gebhart/patrepeval huggingface dataset:
Morphological and molecular characterization of Heterodera dunensis n. sp. (Nematoda: Heteroderidae) from Gran Canaria, Canary Islands (2020)

<i>Heterodera dunensis</i> n. sp. from the coastal dunes of Gran Canaria, Canary Islands, is described. This new species belongs to the <i>Schachtii</i> group of <i>Heterodera</i> with ambifenestrate fenestration, presence of prominent bullae, and a strong underbridge of cysts. It is characterized by vermiform second-stage juveniles having a slightly offset, dome-shaped labial region with three annuli, four lateral lines, a relatively long stylet (27-31 µm), short tail (35-45 µm), and 46 to 51% of tail as hyaline portion. Males were not found in the type population. Phylogenetic trees inferred from D2-D3 of 28S, partial ITS, and 18S of ribosomal DNA and <i>COI</i> of mitochondrial DNA sequences indicate a position in the '<i>Schachtii</i> clade'.
Single‐molecule detection of cancer mutations using a novel PCR‐LDR‐qPCR assay (2020)

Detection of low-abundance mutations in cell-free DNA is being used to identify early cancer and early cancer recurrence. Here, we report a new PCR-LDR-qPCR assay capable of detecting point mutations at a single-molecule resolution in the presence of an excess of wild-type DNA. Major features of the assay include selective amplification and detection of mutant DNA employing multiple nested primer-binding regions as well as wild-type sequence blocking oligonucleotides, prevention of carryover contamination, spatial sample dilution, and detection of multiple mutations in the same position. Our method was tested to interrogate the following common cancer somatic mutations: BRAF:c.1799T>A (p.Val600Glu), TP53:c.743G>A (p.Arg248Gln), KRAS:c.35G>C (p.Gly12Ala), KRAS:c.35G>T (p.Gly12Val), KRAS:c.35G>A (p.Gly12Asp), KRAS:c.34G>T (p.Gly12Cys), and KRAS:c.34G>A (p.Gly12Ser). The single-well version of the assay detected 2-5 copies of these mutations, when diluted with 10,000 genome equivalents (GE) of wild-type human genomic DNA (hgDNA) from buffy coat. A 12-well (pixel) version of the assay was capable of single-molecule detection of the aforementioned mutations at TP53, BRAF, and KRAS (specifically p.Gly12Val and p.Gly12Cys), mixed with 1,000-2,250 GE of wild-type hgDNA from plasma or buffy coat. The assay described herein is highly sensitive, specific, and robust, and potentially useful in liquid biopsies.
Adaptive optics for microscopy and photonic fabrication (2010)

The image resolution and contrast of microscopes are often detrimentally affected by aberrations that are introduced when focusing deep into specimens. These aberrations arise from spatial differences in optical properties of the specimen or refractive index mismatches. This is particularly problematic in multiphoton microscopy, where short pulsed lasers are used to generate contrast through non-linear optical effects, such as two-photon fluorescence or third harmonic generation. The non-linear nature of the signal generation process means that the signal level is strongly affected by changes in the focal spot intensity. We have applied the techniques of adaptive optics to measure and correct the aberrations, restoring image quality. In particular, this has been demonstrated in harmonic generation microscopy of developing mouse embryos. Similar aberration problems affect the resolution and efficiency of three-dimensional optical fabrication systems, such those used for the manufacture of photonic crystals or optical waveguides. These systems are based around microscope optics and use short pulsed laser illumination to induce localized multiphoton effects in a fabrication substrate. In this case, significant aberrations are introduced when focusing deep into the substrate. We report on the development of adaptive optics systems for these applications and discuss the specific challenges for wave front sensing and correction that are presented by these systems.
Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparumpopulation divergence (2008)

The distinct population profile of nonsynonymous variants indicates that natural selection has a significant influence on genomic diversity in P. falciparum, and that many of these changes may reflect functional variants deserving of follow-up study. Our analysis demonstrates the potential for new high-throughput genotyping technologies to enhance studies of population structure, natural selection, and ultimately enable genome-wide association studies in P. falciparum to find genes underlying key phenotypic traits.
Realization of optical pulling forces using chirality (2014)

