gebhart/patrepeval huggingface dataset:
The gene regulatory program of <i>Acrobeloides nanus</i> reveals conservation of phylum-specific expression (2018)

The evolution of development has been studied through the lens of gene regulation by examining either closely related species or extremely distant animals of different phyla. In nematodes, detailed cell- and stage-specific expression analyses are focused on the model <i>Caenorhabditis elegans</i>, in part leading to the view that the developmental expression of gene cascades in this species is archetypic for the phylum. Here, we compared two species of an intermediate evolutionary distance: the nematodes <i>C. elegans</i> (clade V) and <i>Acrobeloides nanus</i> (clade IV). To examine <i>A. nanus</i> molecularly, we sequenced its genome and identified the expression profiles of all genes throughout embryogenesis. In comparison with <i>C. elegans</i>, <i>A. nanus</i> exhibits a much slower embryonic development and has a capacity for regulative compensation of missing early cells. We detected conserved stages between these species at the transcriptome level, as well as a prominent middevelopmental transition, at which point the two species converge in terms of their gene expression. Interestingly, we found that genes originating at the dawn of the Ecdysozoa supergroup show the least expression divergence between these two species. This led us to detect a correlation between the time of expression of a gene and its phylogenetic age: evolutionarily ancient and young genes are enriched for expression in early and late embryogenesis, respectively, whereas Ecdysozoa-specific genes are enriched for expression during the middevelopmental transition. Our results characterize the developmental constraints operating on each individual embryo in terms of developmental stages and genetic evolutionary history.
Impact on Storage Complex Delineation from Injection-induced Pressure Propagation (2014)

Pressure increase during an injection operation for CO2 storage can greatly exceed the delineation of the storage complex. The EC CCS directive do not recommend standards for the pressure development outside the storage complex. In order to evaluate pressure development in that respect regional dynamic modelling can be effective. The paper outlines recommendations for regional pressure modelling and show results on how pressure can propagate much faster and wider that the extension of the CO2 plume and storage complex delineation. Further the use of pressure management through water production is discussed and shown to be a workable technique for pressure controlling undesirable high and fast pressure propagations.
A third Ig light chain gene isotype in Xenopus laevis consists of six distinct VL families and is related to mammalian lambda genes (1996)

Xenopus laevis is a unique model for studying the ontogenetic development of immune functions. A short primer PCR amplification method was employed to amplify fragments from Xenopus genomic DNA that are related to Ig light chains and TCR. One fragment was identified that appeared to represent a novel type of light chain and was used as a probe to recover the corresponding cDNA from a spleen cDNA library. We designate these light chains type III. Using an iterative screening procedure, six families of VL genes, two distinct JL and two distinct CL sequences, were identified. In a comparison of phylogenetically diverse light chains, the type III genes align with higher vertebrate lambda genes. Southern blot hybridization analyses with genomic DNA from different animals showed the VL and CL sequences to be both diverse and polymorphic. Intrafamily sequence comparisons of VL genes revealed additional diversity. Collectively, these studies confirm the existence of a third type of light chain gene in Xenopus, establish a high degree of genetic variation in the sequences encoding the light chain V regions, and provide the most significant evidence to date for the presence of a lambda-like light chain gene at the phylogenetic level of the amphibians.
Mutations Near the N Terminus of Vaccinia Virus G9 Protein Overcome Restrictions on Cell Entry and Syncytium Formation Imposed by the A56/K2 Fusion Regulatory Complex (2020)

