gebhart/patrepeval huggingface dataset:
Aerobic carbon monoxide oxidation in the course of growth of a hyperthermophilic archaeon, Sulfolobus sp. ETSY (2017)

An aerobic hyperthermophilic CO-oxidizing archaeon, Sulfolobus sp. strain ETSY, was isolated and characterized. Presently, it is the only known representative of both hyperthermophiles and Archaea that is capable of aerobic oxidation of CO, a gas of global importance for atmospheric chemistry and of local importance as one of the substrates for the microbial communities of hydrothermal vents. In the genome of Sulfolobus sp. ETSY we found genetic determinants of aerobic CO oxidation: a coxFMSLDE gene cluster and two separately located coxG genes. We also found such gene clusters in the genomes of certain strains of Sulfolobus islandicus and Sulfolobus solfataricus. On the phylogenetic tree of large subunits of aerobic CO-dehydrogenases (CoxLs), these proteins of Sulfolobus representatives formed a compact cluster within one of the branches formed by bacterial form I CoxLs. Thus we argue that the ability to oxidize CO aerobically was acquired by Sulfolobus ancestor from Bacteria relatively late in the evolution, presumably after the formation of the atmosphere with a high oxygen content.
Time-resolved optical characterization of InGaAs/GaAs quantum dots (1994)

We report on the optical characterization of the strained InGaAs/GaAs quantum dots (QDs). The temperature dependence of the photoluminescence (PL) indicates that the onset energy of the thermal quenching in ∼20-nm-diam QDs is enhanced by a factor of ∼2 as compared to a quantum well (QW), due to the additional confinement. At low temperature, an increased carrier lifetime is observed for the QDs as compared to a reference QW (880 vs 330 ps). The carrier lifetime in the QDs was found to be independent of the temperature for T&amp;lt;30 K. In addition to this different dynamics of the localized excitons, we find that in the steady state PL and PL excitation, there is virtually no overlap between the emission and the absorption energies.
Quantitative investigation of impurity distribution in ZMR SOI layers (2003)

Summary form only given. The redistribution of oxygen and nitrogen in zone-melting recrystallized (ZMR) layers is discussed. During the ZMR process the silicon layer is exposed on both sides to SiO/sub 2/ layers at very high temperatures. As a result a high oxygen content may be expected. In-depth SIMS analysis with enhanced sensitivity for oxygen was used to analyze SOI layers with thicknesses ranging from 0.5 to 25 mu m. Typically a symmetric bump-shaped oxygen profile was obtained. A strong redistribution of oxygen takes place after solidification. SIMS profiles were also obtained of the nitrogen distribution. In samples with a compound capping layer consisting of a thin nitride or oxynitride on top of a thick CVD oxide, significant nitrogen peaks were found at the Si-SiO/sub 2/ interfaces immediately after deposition. The peaks increased as the samples were heated and became even more pronounced after ZMR. Different structures in which the nitrogen source was a CVD layer, a NH/sub 3/, a NH/sub 3/ anneal, or a nitrogen implant were investigated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Replication and Transcription of Eukaryotic DNA in Esherichia coli (1974)

Fragments of amplified Xenopus laevis DNA, coding for 18S and 28S ribosomal RNA and generated by EcoRI restriction endonuclease, have been linked in vitro to the bacterial plasmid pSC101; and the recombinant molecular species have been introduced into E. coli by transformation. These recombinant plasmids, containing both eukaryotic and prokaryotic DNA, replicate stably in E. coli. RNA isolated from E. coli minicells harboring the plasmids hybridizes to amplified X. laevis rDNA.
3D shape measurement by thermal fringe projection: optimization of infrared (IR) projection parameters (2018)

