gebhart/patrepeval huggingface dataset:
Normalized Cheeger Cut With Neighborhood Rough Approximation (2018)

A graph-based collecting study recently attracted significant attention from the scientific research community. Normalized Cheeger cut is a balanced graph partition criterion and a generalized version of normalized graph cut. A stress-free resolution of the normalized Cheeger cut can be obtained by employing the eigenvectors of curve p-Laplacian. However, it is highly sensitive for the original Cheeger cut to collect the interference of noise and disrelated properties. Thus, the performance of the Cheeger cut decreases when high-dimensional data are grouped. To decrease the negative influence of outliers and superfluous properties of collecting, we design an efficient attribute decrease method which is based on neighborhood rough approximation. This design aims to improve the collection of the Cheeger cut. The suggested algorithm introduces information entropy to the neighborhood rough sets in order to measure the importance of attributes. This algorithm reserves the most valuable features and removes the redundant features while retaining the maximum category information of raw data. We then build the p-Laplacian array with the optimized attribute sets and obtain the collecting consequences via the eigen-subspace decomposition of graph p-Laplacian. The cogency of the proposed algorithm is established in various standard data collections. Experimentations demonstrated that our method enjoys sturdy robustness to noise or disrelated feature information in high-dimensional figures.
PPARγ regulates adipocyte cholesterol metabolism via oxidized LDL receptor 1 (2005)

In addition to its role in energy storage, adipose tissue also accumulates cholesterol. Concentrations of cholesterol and triglycerides are strongly correlated in the adipocyte, but little is known about mechanisms regulating cholesterol metabolism in fat cells. Here we report that antidiabetic thiazolidinediones (TZDs) and other ligands for the nuclear receptor PPARgamma dramatically upregulate oxidized LDL receptor 1 (OLR1) in adipocytes by facilitating the exchange of coactivators for corepressors on the OLR1 gene in cultured mouse adipocytes. TZDs markedly stimulate the uptake of oxidized LDL (oxLDL) into adipocytes, and this requires OLR1. Increased OLR1 expression, resulting either from TZD treatment or adenoviral gene delivery, significantly augments adipocyte cholesterol content and enhances fatty acid uptake. OLR1 expression in white adipose tissue is increased in obesity and is further induced by PPARgamma ligand treatment in vivo. Serum oxLDL levels are decreased in both lean and obese diabetic animals treated with TZDs. These data identify OLR1 as a novel PPARgamma target gene in adipocytes. While the physiological role of adipose tissue in cholesterol and oxLDL metabolism remains to be established, the induction of OLR1 is a potential means by which PPARgamma ligands regulate lipid metabolism and insulin sensitivity in adipocytes.
Data from The Mitogen-Activated Protein/Extracellular Signal-Regulated Kinase Kinase Inhibitor AZD6244 (ARRY-142886) Induces Growth Arrest in Melanoma Cells and Tumor Regression When Combined with Docetaxel (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Disseminated melanoma is highly therapy resistant. The finding that 66% of melanomas harbor the activating BRAF&lt;sup&gt;V600E&lt;/sup&gt; mutation has raised expectations for targeting the Ras/RAF/mitogen-activated protein (MAP)/extracellular signal-regulated kinase (ERK) kinase (MEK)/ERK pathway in melanoma. This study addresses the anti-melanoma activity of the MEK inhibitor AZD6244 (ARRY-142886).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We recently have shown that growing melanoma cells as three-dimensional collagen-implanted spheroids enhances resistance to the MEK inhibitor U0126. Here, we investigated the anti-melanoma activity of AZD6244 in two-dimensional cell culture, the three-dimensional spheroid model, and an &lt;i&gt;in vivo&lt;/i&gt; model.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; In two-dimensional cell culture, AZD6244 was cytostatic and reduced the growth of melanoma cells in a concentration-dependent fashion through the induction of G&lt;sub&gt;1&lt;/sub&gt;-phase cell cycle arrest. In our three-dimensional spheroid model, the effects of AZD6244 were largely cytostatic and reversible, with drug washout leading to spheroid regrowth. Finally, 1205Lu cells were grown as tumor xenografts in severe combined immunodeficient mice. After tumor establishment, mice were dosed twice daily with 0, 10, or 30 mg/kg AZD6244 p.o. AZD6244 treatment decreased phospho-ERK in the tumors and significantly suppressed tumor growth. The original tumors remained viable, suggesting that AZD6244 monotherapy was largely cytostatic, and not proapoptotic in this model. Further studies showed that co-administration of AZD6244 (30 mg/kg) with docetaxel (15 mg/kg) led to tumor regression, indicating the potential for MEK inhibitor/chemotherapy drug combinations.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Inhibition of MEK is cytostatic as a monotherapy in melanoma, but cytotoxic when combined with docetaxel.&lt;/p&gt;&lt;/div&gt;
A comparison of the solution structures of an LNA:DNA duplex and the unmodified DNA:DNA duplex (2001)

