gebhart/patrepeval huggingface dataset:
Three-dimensional Optical-resolution Photoacoustic Microscopy (2011)

Optical microscopy, providing valuable insights at the cellular and organelle levels, has been widely recognized as an enabling biomedical technology. As the mainstays of in vivo three-dimensional (3-D) optical microscopy, single-/multi-photon fluorescence microscopy and optical coherence tomography (OCT) have demonstrated their extraordinary sensitivities to fluorescence and optical scattering contrasts, respectively. However, the optical absorption contrast of biological tissues, which encodes essential physiological/pathological information, has not yet been assessable. The emergence of biomedical photoacoustics has led to a new branch of optical microscopy optical-resolution photoacoustic microscopy (OR-PAM)1, where the optical irradiation is focused to the diffraction limit to achieve cellular1 or even subcellular2 level lateral resolution. As a valuable complement to existing optical microscopy technologies, OR-PAM brings in at least two novelties. First and most importantly, OR-PAM detects optical absorption contrasts with extraordinary sensitivity (i.e., 100%). Combining OR-PAM with fluorescence microscopy3 or with optical-scattering-based OCT4 (or with both) provides comprehensive optical properties of biological tissues. Second, OR-PAM encodes optical absorption into acoustic waves, in contrast to the pure optical processes in fluorescence microscopy and OCT, and provides background-free detection. The acoustic detection in OR-PAM mitigates the impacts of optical scattering on signal degradation and naturally eliminates possible interferences (i.e., crosstalks) between excitation and detection, which is a common problem in fluorescence microscopy due to the overlap between the excitation and fluorescence spectra. Unique for optical absorption imaging, OR-PAM has demonstrated broad biomedical applications since its invention, including, but not limited to, neurology5, 6, ophthalmology7, 8, vascular biology9, and dermatology10. In this video, we teach the system configuration and alignment of OR-PAM as well as the experimental procedures for in vivo functional microvascular imaging.
Isolation and characterization of Listeria monocytogenes-specific nucleotide sequences (1993)

Subtracter probe hybridization was used to screen a partial genomic library of a clinical isolate of Listeria monocytogenes. Three clones that hybridized with genomic DNA from 174 strains of L. monocytogenes but not with genomic DNA from 32 strains representing other Listeria spp. were recovered. These data establish the utility of subtracter probe hybridization for recovering L. monocytogenes-specific sequences.
Accuracy-Preserving Smoothing Of Color Transformation LUTs (2008)

Color transformations are frequently embodied in look-up tables (LUTs) whose content is the result of computation performed on the basis of color measurements. Noise in color measurements and device output gives LUTs that result in lack of smoothness in color transitions. Smoothing of color LUTs is therefore typically performed, often with a significant loss of accuracy. This paper proposes a method to both smooth LUTs and preserve a significantly greater degree of colorimetric accuracy than conventional methods. The key to such a result is to smooth along 1D paths where lightness change is greatest. E.g., along constant a*b* lines where CIELAB is the indexing space or along paths parallel to the line connecting the black and white points where the indexing space is device–dependent.
Thermoresponsive Bentonite for Water-Based Drilling Fluids (2019)

As an important industrial material, bentonite has been widely applied in water-based drilling fluids to create mud cakes to protect boreholes. However, the common mud cake is porous, and it is difficult to reduce the filtration of a drilling fluid at high temperature. Therefore, this paper endowed bentonite with a thermo response via the insertion of N-isopropylacrylamide (NIPAM) monomers. The interaction between NIPAM monomers and bentonite was investigated via Fourier infrared spectroscopy (FTIR), isothermal adsorption, and X-ray diffraction (XRD) at various temperatures. The results demonstrate that chemical adsorption is involved in the adsorption process of NIPAM monomers on bentonite, and the adsorption of NIPAM monomers accords with the D-R model. With increasing temperature, more adsorption water was squeezed out of the composite when the temperature of the composite exceeded 70 °C. Based on the composite of NIPAM and bentonite, a mud cake was prepared using low-viscosity polyanionic cellulose (Lv-PAC) and initiator potassium peroxydisulfate (KPS). The change in the plugging of the mud cake was investigated via environmental scanning electron microscopy (ESEM), contact angle testing, filtration experiments, and linear expansion of the shale at various temperatures. In the plugging of the mud cake, a self-recovery behavior was observed with increasing temperature, and resistance was observed at 110 °C. The rheology of the drilling fluid was stable in the alterative temperature zone (70-110 °C). Based on the high resistance of the basic drilling fluid, a high-density drilling fluid (ρ = 2.0 g/cm<sup>3</sup>) was prepared with weighting materials with the objective of drilling high-temperature formations. By using a high-density drilling fluid, the hydration expansion of shale was reduced by half at 110 °C in comparison with common bentonite drilling fluid. In addition, the rheology of the high-density drilling fluid tended to be stable, and a self-recovery behavior was observed.
A data-driven approach to four-view image-based hair modeling (2017)