Structured light projection techniques in the visible spectrum of light (VIS) are widely used for fast, contactless, and nondestructive optical three-dimensional (3D) shape measurements. For instance, 3D reconstruction can be performed with a stereo camera system combined with corresponding pixel search and triangulation. Recently, we increased the measurement speed significantly by GOBO projection of aperiodic sinusoidal fringes. Due to their optical properties, such as being glossy, transparent, absorbent, or translucent, some materials cannot be measured in VIS. Changing the spectral range from VIS to infrared (IR) allows measuring the 3D shape of some of these materials. Instead of diffuse reflection of structured light in VIS, the absorption of structured light in IR (e.g., CO<sub>2</sub> laser at 10.6 &mu;m) combined with energy conversion and re-emission of light according to Planck’s law is used. Detection can be carried out at 3–5 &mu;m. Depending on optical and thermal material properties (e.g., complex spectral refractive index, thermal conductivity, specific heat capacity, emissivity), the parameters of the projection unit have to be adjusted, e.g., intensity or illumination time. In this paper, we investigate the influence of material, geometry, and irradiation parameters on the temperature contrast. We present a simulation tool based on the Beer-Lambert law and heat diffusion equation for irradiation-induced thermal pattern on the object’s surface. It allows to determine optimized irradiation settings for well-known material and geometry parameters. We compare the simulation outputs with experimental results.
The Ventricular Defibrillation and Upper Limit of Vulnerability Dose‐Response Curves (1997)

The Box-Tiao dose-response curve is the best single choice for fitting VF induction or defibrillation datasets.
Ultrahigh energy density harvested from domain-engineered relaxor ferroelectric single crystals under high strain rate loading (2017)

Relaxor ferroelectric single crystals have triggered revolution in electromechanical systems due to their superior piezoelectric properties. Here the results are reported on experimental studies of energy harvested from (1-y-x)Pb(In<sub>1/2</sub>Nb<sub>1/2</sub>)O<sub>3</sub>-(y)Pb(Mg<sub>1/3</sub>Nb<sub>2/3</sub>)O<sub>3</sub>-(x)PbTiO<sub>3</sub> (PIN-PMN-PT) crystals under high strain rate loading. Precise control of ferroelectric properties through composition, size and crystallographic orientation of domains made it possible to identify single crystals that release up to three times more electric charge density than that produced by PbZr<sub>0.52</sub>Ti<sub>0.48</sub>O<sub>3</sub> (PZT 52/48) and PbZr<sub>0.95</sub>Ti<sub>0.05</sub>O<sub>3</sub> (PZT 95/5) ferroelectric ceramics under identical loading conditions. The obtained results indicate that PIN-PMN-PT crystals became completely depolarized under 3.9 GPa compression. It was found that the energy density generated in the crystals during depolarization in the high voltage mode is four times higher than that for PZT 52/48 and 95/5. The obtained results promise new single crystal applications in ultrahigh-power transducers that are capable of producing hundreds kilovolt pulses and gigawatt-peak power microwave radiation.
Novel stable resonator for large-volume TEM00 mode operation (1993)

A novel stable resonator is developed to realize stable operation at a TEM00 mode with a large beam diameter. The output coupler has a circular partial-reflection region in the center surrounded by an antireflection region. The transverse mode is mainly selected by the partial-reflection region. An amplified diffraction beam is extracted from the outer antireflection region. By combining part of the ‘‘core’’ beam transmitted from the partial-reflection region with the amplified diffraction beam, a diffraction-limited beam with the M2 factor of 1.3 is obtained from a high power continuous wave CO2 laser as predicted theoretically.
Preliminary results of (18F)FPRGD2 PET/CT imaging of integrin αvβ3 levels in patients with locally advanced rectal carcinoma. (2012)

peer reviewed
Boosting Dilated Convolutional Networks with Mixed Tensor Decompositions (2017)

The driving force behind deep networks is their ability to compactly represent rich classes of functions. The primary notion for formally reasoning about this phenomenon is expressive efficiency, which refers to a situation where one network must grow unfeasibly large in order to realize (or approximate) functions of another. To date, expressive efficiency analyses focused on the architectural feature of depth, showing that deep networks are representationally superior to shallow ones. In this paper we study the expressive efficiency brought forth by connectivity, motivated by the observation that modern networks interconnect their layers in elaborate ways. We focus on dilated convolutional networks, a family of deep models delivering state of the art performance in sequence processing tasks. By introducing and analyzing the concept of mixed tensor decompositions, we prove that interconnecting dilated convolutional networks can lead to expressive efficiency. In particular, we show that even a single connection between intermediate layers can already lead to an almost quadratic gap, which in large-scale settings typically makes the difference between a model that is practical and one that is not. Empirical evaluation demonstrates how the expressive efficiency of connectivity, similarly to that of depth, translates into gains in accuracy. This leads us to believe that expressive efficiency may serve a key role in the development of new tools for deep network design.
Supplementary Figure 1 from The Regulatory T Cell–Associated Transcription Factor FoxP3 Is Expressed by Tumor Cells (2023)

