gebhart/patrepeval huggingface dataset:
Herbicide Rotations and Mixtures (1990)

Herbicide resistant populations have evolved only in monoculture and/or mono-herbicide conditions at the rates we have previously predicted. Contrary to our original model, no populations of atrazine-resistant weeds have appeared in corn where rotations of crops and herbicides or herbicide mixtures were used. This is due to the previous lack of information about the greatly reduced fitness of the resistant individuals, which could be expressed only during rotational cycles, and also to the greater sensitivity of resistant individuals to other herbicides, pests and control practices. Our new model, presented here, describes how these factors reduce the resistant individuals to extremely low frequencies during rotation. It is not yet clear whether such factors will delay the rate of appearance of other types of resistance; e.g. the multiple resistances to grass-killing herbicides in wheat, or to inhibitors of acetolactate synthase, where the fitness of resistant biotypes may be higher.
In vitrovalidation of non-invasive aortic compliance measurements using MRI (2012)

" In vitro validation of non-invasive aortic compliance measurements using MRI." Computer Methods in Biomechanics and Biomedical Engineering, 15(sup1), pp. 83–84
Photonic bound states in periodic dielectric materials (1991)

It is demonstrated that lattice imperfections in a periodic array of dielectric material can give rise to fully localized electromagnetic states. Calculations are performed by using a plane-wave expansion to solve Maxwell's equations. The frequency of these localized states is tunable by varying the size of the defect. Potential device applications in the microwave and millimeter wave regime are proposed.
Luminogenic D‐Luciferin Derivatives as OATP1B1 and 1B3 Substrates in No‐wash Assays† (2021)

The human hepatic organic ion transporting polypeptides OATP1B1 and -1B3 are uptake transporters that influence the disposition of several small molecule drugs and perpetrate certain adverse drug-drug interactions. To predict these in vivo effects, in vitro systems are used to screen new drug entities as potential transporter substrates or inhibitors. To simplify such studies, we synthesized luminogenic derivatives of the OATP1B1 and -1B3 substrate D-luciferin to test as probe substrates in a rapid, no-wash optical approach for substrate and inhibitor identification and characterization. Each derivative is a pro-luciferin containing a self-immolating trimethyl lock quinone linker that is sensitive to intracellular reducing environments that cause the release of free luciferin in proportion to the amount of probe taken up by the transporter. A subsequent luciferin-limited luciferase reaction produces light in proportion to transporter activity. We tested the derivatives in HEK293 cells that overexpress OATP1B1 or OATP1B3 by transient transfection or viral transduction. Derivatives were identified that showed OATP-dependent uptake that was time and concentration dependent, saturable and sensitive to inhibition by known OATP1B1 and -1B3 substrates and inhibitors. These luminogenic transporter probes enabled an add-only multi-well plate protocol suitable for automation and high throughput screening.
Effect of Compression Ratio on Stratified-Charge Direct- Injection Gasoline Combustion (2005)

&lt;div class="htmlview paragraph"&gt;Charge cooling due to fuel evaporation in a direct-injection spark-ignition (DISI) engine typically allows for an increased compression ratio relative to port fuel injection (PFI) engines. It is clear that this results in a thermal efficiency improvement at part load for homogenous-charge DISI engines. However, very little is known regarding the effect of compression ratio on stratified charge operation. In this investigation, DISI combustion data have been collected on a single cylinder engine equipped with a variable compression ratio feature.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The results of experiments performed in stratified-charge direct injection (SCDI) mode show that despite its over-advanced phasing, thermal conversion efficiency improves with higher compression ratios. This benefit is quantified and dissected through an efficiency analysis. Furthermore, since the engine was equipped with both wall-guided DI and PFI systems, direct comparisons are made at part load for fuel consumption and emissions. Interestingly, combustion efficiency deteriorates in SCDI mode as compression ratio increases, albeit not due to crevice loading as is the case in PFI operation. Mechanisms for the observed hydrocarbon emissions behavior are suggested for change in load and compression ratio. The conclusions reached in this investigation provide an experimental basis for adequately selecting a compression ratio in SCDI engines.&lt;/div&gt;
Vitamin K-dependent gamma-carbon-hydrogen bond cleavage and nonmandatory concurrent carboxylation of peptide-bound glutamic acid residues. (1979)

