gebhart/patrepeval huggingface dataset:
Tandemly arranged <i>chalcone synthase A</i> genes contribute to the spatially regulated expression of siRNA and the natural bicolor floral phenotype in <i>Petunia hybrida</i> (2012)

The natural bicolor floral traits of the horticultural petunia (Petunia hybrida) cultivars Picotee and Star are caused by the spatial repression of the chalcone synthase A (CHS-A) gene, which encodes an anthocyanin biosynthetic enzyme. Here we show that Picotee and Star petunias carry the same short interfering RNA (siRNA)-producing locus, consisting of two intact CHS-A copies, PhCHS-A1 and PhCHS-A2, in a tandem head-to-tail orientation. The precursor CHS mRNAs are transcribed from the two CHS-A copies throughout the bicolored petals, but the mature CHS mRNAs are not found in the white tissues. An analysis of small RNAs revealed the accumulation of siRNAs of 21 nucleotides that originated from the exon 2 region of both CHS-A copies. This accumulation is closely correlated with the disappearance of the CHS mRNAs, indicating that the bicolor floral phenotype is caused by the spatially regulated post-transcriptional silencing of both CHS-A genes. Linkage between the tandemly arranged CHS-A allele and the bicolor floral trait indicates that the CHS-A allele is a necessary factor to confer the trait. We suppose that the spatially regulated production of siRNAs in Picotee and Star flowers is triggered by another putative regulatory locus, and that the silencing mechanism in this case may be different from other known mechanisms of post-transcriptional gene silencing in plants. A sequence analysis of wild Petunia species indicated that these tandem CHS-A genes originated from Petunia integrifolia and/or Petunia inflata, the parental species of P. hybrida, as a result of a chromosomal rearrangement rather than a gene duplication event.
Polymeric waveguides (1992)

Techniques for fabricating polymeric waveguides, which are of growing interest for telecommunications, data communications, and optical interconnects within computers at the backplane and multichip-module levels, are described. Fabrication without etching using diffusion techniques or localized reactions and electric field poling, is highlighted. An optical backplane interconnection that uses polyimide waveguide circuits on the daughterboards and motherboard of a multiprocessor system, fabricated as proof of concept, is reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Visualization of chromatin domains created by the <i>gypsy</i> insulator of <i>Drosophila</i> (2003)

Insulators might regulate gene expression by establishing and maintaining the organization of the chromatin fiber within the nucleus. Biochemical fractionation and in situ high salt extraction of lysed cells show that two known protein components of the gypsy insulator are present in the nuclear matrix. Using FISH with DNA probes located between two endogenous Su(Hw) binding sites, we show that the intervening DNA is arranged in a loop, with the two insulators located at the base. Mutations in insulator proteins, subjecting the cells to a brief heat shock, or destruction of the nuclear matrix lead to disruption of the loop. Insertion of an additional gypsy insulator in the center of the loop results in the formation of paired loops through the attachment of the inserted sequences to the nuclear matrix. These results suggest that the gypsy insulator might establish higher-order domains of chromatin structure and regulate nuclear organization by tethering the DNA to the nuclear matrix and creating chromatin loops.
Oral squamous cell carcinoma of tongue (2012)

Squamous Cell Carcinoma is the most common malignant neoplasm of the oral cavity usually affecting individuals over 50–60 years of age and the patients give a long history of tobacco and alcohol use. It rarely occurs in patients who are less than 40 years old (0.4–5.5%). The rarity of this lesion in young patients implies that clinicians might not include it in the differential diagnosis. We hereby present a case of Squamous Cell Carcinoma of the tongue in a 18 year old male.
Rapid prototyping of microfluidic devices for integrating with FT-IR spectroscopic imaging (2010)

A versatile approach for the rapid prototyping of microfluidic devices suitable for use with FT-IR spectroscopic imaging is introduced. Device manufacture is based on the direct printing of paraffin onto the surface of an infrared transparent substrate, followed by encapsulation. Key features of this approach are low running costs, rapid production times, simplicity of design modifications and suitability for integration with FT-IR spectroscopic measurements. In the current experiments, the minimum width of channel walls was found to be approximately 120 mum and approximately 200 when a 25 mum and 12 mum spacer is used, respectively. Water and poly(ethylene glycol) are used as model fluids in a laminar flow regime, and are imaged in both transmission and attenuated total reflection (ATR) modes. It is established that adoption of transmission mode measurements yields superior sensitivity whilst the ATR mode is more suitable for quantitative analysis using strong spectral absorption bands. Results indicate that devices manufactured using this approach are suitable for use with in situ FT-IR spectroscopic imaging.
Modulation of non‐adrenergic, non‐cholinergic neural bronchoconstriction in guinea‐pig airways via GABA<sub>B</sub>‐receptors (1989)