The entry/fusion complex (EFC) consists of 11 conserved proteins embedded in the membrane envelope of mature poxvirus particles. Poxviruses also encode proteins that localize in cell membranes and negatively regulate superinfection and syncytium formation. The vaccinia virus (VACV) A56/K2 fusion regulatory complex associates with the G9/A16 EFC subcomplex, but functional support for the importance of this interaction was lacking. Here, we describe serially passaging VACV in nonpermissive cells expressing A56/K2 as an unbiased approach to isolate and analyze escape mutants. Viruses forming large plaques in A56/K2 cells increased in successive rounds of infection, indicating the occurrence and enrichment of adaptive mutations. Sequencing of genomes of passaged and cloned viruses revealed mutations near the N terminus of the G9 open reading frame but none in A16 or other genes. The most frequent mutation was His to Tyr at amino acid 44; additional escape mutants had a His-to-Arg mutation at amino acid 44 or a duplication of amino acids 26 to 39. An adaptive Tyr-to-Cys substitution at amino acid 42 was discovered using error-prone PCR to generate additional mutations. Myristoylation of G9 was unaffected by the near-N-terminal mutations. The roles of the G9 mutations in enhancing plaque size were validated by homologous recombination. The mutants exhibited enhanced entry and spread in A56/K2 cells and induced syncytia at neutral pH in HeLa cells despite the expression of A56/K2. The data suggest that the mutations perturb the interaction of G9 with A56/K2, although some association was still detected in detergent-treated infected cell lysates.<b>IMPORTANCE</b> The entry of enveloped viruses is achieved by the fusion of viral and cellular membranes, a critical step in infection that determines host range and provides targets for vaccines and therapeutics. Poxviruses encode an exceptionally large number of proteins comprising the entry/fusion complex (EFC), which enables infection of diverse cells. Vaccinia virus (VACV), the prototype member of the poxvirus family, also encodes the fusion regulatory proteins A56 and K2, which are displayed on the plasma membrane and may be beneficial by preventing reinfection and cell-cell fusion. Previous studies showed that A56/K2 interacts with the G9/A16 EFC subcomplex in detergent-treated cell extracts. Functional evidence for the importance of this interaction was obtained by serially passaging wild-type VACV in cells that are nonpermissive because of A56/K2 expression. VACV mutants with amino acid substitutions or duplications near the N terminus of G9 were enriched because of their ability to overcome the block to entry imposed by A56/K2.
An overview of electronic controls for passenger car diesel engines (1980)

The penetration of diesel engine technology into the transportation industry began with heavy trucks in the 1940s and has advanced to passenger cars of the 1980s. The application of control electronics to gasoline powered cars of the 1970s is now expanding to diesel powered cars of the 1980s. The successful application of microprocessor technology, sensors and actuators to gasoline cars provides a technology base for improving the performance and emissions of the diesel engine. The conversion from mechanically controlled diesel injection pumps to electronically controlled pumps can provide improved performance with expanded capabilities and help meet government regulations.
Inspiratory capacity as a preoperative assessment of patients undergoing thoracic surgery (2012)

Although inspiratory capacity (IC) is strongly associated with the disease severity of chronic obstructive pulmonary disease, there was no appropriate equation to compute predicted values for IC. Furthermore, whether assessment of IC can identify the risk of prolonged postoperative stay (PPS) in patients undergoing thoracic surgery also remains unclear. To evaluate whether %IC predicted, for which the new equation to compute the predicted values for IC was utilized, could be applied to identify the risk of PPS, we retrospectively analysed the cases of 412 patients who underwent thoracic surgery in Nagoya University Hospital. The multivariate analysis demonstrated that %IC predicted < 85% was one of the most critical risk predictors for PPS (odds ratio, 1.65; 95% confidence intervals, 1.03-2.648) and, in particular, was independent of percentage predicted forced expiratory volume in 1 s (%FEV1) < 80%. A combined assessment of ICFEV1 Low, defined as %IC predicted <85% or %FEV1 <80%, was able to identify more than double the number of patients with PPS, compared with %FEV1 <80% alone (65.9 vs. 28.5%, respectively). This is the first study to demonstrate the significance of %IC predicted in screening for the risk for PPS in patients undergoing thoracic surgery.
In Situ Measurement of Li-Ion Battery Internal Temperature (2013)

Abstract not Available.
Investigation of thermal management technique in blue LED airport taxiway fixtures (2007)

