gebhart/patrepeval huggingface dataset:
69 Phosphorylation of mechanistic target of rapamycin in porcine blastocyst-stage embryos is dependent on the concentration of glutamine in the medium (2019)

Supplementation of glutamine to porcine embryo culture medium improves blastocyst development, increases leucine consumption, and enhances mitochondrial activity. In cancer cells, glutamine has been implicated in the phosphorylation and activation of mechanistic target of rapamycin (MTOR) to support rapid cellular proliferation. The objective of this study was to determine if phosphorylation of MTOR in porcine blastocysts was dependent upon the concentration of glutamine in the medium and presence of leucine, another activator of MTOR. Presumptive zygotes (n = 732 per treatment across 6 replicates) were split into four groups and cultured in 0, 1, 3.75, or 10 mM GlutaMAX, an L-glutamine alternative, with or without 0.2 mM leucine. On Day 6, percentages of embryos developed to the blastocyst stage were recorded. Blastocyst-stage embryos (n = 100 per treatment) were collected for immunoblotting to detect total MTOR and phosphorylated (Ser2448) MTOR (pMTOR) with 3 replicates per target. To assess MTOR and lysosomal colocalization as another indicator of MTOR activation, blastocyst-stage embryos (n = 15 per treatment) were fixed, probed with antibodies against MTOR and lysosomal associated membrane protein 1 (LAMP1), and imaged on a confocal microscope. Data were analysed by using the GLM procedure in SAS 9.4 (SAS Institute Inc.), and differences between means were detected by using one-way ANOVA followed by a least significant difference test with P &amp;lt; 0.05 declared significant. Compared with the other treatments, culture in 0 mM GlutaMAX resulted in decreased blastocyst development with (26.2 ± 4.8%) or without (23.2 ± 3.0%) leucine. Embryos cultured in 3.75 mM GlutaMAX had increased development to the blastocyst stage (+Leu: 49.7 ± 4.2%; −Leu: 46.2 ± 2.6%) compared with culture in 1 mM (+Leu: 39.5 ± 3.5%; −Leu: 37.8 ± 2.1%). In the presence of leucine, culture in 0 mM GlutaMAX resulted in decreased pMTOR abundance compared with 3.75 or 10 mM GlutaMAX. In the absence of leucine, embryos cultured in 0 mM GlutaMAX had decreased abundance of total MTOR compared with all other groups, and pMTOR abundance was decreased in embryos cultured in 0 or 1 mM compared with 3.75 or 10 mM GlutaMAX. Furthermore, embryos cultured in 0 mM GlutaMAX had decreased colocalization of MTOR and LAMP1 compared with those cultured in 3.75 or 10 mM GlutaMAX. Therefore, glutamine supplementation is sufficient to prompt MTOR phosphorylation in porcine embryos. Further analyses are examining the phosphorylation status of MTOR downstream targets and effects of inhibiting enzymes involved in glutaminolysis. Funding was provided by the United States Department of Agriculture, National Institute of Food and Agriculture (2019-67011-29543) and Food for the 21st Century at the University of Missouri.
Experiment investigation of sampling point selection in fractional sampling OFDM receiver (2009)

In the IEEE802.11a WLAN standard, orthogonal frequency division multiplexing (OFDM) modulation is employed. Diversity techniques are usually utilized to overcome fading channels in OFDM system. Furthermore, a diversity with a single antenna is desirable because the form factor of the terminal is important. Fractional sampling( FS) scheme is one of the diversity technique with a single antenna. Through FS, it is possible to separate multipath components and obtain diversity gain in OFDM communication. In this paper, a novel sampling point selection scheme according to the frequency response of a channel is proposed. Through the experiment the performance of the FS scheme on a IEEE802.11a WLAN system, it is evaluated. Numerical results through the experiment indicate that sampling point selection scheme according to the frequency response of a channel can achieve path diversity.
Photon Paths in Turbid Media: From Smooth to Random (1996)

The path integral formalism is applied to photon migration in turbid media. Our solution spans the range from low diffusive to highly diffusive photons.
LIC-Fusion 2.0: LiDAR-Inertial-Camera Odometry with Sliding-Window Plane-Feature Tracking (2020)