Modified oligonucleotides, containing restricted nucleotides with a 2′-O,4′-C-methylene bridge (LNA), hybridized toward either DNA or RNA display an unprecedented increase in melting temperatures. In order to understand the structural basis for this high stability we have used 1H NMR spectroscopy to determine the high resolution solution structures of an LNA-modified oligonucleotide, as well as the structure of the corresponding unmodified duplex. The modified duplex is an LNA:DNA duplex containing three thymidine LNA modifications (TLL), d(C1TLL2G3A4TLL5A6TLL7G8C9):d(G10C11A12T13A14T15C16A17G18). A full relaxation matrix approach by the program RANDMARDI was used to obtain interproton distance bounds from NOESY cross peak intensities. These distance bounds were used as restraints in molecular dynamics (rMD) calculations. Both duplexes have right-handed helix conformations with all bases in the anti conformation forming normal Watson–Crick base pairs. The LNA strand in the modified duplex has predominantly N-type sugar conformations compared to the S-type conformations of the complementary strand. The unmodified DNA:DNA strand has almost exclusively S-type sugar conformations. The structural strain introduced by the conformational changes of the ribose rings in the LNA:DNA duplex is released by unwinding the helix and widening the minor groove, but as a whole the structure of the duplex is surprisingly unaffected by introducing the modified LNA nucleotides.
Data from Quantifying Treatment Benefit in Molecular Subgroups to Assess a Predictive Biomarker (2023)

&lt;div&gt;Abstract&lt;p&gt;An increased interest has been expressed in finding predictive biomarkers that can guide treatment options for both mutation carriers and noncarriers. The statistical assessment of variation in treatment benefit (TB) according to the biomarker carrier status plays an important role in evaluating predictive biomarkers. For time-to-event endpoints, the hazard ratio (HR) for interaction between treatment and a biomarker from a proportional hazards regression model is commonly used as a measure of variation in TB. Although this can be easily obtained using available statistical software packages, the interpretation of HR is not straightforward. In this article, we propose different summary measures of variation in TB on the scale of survival probabilities for evaluating a predictive biomarker. The proposed summary measures can be easily interpreted as quantifying differential in TB in terms of relative risk or excess absolute risk due to treatment in carriers versus noncarriers. We illustrate the use and interpretation of the proposed measures with data from completed clinical trials. We encourage clinical practitioners to interpret variation in TB in terms of measures based on survival probabilities, particularly in terms of excess absolute risk, as opposed to HR. &lt;i&gt;Clin Cancer Res; 22(9); 2114–20. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
GaN lasers for quantum information science and technology (QIST) applications (2020)

We report on GaN lasers with extremely narrow linewidth (~1MHz) at ‘magic wavelengths’ for cold-atom interferometry quantum sensors, using extended cavity GaN laser diodes and DFB GaN laser diodes.
Visualizing thought: Mapping category and continuum (2011)

thought has roots in the spatial world.Abstractions are expressed in the ways things are arranged in the world as well as the ways people talk and gesture.Mappings to the page should be better when they are congruent, that is, when the abstract concept matches the spatial one.Congruent mappings can be revealed in people's performance and preferences.Congruence is supported here for visual representations of continuum and category.Congruently mapping a continuous concept, frequency, to a continuous visual variable and mapping a categorical concept, class inclusion, to a categorical visual variable were preferred and lead to better performance than the reverse mappings.
The effects of time delay spread on turbo-TCM in a wireless communication channel (2002)

