gebhart/patrepeval huggingface dataset:
TBX3 and Its Isoform TBX3+2a Are Functionally Distinctive in Inhibition of Senescence and Are Overexpressed in a Subset of Breast Cancer Cell Lines (2004)

TBX3 is a transcription factor of the T-box gene family. Mutations of TBX3 cause ulnar-mammary syndrome (MIM 181450) in humans, an autosomal dominant disorder characterized by the absence or underdevelopment of the mammary glands and other congenital anomalies. It recently was found that TBX3 was able to immortalize mouse embryo fibroblast (MEF) cells. In addition, TBX2, a homologue of TBX3, is active in preventing senescence in rodent cells and was found to be amplified in some human breast cancers, suggesting TBX3 plays a role in breast cancer. This study examined the function of TBX3 and its isoform, TBX3 + 2a. TBX3 + 2a differs from TBX3 in the DNA binding domain with an extra 20 amino acids produced by alternative splicing. We first examined the tissue expression and alternative splicing patterns of these two isoforms. We found that TBX3 and TBX3 + 2a are widely expressed in humans and mice, and alternative splicing could be tissue specific and species specific. Overexpression of TBX3 is able to immortalize MEF cells, whereas TBX3 + 2a shows an acceleration of senescence, a functional difference that may be explained by the fact that these two isoforms may have different downstream targets. TBX3, but not TBX3 + 2a, is able to bind to the previously identified T-box binding site in a gel shift assay. A subset of human breast cancer cell lines overexpresses TBX3. Our results indicate that TBX3 and TBX3 + 2a are functionally distinctive in inhibition of senescence of MEF cells and may play a role in breast cancer.
Cyclization of Allyl Silanes — A Novel Approach to 2-Azabicyclo[3.3.0]octanes (1989)

&bsmcl -The methodology which consists in the electrophilic substitution of a-acyl and N-acyl iminium ions on allyl siianes has been used to accede to 2-arabicyclo[3.3.0]octane derivatives and realizes a formal total synthesis of azacarboprostacyclin analogs.Since the discovery of prostacyclins PGI~I, a number of prostacyclin analogs have been reported such as carboprostacyclins and various aza analogs2.The preparation of this class of compounds and its congeners is of considerable interest due to their potentially usefulness in the treatment of thrombotic disease, hypertension.inhibition of platelet aggregation and all forms of vascular disease3.The common structure of azacarboprostacyclins consists in a functionalized 2-azabicyclo[3.3.0loctaneframework.(cf.Scheme 1). Scheme 1Several methods were used to synthesize these azabicyclic compounds2 ; in our approach7 the second ring is created by the intramolecular electrophilic substitution of an a-acyl or N-carboxyiminium ion on an allylsilane derivative (cf.Scheme 2).Allylsilanes constitute a class of nucleophiles which were largely used in organic synthetic field4.These compounds exhibit an excellent reactivity towards electrophiles such as carbonyl derivatives5 and more recently a-acyl iminium ion&.in recent papers, we related intramolecular reactions of cyclic a-acyl iminium ions with allylic silanes ; this strategy was employed with success to accede to indolizidine and quinolizidine bicyclic systems7 and to realize, in four Steps, a formal total synthesis of (t)-mesembrine in a stereospecific manner8.We wish to repon here a new method for the preparation of 2-azabicyclo[3.3.0]octanes based on the electrophilic substitution of a-acyl iminium ions on an allylsilane derivative.Moreover, the formal total synthesis of 2-azacarboprostacyclin analogs was realized by the intramolecular cyclization of an allylsilane on a N-carboxy iminium ion.
The early clinical development of Ebola virus treatments (2016)

Filoviruses are highly pathogenic negative-stranded RNA hemorrhagic fever viruses. First discovered in 1967, filovirus infections in humans have increased, culminating with the recent Ebola virus e...
Temperature-Dependent Empirical Parameters for Polarity in Choline Chloride Based Deep Eutectic Solvents (2017)