The optical force acting on a chiral particle is qualitatively different from that acting on an achiral particle due to chirality-dependent forces which couple mechanical linear momentum with optical spin angular momentum. We show that such chirality-induced coupling can serve as a mechanism to realize optical pulling forces that can be predicted analytically and are also observed in full wave simulations for chiral structures.
Structural and immunochemical relatedness suggests a conserved pathogenicity motif for secondary cell wall polysaccharides in Bacillus anthracis and infection-associated Bacillus cereus (2017)

Bacillus anthracis (Ba) and human infection-associated Bacillus cereus (Bc) strains Bc G9241 and Bc 03BB87 have secondary cell wall polysaccharides (SCWPs) comprising an aminoglycosyl trisaccharide repeat: →4)-β-d-ManpNAc-(1→4)-β-d-GlcpNAc-(1→6)-α-d-GlcpNAc-(1→, substituted at GlcNAc residues with both α- and β-Galp. In Bc G9241 and Bc 03BB87, an additional α-Galp is attached to O-3 of ManNAc. Using NMR spectroscopy, mass spectrometry and immunochemical methods, we compared these structures to SCWPs from Bc biovar anthracis strains isolated from great apes displaying "anthrax-like" symptoms in Cameroon (Bc CA) and Côte d'Ivoire (Bc CI). The SCWPs of Bc CA/CI contained the identical HexNAc trisaccharide backbone and Gal modifications found in Ba, together with the α-Gal-(1→3) substitution observed previously at ManNAc residues only in Bc G9241/03BB87. Interestingly, the great ape derived strains displayed a unique α-Gal-(1→3)-α-Gal-(1→3) disaccharide substitution at some ManNAc residues, a modification not found in any previously examined Ba or Bc strain. Immuno-analysis with specific polyclonal anti-Ba SCWP antiserum demonstrated a reactivity hierarchy: high reactivity with SCWPs from Ba 7702 and Ba Sterne 34F2, and Bc G9241 and Bc 03BB87; intermediate reactivity with SCWPs from Bc CI/CA; and low reactivity with the SCWPs from structurally distinct Ba CDC684 (a unique strain producing an SCWP lacking all Gal substitutions) and non-infection-associated Bc ATCC10987 and Bc 14579 SCWPs. Ba-specific monoclonal antibody EAII-6G6-2-3 demonstrated a 10-20 fold reduced reactivity to Bc G9241 and Bc 03BB87 SCWPs compared to Ba 7702/34F2, and low/undetectable reactivity to SCWPs from Bc CI, Bc CA, Ba CDC684, and non-infection-associated Bc strains. Our data indicate that the HexNAc motif is conserved among infection-associated Ba and Bc isolates (regardless of human or great ape origin), and that the number, positions and structures of Gal substitutions confer unique antigenic properties. The conservation of this structural motif could open a new diagnostic route in detection of pathogenic Bc strains.
Learning and Generalization of Auditory Temporal–Interval Discrimination in Humans (1997)

The sensory encoding of the duration, interval, and order of different stimulus features provides vital information to the nervous system. The present study focuses on the influence of practice on auditory temporal-interval discrimination. The goals of the experiment were to determine (1) whether practice improved the ability to discriminate a standard interval of 100 msec bounded by brief 1 kHz tones from longer intervals, and, if so, (2) whether this improvement generalized to different tonal frequencies or temporal intervals. Learning was examined in 14 human subjects using an adaptive, two-alternative, forced-choice procedure. One hour of training per day for 10 d led to marked improvements in the ability to discriminate between the standard and longer intervals. The generalization of learning was evaluated by independently varying the spectral (tonal frequency) and temporal (interval) components of the stimuli in four conditions tested both before and after the training phase. Remarkably, there was complete generalization to the trained interval of 100 msec bounded by tones at the untrained frequency of 4 kHz, but no generalization to the untrained intervals of 50, 200, or 500 msec bounded by tones at the trained frequency of 1 kHz. Thus, these data show that (1) temporal-interval discrimination using a 100-msec standard undergoes perceptual learning, and (2) the neural mechanisms underlying this learning are temporally, but not spectrally, specific. These results are compared with those from previous investigations of learning in visual spatial tasks, and are discussed in relation to biologically plausible models of temporal processing.
MPI as a Programming Model for High-Performance Reconfigurable Computers (2010)