The pentapeptide Phe-Leu-Glu-Glu-Leu, tritiated at the gamma carbon of each Glu residue, has been synthesized. In a system using microsomal preparations derived from rat liver, vitamin K-dependent tritium release from the L-Glu residues of this substrate can occur without the concurrent gamma-carboxylation of Glu. This tritium release reaction, which indicates cleavage of the gamma C-H bond, although easily uncoupled from CO2-dependent gamma C carboxylation, does require the reduced (hydroquinone) form of vitamin K and oxygen. The data argue against a concerted mechanism for the cleavage of the gamma C-H bond and carboxylation and against a mechanism in which the vitamin functions solely to transfer or activate CO2. Although the tritium release is related clearly to the oxidation of vitamin KH2, it is not yet established how the subsequent carboxylation proceeds. However, two carboxylation mechanisms compatible with the results are discussed.
Expression and function of MIP‐2 are reduced by dexamethasone treatment in vivo (2000)

1. The objective of this study was to examine the effect of dexamethasone on tumour necrosis factor-alpha (TNF-alpha)-induced expression and function of macrophage inflammatory protein-2 (MIP-2) and neutrophil recruitment. For this purpose, we used air pouches raised on the dorsal skin of C57/B16 mice. 2. Initially, we examined the dose-response (0.01 - 0.5 microg ml(-1)) and kinetics (0 - 24 h) of TNF-alpha-induced leukocyte accumulation. The cellular response was maximal at 0.1 microg ml(-1) of TNF-alpha and 4 h after challenge and comprised more than 90% neutrophils. 3. Intraperitoneal (i.p.) pretreatment with 10 mg kg(-1) of dexamethasone for 2 h, but not 1 mg kg(-1), reduced TNF-alpha-induced recruitment of neutrophils by 87%. Administration of dexamethasone had no effect on the expression of CD18 on neutrophils. 4. TNF-alpha (0.1 microg ml(-1)) markedly increased the levels of MIP-2 in the air pouches 1 h after challenge and after 4 h the MIP-2 values returned to baseline. Notably, 2 h pretreatment with dexamethasone (10 mg kg(-1), i.p.) reduced MIP-2 expression by 65% in response to TNF-alpha (0.1 microg ml(-1)). On the other hand, dexamethasone treatment did not change the levels of interleukin-10 (IL-10) in the pouch exudate. 5. Administration of recombinant MIP-2 increased neutrophil accumulation at 0.5 and 1.0 microg ml(-1) after 4 h of challenge. Dexamethasone pretreatment for 2 h (10 mg kg(-1), i.p.) abolished the MIP-2-induced recruitment of neutrophils. 6. Taken together, our data demonstrate that dexamethasone may downregulate TNF-alpha-induced neutrophil recruitment by inhibiting both the expression and function of MIP-2 in vivo.
Alternative splicing of SLAMF6 in human T cells creates a co-stimulatory isoform that counteracts the inhibitory effect of the full-length receptor (2020)

ABSTRACT SLAMF6 is a homotypic receptor of the Ig-superfamily associated with progenitor exhausted T cells. In humans, SLAMF6 has three splice isoforms involving its V-domain. While the canonical 8-exon receptor inhibits T cell activation through SAP recruitment, the short isoform SLAMF6 Δ17-65 has a strong agonistic effect. The costimulatory action depends on protein phosphatase SHP-1 and leads to a cytotoxic molecular profile governed by transcription factors Tbet, Runx3, and Tcf7. In T cells from individual patients treated with immune checkpoint blockade, a shift was noted towards SLAMF6 Δ17-65 . Splice-switching antisense oligonucleotides designed to target the SLAMF6 splice junction, enhanced SLAMF6 Δ17-65 in human tumor-infiltrating lymphocytes and improved their capacity to inhibit human melanoma in mice. The possible emergence of two opposing isoforms from the SLAMF6 gene may represent an immune-modulatory mechanism that can be exploited for cancer immunotherapy.
Specific Photocleavage Activity of N ‐Methylmesoporphyrin IX on G‐Quadruplex DNA Structures (2019)