We introduce a novel four-view image-based hair modeling method. Given four hair images taken from the front, back, left and right views as input, we first estimate the rough 3D shape of the hair observed in the input using a predefined database of 3D hair models, then synthesize a hair texture on the surface of the shape, from which the hair growing direction information is calculated and used to construct a 3D direction field in the hair volume. Finally, we grow hair strands from the scalp, following the direction field, to produce the 3D hair model, which closely resembles the hair in all input images. Our method does not require that all input images are from the same hair, enabling an effective way to create compelling hair models from images of considerably different hairstyles at different views. We demonstrate the efficacy of our method using a wide range of examples.
Efficient Generation of Myelinating Oligodendrocytes from Primary Progressive Multiple Sclerosis Patients by Induced Pluripotent Stem Cells (2014)

Multiple sclerosis (MS) is a chronic demyelinating disease of unknown etiology that affects the CNS. While current therapies are primarily directed against the immune system, the new challenge is to address progressive MS with remyelinating and neuroprotective strategies. Here, we develop a highly reproducible protocol to efficiently derive oligodendrocyte progenitor cells (OPCs) and mature oligodendrocytes from induced pluripotent stem cells (iPSCs). Key elements of our protocol include adherent cultures, dual SMAD inhibition, and addition of retinoids from the beginning of differentiation, which lead to increased yields of OLIG2 progenitors and high numbers of OPCs within 75 days. Furthermore, we show the generation of viral and integration-free iPSCs from primary progressive MS (PPMS) patients and their efficient differentiation to oligodendrocytes. PPMS OPCs are functional, as demonstrated by in vivo myelination in the shiverer mouse. These results provide encouraging advances toward the development of autologous cell therapies using iPSCs.
Optical Scanning Holography - A Review of Recent Progress (2009)

Optical scanning holography (OSH) is a distinct digital holographic technique in that real-time holographic recording a three-dimensional (3-D) object can be acquired by using two-dimensional active optical heterodyne scanning. Applications of the technique so far have included optical scanning cryptography, optical scanning microscopy, 3-D pattern recognition, 3-D holographic TV, and 3-D optical remote sensing. This paper reviews some of the recent progress in OSH. Some possible further works are also discussed.
Macrolide Efflux in <i>Streptococcus pneumoniae</i> Is Mediated by a Dual Efflux Pump ( <i>mel</i> and <i>mef</i> ) and Is Erythromycin Inducible (2005)

Macrolide resistance in Streptococcus pneumoniae due to efflux has emerged as an important worldwide clinical problem over the past decade. Efflux is mediated by the genes of the genetic element mega (macrolide efflux genetic assembly) and related elements, such as Tn1207.1. These elements contain two adjacent genes, mef (mefE or mefA) and the closely related mel gene (msrA homolog), encoding a proton motive force pump and a putative ATP-binding cassette transporter homolog, and are transcribed as an operon (M. Del Grosso et al., J. Clin. Microbiol. 40:774-778, 2004; K. Gay and D. S. Stephens, J. Infect. Dis. 184:56-65, 2001; and M. Santagati et al., Antimicrob. Agents Chemother. 44:2585-2587, 2000). Previous studies have shown that Mef is required for macrolide resistance in S. pneumoniae; however, the contribution of Mel has not been fully determined. Independent deletions were constructed in mefE and mel in the serotype 14 macrolide-resistant strains GA16638 (erythromycin [Em] MIC, 8 to 16 microg/ml) and GA17719 (Em MIC, 2 to 4 microg/ml), which contain allelic variations in the mega element. The MICs to erythromycin were significantly reduced for the independent deletion mutants of both mefE and mel compared to those of the parent strains and further reduced threefold to fourfold to Em MICs of <0.15 microg/ml with mefE mel double mutants. Using quantitative reverse transcription-PCR, the expression of mefE in the mel deletion mutants was increased more than 10-fold. However, in the mefE deletion mutants, the expression of mel did not differ significantly from the parent strains. The expression of both mefE and mel was inducible by erythromycin. These data indicate a requirement for both Mef and Mel in the novel efflux-mediated macrolide resistance system in S. pneumoniae and other gram-positive bacteria and that the system is inducible by macrolides.
Prediction of Radiation Sensitivity Using a Gene (2005)

