gebhart/patrepeval huggingface dataset:
Towards in situ sequencing for life detection (2017)

Due to meteoritic transfer between Earth and Mars, if life on Mars exists, it may be related to life on Earth and utilize nucleic acids as informational polymers. Thus, a Search for Extra-Terrestrial Genomes (SETG) could detect and sequence (deoxy)ribonucleic acids (DNA/RNA) utilized by any extant or recently dead life on Mars. The abiotic synthesis of common organic building blocks, such as nucleobases, sugars, and amino acids, in the solar nebula and potentially in diverse habitable environments could also bias a second genesis of life towards utilizing informational polymers similar to life as we know it. Here we build on prior work and describe the advancement of a SETG instrument to technology readiness level 4 through sample-to-sequence processing with limited manual handling. Another advance includes validation of nucleic acid extraction from Mars analogs at cell counts down to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> per 50 mg sample, equivalent to a limit of detection of approximately 1 part per billion. In addition, we demonstrate that biological nanopore-based single molecule sequencing can be used to detect non-standard bases. Finally, we link sequence data to a statistical test to distinguish between any forward contamination and putative life beyond Earth. Nanopore-based sensing may ultimately enable characterization of non-standard polymers and other molecules, highlighting the potential for nanopore-based life detection and sequencing on Mars or other words such as the icy moons Enceladus or Europa.
Unconventional CHδ+⋯N hydrogen bonding interactions in the stepwise solvation of the naphthalene radical cation by hydrogen cyanide and acetonitrile molecules (2015)

Equilibrium thermochemical measurements using the mass-selected ion mobility (MSIM) technique have been utilized to investigate the binding energies and entropy changes of the stepwise association of hydrogen cyanide (HCN) and acetonitrile (CH3CN) molecules with the naphthalene radical cation (C10H8˙(+)) in the gas phase forming the C10H8˙(+)(HCN)n and C10H8˙(+)(CH3CN)n clusters with n = 1-3 and 1-5, respectively. The lowest energy structures of the C10H8˙(+)(HCN)n and C10H8˙(+)(CH3CN)n clusters for n = 1-2 have been calculated using the M062X and ω97XD methods within the 6-311+G** basis set, and for n = 1-6 using the B3LYP method within the 6-311++G** basis set. In both systems, the initial interaction occurs through unconventional CH(δ+)···N ionic hydrogen bonds between the hydrogen atoms of the naphthalene cation and the lone pair of electrons on the N atom of the HCN or the CH3CN molecule. The binding energy of CH3CN to the naphthalene cation (11 kcal mol(-1)) is larger than that of HCN (7 kcal mol(-1)) due to a stronger ion-dipole interaction resulting from the large dipole moment of CH3CN (3.9 D). On the other hand, HCN can form both unconventional hydrogen bonds with the hydrogen atoms of the naphthalene cation (CH(δ+)···NCH), and conventional linear hydrogen bonding chains involving HCN···HCN interactions among the associated HCN molecules. HCN molecules tend to form "externally solvated" structures with the naphthalene cation where the naphthalene ion is hydrogen bonded to the exterior of an HCN···HCN chain. For the C10H8˙(+)(CH3CN)n clusters, "internally solvated" structures are favored where the acetonitrile molecules are directly interacting with the naphthalene cation through CH(δ+)···N unconventional ionic hydrogen bonds. In both the C10H8˙(+)(HCN)n and C10H8˙(+)(CH3CN)n clusters, the sequential binding energy decreases stepwise to about 6-7 kcal mol(-1) by three HCN or CH3CN molecules, approaching the macroscopic enthalpy of vaporization of liquid HCN (6.0 kcal mol(-1)).
Parametric Finite Element Analysis for Reduced Order Modeling of MEMS (2006)

In this paper we describe a simulation methodology based on FEM to automatic generating reduced order models of coupled microelectro-mechanical systems (MEMS). In particular, the time consuming FE data sampling process should be replaced by a single finite element run. The idea of the new approach is to compute not only the governing system matrices but also high order partial derivatives with regard to design parameters by means of automatic differentiation. As result, Taylor vectors of the model response can be expanded in the vicinity of the initial position with regard to dimensional and physical parameters. The approach is demonstrated on example of a micromirror cell
CHAPTER 7. SILP and SCILL Catalysis (2014)