High-Performance Reconfigurable Computers (HPRCs) consist of one or more standard microprocessors tightly-coupled with one or more reconfigurable FPGAs. HPRCs have been shown to provide good speedups and good cost/performance ratios, but not necessarily ease of use, leading to a slow acceptance of this technology. HPRCs introduce new design challenges, such as the lack of portability across platforms, incompatibilities with legacy code, users reluctant to change their code base, a prolonged learning curve, and the need for a system-level Hardware/Software co-design development flow. This article presents the evolution and current work on TMD-MPI, which started as an MPI-based programming model for Multiprocessor Systems-on-Chip implemented in FPGAs, and has now evolved to include multiple X86 processors. TMD-MPI is shown to address current design challenges in HPRC usage, suggesting that the MPI standard has enough syntax and semantics to program these new types of parallel architectures. Also presented is the TMD-MPI Ecosystem , which consists of research projects and tools that are developed around TMD-MPI to further improve HPRC usability. Finally, we present preliminary communication performance measurements.
Isolable Aryl‐Substituted Silyl Radicals: Synthesis, Characterization, and Reactivity (2014)

Isolable aryl-substituted silyl radicals (tBu2 MeSi)2(Ar)Si(·) (Ar = C6H5, 4-tBuC6H4, 4-PhC6H4, 3,5-tBu2C6H3) were synthesized by the reaction of the corresponding iodosilane with an equimolar amount of potassium graphite (KC8 ) in tetrahydrofuran (THF). The crystal structure of 3,5-tBu2C6H3 derivative, which was determined by X-ray crystallography, showed a planar geometry around the Si atom for the radical center. EPR studies of all four radicals revealed the lack of the delocalization of the unpaired electron over the aromatic ring. Reactivity and spectroscopic studies of the less-hindered phenyl-substituted silyl radical showed that it exists as an equilibrium mixture of the radical and its silene-type dimer in solution.
Spectroscopic Analysis of Liquid/Liquid Interfaces in Multiphase Microflows (2003)

Microscopic quasi-elastic laser scattering (muQELS) spectroscopy has been developed for analysis of interfacial phenomena at laminar multiphase microflow in a microchannel. Transport phenomena of a metal chelate through a water/toluene interface were measured, and transient adsorption of the chelate in the initial step of the transport was measured. A water/methanol miscible interface was also measured, and the interfacial free energy of a miscible interface was determined for the first time. The muQELS is expected to be very effective not only for physicochemical investigations of transport and mixing, but also for elemental process analysis of heterogeneous reactions.
Stimulation of Alloreactive Cytotoxic T Cells by Paternal Major Histocompatibility Antigens during Murine Pregnancy (1985)

In an effort to elucidate T cell reactivity toward paternal major histocompatibility (MHC) antigens during pregnancy, the ability of pregnant mice to develop alloreactive cytotoxic T lymphocytes (CTL) was studied in individual multiparous females mated with MHC congeneic strains of B10 background. Spleen cells obtained from B10.BR females mated to allogeneic males manifested strikingly higher CTL than those from animals mated to syngeneic males or from virgins; syngeneically mated animals were equivalent to virgin controls in CTL responses. The augmented CTL response in allogeneic pregnancy was detected not only by stimulation with the paternal MHC antigens but also by an unrelated MHC haplotype. However, this augmentation was found only during pregnancy in that 2-5 days after the delivery the CTL activity in allopregnant animals returned to a level comparable to that of virgin controls. No suppressor cells were detected at this stage. These observations suggest that maternal T cells recognize MHC disparity with the fetus in some way during pregnancy. Anti-MHC antibodies, immunoglobulin (Ig) M, and IgGs of all subclasses were not detected in these animals throughout multiple pregnancies.
Editorial. (2018)

Effective communication sometimes requires a common language. This is particularly true in science, where communication among health professionals and scientists across national boundaries has become critical because of the rapidity with which new knowledge is acquired. In the modern era, where multinationalism in key medical and scientific discoveries is increasingly common, the language is undoubtedly English. In fact, more than three-quarters of scientific papers today are published in English.
K-NN search using local learning based on regression for neighbor embedding-based image prediction (2013)

The paper describes a K-NN search method aided by local learning of subspace mappings for the problem of neighbor-embedding based image Intra prediction. The local learning of subspace mappings relies on multivariate linear regression. The method is used jointly with Locally Linear Embedding (LLE) as well as with a method inspired from Non Local Means (NLM) for prediction. Linear and kernel ridge regression are also considered directly for predicting the unknown pixels. Rate-distortion performances are then given in comparison with Intra prediction using LLE and classical K-NN search, as well as in comparison with H.264 Intra prediction modes.
Kallikrein Gene Delivery Attenuates Myocardial Infarction and Apoptosis After Myocardial Ischemia and Reperfusion (2000)

