gebhart/patrepeval huggingface dataset:
Ventricular remodeling in global ischemia. (1995)

To determine the effects of chronic constriction of the left coronary artery on the function and structure of the heart, coronary artery narrowing was surgically induced in rats and ventricular pump performance, extent and distribution of myocardial damage, and the hypertrophic and hyperplastic response of myocytes were examined. Alterations in cardiac hemodynamics were found in all rats, but the characteristics of the physiological properties of the heart allowed a separation of the animals into two groups which exhibited left ventricular dysfunction and failure, respectively. Left ventricular hypertrophy occurred in both groups and was characterized by ventricular dilatation and wall thinning which were more severe in the failing animals. Multiple foci of myocardial damage across the wall were seen in all animals but tissue injury was more prominent in the endomyocardium and in failing rats. The anatomical and hemodynamic changes resulted in a significant increase in diastolic wall stress which paralleled the depression in ventricular performance. Myocyte cell loss and myocyte cellular hypertrophy were more severe with ventricular failure than with dysfunction. Finally, diastolic overload appeared to be coupled with activation of the DNA synthetic machinery of myocytes and nuclear mitotic division. In conclusion, a fixed lesion of the left coronary artery leads to abnormalities in cardiac dynamics with marked increases in diastolic wall stress and extensive ventricular remodeling in spite of compensatory myocyte cellular hypertrophy and hyperplasia in the remaining viable tissue.
High-rate quasi-cyclic low-density parity-check codes derived from finite affine planes (2005)

This paper shows that several attractive classes of quasi-cyclic (QC) low-density parity-check (LDPC) codes can be obtained from affine planes over finite fields. One class of these consists of duals of one-generator QC codes. Here, for codes contained in this class, the exact minimum-distance and a lower bound on the multiplicity of the minimum-weight codewords are presented. It is shown that the lower bound on the multiplicity provides a very accurate indication of the bit error performance at moderate and high signal-to-noise ratios, and thus error-floor behavior can be easily predicted. Also discussed is a class consisting of codes from circulant permutation matrices. An explicit formula for the rank of the parity-check matrix is presented for these codes. Furthermore, it is shown that each of these codes can be identified as a code constructed from a constacyclic maximum distance separable (MDS) code in a similar manner to the RS-based LDPC codes presented by Chen et al. and Djurdjevic et al. Experimental results show that a number of high rate QC-LDPC codes with excellent error performance are contained in these classes
Circulating and tumor-based biomarkers predict clinical activity in cancer patients treated with the engineered anti-PD-L1 antibody MPDL3280A (2014)

PD-L1 expressed in the tumor microenvironment regulates Th1 immune responses and mediates cancer immune evasion through interactions with PD-1 or B7.1 receptors on activated T cells. MPDL3280A, an engineered human monoclonal antibody, targets PD-L1 and inhibits its function. To identify immunologic predictive and pharmacodynamic biomarkers of MPDL3280A treatment, we performed a comprehensive analysis of tumors and blood samples collected at baseline and/or on treatment from ≈280 patients with locally advanced or metastatic solid tumors, including NSCLC, RCC, melanoma and bladder cancer. Regardless of tumor type, clinical responses were characterized by PD-L1 expression, the presence of markers of T cell activation (Th1 gene signature and CTLA4), and the absence of fractalkine at baseline in the tumor microenvironment. Elevated baseline expression of IFN-γ and IFN-γ-inducible genes (e.g., IDO1 and CXCL9) was associated with MPDL3280A response in melanoma but not NSCLC or RCC. On treatment, responding tumors showed increased infiltration of Th1-dominant immune infiltrate and evidence of adaptive PD-L1 up-regulation. In contrast, progressing tumors displayed the following patterns of tumor-infiltrating lymphocytes (TILs) and PD-L1 expression: (1) few/no TILs and absent PD-L1 expression (immunologic ignorance), (2) TILs present with minimal/no PD-L1 expression (non-functional immune responses), or (3) TILs residing solely around the tumor cell mass outer edge (excluded infiltrate), suggesting that resistance to MPDL3280A may be associated with impaired T cell trafficking and/or function.