1. Evidence suggests that gamma-aminobutyric acid (GABA) and its receptors are present in the peripheral nervous system. We have now investigated the effect of GABA and related substances on non-adrenergic, non-cholinergic (NANC) neurally-evoked bronchoconstriction in the anaesthetised guinea-pig. 2. Bilateral vagal stimulation (5 V, 5 ms, 3 or 5 Hz) for 30 s, after propranolol (1 mg kg-1 i.v.) and atropine (1 mg kg-1 i.v.) evoked a NANC bronchoconstrictor response manifest as a mean tracheal pressure rise of 21.9 +/- 1.04 cmH2O (n = 70). The bronchoconstrictor response was reproducible for any given animal. 3. GABA (10 micrograms-10 mg kg-1 i.v.) did not alter basal tracheal pressure but reduced the NANC bronchoconstrictor response to vagal stimulation in a dose-dependent manner (ED50 = 186 micrograms kg-1 with a maximal inhibition of 74 +/- 3.4% at 10 mg kg-1). Neither the opioid antagonist naloxone (1 mg kg-1 i.v.) nor the alpha-adrenoceptor antagonist phentolamine (2.5 mg kg-1 i.v.) had any significant effect on the inhibitory response produced by GABA (500 micrograms kg-1). 4. GABA-induced inhibition was not antagonised by the GABAA-antagonist bicuculline (2 mg kg-1 i.v.). 5. The GABAB-agonist baclofen (10 micrograms-3 mg kg-1 i.v.) caused a dose-dependent inhibition of the NANC response (ED50 = 100 micrograms kg-1 with a maximal inhibition of 35.5 +/- 2.8% at 3 mg kg-1). The GABAA-agonist, 4,5,6,7-tetrahydroisoxazolo[5,4-C] pyridin-3-ol (THIP), also inhibited the NANC bronchoconstrictor response. However, the dose of THIP required for this effect was high (3 mg kg- ') and the effect ( <10% inhibition) was small. 6. Substance P (SP; 5upgkg-1 or 25pgkg-1), produced a bronchoconstrictor response equivalent to that produced by NANC vagal stimulation. This response was significantly increased by injection of GABA. Baclofen had no significant effect on responses evoked by exogenous SP. 7. We conclude that GABA inhibits the release of transmitter from NANC nerves via an action at GABAB receptors and that GABA might play a role in the regulation of neurogenic responses in the airways.
Laser scanning cytometry for comet assay analysis (2000)

LSC enables an automated method for cell recognition and evaluation of the comets, thus providing quantitative information about nuclear DNA damage without subjective selection of analyzed comets.
Estimation of PR and ER by immunocytochemistry in breast cancer. Comparison with radioligand binding methods. (1990)

Immunocytochemical assays for progesterone receptor (PR) using monoclonal antirabbit PR antibodies (PR-ICA) and for estrogen receptor (ER) (ER-ICA) were compared with radioligand binding (dextran-coated charcoal [DCC]) methods for receptor determination in patients with breast cancer. Immunocytochemical staining for PR was exclusively nuclear in localization. In this regard, PR staining is similar to previous findings for ER; PR-ICA showed a sensitivity of 89% and specificity of 100%. ER-ICA was also 89% sensitive and similarly specific. There was good correlation between the degree and intensity of staining and quantitative binding of radioligand. Receptor-positive tumors, however, show considerable variation of immunocytochemical staining, suggesting heterogeneity of cellular PR content. The availability of an immunocytochemical assay for PR increases the discriminatory potential for these methods of receptor determination.
Measurement of cardioversion/defibrillation thresholds in man by a truncated exponential waveform and an apical patch-superior vena caval spring electrode configuration. (1984)

