp70S6k. (1995)

The pp70/85-kDa S6 kinases, collectively referred to as pp70S6k, are thought to participate in transit through the G1 phase of the cell cycle. pp70S6k regulates the phosphorylation of the 40S ribosomal protein S6 and the transcription factor CREM tau. pp70S6k is regulated by serine/threonine phosphorylation, and although 1-phosphatidylinositol 3-kinase and phospholipase C have been implicated as upstream regulators, the mechanism of activation and identity of the upstream pp70S6k kinases remain unknown. To improve our understanding of how this mitogen-stimulated protein kinase is regulated by growth factors and the immunosuppressant rapamycin, we have initiated a structure/function analysis of pp70S6k. Our results indicate that both the N and C termini participate in the complex regulation of pp70S6k activity.
Expression Patterns and Post-translational Modifications Associated with Mammalian Histone H3 Variants (2005)

Covalent histone modifications and the incorporation of histone variants bring about changes in chromatin structure that in turn alter gene expression. Interest in non-allelic histone variants has been renewed, in part because of recent work on H3 (and other) histone variants. However, only in mammals do three non-centromeric H3 variants (H3.1, H3.2, and H3.3) exist. Here, we show that mammalian cell lines can be separated into two different groups based on their expression of H3.1, H3.2, and H3.3 at both mRNA and protein levels. Additionally, the ratio of these variants changes slightly during neuronal differentiation of murine ES cells. This difference in H3 variant expression between cell lines could not be explained by changes in growth rate, cell cycle stages, or chromosomal ploidy, but rather suggests other possibilities, such as changes in H3 variant incorporation during differentiation and tissue- or species-specific H3 variant expression. Moreover, quantitative mass spectrometry analysis of human H3.1, H3.2, and H3.3 showed modification differences between these three H3 variants, suggesting that they may have different biological functions. Specifically, H3.3 contains marks associated with transcriptionally active chromatin, whereas H3.2, in contrast, contains mostly silencing modifications that have been associated with facultative heterochromatin. Interestingly, H3.1 is enriched in both active and repressive marks, although the latter marks are different from those observed in H3.2. Although the biological significance as to why mammalian cells differentially employ three highly similar H3 variants remains unclear, our results underscore potential functional differences between them and reinforce the general view that H3.1 and H3.2 in mammalian cells should not be treated as equivalent proteins.
DeepPhys: Video-Based Physiological Measurement Using Convolutional Attention Networks (2018)

Non-contact video-based physiological measurement has many applications in health care and human-computer interaction. Practical applications require measurements to be accurate even in the presence of large head rotations. We propose the first end-to-end system for video-based measurement of heart and breathing rate using a deep convolutional network. The system features a new motion representation based on a skin reflection model and a new attention mechanism using appearance information to guide motion estimation, both of which enable robust measurement under heterogeneous lighting and major motions. Our approach significantly outperforms all current state-of-the-art methods on both RGB and infrared video datasets. Furthermore, it allows spatial-temporal distributions of physiological signals to be visualized via the attention mechanism.
Real-Time Estimation and Prediction of Wave Excitation Forces for Wave Energy Control Applications (2015)

Wave energy is emerging as a new potential source for renewable energy generation. However, wave energy technology is not currently cost competitive with other more mature renewable energy sources such as wind and solar. One approach that researchers and developers are taking to reduce the cost of wave energy is to actively control wave energy converters (WECs) in such a way that the average power produced by the WEC is significantly increased. Most of the proposed control algorithms depend on having predictions of the future wave forces, as the optimal control actions depend on these future forces.
This thesis details a methodology that uses a Kalman filter to estimate the wave forces on a WEC from measured motions of a WEC in real-time. These estimated forces are then used to predict future forces with a recursive, autoregressive least squares prediction model. The methodology is tested on a generic, 3 degree of freedom, point absorbing WEC in simulations, using recorded water surface elevation time series data as input to the WEC model. The effect of different sea states on both estimation and prediction accuracies is investigated. Results show that both estimation and prediction accuracies depend on the hydrodynamic properties of the WEC. It is also observed that low energy sea states result in significantly reduced estimation and prediction accuracies compared to more energetic sea states.
Randomized Trial of Adjuvant Tamoxifen in Node Negative Postmenopausal Breast Cancer (1992)

The paper presents long-term results of a randomized trial of adjuvant tamoxifen (40 mg daily for 2 or 5 years) versus surgery alone including 1,347 postmenopausal patients with histologically negative axillary nodes and a tumour diameter less than or equal to 30 mm. Data on the estrogen receptor status of the primary tumour were available in 1,136 patients (84%). At a median follow-up of 7 years (range 1.7-13.0 years) there was a significant prolongation of the recurrence-free survival among those allocated to tamoxifen (p less than 0.01), significantly fewer deaths due to breast cancer (p = 0.02) and a trend towards improved overall survival (p = 0.11). The treatment benefit was restricted to patients with ER-positive tumours. There was no significant reduction of breast cancer recurrences in the tamoxifen group among patients whose tumours were classified as ER-negative. The results support and extend previous studies in showing a long-term benefit of tamoxifen in postmenopausal breast cancer patients with node-negative, estrogen receptor positive disease.
T Lymphocytes Redirected against the Chondroitin Sulfate Proteoglycan-4 Control the Growth of Multiple Solid Tumors both In Vitro and In Vivo (2013)