Profiling of ≈180 circulating biomarkers revealed that plasma concentrations of IL-18 and interferon-inducible T cell alpha chemoattractant (ITAC) increased in all patients following MPDL3280A treatment, representing a pharmacodynamic measurement of PD-L1 inhibition. In addition, analysis of PBMC showed an increase in T cell activation, as measured by IFN-γ and granzymes A and B gene expression in responders following MPDL3280A treatment, consistent with the observations in responding tumors. Baseline soluble PD-L1 was not associated with response. Some indication-specific biomarkers, such as plasma VEGF, decreased in responders with RCC but not with other indications. In NSCLC, a decrease in tumor burden markers, CA-125 and CEA, was associated with response. Similarly, IL-6 and IL-8 were differentially expressed on treatment in responders vs non-responders. Additionally, responders exhibited a decrease in circulating tumor DNA (ctDNA) in plasma, suggesting that ctDNA may be used to monitor MPDL3280A clinical activity in NSCLC.

In conclusion, these data provide general and indication-specific mechanistic insights into immune checkpoint inhibition, potential mechanisms of response and resistance, as well as identification of potential predictive and pharmacodynamic biomarkers of anti-PD-L1/PD-1 clinical activity across multiple tumor types.
Synthesis, Structure, and Properties of Poly(isoprene)s of Different Constitutions and Configurations from Catalysts Based on Complexes of Nd, Co, and Fe (2023)

Poly(isoprene)s of different molecular structures have been synthesized with various catalysts based on complexes of Nd-, Co-, and Fe-bearing pyridylimine, phosphine, and bipyridine ligands. Poly(isoprene)s with essentially cis-1,4 structure, 3,4 syndiotactic structure, and regular alternating cis-1,4-alt-3,4 structure have been obtained. Moreover, polymers with an unusual prevalent alternating cis-1,4-alt-3,4 structure but containing cis-1,4 units sequences of different lengths (3 or 5 units) within the chain have also been obtained. The structure and mechanical properties of all of the synthesized poly(isoprene)s, some of them completely new, have been investigated. Poly(isoprene)s with a cis-1,4 structure and with a perfectly alternating cis-1,4-alt-3,4 structure or prevalent alternating cis-1,4-alt-3,4 structure are amorphous, exhibiting mechanical behavior with a viscous flow at relatively high deformation. The sample of poly(isoprene) with almost a regular 3,4 syndiotactic structure (about 79% of 3,4 units) crystallizes in the stable orthorhombic form of 3,4-syndiotactic poly(isoprene). This crystalline sample shows better mechanical properties of deformability and flexibility than the other amorphous poly(isoprene)s without a viscous flow with plastic deformation and breaking at relatively high strain around 300–400% and remarkable elastic properties. The plastic deformation and the elastic behavior are associated with a reversible transformation during tensile deformation of the crystalline orthorhombic form into a disordered mesomorphic form, which recrystallizes into the orthorhombic form upon relaxation during elastic recovery. The glass transition temperature of the different poly(isoprene)s decreases linearly with the increasing cis-1,4 content, from 16 °C of the poly(isoprene) with the prevalent 3,4 structure and 21% of cis-1,4 units to −64 °C of the poly(isoprene) with 98% of cis-1,4 units.
A Systematic Review of Reproducibility Research in Natural Language\n Processing (2021)

Against the background of what has been termed a reproducibility crisis in\nscience, the NLP field is becoming increasingly interested in, and\nconscientious about, the reproducibility of its results. The past few years\nhave seen an impressive range of new initiatives, events and active research in\nthe area. However, the field is far from reaching a consensus about how\nreproducibility should be defined, measured and addressed, with diversity of\nviews currently increasing rather than converging. With this focused\ncontribution, we aim to provide a wide-angle, and as near as possible complete,\nsnapshot of current work on reproducibility in NLP, delineating differences and\nsimilarities, and providing pointers to common denominators.\n
Regulation of the Cyclin D3 Promoter by E2F1 (2003)