Supported Ionic Liquid Phase (SILP) catalysts and Solid Catalyst with Ionic Liquid Layer (SCILL) both consist of an ionic liquid dispersed as a thin film on the inner surface of a highly porous solid material. In SILP catalysis the ionic liquid film contains a dissolved homogeneous transition metal complex and in this way a macroscopic solid adopts the chemical reactivity of a homogeneous, ligand-controlled catalyst. In SCILL materials the ionic liquid film modifies the catalytic sites of a classical heterogeneous catalyst in a ligand-like manner. In addition, the specific solubility of the IL film adjusts the local feedstock and product concentrations at the active center. Both, SILP and SCILL materials can be handled like classical heterogeneous catalysts and are suitable for classical fixed-bed technologies, a fact that makes transition to technical applications in larger scale very attractive. Our contribution focuses on some common key technical aspects of both SILP and SCILL technologies. The influence of support structure and support surface chemistry on the functionality of the prepared catalysts is highlighted. Optimization of the ionic liquid loading and large scale preparation technologies for these materials are other important aspects of the chapter.
The gross architecture of an antibody-combining site as determined by spin-label mapping (1977)

1. A series of Dnp (dinitrophenyl) nitroxide spin labels was used to map the dimensions of the combining site of the Dnp-binding immunoglobulin A myeloma protein MOPC 315. The method compares the observed e.s.r. (electron-spin-resonance) hyperfine splittings with those calculated on the basis of different postulated motions for the spin label. The analysis is complicated by the sensitivity of the e.s.r. hyperfine splitting to the overall ;tumbling' time of the antibody-hapten complex and the polarity of the spin-label's environment. When these effects are considered quantitatively, it is then possible to determine the degree of mobility of each hapten which is allowed by the shape of the combining site. 2. The dinitrophenyl ring is rigidly held, and the depth of the site is 1.1-1.2nm and has lateral dimensions at the entrance to the site >/=0.6nmx0.9nm. The analysis of the results for spin-labelled haptens with chiral centres allows these lateral dimensions to be refined to 0.8nm and 1.1nm, and it is shown that the site is asymmetric with respect to the plane of the dinitrophenyl ring. 3. A polarity profile of the combining site was also obtained and a positively charged amino acid residue, possibly arginine-95(L) (light chain), was located at the entrance to the site. 4. The binding of Gd(III) to the antibody-hapten complexes results in quenching of the e.s.r. signal of the nitroxide. By using La(III) as a control, the paramagnetic contribution to the quenching is measured. 5. Analysis of the differential quenchings of the enantiomers of two five-membered nitroxide ring spin labels gives two possible locations of the metal-binding site. One of these is equidistant (0.7nm) from each of the three dinitrophenyl aromatic protons, and nuclear-magnetic-resonance relaxation studies, at 270MHz, on solutions of dinitrobenzene, Gd(III) and the Fv fragment (variable region of heavy and light chain) from protein MOPC 315 support this location for the metal site. 6. The e.s.r. and metal-binding data were then compared with the results of a model of the combining site constructed on the basis of framework invariance in immunoglobulins [Padlan, Davies, Pecht, Givol & Wright (1976) Cold Spring Harbor Symp. Quant. Biol.41, in the press]. The overall agreement is very good. Assignments of possible chelating groups for the metal can be made.
Numerical Analysis of Two-Dimensional Motion of a Freely Falling Circular Cylinder in an Infinite Fluid (2004)