The development of a successful radiation sensitivity predictive assay has been a major goal of radiation biology for several decades. We have developed a radiation classifier that predicts the inherent radiosensitivity of tumor cell lines as measured by survival fraction at 2 Gy (SF2), based on gene expression profiles obtained from the literature. Our classifier correctly predicts the SF2 value in 22 of 35 cell lines from the National Cancer Institute panel of 60, a result significantly different from chance (P = 0.0002). In our approach, we treat radiation sensitivity as a continuous variable, significance analysis of microarrays is used for gene selection, and a multivariate linear regression model is used for radiosensitivity prediction. The gene selection step identified three novel genes (RbAp48, RGS19, and R5PIA) of which expression values are correlated with radiation sensitivity. Gene expression was confirmed by quantitative real-time PCR. To biologically validate our classifier, we transfected RbAp48 into three cancer cell lines (HS-578T, MALME-3M, and MDA-MB-231). RbAp48 overexpression induced radiosensitization (1.5- to 2-fold) when compared with mock-transfected cell lines. Furthermore, we show that HS-578T-RbAp48 overexpressors have a higher proportion of cells in G2-M (27% versus 5%), the radiosensitive phase of the cell cycle. Finally, RbAp48 overexpression is correlated with dephosphorylation of Akt, suggesting that RbAp48 may be exerting its effect by antagonizing the Ras pathway. The implications of our findings are significant. We establish that radiation sensitivity can be predicted based on gene expression profiles and we introduce a genomic approach to the identification of novel molecular markers of radiation sensitivity. (Cancer Res 2005; 65(16): 7169-76)
Quantum Dot Modelocked and Broad-Band Lasers for Optical Interconnect Solutions (2006)

Quantum-dot lasers demonstrate broadband (20 nm) emission spectra and high spectral power densities (>20 mW/nm). Monolithic mode-locked InAs/InGaAs quantum-dot lasers operate at 5 GHz with a peak power of 1.7 W and a pulse width of 3.2 ps
Filaggrin null mutations are associated with increased asthma exacerbations in children and young adults (2008)

In addition to their effect on asthma medication requirements reported previously, there is an association between the presence of FLG null mutations and the risk of asthma exacerbations in asthmatic children and young adults.
Double benefit claims for antimicrobial and antioxidative probiotic (2008)

This paper describes the in vitro assessment of the functional properties of probiotic Lactobacillus fermentum ME-3 (DSM14241) and evaluates the possibility for enhancement of the antioxidative activity of the human organism colonized or not with Helicobacter pylori (Hp) through the use of the synbiotic comprising L. fermentum ME-3, Lactobacillus paracasei 8700:2 and Bifidobacterium longum 46 with Raftilose P95 in a randomized double-blind placebo-controlled volunteer crossover trial. In vitro the probiotic strain ME-3 suppressed both clinical and reference strains of Hp and expressed the highest antioxidative activity among the probiotic bacteria. In a volunteer trial the consumption of the synbiotic suppressed the oxidative stress indices in healthy volunteers colonized or not with Hp. However, this beneficial effect was apparent without systemic antimicrobial influence of probiotic bacteria on Hp colonization. This suggests the possibility to apply the probiotic strain ME-3 with double health claims for reduction of the increased risk of cardiovascular diseases (CVD) in the composition of the synbiotic as an adjunct to Hp antimicrobial therapy. Key words: Helicobacter pylori, antioxidative activity, probiotic, lactobacilli, bifidobacteria, oxidative stress, synbiotic
Design of potent and selective linear antagonists of vasopressor (V1-receptor) responses to vasopressin (1990)