We have previously demonstrated that ectopic expression of E2F1 is sufficient to drive quiescent cells into S phase and that E2F1 expression can contribute to oncogenic transformation. Key target genes in this process include master regulators of the cell cycle, such as cyclin E, which regulates G(1) progression, and cyclin A, which is required for the initiation of DNA synthesis. In the present work, we present novel evidence that a second G(1) cyclin, cyclin D3, is also potently activated by E2F1. First, an estrogen receptor-E2F1 fusion protein (ER-E2F1) potently activates the endogenous cyclin D3 mRNA upon treatment with 4-hydroxytamoxifen, which induces nuclear accumulation of the otherwise cytosolic fusion protein. Furthermore, trans-activation of cyclin D3 by ER-E2F1 occurs even in the presence of the protein synthesis inhibitor cycloheximide and thus appears direct. Second, all of the growth-stimulatory members of the E2F family (E2F1, -2, and -3A) potently activate a cyclin D3 promoter reporter, whereas growth-restraining members of the family (E2F4, -5, and -6) have little effect. Third, recombinant E2F1 binds with high affinity to the cyclin D3 promoter in vitro. Fourth, chromatin immunoprecipitation assays demonstrate that endogenous E2F1 is associated with the cyclin D3 promoter in vivo. Finally, mapping experiments localize the essential E2F regulatory element of the cyclin D3 promoter to a noncanonical E2F site in the promoter between nucleotides -143 and -135 relative to the initiating methionine codon. We conclude that in addition to cyclins E and A, E2F family members can also activate one member of the D-type cyclins, further contributing to the ability of the stimulatory E2F family members to drive cellular proliferation.
The sterol response element binding protein regulates cyclooxygenase-2 gene expression in endothelial cells (2005)

We previously demonstrated that cholesterol deprivation increases endothelial cyclooxygenase-2 (COX-2)-dependent prostacyclin [prostaglandin I2 (PGI2)] production in vitro. Cholesterol directly regulates gene transcription through the sterol response element binding protein (SREBP). In this work, we demonstrate that SREBP directly regulates COX-2 expression. Cholesterol reduces human COX-2 promoter-luciferase reporter construct activity in transiently transfected endothelial cells. Conversely, cotransfection with a constitutively active mutant SREBP increases COX-2 promoter activity. SREBP-1a and -2 specifically bind a putative sterol response element (SRE) sequence in the COX-2 promoter. This sequence competes for SREBP binding to a low density lipoprotein receptor consensus sequence in an electromobility-shift assay. These data indicate that endothelial COX-2 is regulated by cholesterol via the SREBP pathway. The present study identifies COX-2 as the first vascular gene without a clear role in lipid metabolism transactivated by SREBP, and suggests that enhanced production of PGI2 through this pathway may be an additional benefit of cholesterol-lowering therapies.
Learning based Memory Interference Prediction for Co-running Applications on Multi-Cores (2021)

Early run-time prediction of co-running independent applications prior to application integration becomes challenging in multi-core processors. One of the most notable causes is the interference at the main memory subsystem, which results in significant degradation in application performance and response time in comparison to standalone execution. Currently available techniques for run-time prediction like traditional cycle-accurate simulations are slow, and analytical models are not accurate and time-consuming to build. By contrast, existing machine-learning-based approaches for run-time prediction simply do not account for interference. In this paper, we use a machine learning-based approach to train a model to correlate performance data (instructions and hardware performance counters) for a set of benchmark applications between the standalone and interference scenarios. After that, the trained model is used to predict the run-time of co-running applications in interference scenarios. In general, there is no straightforward one-to-one correspondence between samples obtained from the standalone and interference scenarios due to the different run-times, i.e. execution speeds. To address this, we developed a simple yet effective sample alignment algorithm, which is a key component in transforming interference prediction into a machine learning problem. In addition, we systematically identify the subset of features that have the highest positive impact on the model performance. Our approach is demonstrated to be effective and shows an average run-time prediction error, which is as low as 0.3% and 0.1% for two co-running applications.
Autologous Protein Solution processing alters lymphoid and myeloid cell populations and modulates gene expression dependent on cell type (2022)