The two-dimensional motion of a freely falling circular cylinder in an infinite fluid is investigated numerically using combined formulation. The effect of vortex shedding on the motion of a freely falling cylinder is clearly seen: as the streamwise velocity of the cylinder increases due to gravity, the periodic vortex shedding induces a periodic motion of the cylinder. This motion in turn affects the flow field, which is manifested by the generation of the angular velocity vector of the cylinder parallel to the cross product of the gravitational acceleration vector and the transverse velocity vector of the cylinder. A correlation of St-Re relationship for a freely falling circular cylinder is drawn from the present results. The Strouhal number for a freely falling circular cylinder is found to be smaller than that for a fixed circular cylinder when the two Reynolds numbers based on the streamwise terminal velocity of a freely falling circular cylinder and the free stream velocity of a fixed one are the same. From
Quantifying Insulin Sensitivity and Entero-Insular Responsiveness to Hyper- and Hypoglycemia in Ferrets (2014)

Ferrets are an important emerging model of cystic fibrosis related diabetes. However, there is little documented experience in the use of advanced techniques to quantify aspects of diabetes pathophysiology in the ferret. Glycemic clamps are the gold standard technique to assess both insulin sensitivity and insulin secretion in humans and animal models of diabetes. We therefore sought to develop techniques for glycemic clamps in ferrets. To assess insulin sensitivity, we performed euglycemic hyperinsulinemic clamps in 5-6 week old ferrets in the anesthetized and conscious states. To assess insulin secretion, we performed hyperglycemic clamps in conscious ferrets. To evaluate responsiveness of ferret islet and entero-insular hormones to low glucose, a portion of the hyperglycemic clamps were followed by a hypoglycemic clamp. The euglycemic hyperinsulinemic clamps demonstrated insulin responsiveness in ferrets similar to that previously observed in humans and rats. The anesthetic isoflurane induced marked insulin resistance, whereas lipid emulsion induced mild insulin resistance. In conscious ferrets, glucose appearance was largely suppressed at 4 mU/kg/min insulin infusion, whereas glucose disposal was progressively increased at 4 and 20 mU/kg/min insulin. Hyperglycemic clamp induced first phase insulin secretion. Hypoglycemia induced a rapid diminishment of insulin, as well as a rise in glucagon and pancreatic polypeptide levels. The incretins GLP-1 and GIP were affected minimally by hyperglycemic and hypoglycemic clamp. These techniques will prove useful in better defining the pathophysiology in ferrets with cystic fibrosis related diabetes.
Frequency Conversion in a Dielectric Time-Variant Metasurface via Optical Pumping (2020)

We experimentally observe frequency conversion via electromagnetic wave interaction with a high quality-factor resonance in an array of resonators whose refractive indices are varied on an ultrafast timescale. Further, we describe the observations using coupled-mode-theory.
Development of an activation tagging system for maize (2019)

Activation Tagging, distributing transcriptional enhancers throughout the genome to induce transcription of nearby genes, is a powerful tool for discovering the function of genes in plants. We have developed a transposable element system to distribute a novel activation tagging element throughout the genome of maize. The transposon system is built from the Enhancer/Suppressor (<i>En</i>/<i>Spm</i>) transposon system and uses an engineered seed color marker to show when the transposon excises. Both somatic and germinal excision events can be detected by the seed color. The activation tagging element is in a <i>Spm</i>-derived non-autonomous transposon and contains four copies of the <i>S</i>ugar<i>c</i>ane <i>B</i>acilliform <i>V</i>irus-enhancer (<i>SCBV</i>-enhancer) and the AAD1 selectable marker. We have demonstrated that the transposon can give rise to germinal excision events that can re-integrate into non-linked genomic locations. The transposon has remained active for three generations and events displaying high rates of germinal excision in the T2 generation have been identified. This system can generate large numbers of activation tagged maize lines that can be screened for agriculturally relevant phenotypes.
Different effects of five depigmentary compounds, rhododendrol, raspberry ketone, monobenzone, rucinol and AP736 on melanogenesis and viability of human epidermal melanocytes (2015)