CAR.CSPG4-redirected T cells should provide an effective treatment modality for a variety of solid tumors.
Proliferative and cytokine responses to class II HER-2/neu-associated peptides in breast cancer patients. (1998)

Previous studies have characterized the reactivity of CD8+ CTLs with ovarian and breast cancer. There is little information about the antigens and epitopes recognized by CD4+ T cells in these patients. In this study, we analyzed the ability of T cells from peripheral blood mononuclear cells of breast cancer patients to recognize HER-2/neu (HER-2) peptides. We found that 13 of 18 patients responded by proliferation to at least one of the HER-2 peptides tested. Of these peptides, one designated G89 (HER-2: 777-789) was recognized by T cells from 10 patients. Seven of nine responding patients were HLA-DR4+, suggesting that this peptide is recognized preferentially in association with HLA-DR4. Analysis of the specificity and restriction of the cytokine responses to G89 by G89-stimulated T cells revealed that these cells secreted significantly higher levels of IFN-gamma than interleukin 4 and interleukin 10, suggesting priming for a Th0-T helper 1 response. The same pattern of cytokine responses was observed to the intracellular domain of HER-2 protein, suggesting that G89-stimulated T cells recognized epitopes of the HER-2 protein in association with HLA-DR4. Because HLA-DR4 is present in 25% of humans, characterization of MHC class II-restricted epitopes inducing Th0-T helper 1 responses may provide a basis for the development of multivalent HER-2-based vaccines against breast and ovarian cancer.
The allergen specific B‐cell response during immunotherapy (1992)

The paper examines the allergen specific B-cell response in peripheral blood from patients undergoing immunotherapy with house dust mite extract. The 12 patients were part of a double blind placebo controlled study, and they were treated with either Dermatophagoides pteronyssinus (n = 4), Dermatophagoides farinae extract (n = 3) (Alutard SQ, ALK, Denmark) or placebo (n = 5). Blood was taken every fortnight on day seven after hyposensitization and tested for IgM, IgG, IgA and IgE antibody secreting cells (AbSC) to D. pteronyssinus and D. farinae allergens and for the total number of immunoglobulin secreting cells (IgSC). The data showed a maximum of approximately 120 Der f I+II specific AbSC/10(6) mononuclear cells (MNC). A comparison of specific AbSC to the major allergens of the two house dust mites demonstrated that there was no measurable species specificity in the B-cell response that could be correlated to immunotherapy with either of the two extracts. The specific IgM, IgG, and IgA response to Der f I+II was examined in the placebo (39 measurements) and the actively treated (56 measurements) groups, and the results demonstrated a significant rise in specific IgM and IgA AbSC following immunotherapy. The number of specific IgG AbSC did not change. There was a mean of less than one specific IgE AbSC/10(6) MNC, and no detectable change following the treatment. It is speculated that immunotherapy to inhalant allergens causes the induction of specific IgA AbSC. It would then be these partly differentiated plasma cells that are detected on their way to the bronchial or gut mucosa to exert their protective function mediated by allergen specific secretory IgA.
Tumor growth inhibition mediated by lymphotoxin: evidence of B lymphocyte involvement in the antitumor response. (1995)

The antitumor effect of lymphotoxin (LT) and the underlying cellular mechanism were analyzed. To achieve an increased local concentration of LT at the site of tumor growth, which mimics the physiological fashion of cytokine action, we transfected the murine plasmacytoma J558L cells with a human LT expression plasmid and selected several clones that produce varying levels of LT for analysis of their tumorigenicity. The LT produced by the transfected J558L cells effectively suppressed tumor growth in syngeneic BALB/c mice without any obvious side effects. This antitumor function is indirect and LT specific, because the tumor cells did not show altered growth kinetics after the gene transfer in vitro, and tumor growth inhibition in vivo could partially be reversed by an anti-LT mAb. In nude mice, LT producing tumors were initially suppressed, but most mice developed a tumor at the end of the study. However, the requirement of T cells for complete tumor rejection could be compensated for by higher amounts of LT secretion. Furthermore, the antitumor activity of LT seems to involve B lymphocytes in the absence of functional T lymphocytes since a significant difference existed between tumor growth of J558-LT cells in nude and in SCID mice. LT-producing tumors but not parental tumors were massively infiltrated by B220+ cells in nude mice. The secretion of LT by tumor cells also induced a heavy infiltration of Mac-1+ and Mac-3+ cells and a moderate infiltration of Gr-1+ cells, both in nude and in SCID mice. Together, LT-producing J558L cells are rejected by a complex immunological mechanism, which seems to involve T as well as B and other cells. This distinguishes LT from a number of other cytokines analyzed in analogous experiments.