G‐rich regions, at which G‐quadruplexes (G4) are proposed to form, are associated with promoter regions within proto‐oncogenes and may play a role in cell proliferation and carcinogenesis. The ability to identify the formation of G4 structures in these regions, including the temporal aspects of G‐quadruplex formation, is essential to establish the role of these structures in transcriptional regulation. We have focused on identifying highly selective G4 photocleavage agents as molecular probes for establishing the location and timing of G4 formation. N ‐methylmesoporphyrin IX (NMM) has long been known as a G4 ligand; however, there has been little investigation into its DNA photocleavage activity. Here we report the ability of NMM to act as a highly selective photocleavage agent for specific G4 structures. We first studied the interaction of NMM with the G4 structures formed by DNA oligonucleotides containing the c‐MYC promoter or human telomeric (hTel) sequences formed in the presence of either Na + or K + ‐containing buffers using a FRET‐based Tm assay and CD spectroscopy. We employed a fluorescence‐based solution assay for G4 cleavage to establish that NMM effects photocleavage (420 nm) of c‐MYC more efficiently than the hTel G4 under both Na + and K + conditions, and effects photocleavage of c‐MYC G4 even under white light irradiation. Using denaturing polyacrylamide gel electrophoresis (PAGE), we confirmed this selective photocleavage and demonstrate that cleavage occurs at specific guanine residues of the c‐MYC G4. In order to determine if the photocleavage proceeds through the generation of reactive oxygen species like singlet oxygen, we carried out photocleavage reactions in the presence of H 2 O and D 2 O, and employed a turn‐on fluorescent singlet oxygen sensor to detect 1 O 2 generation. We find that NMM acts to destabilize specific G4 topologies, but oligonucleotides annealed in the presence of NMM form alternative topologies that are thermally stabilized. NMM photocleavage is highly selective for G4 DNA versus duplex DNA, and the K + ‐stabilized c‐MYC G4 is preferentially cleaved compared to the Na + ‐stabilized structure and the hTel G4 in either Na + or K + . PAGE analysis indicates that NMM photocleavage of c‐MYC G4 occurs preferentially at the 3′ G‐tetrad residues. This photocleavage does not appear to be due to 1 O 2 . These results indicate that NMM may be a useful tool for elucidating the role of promoter G‐quadruplex structures. Support or Funding Information Support for this work by the Cancer Prevention and Research Institute of Texas (RP160852) and Texas State University is gratefully acknowledged. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Analytical surrogate model for the aberrations of an arbitrary GRIN lens (2016)

Current analytical expressions between Gradient-Index (GRIN) lens parameters and optical aberrations are limited to paraxial approximations, which are not suitable for realizing GRIN lenses with wide fields of view or small f-numbers. Here, an analytical surrogate model of an arbitrary GRIN lens ray-trace evaluation is formulated using multivariate polynomial regressions to correlate input GRIN lens parameters with output Zernike coefficients, without the need for approximations. The time needed to compute the resulting surrogate model is over one order-of-magnitude faster than traditional ray trace simulations with very little losses in accuracy, which can enable previously infeasible design studies to be completed.
Efficiency of Cell-Free and Cell-Associated Virus in Mucosal Transmission of Human Immunodeficiency Virus Type 1 and Simian Immunodeficiency Virus (2013)