Osteoarthritis (OA) is a degenerative disease associated with cartilage degradation, osteophyte formation, and fibrillation. Autologous Protein Solution (APS), a type of autologous anti-inflammatory orthobiologic, is used for pain management and treatment of OA. Various compositions of autologous PRP formulations are in clinical use for musculoskeletal pathologies, by nature of their minimal processing and source of bioactive molecules. Currently, there is no consensus on the optimal composition of the complex mixture. In this study, we focused on elucidating the immune cell subtypes and phenotypes in APS. We identified the immune cell types in APS from healthy donors and investigated phenotypic changes in the immune cells after APS processing. Based on flow cytometric analysis, we found that neutrophils and T cells are the most abundant immune cell types in APS, while monocytes experience the largest fold change in concentration compared to WBCs. Gene expression profiling revealed that APS processing results in differential gene expression changes dependent on immune cell type, with the most significantly differentially regulated genes occurring in the monocytes. Our results demonstrate that the mechanical processing of blood, whose main purpose is enrichment and separation, can alter its protein and cellular composition, as well as cellular phenotypes in the final product.
In Vivo Targeting and Positron Emission Tomography Imaging of Tumor with Intrinsically Radioactive Metal–Organic Frameworks Nanomaterials (2017)

Nanoscale metal-organic frameworks (nMOF) materials represent an attractive tool for various biomedical applications. Due to the chemical versatility, enormous porosity, and tunable degradability of nMOFs, they have been adopted as carriers for delivery of imaging and/or therapeutic cargos. However, the relatively low stability of most nMOFs has limited practical in vivo applications. Here we report the production and characterization of an intrinsically radioactive UiO-66 nMOF (<sup>89</sup>Zr-UiO-66) with incorporation of positron-emitting isotope zirconium-89 (<sup>89</sup>Zr). <sup>89</sup>Zr-UiO-66 was further functionalized with pyrene-derived polyethylene glycol (Py-PGA-PEG) and conjugated with a peptide ligand (F3) to nucleolin for targeting of triple-negative breast tumors. Doxorubicin (DOX) was loaded onto UiO-66 with a relatively high loading capacity (1 mg DOX/mg UiO-66) and served as both a therapeutic cargo and a fluorescence visualizer in this study. Functionalized <sup>89</sup>Zr-UiO-66 demonstrated strong radiochemical and material stability in different biological media. Based on the findings from cellular targeting and in vivo positron emission tomography (PET) imaging, we can conclude that <sup>89</sup>Zr-UiO-66/Py-PGA-PEG-F3 can serve as an image-guidable, tumor-selective cargo delivery nanoplatform. In addition, toxicity evaluation confirmed that properly PEGylated UiO-66 did not impose acute or chronic toxicity to the test subjects. With selective targeting of nucleolin on both tumor vasculature and tumor cells, this intrinsically radioactive nMOF can find broad application in cancer theranostics.
General Total Variation Regularized Sparse Bayesian Learning for Robust\n Block-Sparse Signal Recovery (2021)

Block-sparse signal recovery without knowledge of block sizes and boundaries,\nsuch as those encountered in multi-antenna mmWave channel models, is a hard\nproblem for compressed sensing (CS) algorithms. We propose a novel Sparse\nBayesian Learning (SBL) method for block-sparse recovery based on popular CS\nbased regularizers with the function input variable related to total variation\n(TV). Contrary to conventional approaches that impose the regularization on the\nsignal components, we regularize the SBL hyperparameters. This iterative\nTV-regularized SBL algorithm employs a majorization-minimization approach and\nreduces each iteration to a convex optimization problem, enabling a flexible\nchoice of numerical solvers. The numerical results illustrate that the\nTV-regularized SBL algorithm is robust to the nature of the block structure and\nable to recover signals with both block-patterned and isolated components,\nproving useful for various signal recovery systems.\n
Morphological characteristics of lesions with thin cap fibroatheroma—a substudy from the COMBINE (OCT-FFR) trial (2022)

Within TCFA carrying patients, a smaller MLA, lower FFR values, and TCFA location adjacent to a HP were associated with future MACE. Carpet-like measured lesion area surface was similar, while the TCFA area was smaller in the MACE arm, and predominantly located proximal to the MLA.
A simultaneous wavelength tuning and stabilization scheme of a fiber-optic interferometer filter (1999)

We successfully demonstrated a stabilized fiber-optic Mach­Zehnder interferometer filter with continuous tunability. The tunable scheme was achieved with fine wavelength control of an 1.3<TEX>${\mu}{\textrm}{m}$</TEX> tunable laser diode used as a stabilization light source. The transmission wavelength of the tunable filter was shifted linearly with respect to the wavelength change of the stabilization light source.
Development of an Anisotropic Thermal Transport Material (2014)