The tissue kallikrein-kinin system is present in the heart, and kinin has been shown to have cardioprotective effects. In this study, we investigated the potential role of tissue kallikrein in myocardial ischemia/reperfusion injury through adenovirus-mediated human kallikrein gene delivery. One week after gene delivery, the rats were subjected to a 30-minute coronary occlusion followed by a 2-hour reperfusion. Kallikrein gene delivery caused significant decreases in the ratio of infarct size to ischemic area at risk (from 69.6% to 44.5%, n=10 and 8, P<0.01) and in the incidence of ventricular fibrillation (from 64.3% to 16.7%, n=14 and 24, P<0.01) compared with the group injected with control adenovirus. Kallikrein gene delivery also attenuated programmed cell death in the ischemic area compared with the control area as assessed with the terminal deoxynucleotidyl transferase-mediated nick end labeling assay (n=6, P<0.01). Icatibant, a specific bradykinin B(2) receptor antagonist, abolished these kallikrein-mediated beneficial effects. The expression of human tissue kallikrein mRNA was identified in rat heart, kidney, lung, liver, and adrenal gland. After kallikrein gene delivery, cardiac kinin and cGMP levels were significantly elevated compared with the control (29.6+/-12.7 versus 6.1+/-2.1 pg/mg protein, n=7, P<0.01; 1.30+/-0.06 versus 0.86+/-0.09 pmol/mg protein, n=5, P<0.05). These results indicate that kallikrein gene delivery protects against myocardial infarction, ventricular arrhythmias, and apoptosis in ischemia/reperfusion injury via kinin-cGMP signal pathway. The successful application of this technology may have potential therapeutic value in the treatment of coronary artery diseases.
Group IV mid-IR photonics (2015)

Silicon and germanium are transparent up to approximately 8 μm and 15 μm, respectively, thus offering a range of applications in biochemical and environmental sensing, medicine, astronomy and communications [1]. Silicon-on-insulator (SOI), can be used only up to 4 μm due to the high absorption loss of silicon dioxide, and therefore alternative material platforms have to be utilized for longer wavelengths. Also, to fully exploit the transparency range of SOI, 400 or 500 nm thick overlayers need to be used rather than the most popular 220 nm platform [2]. In this paper we report record low loss MIR SOI strip and slot waveguides, as well as Vernier racetrack configurations. If the buried oxide can be removed and replaced with air, such a platform would be transparent up to 8 μm. We report a robust design based on single etch suspended Si waveguides. Ge-on-Si waveguides have already been demonstrated with losses of 2.5–3.0 dB/cm at λ=5.8 μm by Chang et. al [3] and Shen et. al [4]. We report a record low loss in Ge-on-Si and a demonstration of all optical modulation in such waveguides. Although Si is transparent beyond 1.1 μm, it has been demonstrated that it can be used as a photodetector if mid-bandgap states are created by ion implantation. In this paper we show that detection in Si can be extended to up to 2.5 μm by implantation of SOI waveguides with boron. Finally, we also report theoretical analysis of electroabsorption and electrorefraction in Ge.
Engineering Saccharomyces cerevisiae to produce odd chain‐length fatty alcohols (2015)

Fatty aldehydes and alcohols are valuable precursors used in the industrial manufacturing of a myriad of specialty products. Herein, we demonstrate the de novo production of odd chain-length fatty aldehydes and fatty alcohols in Saccharomyces cerevisiae by expressing a novel biosynthetic pathway involving cytosolic thioesterase, rice α-dioxygenase and endogenous aldehyde reductases. We attained production titers of ∼20 mg/l fatty aldehydes and ∼20 mg/l fatty alcohols in shake flask cultures after 48 and 60 h respectively without extensive fine-tuning of metabolic fluxes. In contrast to prior studies which relied on bi-functional fatty acyl-CoA reductase to produce even chain-length fatty alcohols, our biosynthetic route exploits α-oxidation reaction to produce odd chain-length fatty aldehyde intermediates without using NAD(P)H cofactor, thereby conserving cellular resource during the overall synthesis of odd chain-length fatty alcohols. The biosynthetic pathway presented in this study has the potential to enable sustainable and efficient synthesis of fatty acid-derived chemicals from processed biomass.
Evaluation of Gasoline‐Denatured Ethanol as a Carbon Source for Denitrification (2013)

