gebhart/patrepeval huggingface dataset:
DFMO and 5-Azacytidine Increase M1 Macrophages in the Tumor Microenvironment of Murine Ovarian Cancer (2019)

Although ovarian cancer has a low incidence rate, it remains the most deadly gynecologic malignancy. Previous work has demonstrated that the DNMTi 5-Azacytidine (5AZA-C) activates type I interferon signaling to increase IFNγ<sup>+</sup> T cells and natural killer (NK) cells and reduce the percentage of macrophages in the tumor microenvironment. To improve the efficacy of epigenetic therapy, we hypothesized that the addition of α-difluoromethylornithine (DFMO), an ornithine decarboxylase inhibitor, may further decrease immunosuppressive cell populations improving outcome. We tested this hypothesis in an immunocompetent mouse model for ovarian cancer and found that <i>in vivo</i>, 5AZA-C and DFMO, either alone or in combination, significantly increased survival, decreased tumor burden, and caused recruitment of activated (IFNγ<sup>+</sup>) CD4<sup>+</sup> T cells, CD8<sup>+</sup> T cells, and NK cells. The combination therapy had a striking increase in survival when compared with single-agent treatment, despite a smaller difference in recruited lymphocytes. Instead, combination therapy led to a significant decrease in immunosuppressive cells such as M2 polarized macrophages and an increase in tumor-killing M1 macrophages. In this model, depletion of macrophages with a CSF1R-blocking antibody reduced the efficacy of 5AZA-C + DFMO treatment and resulted in fewer M1 macrophages in the tumor microenvironment. These observations suggest our novel combination therapy modifies macrophage polarization in the tumor microenvironment, recruiting M1 macrophages and prolonging survival. SIGNIFICANCE: Combined epigenetic and polyamine-reducing therapy stimulates M1 macrophage polarization in the tumor microenvironment of an ovarian cancer mouse model, resulting in decreased tumor burden and prolonged survival.
Overcoming the Manley-Rowe Limit for CW Terahertz Generation in Q-Engineered Multimodal Cavity (2021)

We present a method to overcome the Manley-Rowe limit in a Q -factor engineered multimodal nonlinear cavity. Cascading nonlinear processes enable continuous-wave terahertz generation with a theoretical conversion efficiency of 98.8%.
Tranylcypromine and an N-Cyanoethyl Analogue: Effects on Brain Levels of the Trace Amines β-Phenylethylamine and Tryptamine (1985)

Imbalances in the neuronal homeostasis of the trace amines β-phenylethylamine (PE) and tryptamine (T) have been implicated in the aetiology of certain neuropsychiatry disorders, including depression (Dewhurst, 1984 for review). Tranylcypromine (TCP), a monoamine oxidase (MAO) inhibitor used clinically as an antidepressant, has been shown to elevate substantially brain concentrations of these trace amines (Philips and Boulton, 1979). A number of N-alkylated derivatives of TCP have been synthesized in our laboratories to test them as potential prodrugs of TCP. The prodrug N-(2-cyanoethyl)tranylcypromine (CE-TCP) was found to be a potent MAO inhibitor in its own right (Baker et al., 1984). A neurochemical study is now reported in which the effects of TCP and CE-TCP on brain levels of the trace amines PE and T are compared.
ChemInform Abstract: Photochemistry of 1,5‐Hexadien‐3‐ones: Wavelength‐Dependent Selectivity in Intramolecular Enone‐Olefin Photoadditions. (1991)

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.
Metabolomics View on Gut Microbiome Modulation by Polyphenol-rich Foods (2012)

Health is influenced by genetic, lifestyle, and diet determinants; therefore, nutrition plays an essential role in health management. Still, the substantiation of nutritional health benefits is challenged by the intrinsic macro- and micronutrient complexity of foods and individual responses. Evidence of healthy effects of food requires new strategies not only to stratify populations according to their metabolic requirements but also to predict and measure individual responses to dietary intakes. The influence of the gut microbiome and its interaction with the host is pivotal to understand nutrition and metabolism. Thus, the modulation of the gut microbiome composition by alteration of food habits has potentialities in health improvement or even disease prevention. Dietary polyphenols are naturally occurring constituents in vegetables and fruits, including coffee and cocoa. They are commonly associated to health benefits, although mechanistic evidence in vivo is not yet fully understood. Polyphenols are extensively metabolized by gut bacteria into a complex series of end-products that support a significant effect on the functional ecology of symbiotic partners that can affect the host physiology. This review reports recent nutritional metabolomics inspections of gut microbiota-host metabolic interactions with a particular focus on the cometabolism of cocoa and coffee polyphenols.
Myeloid Lineage Restriction Is Prior to and Independent of Lymphoid Lineage Restriction. (2006)