Effective strategies are needed to block mucosal transmission of human immunodeficiency virus type 1 (HIV-1). Here, we address a crucial question in HIV-1 pathogenesis: whether infected donor mononuclear cells or cell-free virus plays the more important role in initiating mucosal infection by HIV-1. This distinction is critical, as effective strategies for blocking cell-free and cell-associated virus transmission may be different. We describe a novel ex vivo model system that utilizes sealed human colonic mucosa explants and demonstrate in both the ex vivo model and in vivo using the rectal challenge model in rhesus monkeys that HIV-1-infected lymphocytes can transmit infection across the mucosa more efficiently than cell-free virus. These findings may have significant implications for our understanding of the pathogenesis of mucosal transmission of HIV-1 and for the development of strategies to prevent HIV-1 transmission.
Sequential analysis of hematopoietic reconstitution achieved by transplantation of hematopoietic stem cells (1993)

We confirmed that murine hematopoietic stem cells express the c-kit molecule but not lymphohematopoietic lineage markers. These lineage marker-negative c-kit-positive (Lin- c-kit+) cells were further divided according to the uptake of rhodamine-123 (Rh-123). Approximately 1,000 Lin- c-kit+ rhodamine-123dull cells, which contained 4.0 +/- 1.3 and 12.5 +/- 1.9 day 8 and day 12 spleen colony-forming units (CFU-S), respectively, rescued the 100% of lethally irradiated mice. One third of these cells formed colonies in the presence of interleukin-3 plus erythropoietin. The time course of the hematopoietic reconstitution of this primitive hematopoietic stem cell fraction was investigated by using Ly-5 congenic mice. Although myeloid cells and B lymphocytes were detected in the peripheral blood 2 to 3 weeks after transplantation, T lymphocytes were not detected until 4 weeks after transplantation. It is generally assumed that myeloid cells and B lymphocytes grow in the bone marrow and that T lymphocytes must pass through the thymus. For the first 2 to 3 weeks after transplantation, donor-type T lymphocytes were not dominant in the thymus, and most donor type cells were CD4/CD8 double-negative or double-positive (including CD4low and CD8low). Four weeks after transplantation, donor-type T lymphocytes were dominant and the ratio of CD4/CD8 cells had recovered to the normal pattern. However, significant numbers of T lymphocytes were detected in the peripheral blood at this stage. Sequential analysis of hematopoietic reconstitution from primitive stem cells demonstrates that myeloid and B-lymphoid lineages occurred earlier than that of the T-lymphoid lineages.
HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes (2020)

Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of hundreds of chosen genes in single cells. HyPR-seq involves hybridizing DNA probes to RNA, distributing cells into nanoliter droplets, amplifying the probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell-type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome single-cell RNA-sequencing, making HyPR-seq a powerful method for targeted RNA profiling in single cells.
Inferring direction of associations between histone modifications using a neural processes-based framework (2022)

Current technologies do not allow predicting interactions between histone post-translational modifications (HPTMs) at a system-level. We describe a computational framework, imputation-followed-by-inference, to predict directed association between two HPTMs using EpiTOF, a mass cytometry-based platform that allows profiling multiple HPTMs at a single-cell resolution. Using EpiTOF profiles of >55,000,000 peripheral mononuclear blood cells from 158 healthy human subjects, we show that neural processes (NP) have significantly higher accuracy than linear regression and <i>k-</i>nearest neighbors models to impute the abundance of an HPTM. Next, we infer the direction of association to show we recapitulate known HPTM associations and identify several previously unidentified ones in healthy individuals. Using this framework in an influenza vaccine cohort, we identify changes in associations between 6 pairs of HPTMs 30 days following vaccination, of which several have been shown to be involved in innate memory. These results demonstrate the utility of our framework in identifying directed interactions between HPTMs.
DNA-Vaccine-Induced Immune Response Correlates with Lower Viral SARS-CoV-2 Titers in a Ferret Model (2022)

The COVID-19 pandemic is entering a new era with the approval of many SARS-CoV-2 vaccines. In spite of the restoration of an almost normal way of life thanks to the immune protection elicited by these innovative vaccines, we are still facing high viral circulation, with a significant number of deaths. To further explore alternative vaccination platforms, we developed COVID-eVax—a genetic vaccine based on plasmid DNA encoding the RBD domain of the SARS-CoV-2 spike protein. Here, we describe the correlation between immune responses and the evolution of viral infection in ferrets infected with the live virus. We demonstrate COVID-eVax immunogenicity as means of antibody response and, above all, a significant T-cell response, thus proving the critical role of T-cell immunity, in addition to the neutralizing antibody activity, in controlling viral spread.
Development of Three-dimensional Hot Bending and Direct Quench Technology (2014)