On airport runways, blue light fixtures denote taxiways between the runway and the airport terminal. Blue optics transmit mostly short-wavelength radiation, which makes traditional incandescent lamps a poor choice of light source; the resulting fixture efficiency could be less than one percent. LEDs are replacing incandescent lamps in this application. But unlike incandescent sources, LEDs do not radiate enough heat to melt ice and snow from the fixture optics. To meet Federal Aviation Administration (FAA) regulations for weatherability, some LED-based fixtures incorporate electric heaters that, when switched on, nearly negate the energy-savings benefit of converting to LED sources. In this study, we explored methods for conduction and convection of LED junction heat to taxiway fixture optics for the purpose of minimizing snow and ice buildup. A more efficient LED-based system compared to incandescent that would require no additional heaters was demonstrated.
Silver nanoparticle array on weakly interacting epitaxial graphene substrate as catalyst for hydrogen evolution reaction under neutral conditions (2021)

The paucity of research on hydrogen evolution reaction (HER) under neutral conditions, which is a more sustainable way to produce H2 compared to acidic and alkaline HER, encourages the development of efficient catalytic materials and devices and deeper investigation of the mechanisms behind neutral HER. We present an electrode concept for facilitating HER under neutral conditions. The concept entails the use of annealing-reshaped silver (Ag) nanoparticle array on monolayer epitaxial graphene (MEG) on 4H-SiC. Measurements of HER performance show more positive onset potential of the cathodic HER for Ag-decorated MEG compared to that for pristine MEG, indicating improved water dissociation at Ag/MEG electrodes. Complementary morphological characterization, absorption measurements, and Raman mapping analysis enable us to ascribe the enhanced catalytic performance of electrodes decorated with 2 nm thick annealed Ag on the synergetic effect originating from simultaneous water reduction on circular Ag nanoparticles of 31 nm in diameter and on compressively strained Ag-free graphene regions. The overall results pave the way toward development of stable van der Waals heterostructure electrodes with a tunable metal–carbon interaction for fast HER under neutral conditions.
On the realization of across wavy water-air-interface diffuse-line-of-sight communication based on an ultraviolet emitter (2019)

We experimentally demonstrated high-speed diffuse line-of-sight optical wireless communication across a wavy water-air-interface. The testbed channel was evaluated, in terms of data rate, coverage and robustness to the dynamic wave movement, based on the performance of different modulation schemes, including non-return-to-zero on-off keying (NRZ-OOK) and quadrature amplitude modulation (QAM)-orthogonal frequency division multiplexing (OFDM). Under the emulated calm water condition, 8-QAM-OFDM offers a data rate of 111.4 Mbit/s at the aligned position, while only 55 Mbit/s is achieved using NRZ-OOK. On the other hand, effective communication can still be maintained at a high data rate of 11 Mbit/s when the photodetector is off aligned laterally by 5 cm based on NRZ-OOK modulation, leading to a coverage of ~79 cm<sup>2</sup>. By utilizing OFDM modulation scheme, a data rate of 30 Mbit/s can be achieved up to 2.5-cm misalignment, leading to a coverage of ~20 cm<sup>2</sup>. Furthermore, in the presence of strong waves (15-mm wave height, causing a scintillation index of 0.667), 4-QAM-OFDM modulation showed a better resilience to channel instability than NRZ-OOK modulation. Our studies pave the way for the eventual realization of communication across a challenging water-air interface without the need for an interface relay, which is much sought-after for implementing a robust and large-coverage underwater-to-terrestrial internet-of-things.
A cost-effective self-sensing biosensor for detection of biological species at ultralow concentrations (2013)