Abstract : The resources provided by this award allowed for the development of two thermally conductive nanofillers whose production at large scale was not previously possible. These fillers, pristine graphene and functionalized boron nitride, have high thermal conductivity coupled with an extreme aspect ratio, making them strong candidates for thermally conductive composites. In the past, the insolubility of pristine graphene required the use of either graphene oxide (GO) or reduced graphene oxide (rGO). While providing solubility, the oxidation also severely reduced the thermal conductivity of the material. The methods developed in the work supported by this grant allow for the use of un-oxidized and un-damaged graphene for thermal composites and include the use of a self-assembling solvent mixture and an interfacial trapping method. Boron nitride was exfoliated for the first time in large quantities. Boron nitride, unlike graphite, is electrically insulating and thus is a complimentary material to graphene. A thermal functionalization and exfoliation procedure was developed and a manuscript describing the work is currently being reviewed. Together, these new materials provide the foundation for a new class of thermally conductive composite materials. Details of the work preformed are available in the archival publications and PhD thesis supported by the award.
assay information of the mouse qualitycontrol samples for HeliScopeCAGE (low quantity ver.) (2017)

a tab delimited flat file (SDRF file) describing the experimental details for mouse quality control samples for the low quantity version of the HeliScopeCAGE protocol
Ventilatory response to isocapnic hyperoxia (1995)

Breathing O2 for up to 1 h has been shown to either not influence or slightly increase (6-13%) minute ventilation. However, end-tidal PCO2 was not kept constant in these experiments. In nine healthy men, we studied the ventilatory, blood pressure, and heart rate responses to 30 min of normobaric hyperoxia (50% O2) at isocapnic conditions. Hyperoxia led to a 60% increase in mean minute ventilation (P = 0.002), largely due to an increase in mean tidal volume from 0.66 +/- 0.04 (SE) to 0.88 +/- 0.05 liter (P = 0.007). Fifteen minutes after the termination of hyperoxia, minute ventilation was still increased (P = 0.02) compared with baseline, although it was reduced compared with hyperoxia (P = 0.02). Arterial blood gas analyses in six subjects before and during hyperoxia showed an increase in arterial PO2 and O2 saturation but no change in arterial PCO2 or pH. Hyperoxia induced no changes in arterial blood pressure or heart rate. We conclude that 1) isocapnic hyperoxia stimulates respiration markedly, an effect that is approximately five times higher than previously measured; 2) the increase in ventilation induced by hyperoxia does not affect arterial blood pressure and heart rate; and 3) in experiments using hyperoxia, its effect on breathing and subsequently on PCO2 has to be taken into account.
Cholesterol functionalized aliphaticN-substituted 8-membered cyclic carbonate (2018)

Straightforward synthesis of cholesterol functionalized aliphatic <i>N</i>-substituted 8-membered cyclic carbonate (Chol-8m) monomer is reported. Well-defined poly(ethylene glycol) (PEG) diblock copolymers were readily accessed via organo catalytic ring opening polymerization. These polymers show promise as building blocks for self-assembled nanostructures and steric stabilizers for liposomes.
Wafer Bonding and Heterogeneous Integration: III-V/Silicon Photonics (2015)

Abstract. The use of bonding technology to integrate III-V opto-electronic components on top of a silicon-on-insulator (SOI) integrated waveguide circuit is presented. III-V laser diodes and photodetectors fabricated on and coupled to an underlying SOI waveguide circuit are considered.
Single polariton nonlinear Faraday rotation (2020)

We present the experimental observation of photon-photon interactions at the single-particle level. The linearly polarized signal beam undergoes Faraday rotation by a nonlinear effective magnetic field induced by a very weak circularly polarized control beam due to the giant Kerr-like interactions between exciton-polaritons in our quantum well-based 0D microcavity structures. We measure a phase shift with a slope of 3.5&times;10^-3 radians per particle for low cavity occupancies between 0.1 and 3 excited by the control beam. These experimental findings are in agreement with theoretical models and pave the way towards the development of scalable photonic quantum gates.