The basic properties of Three-Dimensional Hot Bending and Direct Quench (3DQ), especially the property of bending force were researched. The tensile strength of the product reaches 1470 MPa, and the energy absorption in crash test increases by applying partial quenching. In this report, the basic properties of Three-Dimensional Hot Bending and Direct Quench (3DQ), specially the property of bending force, are introduced. In addition, mass production system using robot and features of products are introduced.
Observations of quantum dynamics by solution‐state NMR spectroscopy (1999)

NMR is emerging as a valuable testbed for the investigation of foundational questions in quantum mechanics.The present paper outlines the preparation of a class of mixed states, called pseudo-pure states, that emulate pure quantum states in the highly mixed environment typically used to describe solution-state NMR samples.It also describes the NMR observation of spinor behavior in spin 1/2 nuclei, the simulation of wave function collapse using a magnetic field gradient, the creation of entangled (or Bell) pseudo-pure states, and a brief discussion of quantum computing logic gates, including the Quantum Fourier Transform.These experiments show that liquid-state NMR can be used to demonstrate quantum dynamics at a level suitable for laboratory exercises.
ChemInform Abstract: A Ca2+‐Mobilizing Carbohydrate‐Based Polyphosphate: Synthesis of 2‐ Hydroxyethyl α‐D‐Glucopyranoside 2′,3,4‐Trisphosphate. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Imprints of Earth Transmission on Seismic Reflections (2013)

Broadband seismic acquisition and advances in amplitude preserving processing have driven the industry toward pre-stack reflection amplitudes that are proportional to the earth’s subsurface reflectivity; resulting in improved drilling success rates and increased production. The amplitude and phase of a reflection is a function of spreading loss, inelastic attenuation, interbed multiples and transmission loss interacting with the spatial distribution of elastic (Vp, Vs, anisotropy and density) and inelastic (Qp, Qs) earth properties. Effective Qp (absorption plus scattering) for near-surface layers is on the order of 5-10 (Mangriotis, et al., 2013) and typically increases with depth to 50-130 for water saturated sediments. Vertical and wide-angle scattering can reduce amplitudes by factors of 2 to 3. Taken together these effects can alter absolute amplitudes by factors of 50 and relative event amplitudes vs. offset by factors of 0.3 to 3.
Cell-Specific Expression of Genes of the Lipid Transfer Protein Family from Arabidopsis thaliana (1999)

We have characterized three cDNAs from a gene family encoding lipid transfer proteins, LTP, from Arabidopsis thaliana (Wassilewskija). In addition to the already characterized Ltp1, our analysis includes Ltp2 and Ltp3, two sequences previously known as expressed sequence tags (EST) only. The deduced amino acid sequences of the three cDNAs share 56 to 57% identity and show unique tissue- and cell-specific expression. Genes Ltp1 and LTp2 are located within approximately 1.4 kb of each other in tandem orientation. RNA hydridizations showed that all three LTP are expressed in flowering meristems, flowers and developing seeds. Ltp1 is expressed in leaves in addition. Ltp3, though not Ltp2, is also expressed in a short segment of the stem close to the flowering meristem. In contrast to the epidermis-specific Ltp1, both Ltp2 and Ltp3 are not restricted to the epidermis, but are also expressed in sub-epidermal layers of the organs in which they are found. In the upper stem segment, Ltp3 is predominantly cortical. It appears that the expression of these three cDNAs is sufficient to account for the formation of LTP in all meristematic and expanding cells of the aboveground plant. Evolutionary analysis allows the conclusion that each Ltp belongs to a different sub-family of genes. Additionally, parsimony analysis provides evidence that several copies of Ltp genes already existed in ancestors of the Brassicaceae family.