This paper presents some simulation results on the performances of turbo-codes with multilevel modulation (turbo-TCM) in a wireless environment. The wireless channel is modeled as a frequency selective fading channel with two time delay spread profiles, namely, a two-ray profile and a one-sided exponential profile. Turbo-TCM codes constructed from punctured turbo-codes combined with different modulation schemes are studied. It is found that turbo-TCM achieves unmatched performance of average irreducible BER. Turbo-TCM has much lower error probability than conventional TCM, especially in channels with high delay spread.
Bacterial Small RNA Regulators (2005)

Small regulatory RNAs can modify the activity of proteins and the stability and translation of mRNAs. They have now been found in a wide range of organisms, and can play previously unsuspected critical regulatory roles. The bacterial small RNAs include two major classes. The largest family(with at least 20 members in Escherichia coli K12) acts by base pairing with target mRNAs to modify mRNA translation or stability; this class of RNAs also uses an RNA chaperone protein, Hfq. DsrA is the best-studied example of this family of RNAs. It has been shown to positively regulate translation of the transcription factor RpoS by opening an inhibitory hairpin in the mRNA, and to negatively regulate translation of hns by pairing just beyond the translation initiation codon. The class of RNAs that modify activity of proteins is exemplified by CsrB and CsrC of E. coli, two RNAs that bind to and inhibit CsrA, a protein translational regulator. Homologs of CsrA and related regulatory RNAs have been implicated in the regulation of gluconeogenesis, biofilm formation,and virulence factor expression in plant and human pathogens.
A GH51 α-l-arabinofuranosidase from Talaromyces leycettanus strain JCM12802 that selectively drives synergistic lignocellulose hydrolysis (2019)

In contrast to other fungal GH51 α-L-arabinofuranosidases, recombinant TlAbf51 showed excellent stability over a broad pH range and high catalytic efficiency. Moreover, TlAbf51 acted synergistically with another hemicellulase to digest arabino-polysaccharides. These favorable enzymatic properties make TlAbf51 attractive for biomass pretreatment and biofuel production.
Ramazzoite, [Mg_8Cu_(12)(PO_4)(CO_3)_4(OH)_(24)(H_2O)_(20)][(H_(0.33)SO_4)_3(H_2O)_(36)], the first mineral with a polyoxometalate cation (2018)

Ramazzoite (IMA2017-090), [Mg_8Cu_(12)(PO_4)(CO_3)_4(OH)_(24)(H_2O)_(20)][(H_(0.33)SO_4)_3(H_2O)_(36)], is a new polyoxometalate (POM) mineral from the Monte Ramazzo mine, near Genova, Liguria, Italy. It occurs on magnetite-rich matrix in association with chlorartinite, chrysotile, dypingite, goethite, lepidocrocite and nesquehonite, and is a late-stage, secondary mineral crystallizing from low-temperature, aqueous solutions. Ramazzoite forms as simple cubes up to about 0.15 mm on edge. The mineral is blue to greenishblue with a vitreous to oily lustre and pale blue streak. Crystals are very brittle with conchoidal fracture, and a perfect cleavage on {100}. The Mohs 'hardness is 2½. The measured density is 1.98(1) g cm^(–3). The mineral is soluble with mild effervescence in dilute HCl at room temperature. Optically, ramazzoite is isotropic with n = 1.491(1) (white light). Electron microprobe analyses (with CO2 from structural data and H2 O from density) gave the empirical formula [(Mg_(8.00))(Cu_(8.00)Mg_(3.78))(PO_4)(CO_3)_4(OH)_(24)(H_2O)_(20)][(H_(0.65)S_(1.01)O_4)_3(H_2O)_(36)], based on 1 P atom per formula unit (apfu). Ramazzoite is cubic, P4 3m, with the unit-cell parameters: a = 13.3887(10) A, V = 2400.0(5) A^3 and Z = 1. The crystal structure, refined to R_1= 0.064 for 803 observed reflections [I> 2 σ I], contains a novel [Mg_8Cu_(12)(PO_4)(CO_3)_4(OH)_(24)(H_2O)_(20)]^(5+)POM cation.
Impact of the generation of EGFR‐TKIs administered as prior therapy on the efficacy of osimertinib in patients with non‐small cell lung cancer harboring EGFR T790M mutation (2020)