In this study concerning denitrification, the performance of three carbon sources, methanol (MeOH), ethanol (EtOH) and gasoline-denatured ethanol (dEtOH), was compared and evaluated on the basis of treatment efficiency, inhibition potential and cost. The gasoline denaturant considered here contained mostly aliphatic compounds and little of the components that typically boost the octane rating, such as benzene, toluene, ethylbenzene and xylenes. Results were obtained using three lab-scale SBRs operated at SRT of 12.0 +/- 0.9 days. After biomass was acclimated, denitrification rates with dEtOH were similar to those of EtOH (201 +/- 50 and 197 +/- 28 NO3-N/g MLVSS x d, respectively), and higher than those of MeOH (165 +/- 49 mg NO3-N/g MLVSS x d). The denaturant did not affect biomass production, nitrification or denitrification. Effluent soluble COD concentrations were always less than the analytical detection limit. Although the cost of dEtOH ($2.00/kg nitrate removed) was somewhat higher than that of methanol ($1.63/kg nitrate removed), the use of dEtOH is very promising and utilities will have to decide if it is worth paying a little extra to take advantage of its benefits.
Identifying Drivers of Catalytic Activity through Systematic Surface Modification of Cathode Materials (2009)

To systematically study the effect of surface composition on the catalytic activity for oxygen exchange, strontium doped lanthanum manganite (LSM) powder was infiltrated with various metal nitrate solutions (La, Sr, Co, Fe) and then calcined to deposit the resultant metal oxide on the surface of the powder. The elements chosen for LSM infiltration were selected because they are the metal constituents of strontium doped cobalt ferrite (LSCF), which is initially a much more active cathode material. Results from LSM show a stronger effect from the addition of B site elements, thus LSCF was correspondingly infiltrated with manganese. By comparing the different surfaces, a better understanding of the underlying drivers of catalytic activity is gained. Two key properties for good catalytic activity are recognized: ionic conductivity and active metal sites on the surface which serve as either redox centers or adsorption sites.
Topology optimization of freeform large-area metasurfaces (2019)

We demonstrate optimization of optical metasurfaces over 10<sup>5</sup>-10<sup>6</sup> degrees of freedom in two and three dimensions, 100-1000+ wavelengths (λ) in diameter, with 100+ parameters per λ<sup>2</sup>. In particular, we show how topology optimization, with one degree of freedom per high-resolution "pixel," can be extended to large areas with the help of a locally periodic approximation that was previously only used for a few parameters per λ<sup>2</sup>. In this way, we can computationally discover completely unexpected metasurface designs for challenging multi-frequency, multi-angle problems, including designs for fully coupled multi-layer structures with arbitrary per-layer patterns. Unlike typical metasurface designs based on subwavelength unit cells, our approach can discover both sub- and supra-wavelength patterns and can obtain both the near and far fields.
Each side chain of cyclosporin A is not essential for high passive permeability across lipid bilayers (2023)

We compared the passive permeability of cyclosporin A (CsA) derivatives with side chain deletions across lipid bilayers. CsA maintained passive permeability after losing any one of the side chains, which suggests that the propensity of the backbone of CsA is an important component for high passive permeability.
Math Doesn't Have to be Hard (2019)

Recent work has shown that using low-precision arithmetic in Deep Neural Network (DNN) inference acceleration can yield large efficiency gains with little or no accuracy degradation compared to half or single precision floating-point by enabling more MAC operations per unit area. The most efficient precision is a complex function of the DNN application, structure and required accuracy, which makes the variable precision capabilities of FPGAs very valuable. We propose three logic block architecture enhancements to increase the density and reduce the delay of multiply-accumulate (MAC) operations implemented in the soft fabric. Adding another level of carry chain to the ALM (extra carry chain architecture) leads to a 1.5x increase in MAC density, while ensuring a small impact on general designs as it adds only 2.6% FPGA tile area and a representative critical path delay increase of 0.8%. On the other hand, our highest impact option, which combines our 4-bit Adder architecture with a 9-bit Shadow Multiplier, increases MAC density by 6.1x, at the cost of larger tile area and representative critical path delay overheads of 16.7% and 9.8%, respectively.