gebhart/patrepeval huggingface dataset:
SOX2 Modulates Reprogramming of Gene Expression in Two-Cell Mouse Embryos1 (2011)

Sox2 is a key gene that controls transcriptional networks required for pluripotency. The role of Sox2 in the developmental transition of a highly differentiated oocyte to totipotent blastomeres of the early preimplantation embryo, however, is not known. We report that Sox2, which is localized in the nucleus, is first zygotically expressed during the 2-cell stage and that its expression dramatically increases between the morula and blastocyst stages. Injecting a cRNA encoding Sox2 into 1-cell embryos resulted in overexpression of SOX2 by approximately 70% and developmental arrest at the 2-cell stage, whereas injecting cRNAs encoding Pou5f1, Myc (also known as c-Myc), or Klf4 has little effect on the ability of 2-cell embryos to cleave to the 4-cell stage. Global transcription assessed by bromo uridine triphosphate incorporation is reduced by approximately 15%, and transcript profiling revealed that approximately 15% of zygotically expressed genes are dramatically repressed in 2-cell embryos overexpressing SOX2. Furthermore, overexpressing a dominant-negative SOX2 perturbs reprogramming of gene expression in 2-cell embryos, though to a much lesser extent than that observed following overexpression of SOX2, and leads to developmental failure after the 2-cell stage but before the 8-cell stage. Results of these experiments implicate Sox2 as a critical transcriptional regulator in the oocyte-to-embryo transition that entails formation of totipotent blastomeres and indicate that the amount of Sox2 is critical for successful execution of this transition.
Mechanisms of smooth muscle responses to inflammation (2012)

In this review we discuss the various types of inflammation and the established and emerging mechansims of inflammation-induced changes in smooth muscle morphology and function.
Quantum Interferometric Optical Lithography: Exploiting Entanglement to Beat the Diffraction Limit (2000)

Classical optical lithography is diffraction limited to writing features of a size lambda/2 or greater, where lambda is the optical wavelength. Using nonclassical photon-number states, entangled N at a time, we show that it is possible to write features of minimum size lambda/(2N) in an N-photon absorbing substrate. This result allows one to write a factor of N2 more elements on a semiconductor chip. A factor of N = 2 can be achieved easily with entangled photon pairs generated from optical parametric down-conversion. It is shown how to write arbitrary 2D patterns by using this method.
The Lutheran blood group glycoprotein, another member of the immunoglobulin superfamily, is widely expressed in human tissues and is developmentally regulated in human liver. (1995)

Glycoproteins expressing the Lutheran blood group antigens were isolated from human erythrocyte membranes and from human fetal liver. Amino acid sequence analyses allowed the design of redundant oligonucleotides that were used to generate a 459-bp, sequence-specific probe by PCR. A cDNA clone of 2400 bp was isolated from a human placental lambda gt 11 library and sequenced, and the deduced amino acid sequence was studied. The predicted mature protein is a type I membrane protein of 597 amino acids with five potential N-glycosylation sites. There are five disulfide-bonded, extracellular, immunoglobulin superfamily domains (two variable-region set and three constant-region set), a single hydrophobic, membrane-spanning domain, and a cytoplasmic domain of 59 residues. The overall structure is similar to that of the human tumor marker MUC 18 and the chicken neural adhesion molecule SC1. The extracellular domains and cytoplasmic domain contain consensus motifs for the binding of integrin and Src homology 3 domains, respectively, suggesting possible receptor and signal-transduction function. Immunostaining of human tissues demonstrated a wide distribution and provided evidence that the glycoprotein is under developmental control in liver and may also be regulated during differentiation in other tissues.
Electrochemical impedance spectroscopy investigations focused on food allergens (2014)

In this article, we survey recent literature related to the development of impedimetric sensors and methods for allergen proteins in food. Electrochemical impedance spectroscopy is&#13;\nan electrochemical method that allows label-free monitoring of analyte-ligand interactions and&#13;\nwas largely used for characterising various steps in the development of (bio)sensors. Both faradaic impedance spectroscopy – using a redox probe added to the analytical system to be investigated – and non-faradaic impedance spectroscopy were used for the detection of food allergens. Several approaches leading to high sensitivity and application to the analysis of real samples are particularly emphasized. The challenges in using EIS for the determination of allergens are discussed.
Expansion of microvascular bed and increased solute flux in human Basal cell carcinoma in vivo, measured by fluorescein video angiography. (2003)