Abstract It has been widely accepted that hematopoietic stem cells (HSCs) exclusively give rise to either myeloid or lymphoid lineage along their differentiation. Phenotypically defined as FcRloCD34+IL-7R−Sca-1−Kit+Lin− cells, common myeloid progenitors (CMPs) are supposedly at the first branched point for myeloid lineage commitment. Phenotypically defined as Thy1.1−IL-7R+KitloSca-1loLin− cells, common lymphoid progenitors are supposedly at the first branched point for both B- and T-lymphoid lineage commitment. Contradicting this model, we previously made observations of the myeloid lineage restriction in very early stages of HSC differentiation. We therefore decided to compare the myeloid and lymphoid differentiation potentials in long-term HSCs, short-term HSCs, multipotent progenitors (MPPs), CMPs, granulocyte/macrophage progenitors (GMPs), megakaryocyte/erythrocyte progenitors (MEPs), and CLPs at the single cell level. Because any available assays are not so sensitive enough for detection of lymphoid lineage differentiation potential, we primarily focused on myeloid differentiation potentials in this study. Here we provide data indicative of the absence of CMPs in the adult mouse bone marrow. Long-term HSCs (CD34−Kit+Sca-1+Lin− cells), short-term HSCs (Flt-3−CD34+Kit+Sca-1+Lin− cells), MPPs (Flt-3+CD34+Kit+Sca-1+Lin− cells), CMPs (FcRloCD34+IL-7R−Sca-1−Kit+Lin− cells), GMPs (FcRhiCD34+IL-7R−Sca-1−Kit+Lin− cells), MEPs (FcRloCD34−IL-7R−Sca-1−Kit+Lin− cells), and CLPs (IL-7R+KitloSca-1loLin− cells) were purified from adult B6 mice by flow cytometry. Single cell cultures were performed in the presence of SCF+TPO+IL-3+EPO. All colonies made by single cells were subjected to Cytospin preparations, followed by May-Gruenwald-Giemsa staining, for morphological classifications of colony cells: neutrophil (n), macrophage (m), erythroblast (E), or megakaryocyte (M). Cells with all n, m, E, M differentiation potentials (nmEM cells) were detected in on average 31%, 5%, and fewer than 1 % of long-term HSCs, short-term HSCs, and MPPs, repectively. Notably, none of a total of over 800 CMPs showed the full nmEM differentiation potential. These CMPs instead showed potentials belonging to members of GMPs and MEPs, suggesting CMPs are mostly an overlaping population of GMPs and MEPs rather than a distinct population. Single cell transplantation experiments revealed the coexistence of cells with the myleoid and B-lymphoid potentials or cells with the myeloid and T-lymphoid potentials among CD34−Kit+Sca-1+Lin− long-term HSC population. These progentiors are likely to be immediate progeny of HSCs. Together, these data support our view that myeloid lineage restriction takes place prior to and independent of lymphoid lineage restriction.
Abstract 20897: Patient-Reported Outcomes in Tetralogy of Fallot: Baseline Results From a Prospective, International, Multi-Site Study (2017)