Deep eutectic solvents have emerged as a promising and economically viable alternative to address our need for environmentally benign media. Efficient utilization of deep eutectic solvents in various fields will require adequate knowledge about their physicochemical properties. In this work, independent polarity scales pertaining to solvent polarizability, dipolarity, acidity and basicity have been determined for some commonly used deep eutectic solvents based on choline chloride. The three eutectic mixtures selected for the study include reline (1:2 mixture of choline chloride and urea), ethaline (1:2 mixture of choline chloride and ethylene glycol), and glyceline (1:2 mixture of choline chloride and glycerol). The variation of the probe response as a function of temperature revealed some interesting details about the polarity of neoteric solvents being investigated. Our observations indicate that while the polarity parameters for ethaline and glyceline are easily determined, the instability of probe molecules in reline poses a potential challenge for the determination of its polarity parameters. Attempts to correlate the empirical polarity parameters with solvatochromic response of Reichardt's dye (E<sub>T</sub><sup>N</sup> parameter) also led to surprising observations. Use of alternative probes to measure the polarity in reline indicated that the polarity scales using different probes need to be normalized for DESs. The results emphasize the extent of applicability of currently employed polarity scales to determine the polarity of DES, the need to develop appropriate probe molecules, and the factors limiting our understanding of these extremely interesting class of solvents.
218. 2-butyne-1 : 4-diol. Part I. Reactions of the hydroxyl groups (1946)

A. W. Johnson, J. Chem. Soc., 1946, 1009 DOI: 10.1039/JR9460001009
2'-Pyrene modified oligonucleotide provides a highly sensitive fluorescent probe of RNA (1999)

Oligonucleotide 9mers containing 2'-O-(1-pyrenylmethyl)uridine [U(pyr)] at the center position were synthesized by using a protected U(pyr) phosphoramidite. The UV melting behaviors indicate that the pyrene-modified oligonucleotides can bind to both their complementary DNA and RNA in aqueous solution. When compared with the unmodified oligonucleotides, the pyrene-modified oligonucleotides showed higher affinity for DNA while exhibiting lower affinity for RNA. The pyrene-modified oligonucleotides in diluted solution exhibited fluorescence typical of pyrene monomer emission [lambdamax 378 (band I) and 391 nm (band III)]. When these oligomers bound to DNA, the fluorescence intensity ratio of band III/band I was increased. With this fluorescence change, a new broad emission (lambdamax 450 nm) due to exciplex between the pyrene and an adjacent nucleobase appeared. In contrast, addition of RNA to the pyrene oligonucleotides resulted in enhancement of the pyrene monomer emission with decrease in the fluorescence band ratio. The extent of the emission enhancement was found to be highly dependent on the nucleobase adjacent to the U(pyr) in the pyrene oligomers. The pyrene oligonucleotide containing dC at the 3'-site of the modification showed remarkable increase (approximately 250 times) in fluorescence (375 nm) upon binding to complementary RNA. The present findings would open the way to the design of a highly sensitive fluorescent probe of RNA.
Impact of the Laser on Nevi And Melanomas (1964)

The incident energy of the powerful beam of the ruby laser has been shown to be absorbed more effectively by colored tissues. 1-3 Nevi and melanomas in an accessible organ, such as the skin, provide adequate masses of such tissues. Superficial changes in pigmented nevi and in melanoma were produced in experiments with low energy lasers (0.5-1.0 joules of exit energy from the laser head) . 1-3 Continued work with high energy lasers (25 to 125 joules of exit energy) has produced more extensive change. Outputs of laser energy were measured by a TRG calorimeter in conjunction with a Keithley microvolt-ammeter. The cellular nevi exposed to the laser included two junctional, seven mixed, and three dermocellular types. The nevi were excised, moistened with saline, and placed on glass slides. In three of the dermocellular nevi, 1% aqueous solution of Evans blue dye was injected into portions of the tissue to determine
Pharmacokinetics and Tissue Distribution of Cisplatin and Conjugates of Cisplatin with Carboxymethyldextran and A5B7 Monoclonal Antibody in CD1 Mice (1997)