Multi-sensor fusion of multi-modal measurements from commodity inertial, visual and LiDAR sensors to provide robust and accurate 6DOF pose estimation holds great potential in robotics and beyond. In this paper, building upon our prior work (i.e., LIC-Fusion), we develop a sliding-window filter based LiDAR-Inertial-Camera odometry with online spatiotemporal calibration (i.e., LIC-Fusion 2.0), which introduces a novel sliding-window plane-feature tracking for efficiently processing 3D LiDAR point clouds. In particular, after motion compensation for LiDAR points by leveraging IMU data, low-curvature planar points are extracted and tracked across the sliding window. A novel outlier rejection criteria is proposed in the plane-feature tracking for high quality data association. Only the tracked planar points belonging to the same plane will be used for plane initialization, which makes the plane extraction efficient and robust. Moreover, we perform the observability analysis for the IMU-LiDAR subsystem under consideration and report the degenerate cases for spatiotemporal calibration using plane features. While the estimation consistency and identified degenerate motions are validated in Monte-Carlo simulations, different real-world experiments are also conducted to show that the proposed LIC-Fusion 2.0 outperforms its predecessor and other state-of-the-art methods.
Winnability Prediction for IT Services Bids (2019)

Different service providers compete to win highly valued IT service contracts in a lengthy tender bidding process. These multimillion-dollar deals are complex in both solution design and service delivery. A successful bidding outcome does not solely depend on pricing. Hence, we experiment on a selection of deal factors that play critical roles in winning a deal. In this paper, we describe two machine learning models that use structured data to predict the bidding outcome of sales opportunities.
DNA index and S-phase fraction and their combination as prognostic factors in operable ductal breast carcinoma (1990)

The prognostic significance of DNA ploidy, DNA index (DI), and S-phase fraction (SPF) and their various combinations were studied together with 16 other clinicopathologic factors in 222 patients with operable invasive ductal breast carcinoma. The patients have been followed for a minimum of 22 years after the diagnosis or until death. Nuclear DNA content was determined by flow cytometry from paraffin-embedded tissue. Patients with DNA diploid cancer (n = 57, 26%) had better survival rate corrected for intercurrent deaths than patients with nondiploid cancer (P = 0.002), and also, a small SPF (less than or equal to 14%, calculated in 134 cases) was associated with a favorable outcome in a univariate analysis (P = 0.01). The prognostic value of the DI and SPF was increased if they were combined. The most effective combination was obtained if diploid cancers were grouped together with DNA aneuploid cancers with a DI less than 2.1 and an SPF less than 14%. This combination had considerable prognostic value in a univariate analysis (P = 0.0002) and had independent prognostic value (P = 0.04) in Cox's multivariate analysis together with the primary tumor size (P less than 0.001) in axillary node negative patients but not in axillary node positive patients. In the whole series the presence of axillary nodal metastases (P less than 0.001), high mitotic count (P less than 0.001), a large primary tumor size (P = 0.001), poorly circumscribed tumor margin (P = 0.005), and slight or absent tubule formation (P = 0.05) were the only independent prognostic factors in a multivariate analysis.
“Reverse-Schur” Approach to Optimization with Linear PDE Constraints: Application to Biomolecule Analysis and Design (2009)

We present a partial-differential-equation (PDE)-constrained approach for optimizing a molecule's electrostatic interactions with a target molecule. The approach, which we call reverse-Schur co-optimization, can be more than two orders of magnitude faster than the traditional approach to electrostatic optimization. The efficiency of the co-optimization approach may enhance the value of electrostatic optimization for ligand-design efforts-in such projects, it is often desirable to screen many candidate ligands for their viability, and the optimization of electrostatic interactions can improve ligand binding affinity and specificity. The theoretical basis for electrostatic optimization derives from linear-response theory, most commonly continuum models, and simple assumptions about molecular binding processes. Although the theory has been used successfully to study a wide variety of molecular binding events, its implications have not yet been fully explored, in part due to the computational expense associated with the optimization. The co-optimization algorithm achieves improved performance by solving the optimization and electrostatic simulation problems simultaneously, and is applicable to both unconstrained and constrained optimization problems. Reverse-Schur co-optimization resembles other well-known techniques for solving optimization problems with PDE constraints. Model problems as well as realistic examples validate the reverse-Schur method, and demonstrate that our technique and alternative PDE-constrained methods scale very favorably compared to the standard approach. Regularization, which ordinarily requires an explicit representation of the objective function, can be included using an approximate Hessian calculated using the new BIBEE/P (boundary-integral-based electrostatics estimation by preconditioning) method.
beta2-Microglobulin mutations, HLA class I antigen loss, and tumor progression in melanoma. (1998)