Numerous medications are used to treat hyperpigmentation. However, several reports have indicated that repeated application of some agents, such as rhododendrol (RD), raspberry ketone (RK) and monobenzone (MB), can be toxic to melanocytes. Although these agents had severe side effects in human trials, no current in vitro methods can predict the safety of such drugs. This study assessed the in vitro effects of five depigmentary compounds including leukoderma-inducing agents. In particular, we determined the effects of different concentrations and exposure times of different depigmentary agents on cell viability and melanogenesis in the presence and absence of ultraviolet B (UVB) radiation. Concentrations of RD, RK and MB that inhibit melanogenesis are similar to concentrations that are cytotoxic; however, concentrations of rucinol (RC) and AP736 that inhibit melanogenesis are much lower than concentrations that are cytotoxic. Furthermore, the concentrations that cause toxic effects depend on exposure duration, and prolonged exposure to RD, RK and MB had more cytotoxic effects than prolonged exposure to RC and AP736. The cytotoxic effects of RD and RK appear to be mediated by apoptosis due to increased expression of caspase-3 and caspase-8; UVB radiation increased the cytotoxicity of these agents and also increased caspase activity. Our results indicate that different leukoderma-inducing compounds have different effects on the viability of normal epidermal melanocytes and suggest that the in vitro assay used here can be used to predict whether an investigational compound that induces leukoderma may lead to adverse effects in human trials.
Biosynthetic thiolase from Zoogloea ramigera. Mutagenesis of the putative active-site base Cys-378 to Ser-378 changes the partitioning of the acetyl S-enzyme intermediate. (1992)

The proposed active-site base Cys-378 of thiolase, responsible for deprotonation of acetyl-CoA, has been converted to a less acidic residue Ser-378 by mutagenesis. Comparison of the CD spectra and dimethyl suberimidate cross-linking experiments of the wild type, mutant Ser-378, and Gly-378 enzymes indicated that there have been no major conformational changes. The Ser-378 enzyme retains 0.1% of the Vmax of wild type in the direction of acetoacetyl-CoA thiolytic cleavage and 0.07% of the Vmax in the Claisen condensation direction. Analysis of the acetyl S-enzyme intermediate partitioning, that is capture of the acetyl enzyme by 1) the thiolate of coenzyme A relative to 2) the C-2 carbanion of acetyl-CoA, is changed to favor reaction 2 in the case of the Ser-378 mutant enzyme.
ChemInform Abstract: Highly Modular P—OP Ligands for Asymmetric Hydrogenation: Synthesis, Catalytic Activity, and Mechanism. (2010)

Abstract A new P—OP ligand, easily prepared in two synthetic steps from enantiopure epoxide, is used as a highly efficient ligand in the rhodium‐catalyzed asymmetric hydrogenation of functionalized alkenes.
Global, regional, and national incidence, prevalence, and years lived with disability for 310 diseases and injuries, 1990–2015: a systematic analysis for the Global Burden of Disease Study 2015 (2020)

BACKGROUND: Non-fatal outcomes of disease and injury increasingly detract from the ability of the world's population to live in full health, a trend largely attributable to an epidemiological trans ...
python-pillow/Pillow 7.1.1 (2020)

https://pillow.readthedocs.io/en/stable/releasenotes/7.1.1.html
Widely tunable narrow-line RF source based on modulation sideband injection-locked lasers (2013)

We have developed and demonstrated a photonic RF source architecture with a tuning range of more than 7 octaves. It is based on the photomixing of a pair of tuned lasers. Narrow linewidth is obtained by modulating one laser with a reference signal and injection seeding the other with a harmonic sideband. Tuning is accomplished by selecting a specific sideband, i.e. a particular harmonic of the drive signal, for injection locking, combined with tuning the modulator drive signal. In this paper we discuss the operation of the system and present experimental results characterizing its performance. We also discuss planned improvements to the system, including the implementation of low-noise VCOs for the reference signal, and increased RF signal power through the use of high-performance photodiode detectors.
Embedded Modules for Speaker Classification (2008)

Classifying speakers and their context is a research topic that increasingly finds its way into market-ready products. This paper describes how a speech-based classification problem can be split into components that are then combined in a classification module, which can be compiled for a specific platform and scenario with its respective technical requirements and limitations. We are focusing on the AGENDER Speaker Classification approach to show how a theoretic model can be transformed into a finished embedded module and present a tool that facilitates this in a fully automated build process.
Rate and distortion redundancies for universal source coding with respect to a fidelity criterion (2005)