Supplementary Figure 1 from The Regulatory T Cell–Associated Transcription Factor FoxP3 Is Expressed by Tumor Cells
Textpresso for oro‐pharyngeal anatomy: a system for searching the full text of anatomy literatures (338.3) (2014)

Biological databases are a useful resource for parlaying existing data into new experimental hypotheses. Populating such databases with information from the published literature, however, can be labor intensive and thus is aided greatly by text mining tools capable of retrieving key facts from full text. The Textpresso information retrieval system ( http://www.textpresso.org ) is used by several Model Organism Database (MOD) communities to assist in curation [Müller HM, Kenny EE, Sternberg PW. 2004. PLoS Biol. Nov;2(11):e309; Van Auken KM, Fey P, Berardini TZ, et al. 2012. Database (Oxford). Nov 17;2012:bas040.] Textpresso searches the full text of literature using keywords and/or categories, groups of semantically related words, to identify sentences within a paper that describe specific aspects of biology. Using the anatomy ontology of oro‐pharyngeal structures developed in the FEED project [Druzinsky R, et al., in prep ], we are constructing a Textpresso site to aid in curation of the oro‐pharyngeal muscle literature. At this time, we have amassed a database of over 2000 searchable references. We will present a demonstration of Textpresso for Oro‐Pharyngeal Anatomy and show how it can be used to construct meaningful queries on the full text of the literature.
Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments (2001)

In this paper we focus on the detection of differentially expressed genes according to changes in hybridization signals using statistical tests. These tests were applied to 14 208 zebrafish cDNA clones that were immobilized on a nylon support and hybridized with radioactively labeled target mRNA from wild-type and lithium-treated zebrafish embryos. The methods were evaluated with respect to 16 control clones that correspond to eight different genes which are known to be involved in dorso-ventral axis specification. Moreover, 4608 Arabidopsis thaliana clones on the same array were used to judge statistical significance of expression changes and to control the false positive rates of the test decisions. Utilizing this special array design we show that differential expression of a high proportion of cDNA clones (15/16) and the respective genes (7/8) were identified, with a false positive error of <5% using the constant control data. Furthermore, we investigated the influence of the number of repetitions of experiments on the accuracy of the procedures with experimental and simulated data. Our results suggest that the detection of differential expression with repeated hybridization experiments is an accurate and sensitive way of identifying even small expression changes (1:1.5) of a large number of genes in parallel.
Carbon nanotube thin-film transistors featuring transfer-printed metal electrodes and a thin, self-grown aluminum oxide gate dielectric (2015)

We report on a novel fabrication scheme to define metal source and drain contacts for short-channel thin-film transistors utilizing a purely additive transfer-printing process. We demonstrate the viability of this approach by realizing carbon nanotube thin-film transistors featuring a very thin aluminum oxide gate dielectric The active layer of the transistors is spray-deposited from an aqueous carbon-nanotube suspension with 90% semiconducting content. Full gate control is demonstrated for gate-source voltages below 2.0 V.
Adamantyl-Substituted Retinoid-Derived Molecules That Interact with the Orphan Nuclear Receptor Small Heterodimer Partner: Effects of Replacing the 1-Adamantyl or Hydroxyl Group on Inhibition of Cancer Cell Growth, Induction of Cancer Cell Apoptosis, and Inhibition of Src Homology 2 Domain-Containing Protein Tyrosine Phosphatase-2 Activity (2008)