Defibrillation/cardioversion thresholds were measured in 33 patients undergoing defibrillator implants. Each patient had a 12 cm2 patch placed near the left ventricular apex via a thoracotomy and a 10 cm2 spring lead placed pervenously at the right atrial-superior vena caval junction. Ventricular tachycardia of stable morphology, polymorphic ventricular tachycardia, or ventricular fibrillation was induced four times in each patient and 1, 5, 10, and 25 J truncated exponential shocks with 60% tilt were given in a random sequence. The conversion rate was constant (77%, 86%, 87%, 85%) with increasing energy for ventricular tachycardia but progressively increased for polymorphic ventricular tachycardia and ventricular fibrillation (8%, 33%, 58%, 92%). The ventricular tachycardia acceleration rates for 1, 5, 10, and 25 J were 23%, 14%, 10%, and 15%. Patients not reliably converted with 25 J may require repositioning of leads or two patches. We conclude that for the spring-patch electrodes, increasing energy from 1 to 25 J improves the conversion rate for polymorphic ventricular tachycardia and ventricular fibrillation; the ventricular tachycardia conversion rate is constant. Acceleration of ventricular tachycardia occurs at all energies. Defibrillator implantation requires extensive intraoperative electrophysiologic testing to ensure safe and reliable termination of ventricular tachycardia and fibrillation.
Assembly of Bacteriophage Lambda Terminase into a Viral DNA Maturation and Packaging Machine (2006)

Terminase enzymes are common to complex double-stranded DNA viruses and function to package viral DNA into the capsid. We recently demonstrated that the bacteriophage lambda terminase gpA and gpNu1 proteins assemble into a stable heterotrimer with a molar ratio gpA1/gpNu1(2). This terminase protomer possesses DNA maturation and packaging activities that are dependent on the E. coli integration host factor protein (IHF). Here, we show that the protomer further assembles into a homogeneous tetramer of protomers of composition (gpA1/gpNu1(2))4. Electron microscopy shows that the tetramer forms a ring structure large enough to encircle duplex DNA. In contrast to the heterotrimer, the ring tetramer can mature and package viral DNA in the absence of IHF. We propose that IHF induced bending of viral DNA facilitates the assembly of four terminase protomers into a ring tetramer that represents the catalytically competent DNA maturation and packaging complex in vivo. This work provides, for the first time, insight into the functional assembly state of a viral DNA packaging motor.
Anion coordination and anion-templated assembly under halogen bonding control (2009)

This highlight discusses a selected set of halogen-bonded architectures reported in the literature wherein anions function as halogen bonding acceptors. Some of these architectures have been assembled purposefully, others have been obtained serendipitously. This paper is perhaps the first attempt to prove the effectiveness of halogen bonding in anion coordination and anion-templated assembly. A corollary of this attempt is that anions are particularly robust tectons in halogen bonding driven self-assembly processes. The focus here is particularly on halide anions and their ability to afford a wide variety of supramolecular architectures in a rational and predictable way. A brief inventory of other anions and their behaviour in self-assembly processes based on halogen bonding is also given.
Tuning hierarchical architecture of 3D polymeric scaffolds for cardiac tissue engineering (2008)

Tissue engineering combines the fields of engineering, chemistry, biology, and medicine to fabricate replacement tissues able to restore, maintain, or improve structurally and functionally damaged organs. The approach of regenerative medicine is of paramount importance for treating patients with severe cardiac diseases. For successful exploitation, the challenge for cardiac regenerative medicine is to identify the suitable combination between the best cell source for cardiac repair and the design of the optimal scaffold as a template for tissue replacement. Adult stem cells have the potential to improve regenerative medicine with their peculiar feature to self-renew and differentiate into various phenotypes. Insights into the stem cell field lead to the identification of the suitable scaffold features that enhance the ex vivo proliferation and differentiation of stem cells. Scaffolds composed of natural and/or synthetic polymers can organise stem cells into complex architectures that mimic native tissues....
Distinguishing Attacks from Legitimate Authentication Traffic at Scale (2019)

Online guessing attacks against password servers can be hard to address. Approaches that throttle or block repeated guesses on an account (e.g., three strikes type lockout rules) can be effective against depth-first attacks, but are of little help against breadth-first attacks that spread guesses very widely. At large providers with tens, or hundreds, of millions of accounts breadth-first attacks offer a way to send millions or even billions of guesses without ever triggering the depth-first defenses. The absence of labels and non-stationarity of attack traffic make it challenging to apply machine learning techniques.
Tunable <i>n</i>-Type Doping of Carbon Nanotubes through Engineered Atomic Layer Deposition HfO<sub>X</sub> Films (2018)