Rissanen has shown that there exist universal noiseless codes for {Xi} with per-letter rate redundancy as low as (K log N)/2N, where N is the blocklength and K is the number of source parameters. we derive an analogous result for universal source coding with respect to the squared error fidelity criterion: there exist codes with per-letter rate redundancy as low as (K log N)/2N and per-letter distortion (averaged over X^N and θ) at most D(R)[1 + K/N], where D(r) is an average distortion-rate function and K is now the number of parameters in the code.
Evaluation of Oxygen Plasma and UV Ozone Methods for Cleaning of Occluded Areas in MEMS Devices (2010)

UV ozone and oxygen plasma treatments are two common procedures for cleaning silicon surfaces. The extent to which hidden surfaces of microelectromechanical systems (MEMS) are cleaned by these methods has not been well documented. To probe and compare the effectiveness of the two methods for cleaning occluded regions in MEMS, devices consisting of large movable flaps were fabricated to produce hidden surfaces whose occluded regions exceeded the aspect ratios that typically occur in MEMS devices. The gaps between the flap and the substrate in the custom flap devices were designed to be variable in extent. Their interior regions were initially coated with chemisorbed monolayers and then subjected to cleaning. Both techniques removed monolayers on exposed surfaces and both, to some extent, removed monolayers present on the occluded surfaces. Oxygen plasma was found to be a far more effective method for cleaning the occluded surfaces than the UV ozone method. However, in occlusions with exceptionally large aspect ratios of 1700 : 1, even oxygen plasma could not remove all traces of the chemisorbed monolayers. <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\hfill$</tex></formula> [2009-0103]
Delay-Throughput Analysis in Decentralized Single-Hop Wireless Networks (2007)

In this paper, an asymptotic analysis for the delay- throughput of a single-hop wireless network with n pairs of nodes is presented. The analysis relies on the decentralized on-off power allocation strategy, in which the on-off transmission policy for each link is based on comparing its direct channel gain with optimum threshold taun. We first provide a new definition of the transmission delay in a homogenous network. It is proved that the delay threshold level that results in dropping probability for each link tends to zero, while achieving the maximum average sum-rate scales as omega(n/ log n). Also, the minimum delay in order to make the dropping probability for the whole network approach zero scales as omega(n/ log n) + n. Furthermore, we drive lower and upper bounds for the link activation probability, q, such that the order of the average sum-rate is preserved. Based on the upper bound on q, an asymptotic analysis shows that the delay in each link and in the network improves without any significant impact on the the average sum-rate. Finally, we present a new definition of the throughput for the link in the cases of one and infinite buffer size. It is demonstrated that the maximum average throughput of the network with the decentralized on-off power allocation strategy is independent of the buffer size.
Polyadenylic acid on poliovirus RNA. II. poly(A) on intracellular RNAs (1975)

The content, size, and mechanism of synthesis of 3'-terminal poly(A) on the various intracellular species of poliovirus RNA have been examined. All viral RNA species bound to poly(U) filters and contained RNase-resistant stretches of poly(A) which could be analyzed by electrophoresis in polyacrylamide gels. At 3 h after infection, the poly(A) on virion RNA, relicative intermediate RNA, polyribosomal RNA, and total cytoplasmic 35S RNA was heterogeneous in size with an average length of 75 nucleotides. By 6 h after infection many of the intracellular RNA's had poly(A) of over 150 nucleotides in length, but the poly(A) in virion RNA did not increase in size suggesting that the amount of poly(A) which can be encapsidated is limited. At all times, the double-stranded poliovirus RNA molecules had poly(A) of 150 to 200 nucleotides. Investigation of the kinetics of poly(A) appearance in the replicative intermediate and in finished 35S molecules indicated that poly(A) is the last portion of the 35S RNA to be synthesized; no nascent poly(A) could be detected in the replicative intermediate. Although this result indicates that poliovirus RNA is synthesized 5' leads to 3' like other RNA's, it also suggests that much of the poly(A) found in the replicative intermediate is an artifact possibly arising from the binding of finished 35S RNA molecules to the replicative intermediate during extraction. The addition of poly(A) to 35S RNA molecules was not sensitive to guanidene.