Human basal cell carcinoma (BCC) offers a unique opportunity to assess directly the microvascular abnormalities in a human cancer in vivo. Our objectives were to assess angiogenesis, perfusion, and changes in small solute exchange kinetics. The microcirculation of BCC and a normal (control) skin site was studied in 15 patients by laser Doppler fluximetry and videoangiography after rapid i.v. fluorescein injection. Microvascular morphometry was analyzed off line. Sodium fluorescein accumulation/clearance was recorded for 30 min, and fluorescence intensity (FI) was quantified by computer analysis of videotape image gray levels. In BCCs, the microvascular area fraction was 2.6-fold greater, microvessel length density 2.0-fold greater, average vessel image width 2.1-fold greater, and red cell flux 3.9-fold greater than in control sites (P < 0.01, paired t tests). The initial rate of rise of FI over 10 s was approximately 3-fold greater in BCC than control and correlated with vascular area fraction and red cell flux. Tissue then equilibrated faster in BCC, rate constant -(13.0 +/- 5.6) x 10(-3) s(-1) (mean +/- SD), than controls -(5.3 +/- 1.7) x 10(-3) s(-1), and plasma clearance was 2.6-fold higher in BCC than controls (P < 0.01, paired t test). Similarly, the rate constant of the subsequent clearance phase was approximately 2-fold greater in BCC, -(0.53 +/- 0.19) x 10(-3) s(-1), than controls, -(0.27 +/- 0.22) x 10(-3) s(-1) (P < 0.01). Removal rate constants were an order of magnitude slower than accumulation rate constants. The results demonstrate angiogenesis, increased perfusion, and a more rapid exchange of small solute in human BCC. FI itself is rejected as an index of permeability to small solutes (cf. 29) because it depends also on blood flow, endothelial area, microvascular volume, and interstitial fluid volume.
Spermicidal activity of chelated complexes of bis(cyclopentadienyl)vanadium(IV) (1998)

Transition metal complexes containing vanadium IV have been shown to modulate the cellular redox potential and catalyse the generation of reactive oxygen intermediates (ROI). Since sperm function is exquisitely susceptible to ROI, we examined the effects of stable chelate complexes of vanadocenes on human sperm motility. We synthesized seven structurally distinct chelate complexes of bis(cyclopentadienyl)vanadium(IV) with bidentate ligands [i.e. vanadocene acetylacetonato monotriflate (VDacac), vanadocene hexafluoro acetylacetonato monotriflate (VDHfacac), vanadocene N-phenyl benzohydroxamato monotriflate (VDPH), vanadocene acethydroxamato monotriflate (VDH), vanadocene catecholate (VDCAT), vanadocene bipyridino ditriflate (VDBPY), and vanadocene dithiocarbamate monotriflate (VDDTC)], and evaluated their spermicidal activity using computer-assisted sperm analysis (CASA; Hamilton-Thorne). All seven chelate complexes of vanadocene elicited potent spermicidal activity at micromolar concentrations (EC50 values: 3.9-106 microM) without affecting the sperm acrosome integrity. The catecholate and acetylacetonate complexes of vanadocene were the most active and the bipyridyl complex the least active with an order of efficacy VDCAT > VDacac > VDDTC > VDPH > VDH > VDHfacac > VDBPY. The spermicidal activity of chelate complexes of vanadocenes was rapid and irreversible since the treated spermatozoa underwent apoptosis, as determined by the flow cytometric analysis of mitochondrial membrane potential, surface annexin V binding assay, in-situ nick-end labelling of sperm nuclei, and confocal laser scanning microscopy. These results provide unprecedented evidence that chelate complexes of vanadocene with bidentate ligands have spermicidal and apoptosis inducing properties. These vanadocene complexes, especially VDacac, may be useful as contraceptive agents.
Bidirectional-Barbed Sutured Knotless Running Anastomosis v Classic Van Velthoven Suturing in a Model System (2007)

It appears from our preliminary work that a bidirectional-barbed suture might improve the vesicourethral anastomosis during a robotic radical prostatectomy. Further investigations should be done to measure the disruptive force necessary to distract these sutures, whether the applied forces of the barbs are adequate for maintaining a watertight seal, and the reproducibility of our results by other surgeons. All of these investigations are in progress in our laboratory.
Algebraic Implementation of Model Checking (1996)