The plasma disposition kinetics and tissue distribution of platinum was evaluated following intravenous bolus administration to CD1 immune-competent mice of cisplatin, cisplatin conjugated to anti-CEA monoclonal antibody A5B7 via a carboxymethyl dextran (CMdextran) carrier molecule, and cisplatin coupled to the CMdextran in the absence of antibody. In addition, the in vivo characteristics of 125I-labeled A5B7 were compared with and without conjugation to CMdextran. Conjugation of cisplatin [clearance (CL = 0.62 mL/min/g, volume of distribution at steady-state (Vdss) = 16 mL/g] to CMdextran restricted its tissue distribution (Vdss = 0.43 mL/g) and reduced its systemic clearance (CL = 0.055 mL/min/g). Subsequent conjugation of the complex to A5B7 further reduced both its distribution (Vdss = 0.20 mL/g) and clearance (CL = 0.016 mL/min/g). Clearance of A5B7 (CL = 0.002 mL/min/g) was increased by conjugation to CMdextran (CL = 0.014 mL/min/g); tissue distribution was unchanged. A5B7-CMdextran-cisplatin was relatively stable in plasma and other tissues, except the liver. The extent of distribution of platinum into tissues (lung, liver, muscle, kidney) was markedly influenced by conjugation, with the influence being greatest for unmodified cisplatin and least for the A5B7-CMdextran conjugate. However, the time courses of tissue distribution, expressed in mean residence time scales, were similar, implying a common mechanism controlling tissue uptake.
Nutraceutical and Specialty Lipids and their Co-Products (2006)

Nutraceutical and Specialty Lipids F. Shahidi and S.P.J.N. Senanayake Medium-Chain Triacylglycerols Y. B. Che Man and M. Abdul Manaf Cereal Grain Oils R. Przybylski Fruit Seed Oils L. Yu, J.W. Parry, and K. Zhou Minor Specialty Oils F. D. Gunstone Sphingolipids F. Fang, H. Chen, C.-T. Ho, and R.T. Rosen Modification and Purification of Sphingolipids and Gangliosides S. Bloomer Hydroxy Fatty Acids T.A. McKeon, C.T.X. Hu, G. Chen, and J.-T. Lin Tree Nuts, Oils, and Byproducts: Compositional Characteristics and Nutraceutical Applications F. Shahidi and H. Miraliakbari Gamma-Linolenic Acid (GLA) Y-W. Huang and C-Y. Huang Diacylglycerols (DAGs) and their Mode of Action B.D. Flickinger Conjugated Linoleic Acids (CLAs): Food, Nutrition, and Health B.A. Watkins and Yong Li Occurrence of Conjugated Fatty Acids in Aquatic and Terrestrial Plants and their Physiological Effects B. Narayan, M. Hosokawa, and K. Miyashita Marine Conjugated Polyunsaturated Fatty Acids Y. Endo, S.-B. Park, and K. Fujimoto Marine Oils: Compositional Characteristics and Health Effects F. Shahidi and H. Miraliakbari Single-Cell Oils as Sources of Nutraceutical and Specialty Lipids: ProcessingTechnologies and Applications S.P.J.N. Senanayake and J. Fichtali Emulsions for the Delivery of Nutraceutical Lipids K. Mootoosingh and D. Rousseau Lipid Emulsions for Total Parenteral Nutrition (TPN) Use and as Carriers for Lipid-Soluble Drugs H. Lui and L. Wang Modified Oils F. D. Gunstone Fat Replacers: Mimetics and Substitutes B. G. Swanson Application of Functional Lipids in Foods C. Jacobsen, M. Timm-Heinrich, and N. Skall Nielsen Application of Multistep Reactions with Lipases to the Oil and Fat Industry Y. Shimada, T. Nagao, and Y. Watanabe Structure-Related Effects on Absorption and Metabolism of Nutraceutical and Specialty Lipids A.B. Christophe Lipid Oxidation in Specialty Oils K. Schaich TransFatty Acids in Specialty Lipids G.R. List, R.O. Adlof, and J.W. King Tocopherols and Tocotrienols as Byproducts of Edible Oil Processing Vitamin E: A New Perspective A.M. Papas Plant Sterols and Steryl Esters in Functional Foods and Nutraceuticals N. Weber and K.D. Mukherjee Phospholipids/Lecithin: A Class of Nutraceutical Lipids F.T. Orthoefer and G.R. List Centrifugal Partition Chromatography (CPC) as a New Tool for Preparative-Scale Purification of Lipid and Related Compounds U. Wanasundara and P. Fedec Oilseed Medicinals: Applications in Drugs and Functional Foods R. D. Reichert
Scribbler: Controlling Deep Image Synthesis with Sketch and Color (2017)