Introduction: In addition to understanding causes of morbidity and mortality following tetralogy of Fallot repair (rTOF), the importance of patient-reported outcomes (PROs) such as quality of life (QOL) is increasingly being recognized. Hypothesis: We hypothesized that PROs in rTOF would be associated with selected sociodemographic factors, functional status, and/or clinical variables. Methods: As part of a prospective study of patients ≥12 years with rTOF and significant pulmonary regurgitation, participants completed PRO surveys: SF-12 Health Status (physical component summary [PCS] and mental component summary [MCS] t-scores), EQ-5D (5 dimensions: mobility, self-care, usual activities, pain/discomfort, and anxiety/depression), and a 0-100 QOL linear analogue scale (QOL-LAS). With multivariable regression analysis, we determined the association between PROs and selected predictors. Results: We studied n=627 participants (55% male, 26±13 years, 75% adult) at 14 sites (North America, Europe and Asia). Median age at repair was 1.6 years (IQR 0.6, 4.2). In general, scores on the SF-12 and QOL-LAS suggested good outcomes: SF-12 PCS &lt;18 years 52±6 and ≥18 years 51±9; SF-12 MCS &lt;18 years 52±9 and ≥18 years 49±10; QOL-LAS &lt;18 years 83±14 and ≥18 years 78±16. On the EQ-5D, difficulties were reported with usual activities (16%), pain (25%) and anxiety/depression (38%). In multivariable regression analysis, younger age at enrollment emerged as an independent predictor of better physical health status and worse mental health status (p=0.0005 and p=0.029, respectively), but not QOL. Better NYHA functional class was a predictor of better SF-12 PCS and MCS (p&lt;0.0005 and p=0.002) as well as better QOL (p&lt;0.0001). Other factors (including complexity of underlying TOF anatomy, previous shunt palliation and need for arrhythmia intervention) were not associated with PROs. Conclusions: Age and NYHA functional class at enrollment were found to be predictors of PROs in rTOF. While global measures of health status and QOL (SF-12 and QOL-LAS) suggest relatively good PROs, this study demonstrates the importance of inquiring about specific health problems (EQ-5D) to achieve a richer understanding of PROs in order to potentially maximize patient well-being.
Nonuniformity of Carbohydrate Degradation during Kraft Pulping−Measurement and Modeling Using a Modified G-Factor (2000)

Nonuniform carbohydrate degradation during pulping can be more harmful to pulp strength than the same degree of degradation occurring uniformly. A modified G-factor model that incorporates the history of both temperature and [OH-] changes in wood chips during cooking is presented. This method requires knowing the variation in [OH-] across the thickness of the wood chip and during the cooking. These variations can be determined by numerically solving a set of mass-transfer equations with kinetic reaction terms using a computer program. The G-factor values are then converted to pulp viscosity. The model was experimentally validated by measuring the viscosity profiles over the thickness direction of hand-cut wood chips. Both measured and calculated profiles showed that the viscosity of the cellulose at the chip center was 50−100% higher than that at the edge of the 10-mm-thick chips. The difference in these viscosities for a 3-mm-thick chip was only 10−15%.
Versatile functionalization of carbon electrodes with a polypyridine ligand: metallation and electrocatalytic H+ and CO2 reduction (2015)

A strategy is proposed for immobilization of homogeneous catalysts whereby a glassy carbon electrode is functionalized by electro-grafting of a ligand, terpyridine. The modified electrode can easily be metallated with cobalt and shows activity towards catalytic proton and CO2 reduction. The metal can be removed and the electrode re-metallated at will.
MALDI MS Peptide Mapping Performance by In-Gel Digestion on a Probe with Prestructured Sample Supports (2004)

Matrix-assisted laser desorption/ionization (tandem) mass spectrometry (MALDI MS) is widely used in protein chemistry and proteomics research for the identification and characterization of proteins isolated by polyacrylamide gel electrophoresis. In an effort to minimize sample handling and increase sample throughput, we have developed a novel in-gel digestion protocol where sample preparation is performed directly on a MALDI probe with prestructured sample support. The protocol consists of few sample-handling steps and has minimal consumption of reagents, making the protocol sensitive, timesaving, and cost-efficient. Performance of the on-probe sample preparation protocol was demonstrated by analysis of a set of rat liver proteins obtained from a fluorescently stained (Cy3 and SyproRuby) two-dimensional polyacrylamide gel. The success rate of protein identification by on-probe tryptic digestion and MALDI peptide mass mapping was 89%. The on-probe in-gel digestion procedure provided superior sensitivity and peptide mass mapping performance as compared to our standard in-gel digestion protocol. The on-probe digestion technique resulted in significantly improved amino acid sequence coverage of proteins, mainly due to efficient recovery and detection of large (>1.5 kDa) hydrophobic peptides. These observations indicate that numerous tryptic peptides are lost when using the standard in-gel digestion methods and sample preparation techniques for MALDI MS. This study also demonstrates that the on-probe digestion protocol combined with MALDI tandem mass spectrometry provides a robust platform for proteomics research, including protein identification and determination of posttranslational modifications.
Multi-Scale Geometric Consistency Guided and Planar Prior Assisted Multi-View Stereo (2022)