We apply the algebraic methodology for compiler design and implementation to deduce an algebraic specification and implementation of a CTL model checker algorithm. For that we start by observing that an algebraic compiler C : L s ! L t is a language-to-language translator embedding a source language L s into a target language L t . We take the source language to be the set of CTL formulas for a given model M and the target language to be the power set of the set of states of the model M . The algebraic compiler thus specified translates a CTL formula f , to the set of states, S 0 , on which f is satisfied. That is, C(f) = S 0 where S 0 = fsjs 2 S M; s j= fg. This approach has significant advantages over the traditional approach. Among others, we note that this algorithm is automatically generated from an algebraic specification of the source and target languages, and since it is based on homomorphism computation it is naturally parallel.
Growth and Antigen Recognition of Tumor-Infiltrating Lymphocytes from Human Breast Cancer (1998)

In the present study, we isolated tumor-infiltrating lymphocytes (TIL) from 21 primary solid tumors and tumor-associated lymphocytes (TAL) from 9 malignant effusions, respectively, of breast cancer patients. Significant proliferation and expansion of T cells was observed in 23 of 30 distinct samples. TIL were isolated from primary tumors by either enzymatic digestion or mechanical disruption. The TIL cultures were initiated using OKT3 mAb in the presence of moderate concentrations (25-50 U/ml) of IL-2, followed by 100 U/ml of tumor necrosis factor (TNF)-alpha. TAL were not stimulated with OKT3 mAb, but all were successfully expanded in culture in the presence of IL-2 alone or together with TNF-alpha. Seven of nine distinct TAL grew in culture as predominantly CD4+ lines. In contrast, only 14 of 21 (66%) of primary breast TIL expanded in culture and were predominantly of CD8+ phenotype. Autologous tumor lysis was observed in seven of eight cases tested. Only one of the four TIL tested and one of the four TAL tested preferentially lysed autologous tumor. HER-2 peptide E75 (369-377) was recognized by two TIL lines of the five primary TIL tested and three of the four TAL tested. This suggests that E75 may be recognized by primary breast tumors. This may be of interest in developing vaccine strategies for therapeutic management of breast cancer.
Immunoproteasomes are essential for survival and expansion of T cells in virus‐infected mice (2010)

Immunoproteasomes containing the IFN-inducible subunits β1i (LMP2), β2i (MECL-1) and β5i (LMP7) alter proteasomal cleavage preference and optimize the generation of peptide ligands of MHC class I molecules. Here, we report on an unexpected new function of immunoproteasome subunits for the survival and expansion of CD4(+) and CD8(+) T cells during viral infection of mice. The effect of immunoproteasome subunit deficiency on T-cell survival upon adoptive transfer was most prominent for the lack of LMP7 followed by MECL-1 and LMP2. The survival of T cells in uninfected mice or the homeostatic expansion after transfer into RAG-2(-/-) mice was not affected by the lack of the immunosubunits. Lymphocytic choriomeningitis virus (LCMV)-specific CD8(+) T cells lacking LMP7 or MECL-1 started to divide after transfer into LCMV-infected mice but experienced a considerable cell loss within 2 days after transfer. We provide strong evidence that the loss of immunoproteasome-deficient T cells after transfer is not a consequence of graft rejection by the host, but instead is based on the requirement for immunoproteasomes for the survival of T cells in LCMV-infected mice. Therefore, the immunoproteasome may qualify as a potential new target for the suppression of undesired proinflammatory T-cell responses.
Topical Poloxamer-188 Improves Blood Flow Following Thermal Injury in Rat Mesenteric Microvasculature (2008)

Microvascular changes of sludging and stasis are indications of thermal injury in tissue. This study investigates whether microvascular thermal injury can be decreased via topical application of poloxamer-188. Rat mesenteric microvessels were thermally injured and topically suffused with either Ringer's solution (control) or 5% poloxamer-188 in Ringer's solution (experiment). Blood flow was characterized in microvessels as normal or abnormal (ie, sludging and stasis). Topical treatment with poloxamer-188 reduced the percentage of capillaries with abnormal blood flow from 62% to 23%. In venules, this treatment resulted in a decrease from 54% to 34%. These results demonstrated that topically applied poloxamer-188 dramatically reduces the microvascular changes of sludging and stasis because of thermal injury in rat mesenteric microvessels.
A mild procedure for solid phase peptide synthesis: use of fluorenylmethoxycarbonylamino-acids (1978)