Several recent works have used deep convolutional networks to generate realistic imagery. These methods sidestep the traditional computer graphics rendering pipeline and instead generate imagery at the pixel level by learning from large collections of photos (e.g. faces or bedrooms). However, these methods are of limited utility because it is difficult for a user to control what the network produces. In this paper, we propose a deep adversarial image synthesis architecture that is conditioned on sketched boundaries and sparse color strokes to generate realistic cars, bedrooms, or faces. We demonstrate a sketch based image synthesis system which allows users to scribble over the sketch to indicate preferred color for objects. Our network can then generate convincing images that satisfy both the color and the sketch constraints of user. The network is feed-forward which allows users to see the effect of their edits in real time. We compare to recent work on sketch to image synthesis and show that our approach generates more realistic, diverse, and controllable outputs. The architecture is also effective at user-guided colorization of grayscale images.
Per què està de moda la bioinformàtica? Les papallones ens ajuden a descobrir-ho (2018)

Us heu preguntat mai per que tenim dos bracos o com es que no tenim cua i, en canvi, els taurons i els cangurs si que en tenen? Per que al desert hi ha cactus pero no hi ha roses o com troben parella les papallones? I per que els grills tenen tants fills i, en canvi, els ximpanzes tan pocs? Com sabem que els animals estem mes emparentats amb els fongs que amb les plantes? Com demostrem que els humans som cosins germans dels ximpanzes? I com hem descobert que els mitocondris probablement eren bacteris que van ser engolits per una altra cel·lula? La cerca de respostes a totes aquestes preguntes ha ocupat i apassionat a naturalistes i cientifics des de fa molts anys. I no es estrany, perque som davant de questions molt profundes i complexes que expliquen el perque del que ens envolta, quins passos ha seguit la natura per anar modelant el nostre entorn i, sobretot, ens ajuden a descobrir d’on venim. Estudiem l’evolucio de les especies per coneixer la causa ultima del la biodiversitat que observem, i aixi, poc a poc, anar entenent com funciona la natura. En l’actualitat gran part d’aquests estudis evolutius es duen a terme gracies a eines informatiques aplicades a la biologia, que es el que anomenem bioinformatica. Si voleu saber que pot fer la bioinformatica per nosaltres, i a mes, descobrir com funciona el gust i l’olfacte de les papallones, continueu llegint.
Comparison of direct blind deconvolution methods for motion-blurred images (1999)

Direct methods for restoration of images blurred by motion are analyzed and compared. The term direct means that the considered methods are performed in a one-step fashion without any iterative technique. The blurring point-spread function is assumed to be unknown, and therefore the image restoration process is called blind deconvolution. What is believed to be a new direct method, here called the whitening method, was recently developed. This method and other existing direct methods such as the homomorphic and the cepstral techniques are studied and compared for a variety of motion types. Various criteria such as quality of restoration, sensitivity to noise, and computation requirements are considered. It appears that the recently developed method shows some improvements over other older methods. The research presented here clarifies the differences among the direct methods and offers an experimental basis for choosing which blind deconvolution method to use. In addition, some improvements on the methods are suggested.
Type 1 transforming growth factor beta: amplified expression and secretion of mature and precursor polypeptides in Chinese hamster ovary cells. (1987)

Recombinant type 1 transforming growth factor beta (TGF-beta) was expressed to high levels in CHO cells by using dihydrofolate reductase (dhfr) gene amplification. The expression plasmid was derived from the pSV2 vectors and contained, in tandem, the simian TGF-beta and mouse dhfr cDNAs. Transcription of both cDNAs was controlled by the simian virus 40 early promoter. Stepwise selection of transfected CHO cells in increasing concentrations of methotrexate yielded cell lines that expressed amplified TGF-beta nucleic acid sequences. The expression plasmid DNA was amplified greater than 35-fold in one of the methotrexate-selected transfectants. The major proteins secreted by these cells consisted of latent TGF-beta and TGF-beta precursor polypeptides, as judged by immunoblots by using site-specific anti-peptide antibodies derived from various regions of the TGF-beta precursor. Levels of recombinant TGF-beta protein secreted by these cells approached 30 micrograms/24 h per 10(7) cells and required prior acidification for optimal activity; nonacidified supernatants were approximately 1% as active as acidified material. Antibodies directed toward sequences present in the mature growth factor readily identified a proteolytically processed recombinant TGF-beta which, on sodium dodecyl sulfate-polyacrylamide gels, comigrated with highly purified natural TGF-beta. In addition to mature recombinant TGF-beta, site-specific antibodies demonstrated the existence of larger TGF-beta precursor polypeptides. The availability of biologically active recombinant type 1 TGF-beta and precursor forms should provide a means to examine the structure, function, and potential in vivo therapeutic use of this growth factor.
Tumour-amplified kinase BTAK is amplified and overexpressed in gastric cancers with possible involvement in aneuploid formation (2001)