The potential negative impact of HLA class I antigen abnormalities on the outcome of T cell-based immunotherapy of melanoma has prompted us to investigate the mechanisms underlying lack of HLA class I antigen expression by melanoma cell lines Me18105, Me9923, and Me1386. Distinct mutations in the beta2-microglobulin (beta2m) gene were identified in each cell line which result in loss of functional beta2m. In Me18105 cells, an aberrant splicing mechanism caused by an A--> G point mutation in the splice acceptor site of intron 1 of the beta2m gene, deletes 11 bp from the beta2m mRNA creating a shift in the reading frame. In Me9923 cells a 14-bp deletion in exon 2 and in Me1386 cells a CT deletion in exon 1 of the beta2m gene produce a frameshift mutation. The beta2m gene mutations identified in Me18105, Me9923, and Me1386 cells were also detected in the surgically removed melanoma lesions from which the cell lines originated. Transfection of each melanoma cell line with a wild-type beta2m gene restored HLA class I antigen expression and, in Me18105 cells, recognition by Melan-A/MART-1-specific, HLA-A2-restricted cytotoxic T lymphocytes. Interestingly, the beta2m mutation present in Me9923 cells that were derived from a metastatic lesion was also found in the Me9923P cell line that originated from the autologous primary lesion. These data suggest that beta2m mutations in melanoma cells may be an early event in progression to the malignant phenotype.
On tuning the cytotoxicity of Ti3C2 (MXene) flakes to cancerous and benign cells by post-delamination surface modifications (2020)

Abstract Despite intensive research on the application of two-dimensional (2D) materials, including MXenes, in nanomedicine, the knowledge concerning the mechanisms responsible for their observed bio-effects is far from being understood. Here we present insight into the mechanism of toxicity in vitro of the 2D Ti 3 C 2 MXene. The most important results of this work are that using simple, inexpensive, post-delamination treatments, such as ultrasonication or mild thermal oxidation it is possible to ‘tune’ the cytotoxicity of the Ti 3 C 2 T z flakes. Sonication of Ti 3 C 2 T z flakes, or sonication followed by mild oxidation in the water at 60 °C, renders them selectively toxic to cancer cells as compared to non-malignant ones. It relates to the appearance of superficial titanium (III) oxide (Ti 2 O 3 ) layer corresponding to the type of post-treatment. The presence of surface-Ti 2 O 3 results in a noticeably higher generation of oxidative stress compared to pristine 2D Ti 3 C 2 . Our findings give evidence that the sonication and thermal treatments were successful in changing the nature of the surface terminations on the Ti 3 C 2 T z surfaces. This study makes a significant contribution to the future rationalized surface-management of 2D Ti 3 C 2 MXene as well as encourages new rationalized applications in biotechnology and nanomedicine. Bullet points: 1. First study on 2D Ti 3 C 2 MXene superficially oxidized to titanium (III) oxide i.e. Ti 2 O 3 . 2. By sonication Ti 3 C 2 Tz MXene flakes followed by mild thermal oxidation in the water at 60 °C for 24 h, it is possible to ‘tune’ the toxicity of the flakes to cancerous cell lines. 3. Decreases in cell viabilities were dose-dependent. 4. Highest cytotoxic effect was observed for thermally oxidized samples. 5. The thermally oxidized samples were also selectively toxic towards all cancerous cell lines up to 375 mg l −1 . 6. Reactive oxygen species generation was identified as a mechanism of toxicity.
Alkyne Complexes of Tungsten(IV) (1983)