Although digital systems fabricated from carbon-nanotube-based field-effect transistors (CNFETs) promise significant energy efficiency benefits, realizing these benefits requires a complementary CNFET technology, i.e., CNFET CMOS, comprising both PMOS and NMOS CNFETs. Furthermore, this CNFET CMOS process must be robust ( e.g., air-stable), tunable ( e.g., ability to control CNFET threshold voltages), and silicon CMOS compatible (to integrate within existing manufacturing facilities and process flows). Despite many efforts, such a silicon CMOS compatible CNT doping strategy for forming NMOS CNFETs does not exist. Techniques today are either not air-stable (using reactive low work function metals), not solid-state or silicon CMOS compatible (employing soluble molecular dopants in ionic solutions), or have not demonstrated precise control over the amount of doping (for setting threshold voltage, V<sub>T</sub>). Here, we demonstrate an electrostatic doping technique that meets all of these requirements. The key to our technique is leveraging atomic layer deposition (ALD) to encapsulate CNTs with nonstoichiometric oxides. We show that ALD allows for precise control of oxide stoichiometry, which translates to direct control of the amount of CNT doping. We experimentally demonstrate the ability to modulate the strength of the p-type conduction branch by >2500× (measured as the change in current at fixed bias), realize NMOS CNFETs with n-type conduction ∼500× stronger than p-type conduction (also measured by the relative current at fixed biases), and tune V<sub>T</sub> over a ∼1.5 V range. Moreover, our technique is compatible with other doping schemes; as an illustration, we combine electrostatic doping and low work function contact engineering to achieve CNFET CMOS with symmetric NMOS and PMOS ( i.e., CNFET ON-current for NMOS and PMOS is within 6% of each other). Thus, this work realizes a solid-state, air-table, very large scale integration and silicon CMOS compatible doping strategy, enabling integration of CNFET CMOS within standard fabrication processes today.
Stabilizing Superionic-Conducting Structures via Mixed-Anion Solid Solutions of Monocarba-<i>closo</i>-borate Salts (2016)

Solid lithium and sodium closo-polyborate-based salts are capable of superionic conductivities surpassing even liquid electrolytes, but often only at above-ambient temperatures where their entropically driven disordered phases become stabilized. Here we show by X-ray diffraction, quasielastic neutron scattering, differential scanning calorimetry, NMR, and AC impedance measurements that by introducing “geometric frustration” via the mixing of two different closo-polyborate anions, namely, 1-CB9H10– and CB11H12–, to form solid-solution anion-alloy salts of lithium or sodium, we can successfully suppress the formation of possible ordered phases in favor of disordered, fast-ion-conducting alloy phases over a broad temperature range from subambient to high temperatures. This result exemplifies an important advancement for further improving on the remarkable conductive properties generally displayed by this class of materials and represents a practical strategy for creating tailored, ambient-temperature, solid, superionic conductors for a variety of upcoming all-solid-state energy devices of the future.
A framework for structure, layout & function in documents (2005)

The Document Description Framework (DDF) is a representation for variable-data documents. It supports very high flexibility in the type and extent of variation supported, considerably beyond the 'copy-hole' or flow-based mechanisms of existing formats and tools. DDF is based on holding application data, logical data struc-ture and presentation as well as constructional 'programs' together within a single document. DDF documents can be merged with other documents, bound to variable values incrementally, combine several types of layout and styling in the same document and support final delivery to different devices and page-ready formats. The framework uses XML syntax and fragments of XSLT to describe 'programmatic construction' of a bound document. DDF is extensible, especially in the ability to add new types of layout and inter-operability between components in different formats. In this paper we describe the motivation for DDF, the major design choices and how we evaluate a DDF document with specific data values. We show through implemented examples how it can be used to construct high-complexity and variability presentations and how the framework complements and can use many existing XML-based documents formats, such as SVG and XSL-FO.
Wavelet video coding via a spatially adaptive lifting structure (2003)