Additional mutations other than EGFR T790M may affect the efficacy of osimertinib treatment.
Low Density Lipoprotein Receptor-Related Proteins (LRPs), Alzheimers and Cognition (2005)

This review will focus primarily on the role of the low density lipoprotein receptor-related protein (LRP-1) in neuronal synapse formation and function in Alzheimer's Disease (AD). We review the role that its ligands may have in cognition or AD: apolipoprotein E (ApoE), alpha2-macroglobulin, Transforming Growth Factor-Beta (TGFbeta, Tissue Plasminogen Activator (tPA), insulin growth factor binding protein-3 (IGFBP-3), which all bind LRP-1 and apolipoprotein J (ApoJ), which is a ligand for LRP-2. After reviewing its role as a signaling receptor, we discuss the connection between LRP and the NMDA glutamate receptor via the post synaptic density 95 (PSD-95) neuronal scaffold protein and the implications it may have for memory and cognition. Finally, we discuss the evidence supporting a role for LRP in AD. Although the evidence for LRP as a genetic risk factor is weak, many of its ligands impose genetic risk, and have been implicated in AD pathogenic cascades. We discuss the role of LRP in amyloid precursor protein (APP) processing and production of beta-amyloid (Abeta. We identify LRP ligands that accelerate aggregation of toxic Abeta species. LRP mediates crucial pathways in AD pathogenesis such as Abeta clearance, Abeta uptake, intraneuronal Abeta accumulation and Abeta-associated neuron death. Interestingly, the TGFbeta -V receptor is LRP-1. Data show that one critical ligand TGFbeta2, associated with neurodegeneration in amyloid diseases, induces LRP expression in PC12 cells. Data from rodent infusion models demonstrate the impact of TGFbeta2 in modifying Abeta- induced Long Term Potentiation (LTP) responses, presynaptic proteins, lipid peroxidation, gliosis and staining for neuronal nuclei. The evidence supports a complex and significant role of LRP in cognition and AD.
Subcellular Distribution and Membrane Topology of the Mammalian Concentrative Na+-Nucleoside Cotransporter rCNT1 (2001)

The rat transporter rCNT1 is the archetype of a family of concentrative nucleoside transporters (CNTs) found both in eukaryotes and in prokaryotes. In the present study we have used antibodies to investigate the subcellular distribution and membrane topology of this protein. rCNT1 was found to be expressed predominantly in the brush-border membranes of the polarized epithelial cells of rat jejunum and renal cortical tubules and in the bile canalicular membranes of liver parenchymal cells, consistent with roles in the absorption of dietary nucleosides, of nucleosides in the glomerular filtrate, or of nucleosides arising from the action of extracellular nucleotidases, respectively. The effect of endoglycosidase F treatment on wild-type and mutant rCNT1 expressed in Xenopus oocytes revealed that the recombinant transporter could be glycosylated at either or both of Asn605 and Asn643, indicating that its C terminus is extracellular. In contrast, potential N-glycosylation sites introduced near the N terminus, or between putative transmembrane (TM) helices 4 and 5, were not glycosylated. The deduced orientation of the N terminus in the cytoplasm was confirmed by immunocytochemistry on intact and saponin-permeabilized Chinese hamster ovary cells expressing recombinant rCNT1. These results, in conjunction with extensive analyses of CNT family protein sequences using predictive algorithms, lead us to propose a revised topological model, in which rCNT1 possesses 13 TM helices with the hydrophilic N-terminal and C-terminal domains on the cytoplasmic and extracellular sides of the membrane, respectively. Furthermore, we show that the first three TM helices, which are absent from prokaryote CNTs, are not essential for transporter function; truncated proteins lacking these helices, derived either from rCNT1 or from its human homolog hCNT1, were found to retain significant sodium-dependent uridine transport activity when expressed in oocytes.
Imaging the mechanical, electrical, and physiological properties of the heart (2002)