We report the solid-phase synthesis of 21 linear analogues of A and D, two nonselective antagonists of the vasopressor (V1) and antidiuretic (V2) responses to arginine vasopressin (AVP). A is Aaa-D-Tyr(Et)-Phe-Val-Asn-Abu-Pro-Arg-Arg-NH2 (where Aaa = adamantylacetyl at position 1). D is the des-Arg9 analogue of A. Nine new analogues of A (1-9) and 12 new analogues of D (10-21) were obtained. The following substitutions either alone or in combination were incorporated in A and/or in D: phenylacetic acid (Phaa) and tert-butylacetic acid (t-Baa) at position 1; D-Tyr2, D-Tyr(Me)2; Gln4; Arg6, Lys6, Orn6, MeAla7. The nine new analogues of A are (1) [Arg6], (2) [Lys6], (3) [Orn6], (4) [Phaa1,Lys6], (5) [Phaa1,Orn6], (6) [D-Tyr2], (7) [D-Tyr2,Arg6], (8) [Phaa1,D-Tyr2], (9) [Phaa1,D-Tyr2,Arg6]. The 12 new analogues of D are (10) [Arg6], (11) [Lys6], (12) [Orn6], (13) [Phaa1,Lys6], (14) [Phaa1,Gln4,Lys6], (15) [Phaa,D-Tyr(Me)2,Lys6], (16) [Phaa,D-Tyr(Me)2,Gln4,Lys6], (17) [Phaa1,D-Tyr2,Gln4,Lys6], (18) [t-Baa1,Lys6], (19) [t-Baa1,Gln4,Lys6], (20) [Arg6,MeAla7], (21) [t-Baa1,Arg6,MeAla7]. All 21 peptides were examined for agonistic and antagonistic potencies in AVP V2 and V1 assays in rats. With the exception of 6, the eight remaining new analogues of A are equipotent or more potent than A as V1 antagonists. Peptides 2-9 are less potent than A as V2 antagonists. Three, 4, 5, and 9, exhibit significant gains in anti-V1/anti-V2 selectivities (selectivity ratio = 41, 14, and infinite, respectively), compared to A (anti-V1, pA2 = 7.75 +/- 0.07; selectivity ratio = 0.44). Peptide 9 is unique in both series. It is a highly potent V1 antagonist (anti-V1 pA2 = 8.62 +/- 0.11 and is the first linear peptide to exhibit substantial antidiuretic agonism (4.1 +/- 0.2 units/mg). With the exception of 12, the remaining 11 analogues of D are 8-40 times more potent than D as V1 antagonists. Eight of these peptides exhibit significant gains in anti-V1/anti-V2 selectivities compared to D (anti-V1 pA2 = 7.43 +/- 0.06; selectivity ratio = 1.6).(ABSTRACT TRUNCATED AT 400 WORDS)
<i>Pseudomonas</i> Exotoxin and Recombinant Immunotoxins Derived from It (1993)

Pseudomonas exotoxin (PE) is a bacterial toxin that kills mammalian cells by gaining entry to the cytosol and inactivating protein synthesis. The toxin binds and enters cells via the alpha 2-macroglobulin receptors. Within cells, the toxin is processed in several steps to produce an enzymatically active 37-kDa C-terminal fragment which translocates to the cytosol and ADP-ribosylates elongation factor 2. Because PE is a very potent toxin, derivatives of it have been produced which, when joined to various binding ligands, are capable of killing specific target cells. It is hoped that this strategy will lead to the development of effective therapeutic agents for the treatment of human diseases such as cancer, AIDS, and various immunologic disorders.
Magnetic resonance elastography of the lung: Technical feasibility (2006)