Abstract The complete manuscript of this communication appears in: Angew. Chem. Suppl. 1983 , 1409. DOI: 10.1002/anie.198314090
Resist Patterning Characteristics using KrF Laser-ablation Process (2019)

The patterning characteristics of a variety of resist material platforms were investigated using a KrF laser ablation process. The results showed that a fullerene-based resist material with a 170-nm film thickness is capable of sub-micron resolution up to 0.8 μm 1:1 lines and spaces (L/S). Moreover, using a novolac-based resist material, the dependence of laser ablation patterning performance on the resist process conditions was determined. An increase in the total exposure energy (exposure energy per pass × total number of passes) is necessary as the film thickness increases. Moreover, using the same novolac-based resist material fixed at a 5-μm film thickness, results suggested that exposure energy has a more significant impact on the effective formation of laser ablation patterns (compared to number of exposure passes). Finally, preliminary investigations using a metal resist (at a 90-nm film thickness) resulted in resolution capabilities up to 2 μm 1:1 L/S at a relatively lower total exposure energy. This showed the potential of the metal resist material for application in laser ablation patterning.
Catalyseurs Ziegler‐Natta supportés sur MgCl2 pour la polymérisation du propène. I. Etude de la réaction entre le triéthylaluminium et le benzoate d'ethyle (1984)

Abstract In this article we describe a study of the reaction between triethylaluminium (TEA) and ethylbenzoate (BE) in a heptane solution by Fourier transform, infrared (IR), and ultraviolet (UV) spectroscopy. These compounds were chosen as a model of the cocatalytic solution used with a Ziegler‐Natta catalyst supported on MgCl 2 for the stereospecific polymerization of propene. In the polymerization concentration range a 2 TEA:1 BE yellow complex was added to the solution and no free BE could be detected at a AI/BE molar ratio above 2: the solution contained only free and complexed TEA. The complex decomposed spontaneously to a colorless aluminium alcoholate. The rate of decomposition remained slow at room temperature and the reaction was enhanced by heating or by a high AI/BE ratio or high AI concentration. The decomposition was inhibited in the presence of an olefin.
The Acoustic Lever Loudspeaker Enclosure (1999)

A new form of loudspeaker enclosure design is presented which is based on a concept that the author calls Acoustic Lever. The basic design approach is illustrated along with some examples for two types of systems-a single Acoustic Lever and a double Acoustic Lever.
The relationship between cardiac output and posthyperventilation hyperpnoea in patients with essential hypertension (1998)

Posthyperventilation hyperpnoea (PHVH) is the progressive decline in minute ventilation (V'E) that follows abrupt cessation of voluntary hyperventilation. It has been hypothesized that the increase in cardiac output (CO) during hyperventilation could contribute to the duration of PHVH. This hypothesis was tested by measuring the duration of PHVH in patients with essential hypertension, in whom the increase in CO as a result of various stimuli is less pronounced. Twenty male hypertensives (mean arterial blood pressure+/-SEM: 178/ 107+/-3/1 mmHg), and 12 age-matched male healthy subjects were studied. The study consisted of three periods: control (5 min), voluntary hyperventilation (2 min), and recovery (3 min). V'E, CO, end-tidal CO2 and O2 tensions were measured, and the time constant (tau) of the V'E decay during recovery calculated. The V'E decay was faster in hypertensives (tau: 0-8.4 s) than in healthy subjects (tau: 12-59 s; p<0.01). During voluntary hyperventilation, CO increased to a lesser extent in hypertensives (6.8+0.7 L.min(-1)) than in healthy subjects (12.9+/-1.1 L.min(-1); p<0.01). In hypertensives, changes in CO during voluntary hyperventilation were significantly related to tau (r=0.646; n=20; p=0.002). The less pronounced rise in cardiac output during hyperventilation in hypertensives could account for the shorter duration of posthyperventilation hyperpnoea.
Data from Intratumoral Induction of CD103 Triggers Tumor-Specific CTL Function and CCR5-Dependent T-Cell Retention (2023)