In this paper, we propose some efficient multi-view stereo methods for accurate and complete depth map estimation. We first present our basic methods with Adaptive Checkerboard sampling and Multi-Hypothesis joint view selection (ACMH & ACMH+). Based on our basic models, we develop two frameworks to deal with the depth estimation of ambiguous regions (especially low-textured areas) from two different perspectives: multi-scale information fusion and planar geometric clue assistance. For the former one, we propose a multi-scale geometric consistency guidance framework (ACMM) to obtain the reliable depth estimates for low-textured areas at coarser scales and guarantee that they can be propagated to finer scales. For the latter one, we propose a planar prior assisted framework (ACMP). We utilize a probabilistic graphical model to contribute a novel multi-view aggregated matching cost. At last, by taking advantage of the above frameworks, we further design a multi-scale geometric consistency guided and planar prior assisted multi-view stereo (ACMMP). This greatly enhances the discrimination of ambiguous regions and helps their depth sensing. Experiments on extensive datasets show our methods achieve state-of-the-art performance, recovering the depth estimation not only in low-textured areas but also in details. Related codes are available at https://github.com/GhiXu.
Fast and Accurate Modeling of PCB Differential Trace Skew Compensation using ML (2021)

High Speed Serial interfaces using differential routing require intra-pair delay matching to minimize loss and electromagnetic interference due to differential to common mode conversion. Existing layout methods using geometric length are useful to avoid gross errors, but fall short as the electrical length is a non-linear 3D problem that is dependent on self-coupling and return path. This paper investigates this issue and compares different regression models to improve skew compensation accuracy and speed.
Flame Behavior and Thermal Structure of Combusting Nonpulsating and Pulsating Plane Jets (2012)

The flame behavior, thermal structure, and combustion product concentrations of the flames of nonpulsating and pulsating plane jets were examined and compared. A nonpulsating plane jet was modified into a pulsating plane jet by introducing the jet fluids through a jet-impingement fluidic oscillator. The flame behavior was analyzed by photographing the flame from the lateral direction and focusing on the near burner region. The flame length was taken from long-exposure photographs. The temperature and combustion product concentrations were measured by using a fine-wire thermocouple and a gas analyzer, respectively. The results showed that the pulsating jet flame is significantly shorter and wider than the nonpulsating jet flame. A difference in the flame length larger than 30% was typical. The central region temperature distributions of the pulsating jet flame presented wide plateaus of high temperatures. The maximum temperature that the pulsating jet flame may attain was higher than that of the nonpulsating jet flame by about 250°C. The pulsating jet flame presented significantly larger concentration, smaller CO concentration, and smaller unburned than those of the nonpulsating jet flame, which implied that the combustion happening in the pulsating jet is more complete than that happening in the nonpulsating jet.
Nanoelectronic architecture for Boolean logic (1997)

A nanoelectronic implementation of Boolean logic circuits is described where logic functionality is realized through charge interactions between metallic dots self-assembled on the surface of a double-barrier resonant tunneling diode (RTD) structure. The primitive computational cell in this architecture consists of a number of dots with nearest neighbor (resistive) interconnections. Specific logic functionality is provided by appropriate rectifying connections between cells. We show how basic logic gates, leading to combinational and sequential circuits, can be realized in this architecture. Additionally, architectural issues including directionality, fault tolerance, and power dissipation are discussed. Estimates based on the current-voltage characteristics of RTD's and the capacitance and resistance values of the interdot connections indicate that static power dissipation as small as 0.1 nW/gate and switching delay as small as a few picoseconds can be expected. We also present a strategy for fabricating/synthesizing such systems using chemical self-organizing/self-assembly phenomena. The proposed synthesis procedure utilizes several chemical self-assembly techniques which have been demonstrated recently, including self-assembly of uniform arrays of close-packed metallic dots with nanometer diameters, controlled resistive linking of nearest neighbor dots with conjugated organic molecules and organic rectifiers.
Chromodomains direct integration of retrotransposons to heterochromatin (2008)