Detection of ultrasmall masses and identification of biological molecules have been made possible as a result of advances in nanotechnology. Development of biosensing tools has significantly contributed to high-throughput diagnosis and analytical sensing exploiting high affinity of biomolecules. MicroCantilever (MC)-based detection has emerged as a promising biosensing tool for offering label-free and cost-effective sensing capabilities. One of the main criteria determining the success of each biosensor is the capability of the sensing platform to operate in aqueous media. Although being characterized with high sensitivity and simplicity, MCs do not provide an effective tool for measurement of marker proteins in liquid media due to large hydrodynamic damping and losses in the surrounding liquid. In this study, we describe two approaches to high sensitivity biomolecular detection using piezoelectric microcantilevers. (i) Immobilized Mass Detection in Air using electro-mechanical resonance: a unique self-sensing measurement technique is reported utilizing a self-sensing circuit consisting of a piezoelectric MC to address the mentioned limitation. The capability of the self-sensing measurement technique was first verified by detecting ultrasmall biological masses immobilized over the surface of MC by monitoring the shift in fundamental mechanical resonance frequency of the system in air and comparing it with optical-based measurement. This was further utilized for calibration of mass detection in liquid media. (ii) Immobilized Mass Detection in Liquid using the electrical self-sensing circuit's resonance: Once the capability to detect adsorbed mass was verified, the self-sensing platform was implemented to detect different concentrations of target molecule (glucose in this study) in liquid media by adopting the highly sensitive resonance frequency of the whole circuit instead of the mechanical response of MC. Molecular binding occurring over the surface of MC changes the capacitance of the total interface thus changing the resonance frequency of the circuit. The amount of shift in the measured circuit's resonance frequency provides qualitative and quantitative insight into the amount of target protein concentration. The reported diagnostic platform offers a simple, cost-effective, all-electronics method of detection where the need for any bulky, expensive optical based measurement is eliminated. Utilizing this technique, physiological concentration of glucose as low as 500 nM was measured in liquid media. This sensitivity is significantly higher than what has been previously reported using other mechanical resonance techniques.
The development of high-content screening (HCS) technology and its importance to drug discovery (2016)

Recent advances in cellular assay technologies, such as the introduction of three-dimensional (3D) cultures, induced pluripotent stem cells (iPSCs) and genome editing technologies (e.g., CRISPR/Cas9), have tremendously expanded the potential of high-content assays to contribute to the drug discovery process. Increasingly predictive cellular models and readouts, together with the development of more sophisticated and affordable HCS readers, will further consolidate the role of HCS technology in drug discovery.
Soluble MICA in malignant diseases (2005)

The immunoreceptor NKG2D activates natural killer cells and costimulates CD8 T cells. The MHC class I-related MICA molecules are ligands of NKG2D and are expressed on malignant, but not on normal, cells. As NKG2D plays an important role in the immunosurveillance of tumors, studies suggest that release of MICA from cancer cells constitutes an immune escape mechanism that systemically impairs antitumor immunity. Here, we investigated the potential of soluble MICA (sMICA) as a marker in cancer. Analysis of sMICA in sera of 512 individuals revealed significantly (p < 0.0001) higher levels in patients with various malignancies (n = 296, median 161 pg/ml) than in healthy individuals (n = 62, median <30 pg/ml). Patients with benign diseases (n = 154, median 84 pg/ml) exhibited intermediate sMICA levels. In cancer patients, elevated sMICA levels correlated significantly with cancer stage and metastasis (p = 0.015 and p = 0.007, respectively). While release of MICA is thought to impair tumor immunity, determination of sMICA levels may provide useful additional information in the diagnosis and staging of cancer.
Characteristics and Performance of Surfaces Created by Various Finishing Methods (Invited Paper) (2016)

The functional performance of mechanical components depends on their surface characteristics, surface integrity and geometric accuracy. It is critical to understand the influence of these surface properties on product performance, so the manufacturing processes can be designed to deliver the required performance. This paper presents the influence of surface characteristics on functional performance including surface topography, surface 2D/3D parameters, tribological parameters and residual stresses. It then discusses the surface properties created by various finishing methods such as hard turning, grinding, superfinishing, mass finishing, etc. Finally, it provides guidelines for the design and selection of finishing processes in order to yield the critical product performance characteristics.
Polyclonal B cell activation in hamsters infected with parasites of the genus Leishmania (1982)

Mesocricetus auratus (golden hamsters) infected with leishmania developed characteristic B cell immune responses that depended on the infecting species of leishmania. Thus, hamsters infected with viscerotropic leishmania (Leishmania donovani) developed antileishmania antibodies and hypergammaglobulinemia due to polyclonal activation of B cells as measured by reverse hemolytic plaque assay. In contrast, dermotropic leishmanias (L. braziliensis braziliensis and L. mexicana amazonensis) stimulated antileishmania antibodies with no increase in either serum immunoglobulin concentration or in the number of antibody-forming cells per spleen. The dermotropic leishmanias were unable to stimulate polyclonal activation even in hamsters in which visceralization had occurred with high splenic parasitization. These findings suggest that species-specific leishmania antigens (or factors) might be the modulators of the altered immune response present in these diseases.
On the Phase Sequence Set of SLM Scheme for Crest Factor Reduction in OFDM System (2006)