Two of the most formidable challenges when diagnosing cardiac disease are detecting blood perfusion defects and ascertaining whether those defects are ischemic and viable myocardial tissue or infarcted tissue. Current medical imaging techniques can help answer these important clinical questions through imaging of the mechanical, electrical, and physiological properties of the heart. This paper summarizes mathematical models that have been developed to investigate these properties of the heart through the use of medical imaging. Particular attention is given to the following three problems: 1. The evaluation of myocardial deformation using gated single photon emission computed tomography (SPECT) in conjunction with a mechanical boundary value problem; 2. the evaluation of myocardial conduction using magnetocardiography (MCG); and 3. the evaluation of perfusion and metabolism using dynamic cardiac SPECT. The use of medical imaging to better model myocardial properties has the potential to enable better care for cardiac patients and holds promise for even greater standards of care in the future.
Convergent coexpression of autism-associated genes suggests some novel risk genes may not be detectable in large-scale genetic studies (2023)

Autism spectrum disorder (ASD) is a heritable neurodevelopmental disorder characterized by deficits in social interactions and communication. Protein-altering variants in many genes have been shown to contribute to ASD; however, understanding the convergence across many genes remains a challenge. We demonstrate that coexpression patterns from 993 human postmortem brains are significantly correlated with the transcriptional consequences of CRISPR perturbations in human neurons. Across 71 ASD risk genes, there was significant tissue-specific convergence implicating synaptic pathways. Tissue-specific convergence was further demonstrated across schizophrenia and atrial fibrillation risk genes. The degree of ASD convergence was significantly correlated with ASD association from rare variation and differential expression in ASD brains. Positively convergent genes showed intolerance to functional mutations and had shorter coding lengths than known risk genes even after removing association with ASD. These results indicate that convergent coexpression can identify potentially novel genes that are unlikely to be discovered by sequencing studies.
Conductive-probe atomic force microscopy characterization of silicon nanowire (2011)

The electrical conduction properties of lateral and vertical silicon nanowires (SiNWs) were investigated using a conductive-probe atomic force microscopy (AFM). Horizontal SiNWs, which were synthesized by the in-plane solid-liquid-solid technique, are randomly deployed into an undoped hydrogenated amorphous silicon layer. Local current mapping shows that the wires have internal microstructures. The local current-voltage measurements on these horizontal wires reveal a power law behavior indicating several transport regimes based on space-charge limited conduction which can be assisted by traps in the high-bias regime (> 1 V). Vertical phosphorus-doped SiNWs were grown by chemical vapor deposition using a gold catalyst-driving vapor-liquid-solid process on higly n-type silicon substrates. The effect of phosphorus doping on the local contact resistance between the AFM tip and the SiNW was put in evidence, and the SiNWs resistivity was estimated.
Support versus inhibition of hematopoiesis by two characterized stromal cell types (1995)

Stromal cells are believed to regulate hematopoiesis through direct cell-cell contact interactions and the release of growth factors. Many questions remain, however, about their lineage derivation and functional heterogeneity. We have previously shown that the adherent nontransformed, nonimmortalized murine bone marrow stromal cell population consists of three cell types which could be grown separately in vitro. Based on the phenotype characterization and expression of surface antigens, we proposed a classification listing for murine bone marrow stromal cells as macrophages, endothelial-like cells and myofibroblasts that display smooth muscle-like characteristics in culture. The present study describes the ability of each of these freshly isolated separated murine stromal cell populations to support the growth of primitive hematopoietic stem cells previously characterized as highly enriched in long-term repopulating cells (LTRC). Of the three stromal cell types tested only the myofibroblasts were capable of support for multilineage hematopoiesis derived in vitro from LTRC in a cloning ring culture system. Endothelial-like cells had an inhibitory effect on the proliferation of LTRC and their descendant cells that was induced by exogenous growth factors. This inhibitory activity was present in a low molecular weight filtrate of endothelial-like cells culture medium. This suggests an essential role for marrow stroma myofibroblasts in the support of proliferation of hematopoietic cells at the stage of early divisions of primitive hematopoietic stem cells and endothelial-like cells as negative regulators of this proliferation.