Magnetic resonance elastography (MRE) is a phase-contrast technique that can spatially map shear stiffness within tissue-like materials. To date, however, MRE of the lung has been too technically challenging-primarily because of signal-to-noise ratio (SNR) limitations and phase instability. We describe an approach in which shear wave propagation is not encoded into the phase of the MR signal of a material, but rather from the signal arising from a polarized noble gas encapsulated within. To determine the feasibility of the approach, three experiments were performed. First, to establish whether shear wave propagation within lung parenchyma can be visualized with phase-contrast MR techniques, MRE was performed on excised porcine lungs inflated with room air. Second, a phantom consisting of open-cell foam filled with thermally polarized (3)He gas was imaged with MRE to determine whether shear wave propagation can be encoded by the gas. Third, preliminary evidence of the feasibility of MRE in vivo was obtained by using a longitudinal driver on the chest of a normal volunteer to generate shear waves in the lung. The results suggest that MRE in combination with hyperpolarized noble gases is potentially useful for noninvasively assessing the regional elastic properties of lung parenchyma, and merits further investigation.
Using Hermite-Gaussian modes for free-space optical communication (Conference Presentation) (2018)

There is interest in using spatial modes of light to increase the data speed of free-space optical communication where, each spatial mode can be used as a state or channel with which to encode or carry data, respectively. Here, the use of Hermite-Gaussian modes for free-space optical communication is investigated. It is shown that due their symmetry with respect to lateral displacement, as compared to other spatial modes, such as, orbital angular momentum modes, a subset of Hermite-Gaussian modes can experience less mode-crosstalk and -dependent loss when laterally displaced at the data receiver.
Defining the genetic components of callus formation: A GWAS approach (2018)

A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture propagation of recalcitrant plant species and genetic engineering for desired phenotypes typically depends on efficient in vitro callus generation. Callus formation is under genetic regulation, and consequently, a molecular understanding of this process underlies successful generation for propagation materials and/or introduction of genetic elements in experimental or industrial applications. Herein, we identified 11 genetic loci significantly associated with callus formation in Populus trichocarpa using a genome-wide association study (GWAS) approach. Eight of the 11 significant gene associations were consistent across biological replications, exceeding a chromosome-wide-log10 (p) = 4.46 [p = 3.47E-05] Bonferroni-adjusted significance threshold. These eight genes were used as hub genes in a high-resolution co-expression network analysis to gain insight into the genome-wide basis of callus formation. A network of positively and negatively co-expressed genes, including several transcription factors, was identified. As proof-of-principle, a transient protoplast assay confirmed the negative regulation of a Chloroplast Nucleoid DNA-binding-related gene (Potri.018G014800) by the LEC2 transcription factor. Many of the candidate genes and co-expressed genes were 1) linked to cell division and cell cycling in plants and 2) showed homology to tumor and cancer-related genes in humans. The GWAS approach based on a high-resolution marker set, and the ability to manipulate targets genes in vitro, provided a catalog of high-confidence genes linked to callus formation that can serve as an important resource for successful manipulation of model and non-model plant species, and likewise, suggests a robust method of discovering common homologous functions across organisms.
Recombinant bacteria for mosquito control (2003)

Bacterial insecticides have been used for the control of nuisance and vector mosquitoes for more than two decades. Nevertheless, due primarily to their high cost and often only moderate efficacy, these insecticides remain of limited use in tropical countries where mosquito-borne diseases are prevalent. Recently, however, recombinant DNA techniques have been used to improve bacterial insecticide efficacy by markedly increasing the synthesis of mosquitocidal proteins and by enabling new endotoxin combinations from different bacteria to be produced within single strains. These new strains combine mosquitocidal Cry and Cyt proteins of Bacillus thuringiensis with the binary toxin of Bacillus sphaericus, improving efficacy against Culex species by 10-fold and greatly reducing the potential for resistance through the presence of Cyt1A. Moreover, although intensive use of B. sphaericus against Culex populations in the field can result in high levels of resistance, most of this can be suppressed by combining this bacterial species with Cyt1A; the latter enables the binary toxin of this species to enter midgut epithelial cells via the microvillar membrane in the absence of a midgut receptor. The availability of these novel strains and newly discovered mosquitocidal proteins, such as the Mtx toxins of B. sphaericus, offers the potential for constructing a range of recombinant bacterial insecticides for more effective control of the mosquito vectors of filariasis, Dengue fever and malaria.