The crest factor distribution of orthogonal frequency division multiplexing (OFDM) symbol sequences is evaluated and it is shown that OFDM symbol sequences with a short period are expected to have a high crest factor. The crest factor relationship between two input symbol sequences, Hamming distance D apart is also derived. Using these two results, we propose two criteria for a phase sequence set of the selected mapping (SLM) scheme and suggest the rows of the cyclic Hadamard matrix constructed from an m-sequence as the near optimal phase sequence set of the SLM scheme.
Core–shell-like Au sub-nanometer clusters in Er-implanted silica (2015)

The very early steps of Au metal cluster formation in Er-doped silica have been investigated by high-energy resolution fluorescence-detected X-ray absorption spectroscopy (HERFD-XAS). A combined analysis of the near-edge and extended part of the experimental spectra shows that Au cluster nucleation starts from a few Au and O atoms covalently interconnected, likely in the presence of embryonic Au-Au correlation. The first Au clusters, characterized by a well defined Au-Au coordination distance, form upon 400 °C inert annealing. The estimated upper limit of the Gibbs free energy for the associated heterogeneous nucleation is 0.06 eV per atom, suggesting that the Au nucleation is assisted by matrix defects, most likely non-bridging oxygen atoms. The experimental results indicate that the formed subnanometer Au clusters can be applied as effective core-shell systems in which the Au atoms of the 'core' develop a metallic character, whereas the Au atoms in the 'shell' can retain a partially covalent bond with O atoms of the silica matrix. High structural disorder at the Au site is found upon neutral annealing at a moderate temperature (600 °C), likely driven by the configurational disorder of the defective silica matrix. A suitable choice of the Au concentration and annealing temperature allows tailoring of the Au cluster size in the sub-nanometer range. The interaction of the Au cluster surface with the surrounding silica matrix is likely responsible for the infrared luminescence previously reported on the same systems.
Complete Genome Sequence of Neonatal Clinical Group B Streptococcal Isolate CJB111 (2021)

Group B <i>Streptococcus</i> (GBS) is an asymptomatic colonizer of the female reproductive tract but can cause maternal and neonatal infections and adverse pregnancy outcomes. Here, we closed the genome sequence of strain CJB111, a neonatal GBS clinical isolate from a case of late-onset bacteremia without focus (Houston, TX; 1990).
Abstract P131: What Drives Greater Assimilation of Telestroke in Emergency Departments? (2021)

Objective: Although many emergency departments (EDs) have telestroke capacity, it is unclear why some EDs consistently use telestroke and others do not. We compared the characteristics and practices of EDs with robust and low assimilation of telestroke. Methods: We conducted semi-structured interviews with representatives of EDs that received telestroke services from 10 different networks and had used telestroke for a minimum of two years. We used maximum diversity sampling to select EDs for inclusion and applied a positive deviance approach, comparing programs with robust and low assimilation. Data collection was informed by the Consolidated Framework for Implementation Research. For the qualitative analysis, we created site summaries and conducted a supplemental matrix analysis to identify themes. Results: Representatives from 21 EDs with telestroke, including 11 with robust assimilation and 10 with low assimilation, participated. In EDs with robust assimilation, telestroke workflow was highly protocolized, programs had the support of leadership, telestroke use and outcomes were measured, and individual providers received feedback about their telestroke use. In EDs with low assimilation, telestroke was perceived to increase complexity, and ED physicians felt telestroke did not add value or had little value beyond a telephone consult. EDs with robust assimilation identified four sets of strategies to improve assimilation: strengthening relationships between stroke experts and ED providers, improving and standardizing processes, addressing resistant providers, and expanding the goals and role of the program. Conclusion: Greater assimilation is associated with standardized workflow, leadership support, ongoing evaluation and quality improvement efforts, and mechanisms to address resistant ED providers.