Use of base-labile N-fluorenylmethoxycarbonylamino-acids, t-butyl based side chain protecting groups, and a p-alkoxybenzyl ester resin linkage provides a simple, rapid, and exceptionally mild strategy in solid phase peptide synthesis.
Effects of water- and lipid-soluble antioxidants on turkey sperm viability, membrane integrity, and motility during liquid storage (1997)

Aerobic conditions are required to maintain the viability of turkey sperm in vitro. In mammalian sperm, excess oxygen during in vitro storage results in lipid peroxidation, causing membrane damage and reduced sperm motility and subsequent fertility. The effect of adding antioxidants to turkey sperm during liquid storage was studied. Semen was collected and pooled from 20 toms and antioxidants were tested at a minimum of six concentrations, n = 6 observations per concentration. Semen was diluted into Beltsville Poultry Semen Extender. Extended semen served as a control; treatments were extended semen supplemented with tocopherol (vitamin E, 1 to 80 micrograms/mL); butylated hydroxytoluene (BHT, 0.02 to 1.25 mM); Tempo (0.039 to 1.25 microM), or vitamin C (1 to 400 micrograms/mL) and stored at 5 C for 48 h. Sperm viability in extended semen was evaluated after 0, 24, or 48 h storage. Membrane integrity and motility were also measured. Flow cytometric analysis was done using the live/dead stain combination (SYBR-14/propidium iodide) for sperm viability, and membrane integrity was assessed using a hypo-osmotic stress test. Sperm motility was evaluated subjectively. Control sperm viability was reduced almost 50% between 0 and 48 h. However, supplementation with vitamin E, Tempo, and BHT maintained populations of viable sperm similar to the 0 h levels at 48 h. Hypo-osmotic membrane integrity in the control sperm was reduced to approximately 22% (at 24 h, P < or = 0.05) and 5% (at 48 h, P < or = 0.05) of the total sperm population. Similar to controls after 24 h in vitro storage, sperm treated with the antioxidants vitamin E, Tempo, and BHT had reduced hypo-osmotic membrane integrity compared to 0 h samples. However, many of these treated samples maintained hypo-osmotic membrane integrity observed from 24 through 48 h (range, 21.5 to 44.6%), whereas hypo-osmotic membrane integrity fell to 4.6% at 48 h for the control (P < or = 0.05). Vitamin C treatments were similar to controls at all time points. Addition of the antioxidants vitamin E, BHT, and Tempo to extended turkey semen improves sperm survival, membrane integrity, and reduces the loss of motility after 48 h storage.
Numerical Methods of Bibliographic Analysis (1973)

Owing to the high demand for drone operation in high-elevation masked areas, it is necessary to develop a more effective method of transmitting and applying Satellite-Based Augmentation System (SBAS) messages for drones. This study proposes an onboard module including correction conversion, integrity information calculation, and fast initialization requests, which can enable the application of an online SBAS to drone operation. The proposed system not only improves the position accuracy with timely and proper protection levels in an open sky, but also reduces the initialization time from 70-100 s to 1 s, enabling a drone of short endurance to perform its mission successfully. In SBAS signal-denied cases, the position accuracy was improved by 40% and the uncorrected 13.4 m vertical error was reduced to 5.6 m by applying an SBAS message delivered online. The protection levels calculated with the accurate position regardless of the current location could denote the thrust level and availability of the navigation solution. The proposed system can practically solve the drawbacks of the current SBAS, considering the characteristics of the low-cost receivers on the market. Our proposed system is expected to be a useful and practical solution to integrate drones into the airspace in the near future.
Space Efficient Streaming Algorithms for the Maximum Error Histogram (2007)

We propose new algorithms for constructing maximum error (L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> ) histograms in the data stream model. Our first algorithm (Min-Merge) achieves the following performance guarantee: using O(B) memory, it constructs a 2B-bucket histogram whose approximation error is at most the error of the optimal B-bucket histogram. Our second algorithm (Min-Increment) achieves a (1 + ε)-approximation of a B-bucket histogram using O(ε <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> B log U) space, where U is the size of the domain for data values. The memory requirements of these algorithms are a significant improvement over the previous best schemes for constructing near-optimal histograms in the data stream model, making them ideal for data summary applications where memory is at a premium, such as wireless sensor networks. Our Min-Increment algorithm also extends to the sliding window model without any asymptotic increase in space. Finally, using synthetic and real-world data, we show that our algorithms are indeed as space-efficient in practice as their theoretical analysis predicts - compared to previous best algorithms, they require two or more orders of magnitude less memory for the same approximation error.
A Bayesian decision model for watercolour analysis (2007)