(E)-4-[3-(1-Adamantyl)-4'-hydroxyphenyl]-3-chlorocinnamic acid (3-Cl-AHPC) induces the cell-cycle arrest and apoptosis of leukemia and cancer cells. Studies demonstrated that 3-Cl-AHPC bound to the atypical orphan nuclear receptor small heterodimer partner (SHP). Although missing a DNA-binding domain, SHP heterodimerizes with the ligand-binding domains of other nuclear receptors to repress their abilities to induce or inhibit gene expression. 3-Cl-AHPC analogues having the 1-adamantyl and phenolic hydroxyl pharmacophoric elements replaced with isosteric groups were designed, synthesized, and evaluated for their inhibition of proliferation and induction of human cancer cell apoptosis. Structure-anticancer activity relationship studies indicated the importance of both groups to apoptotic activity. Docking of 3-Cl-AHPC and its analogues to an SHP computational model that was based on the crystal structure of ultraspiracle complexed with 1-stearoyl-2-palmitoylglycero-3-phosphoethanolamine suggested why these 3-Cl-AHPC groups could influence SHP activity. Inhibitory activity against Src homology 2 domain-containing protein tyrosine phosphatase 2 (Shp-2) was also assessed. The most active Shp-2 inhibitor was found to be the 3'-(3,3-dimethylbutynyl) analogue of 3-Cl-AHPC.
Experimental assessment of transmission reach for uncompensated 32-GBaud PDM-QPSK and PDM-16QAM (2012)

We experimentally compare the transmission reach of PDM-16QAM and PDM-QPSK at 32 Gbaud over an uncompensated transmission link and characterize the impact of the hardware limitations stemming from the practical implementation of PDM-16QAM.
Isolation and Characterization of Two Verrucarins from Myrothecium roridum (2006)

In the course of a screening for compounds inhibiting the growth of two human breast cancer cells lines, two highly cytotoxic compounds were isolated from fermentations of Myrothecium roridum. The elucidation of their structures revealed that they are macrocyclic trichothecenes of the verrucarin type, 16-hydroxyverrucarin A (1), reported here as a natural product for the first time, and verrucarin X (2), a new compound. Both 1 and 2 exhibit moderate antifungal activity and pronounced cytotoxic activity, with IC50 values in the nanomolar (1) and micromolar (2) range. Both compounds preferentially inhibit in vivo protein biosynthesis.
Improvements in English ASR for the MALACH project using syllable-centric models (2004)

LVCSR systems have traditionally used phones as the basic acoustic unit for recognition. Syllable and other longer length units provide an efficient means for modeling long-term temporal dependencies in speech that are difficult to capture in a phone based recognition framework. However, it is well known that longer duration units suffer from training data sparsity problems since a large number of units in the lexicon will have little or no acoustic training data. Previous research has shown that syllable-based modeling provides improvements over word internal systems, but performance has lagged behind cross-word context-dependent systems. In this paper, we describe a syllable-centric approach to English LVCSR for the MALACH (Multilingual Access to Large spoken Archives) project. The combined modeling of syllables and context-dependent phones provides a 0.5% absolute improvement in recognition accuracy over the state-of-the-art cross-word system for the heavily accented and spontaneous speech seen in oral history archives. More importantly, we report on the importance of the improved recognition of names and concepts that is crucial for subsequent search and retrieval.
Reversible Carbon–Carbon Bond Formation Induced by Oxidation and Reduction at a Redox-Active Cobalt Complex (2013)

The electronic structure of the diamagnetic pyridine imine enamide cobalt dinitrogen complex, (iPrPIEA)CoN2 (iPrPIEA = 2-(2,6-iPr2–C6H3N═CMe)-6-(2,6-iPr2–C6H3NC═CH2)C5H3N), was determined and is best described as a low-spin cobalt(II) complex antiferromagnetically coupled to an imine radical anion. Addition of potential radical sources such as NO, PhSSPh, or Ph3Cl resulted in C–C coupling at the enamide positions to form bimetallic cobalt compounds. Treatment with the smaller halocarbon, PhCH2Cl, again induced C–C coupling to form a bimetallic bis(imino)pyridine cobalt chloride product but also yielded a monomeric cobalt chloride product where the benzyl group added to the enamide carbon. Similar cooperative metal–ligand addition was observed upon treatment of (iPrPIEA)CoN2 with CH2═CHCH2Br, which resulted in allylation of the enamide carbon. Reduction of Coupled-(iPrPDI)CoCl (Coupled-(iPrPDI)CoCl = [2-(2,6-iPr2–C6H3N═CMe)-C5H3N-6-(2,6-iPr2–C6H3N═CCH2−)CoCl]2) with NaBEt3H led to quantitative formation of (iPrPIEA)CoN2, demonstrating the reversibility of the C–C bond forming reactions. The electronic structures of each of the bimetallic cobalt products were also elucidated by a combination of experimental and computational methods.
Vulnerability of Network Traffic under Node Capture Attacks Using Circuit Theoretic Analysis (2008)