The enrichment of mobile genetic elements in heterochromatin may be due, in part, to targeted integration. The chromoviruses are Ty3/gypsy retrotransposons with chromodomains at their integrase C termini. Chromodomains are logical determinants for targeting to heterochromatin, because the chromodomain of heterochromatin protein 1 (HP1) typically recognizes histone H3 K9 methylation, an epigenetic mark characteristic of heterochromatin. We describe three groups of chromoviruses based on amino acid sequence relationships of their integrase C termini. Genome sequence analysis indicates that representative chromoviruses from each group are enriched in gene-poor regions of the genome relative to other retrotransposons, and when fused to fluorescent marker proteins, the chromodomains target proteins to specific subnuclear foci coincident with heterochromatin. The chromodomain of the fungal element, MAGGY, interacts with histone H3 dimethyl- and trimethyl-K9, and when the MAGGY chromodomain is fused to integrase of the Schizosaccharomyces pombe Tf1 retrotransposon, new Tf1 insertions are directed to sites of H3 K9 methylation. Repetitive sequences such as transposable elements trigger the RNAi pathway resulting in their epigenetic modification. Our results suggest a dynamic interplay between retrotransposons and heterochromatin, wherein mobile elements recognize heterochromatin at the time of integration and then perpetuate the heterochromatic mark by triggering epigenetic modification.
PI Stabilization of Power Converters With Partial State Measurements (2012)

In a recent paper a procedure to design globally asymptotically stabilizing linear proportional plus integral controllers for switched power converters was proposed. The construction requires the measurement of the full state of the system, which is often unavailable in practice. In this note we identify a class of converters for which an asymptotically convergent reduced order observer, preserving the aforementioned stability property of the closed-loop, can be designed. The class is characterized by a simple linear matrix inequality. The new controller is illustrated with the widely-popular, and difficult to control, single-ended primary inductor converter, for which simulation and experimental results are presented.
Correction: Loss of tuberous sclerosis complex 2 sensitizes tumors to nelfinavir–bortezomib therapy to intensify endoplasmic reticulum stress-induced cell death (2019)

This article was originally published under standard licence, but has now been made available under a CC BY 4.0 license. The PDF and HTML versions of the paper have been modified accordingly.
Plasmonic oxidation of glycerol using AuPd/TiO2 catalysts (2019)

AuPd nanoparticles supported on P25 TiO<sub>2</sub> (AuPd/TiO<sub>2</sub>) were prepared by a facile sol-immobilisation method and investigated for surface plasmon-assisted glycerol oxidation under base-free conditions.
Human Umbilical Cord Stem Cell Xenografts Improve Cognitive Decline and Reduce the Amyloid Burden in a Mouse Model of Alzheimer's Disease (2016)

Human umbilical cord mesenchymal stem cells appear to reduce AD pathology in a transgenic mouse model as documented by a reduction of the amyloid plaque burden compared to controls. This amelioration of pathology correlates with improvements on cognitive and sensorimotor tasks.
Protein‐coding and MicroRNA Biomarker Gene Panels Predictive of Clinical Recurrence in Prostate Cancer (2009)

An important challenge in prostate cancer research is to develop effective predictors of tumor recurrence following surgery. To identify predictive biomarkers, we performed DASL expression profiling with a custom‐designed panel of 522 prostate cancer relevant genes on 71 FFPE radical prostatectomy specimens with long‐term outcome. We identified a panel of eight genes that could be used to predict recurrence (p = 0.001). Furthermore, this gene panel could separate patients with and without recurrence in the subset of 46 patients with Gleason 7 tumors (p = 0.022) for whom the decision regarding adjuvant therapy is particularly important and difficult. We also performed comprehensive miRNA profiling of these samples, and identified six miRNAs predictive of recurrence (p=0.001) for all 71 patients and for the subset of 46 Gleason 7 patients (p=0.032). Following promoter analysis of these miRNA genes, we determined that four of them are directly bound by SOX4 in chromatin immunoprecipitations, suggesting that SOX4 may regulate their expression. Among the potential downstream targets of these miRNA genes are several tumor suppressors involved in cell‐cycle arrest and apoptosis. It may therefore now be possible to increase the accuracy of prognostication for individual patients following radical prostatectomy using universally available archived specimens.