Bayesian Classification methods can be applied to images of watercolour paintings in order to characterize blue and green pigments used in these paintings. Pigments found in watercolour paintings are semi-transparent materials and their analysis provides important information on the date, the painter, the place of the production of watercolour paintings and generally on the authenticity of these works of art. However, watercolour pigments are difficult to characterize because their intensity depends on the amount of liquid spread during painting and the reflective properties of the underlying support. The method describedin this paper is non-destructive, non invasive, does not involve sampling and can be applied in situ. The methodology is based on the photometric properties of pigments and produce computational models which classify diverse types of pigments found in watercolour paintings. These pigments are photographed in the visible and infrared area of electromagnetic spectrum and models based on statistical characteristics of intensity values using a mixture of Gaussian functions are created. Finally the pigments are classified using a Bayesian classification algorithm to process the generate models.
A New Catalytic Route to Monoalkynyl-Functionalized Di- and Trivinyl-Substituted Cyclosiloxanes and Divinylcyclosilazanes (2008)

Series of alkynyltrimethyldivinylcyclotrisiloxanes and -trisilazanes, and of alkynyltetramethyltrivinylcyclotetrasiloxanes have been synthesized by means of a new catalytic coupling of the appropriate tri- and tetra-vinylcyclosiloxanes (1, 2) and trivinylcyclosilazane (3) with terminal alkynes R-C≡C−H (where R = SiEt3, SiMe2Ph, GeEt3, or alkyl) in the presence of a ruthenium hydride complex [RuHCl(CO)(PCy3)2] (I), as a catalyst. Twenty-one new functionalized monoalkynyl-substituted cyclosiloxanes and cyclosilazanes were isolated in high to moderate (70−95%) yields and characterized by 1H, 13C, and 29Si NMR spectroscopy. Selected alkynyldivinyl- and alkynyltrivinyl-cyclic products have been further functionalized by silylative coupling of the remaining vinyl groups with styrene to give cyclosiloxanes and cyclosilazanes containing one alkynyl and two or three styryl substituents at silicon in high yields and selectivity ((E)-styryl products).
Identification of the Wax Ester Synthase/Acyl-Coenzyme A:Diacylglycerol Acyltransferase WSD1 Required for Stem Wax Ester Biosynthesis in Arabidopsis (2008)

Wax esters are neutral lipids composed of aliphatic alcohols and acids, with both moieties usually long-chain (C(16) and C(18)) or very-long-chain (C(20) and longer) carbon structures. They have diverse biological functions in bacteria, insects, mammals, and terrestrial plants and are also important substrates for a variety of industrial applications. In plants, wax esters are mostly found in the cuticles coating the primary shoot surfaces, but they also accumulate to high concentrations in the seed oils of a few plant species, including jojoba (Simmondsia chinensis), a desert shrub that is the major commercial source of these compounds. Here, we report the identification and characterization of WSD1, a member of the bifunctional wax ester synthase/diacylglycerol acyltransferase gene family, which plays a key role in wax ester synthesis in Arabidopsis (Arabidopsis thaliana) stems, as first evidenced by severely reduced wax ester levels of in the stem wax of wsd1 mutants. In vitro assays using protein extracts from Escherichia coli expressing WSD1 showed that this enzyme has a high level of wax synthase activity and approximately 10-fold lower level of diacylglycerol acyltransferase activity. Expression of the WSD1 gene in Saccharomyces cerevisiae resulted in the accumulation of wax esters, but not triacylglycerol, indicating that WSD1 predominantly functions as a wax synthase. Analyses of WSD1 expression revealed that this gene is transcribed in flowers, top parts of stems, and leaves. Fully functional yellow fluorescent protein-tagged WSD1 protein was localized to the endoplasmic reticulum, demonstrating that biosynthesis of wax esters, the final products of the alcohol-forming pathway, occurs in this subcellular compartment.