&lt;div&gt;Abstract&lt;p&gt;We have reported previously that the interaction of α&lt;sub&gt;E&lt;/sub&gt;(CD103)β&lt;sub&gt;7&lt;/sub&gt; integrin, expressed on a CD8&lt;sup&gt;+&lt;/sup&gt; tumor-infiltrating lymphocyte (TIL) clone but not on a peripheral blood lymphocyte (PBL) counterpart, with the epithelial marker E-cadherin on human lung tumor cells plays a crucial role in T-cell receptor–mediated cytotoxicity. We show here that both TIL and PBL clones are able to migrate toward autologous tumor cells and that chemokine receptor CCR5 is involved in this process. Adoptive transfer of the PBL clone in the cognate tumor engrafted in nonobese diabetic/severe combined immunodeficient mice and subsequent coengagement of T-cell receptor and transforming growth factor-β1 receptor triggers CD103 expression on T-cell surface resulting in strong potentiation of antitumor lytic function. Moreover, interaction of α&lt;sub&gt;E&lt;/sub&gt;β&lt;sub&gt;7&lt;/sub&gt; integrin with E-cadherin, but not lymphocyte function-associated antigen-1 with intercellular adhesion molecule-1, promotes CCR5 recruitment at the immunologic synapse formed between TIL and tumor cells, leading to inhibition of T-cell sensitivity to CCL5 chemotactic gradient. These results provide evidence for a role of tumor microenvironment, namely MHC class I–restricted antigen presentation and transforming growth factor-β1 secretion, in regulating the effector phase of tumor-specific CTL response. They also suggest a unique role of CD103 in T-cell retention at the tumor site by a CCR5-dependent mechanism. [Cancer Res 2009;69(15):6249–55]&lt;/p&gt;&lt;/div&gt;
Inside Cover: Fluorescent Nanowires Self‐Assembled through Host–Guest Interactions in Modified Calcein (Angew. Chem. Int. Ed. 32/2011) (2011)

Highly fluorescent nanowires self-assemble by host–guest interactions of cyclodextrin- and adamantane-modified calcein in aqueous solution. In their Communication on page 7407 ff., H. Ritter and co-workers show by transmission electron and scanning electron microscopy that the combination of these modified fluorescent dyes resulted in wires of several micrometers, which will find applications in microbiology.
Examination of the Effect of the Annealing Cation on Higher Order Structures Containing Guanine or Isoguanine Repeats (2009)

Isoguanine (2-oxo-6-amino-guanine), a natural but non-standard base, exhibits unique self-association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. The guanine-containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI-MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads.
Self-assembling elastin-like peptides growth factor chimeric nanoparticles for the treatment of chronic wounds (2010)

Chronic wounds are associated with poor epidermal and dermal remodeling. Previous work has shown the efficacy of keratinocyte growth factor (KGF) in reepithelialization and elastin in dermal wound healing. Here we demonstrate the fabrication of a fusion protein comprising of elastin-like peptides and KGF. This fusion protein retains the performance characteristics of KGF and elastin as evidenced by its enhancement of keratinocyte and fibroblast proliferation. It also preserved the characteristic elastin-like peptides inverse phase transitioning allowing the recombinant protein to be expressed in bacterial hosts (such as Escherichia coli) and purified rapidly and easily using inverse temperature cycling. The fusion protein self-assembled into nanoparticles at physiological temperatures. When applied to full thickness, wounds in Lepr(db) diabetic mice these particles enhanced reepithelialization and granulation, by 2- and 3-fold respectively, when compared to the controls. The data strongly suggests that these self-assembled nanoparticles may be beneficial in the treatment of chronic wounds resulting from diabetes or other underlying circulatory conditions.
A Synthetic Approach to a Peptide α‐Thioester from an Unprotected Peptide through Cleavage and Activation of a Specific Peptide Bond by N‐Acetylguanidine (2011)

Ein anderer Weg zu Peptid-α-thioestern führt über die Peptidbindungsspaltung an einem Cysteinrest durch S-Thiocarbonylierung und die anschließende Behandlung mit N-Acetylguanidin. Das erhaltende Peptidyl-N-acetylguanidin kann in den entsprechenden α-Thioester überführt oder als Alternative zu einem Peptid-α-Thioester verwendet werden. Diese Methode ermöglicht eine effiziente kinetisch kontrollierte Ligation in Gegenwart von Thiolen. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.