We investigate the impact of node capture attacks on the confidentiality and integrity of network traffic. We map the compromise of network traffic to the flow of current through an electric circuit and propose a metric for quantifying the vulnerability of the traffic using the circuit mapping. We compute the vulnerability metric as a function of the routing and the cryptographic protocols used to secure the network traffic. We formulate the minimum cost node capture attack problem as a nonlinear integer programming problem. Due to the NP-hardness of the minimization problem, we provide a greedy heuristic that approximates the minimum cost attack. We provide examples of node capture attacks using our vulnerability metric and show that the adversary can expend significantly less resources to compromise target traffic by exploiting information leakage from the routing and cryptographic protocols.
Single-stranded DNA oligonucleotides inhibit TLR3-mediated responses in human monocyte-derived dendritic cells and in vivo in cynomolgus macaques (2012)

TLR3 is a key receptor for recognition of double-stranded RNA and initiation of immune responses against viral infections. However, hyperactive responses can have adverse effects, such as virus-induced asthma. Strategies to prevent TLR3-mediated pathology are therefore desired. We investigated the effect of single-stranded DNA oligonucleotides (ssDNA-ODNs) on TLR3 activation. Human monocyte-derived dendritic cells up-regulate maturation markers and secrete proinflammatory cytokines on treatment with the synthetic TLR3 ligand polyinosine-polycytidylic acid (poly I:C). These events were inhibited in cultures with ssDNA-ODNs. Poly I:C activation of nonhematopoietic cells was also inhibited by ssDNA-ODNs. The uptake of poly I:C into cells was reduced in the presence of ssDNA-ODNs, preventing TLR3 engagement from occurring. To confirm this inhibition in vivo, we administered ssDNA-ODNs and poly I:C, alone or in combination, via the intranasal route in cynomolgus macaques. Proinflammatory cytokines were detected in nasal secretions in the poly I:C group, while the levels were reduced in the groups receiving ssDNA-ODNs or both substances. Our results demonstrate that TLR3-triggered immune activation can be modulated by ssDNA-ODNs and provide evidence of dampening proinflammatory cytokine release in the airways of cynomolgus macaques. These findings may open novel perspectives for clinical strategies to prevent or treat inflammatory conditions exacerbated by TLR3 signaling.
Impact of voids in Ti-salicided p/sup +/ polysilicon lines on TiSi/sub 2/ electrical properties (1999)

We report the effect of voids in Ti-salicided narrow p/sup +/-doped polysilicon lines on the electrical performance of the TiSi/sub 2/ films. The variation in the TiSi/sub 2/ sheet resistance was found to correlate well to the void density, which is a function of the poly-Si implant species and dose, the gate line-width and the p/sup +/ anneal. In addition, we find that the low frequency noise measurements are a good diagnostic method to determine the extent of voiding in silicided films.
Aerodynamic Design and Analysis of a High Pressure Ratio Aspirated Compressor Stage (2000)

The pressure ratio of axial compressor stages can be significantly increased by controlling the development of blade and endwall boundary layers in regions of adverse pressure gradient by means of boundary layer suction. This concept is validated and demonstrated through the design and analysis of a unique aspirated compressor stage which achieves a total pressure ratio of 3.5 at a tip speed of 1500 ft/s. The aspirated stage was designed using an axisymmetric through-flow code coupled with a quasi three-dimensional cascade plane code with inverse design capability. Validation of the completed design was carried out with three-dimensional Navier-Stokes calculations. Spanwise slots were used on the rotor and stator suction surfaces to bleed the boundary layer with a total suction requirement of 4% of the inlet mass flow. Additional bleed of 3% was also required on the hub and shroud near shock impingement locations. A three-dimensional viscous evaluation of the design showed good agreement with the quasi three-dimensional design intent, except in the endwall regions. The three-dimensional viscous analysis predicted a mass averaged total pressure ratio of 3.7 at an isentropic efficiency of 93% for the rotor, and a mass averaged total pressure ratio of 3.4 at an isentropic efficiency of 86% for the stage.
3‐(4‐Piperidinyl)indoles and 3‐(4‐Piperidinyl)pyrrolo[2,3‐b]pyridines as Ligands for the ORL‐1 Receptor. (2006)

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