Our recent analysis of gastric cancers using comparative genomic hybridization (CGH) revealed a novel high frequent copy number increase in the long arm of chromosome 20. Tumour-amplified kinase BTAK was recently cloned from breast cancers and mapped on 20q13 as a target gene for this amplification in human breast cancers. In the study presented here, we analysed BTAK copy-number and expression, and their relation to the ploidy pattern in 72 primary gastric cancers. Furthermore, wild-type BTAK and its deletion mutants were transfected to gastric cancers to examine changes in cell proliferation and DNA ploidy pattern. Evaluation of 72 unselected primary gastric cancers found BTAK amplification in 5% and overexpression in more than 50%. All four clinical samples with BTAK amplification showed aneuploidy and poor prognosis. Transfection of BTAK in near-diploid gastric cancers induced another aneuploid cell population. In contrast, the c-terminal-deleted mutant of BTAK induced no effect in DNA ploidy pattern and inhibited gastric cancer cell proliferation. These results suggest that BTAK may be involved in gastric cancer cell aneuploid formation, and is a candidate gene for the increase in the number of copies of the 20q, and thus may contribute to an increase in the malignant phenotype of gastric cancer.
Experimental demonstration of a tunable laser using an SOA and an Opto-VLSI Processor (2007)

In this paper we propose and experimentally demonstrate a tunable laser structure cascading a semiconductor optical amplifier (SOA) that generates broadband amplified spontaneous emission and a reflective Opto-VLSI processor that dynamically reflects arbitrarily wavelengths and injects them back into the SOA, thus synthesizing an output signal of variable wavelength. The wavelength tunablility is performed using digital phase holograms uploaded on the Opto-VLSI processor. Experimental results demonstrate a tuning range from 1524nm to 1534nm, and show that the proposed tunable laser structure has a stable performance.
Interference Testing of Horizontal Wells (1991)

ABSTRACT Solution to the problem of interference testing of horizontal wells is a major step forward in understanding the fluid flow behavior of horizontal wells and, therefore, to the efficient implementation of the horizontal well technology. These tests provide valuable information about reservoir characteristics such as areal average transmissibility, storage, and degree of communication between wells. Due to the larger radius of influence and larger contact area of a horizontal well with the formation than its vertical counterpart, this paper suggests that the transmissibility and storage obtained from interference testing of horizontal wells would be much more representative of the formation than the ones obtained from interference testing of vertical wells. This paper provides the dimensionless pressure and dimensionless pressure derivative type curves for interference testing of horizontal wells and the appropriate equations to be used in conjunction with the type curves in order to determine transmissibility and storage from field data. Solutions were also obtained for interference testing between horizontal and vertical wells. In addition, this paper recommends that the determination of dimensionless pressure at the horizontal wellbore requires calculating the PD function at small values of both YD and ZD
Cyclin-Dependent Regulation of G 1 in Mammalian Fibroblasts (1993)

Eukaryotic cells become committed to proliferate during the G1 phase of the cell cycle. In budding yeast, commitment occurs when the catalytic subunit of a protein kinase, encoded by the CDC28 gene (the homolog of the fission yeast cdc2+ gene), binds to a positively acting regulatory subunit, a cyclin. Related kinases are also required for progression through the G1 phase in higher eukaryotes. The role of cyclins in controlling G1 progression in mammalian cells was tested by construction of fibroblasts that constitutively overexpress human cyclin E. This was found to shorten the duration of G1, decrease cell size, and diminish the serum requirement for the transition from G1 to S phase. These observations show that cyclin levels can be rate-limiting for G1 progression in mammalian cells and suggest that cyclin synthesis may be the target of physiological signals that control cell proliferation.
Band-gap engineering in periodic elastic composites (1994)

Periodic elastic composites can give rise to complete band gaps in which vibrations, sound, and phonons are forbidden. This is of interest for applications such as creation of vibrationless environment and improvements in transducers, as well as for pure physics related to localized vibrations and phonons. We present rudimentary ideas of the ‘‘band-gap engineering’’ necessary for designing suitable frequency gaps. This is illustrated by means of acoustic band structures, computed for periodic, binary composites of long, elastic cylinders that form a hexagonal lattice.