We present a spatially adaptive wavelet video coding technique with an update-first lifting structure. A common problem in many adaptive-transform frameworks is the introduction of a large overhead to address side information. We demonstrate that our structure does not need to transmit any side information to synchronize the encoder and decoder. We incorporate this technique in a motion compensated wavelet video codec. The experimental results confirm the performance improvement.
Interaction of Gold with Cerium Oxide Supports: CeO<sub>2</sub>(111) Thin Films vs CeO<i><sub>x</sub></i> Nanoparticles (2009)

Morphology, electronic structure, and CO adsorption of gold supported on well-ordered CeO2(111) thin films and CeOx nanoparticles were studied by scanning tunneling microscopy (STM), photoelectron spectroscopy (XPS), and infrared reflection absorption spectroscopy (IRAS). Ceria nanoparticles grown on crystalline thin silica films possess Ce in both the 3+ and 4+ oxidation states, with the former dominating in smaller particles. Upon deposition on CeO2(111) films, most of the Au particles are formed at the step edges. The particles on terraces grow presumably through the decoration of point defects, which are more numerous on reduced surfaces. Combined XPS and IRAS data show that partially charged Auδ+ species are formed by deposition at low temperatures (∼100 K) and low coverages on both ceria supports. Formation of Auδ+ on CeO2(111) films is kinetically limited and is attributed to the interaction of the gold ad-atoms with defects. In variance to extended ceria surfaces, where only metallic Au nanoparticles are observed at 300 K, the “cationic” gold species are formed in abundance on nano-CeOx and exhibit enhanced thermal stability. It is shown that nanoceria stabilizes small Au clusters, which may even be incorporated into the ceria nanoparticles at elevated temperatures.
Facile and Efficient Conversion of Furfuryl Alcohol into n-Butyl Levulinate Catalyzed by Extremely Low Acid Concentration (2014)

Alkyl levulinates have been identified as promising chemicals with various industrial applications. Here, a catalytic process for the synthesis in an n-butanol medium of n-butyl levulinate via the alcoholysis of biomass-derived furfuryl alcohol was performed using an extremely low concentration of sulfuric acid ( 0.01 M) as the catalyst. A study was conducted that was designed to optimize the process variables, which include acid concentration, reaction temperature, initial substrate concentration, and water content, as a function of time. The optimum conditions resulted in a furfuryl alcohol conversion of nearly 100% and a high n-butyl levulinate yield of up to 97%, which was confirmed by isolated yield. An advantage of this catalyst system is that negligible undesired oligomeric products were formed from the side reaction for the polymerization of furfuryl alcohol, the catalyst cost is low, and less solid waste was discharged from the neutralization of spent acid. Overall, this catalytic strategy is a facile, efficient, and economical approach to the conversion of biomass-derived furfuryl alcohol into alkyl levulinates.
Crystal Structure of a Hyperactive <i>Escherichia coli</i> Glycerol Kinase Mutant Gly230 → Asp Obtained Using Microfluidic Crystallization Devices<sup>,</sup> (2007)

The crystal structure of an Escherichia coli glycerol kinase mutant Gly230 --> Asp (GKG230D) was determined to 2.0 A resolution using a microfluidics based crystallization platform. The crystallization strategy involved a suite of microfluidic devices that characterized the solubility trends of GKG230D, performed nanoliter volume free interface diffusion crystallization experiments, and produced diffraction-quality crystals for in situ data collection. GKG230D displays increased enzymatic activity and decreased allosteric regulation by the glycolytic pathway intermediate fructose 1,6-bisphosphate (FBP) compared to wild-type GK (GKWT). Structural analysis revealed that the decreased allosteric regulation is a result of the altered FBP binding loop conformations in GKG230D that interfere with the wild-type FBP binding site. The altered FBP binding loop conformations in GKG230D are supported through a series of intramolecular loop interactions. The appearance of Asp230 in the FBP binding loops also repositions the wild-type FBP binding residues away from the FBP binding site. Light scattering analysis confirmed GKG230D is a dimer and is resistant to tetramer formation in the presence of FBP, whereas GKWT dimers are converted into putatively inactive tetramers in the presence of FBP. GKG230D also provides the first structural evidence for multiple GK monomer conformations in the presence of glycerol and in the absence of a nucleotide substrate and verifies that glycerol binding is not responsible for locking GK into the closed conformation necessary for GK activity.