gebhart/patrepeval huggingface dataset:
Residual pathologic stage at radical cystectomy and risk stratification of patients with pT2N0 bladder cancer (2009)

5076 Background: We hypothesized that in patients with pT2N0 transitional cell carcinoma (TCC) of the urinary bladder, residual muscle-invasive disease at radical cystectomy (RC) may confer poorer outcomes than residual non-muscle invasive disease due to larger tumor volume and/or biologically more aggressive disease. Patients with high-risk pT2N0 disease may be candidates for trials of adjuvant therapy. Methods: Patients from the BCRC database with pT2N0 stage (N = 208) at TUR (transurethral resection) whose tumors were organ-confined at RC (≤pT2N0) were analyzed. T1N0 patients (N=33) with pT2 disease at RC were also examined in order to include all pT2 patients. None of the patients had received perioperative chemotherapy. The effect of residual pT-stage at RC on outcomes was evaluated in Kaplan-Meier, as well as in univariable and multivariable Cox-regression models. Covariates consisted of age, gender, grade, lymphovascular invasion, concomitant carcinoma-in-situ (CIS), number of lymph nodes removed, and the year of surgery. Results: Among baseline T2N0 patients, residual pT-stage at RC was pT0 in 24 (11.5%), pTa in 9 (4.3%), pCIS in 22 (10.6%), pT1 in 35 (16.8%), and pT2 in 118 patients (56.7%). The median follow-up was 50.1 months. The 5-year recurrence-free survivals of patients with residual pT0/pTa/pCis, pT1 and pT2 were 100%, 85% and 75%, respectively. The 5-year cancer-specific survival rates for the same patient cohorts were 100%, 93%, and 81%, respectively. In multivariable analyses, the effect of residual stage &lt;pT2 at RC achieved independent predictor status for recurrence (adjusted HR 0.20; p = 0.002), as well as for cancer-specific survival (adjusted HR: 0.24; p = 0.02). Initial T1 patients who were pT2 at RC did not have statistically different outcomes compared to initial T2 followed by pT2 at RC. Conclusions: Patients with pT2N0 TCC of the urinary bladder with residual non-muscle invasive disease at RC have significantly better long-term outcomes compared to residual muscle-invasive disease. With further validation, these data may facilitate the risk-stratification of patients with pT2N0 disease and enable the selection of high-risk patients for trials of adjuvant therapy. No significant financial relationships to disclose.
Equitable Outcomes in Online Programs through Wrap-Around Student Support (2022)

This chapter details a case study of an Hispanic-Serving Institution (HSI) in an urban setting that made a commitment to online programming. The wrap-around services the institution has built over the last 5 years for online students have produced gains in persistence and satisfaction and have led to a better understanding of online student support university-wide. This system of virtual wrap-around support for online students is contextualized using a scenario of a student navigating her online program. Other institutions focused on providing equitable support to their online students can emulate this proactive, collaborative, and student-centered system. These practices improve institutional and student-based outcomes, leading to more satisfied online student graduates. Moreover, a case can be made for closing the gap between the services offered to on-campus and online students in order to create a more inclusive experience for all students.
Low-Density Lipoprotein Particle Size Subfractions and Cerebral Amyloidosis (2019)

Cerebral beta-amyloidosis (CA) is a condition in which amyloid-β (Aβ) proteins are deposited in the cerebral cortex and is a predictor of Alzheimer's disease (AD). The Aging Brain Study (ABS) investigated risk factors for CA in persons with diabetes and dyslipidemia. In the ABS, we identified that greater levels of LDL cholesterol and lower levels of HDL cholesterol were associated with increased CA. LDL particles comprise multiple species of varying size, density, and protein composition. For example, within a lipoprotein profile characteristic for persons with obesity and diabetic dyslipidemia, larger LDL particles have a greater ApoE to ApoB ratio, enhancing their binding affinity to LDL receptors. The goal of this study was to identify LDL particles that associate with CA in ABS. LDL particle size fractions were measured by ion mobility in plasma samples of 58 participants (40 women and 18 men). CA was assessed using Pittsburgh Compound B index-Positron Emission Tomography (PiB-PET) imaging. Among the LDL subfractions, greater plasma levels of large LDL particles were significantly associated with greater cerebral amyloidosis and lower hippocampal volumes independent of LDL cholesterol or triglyceride levels. Since Aβ is cleared by the LDL receptor family, such as lipoprotein-like receptor 1 (LRP1), one potential mechanism for our findings is competition between ApoE enriched larger LDL particles and brain-derived Aβ on hepatic Aβ clearance and degradation. We conclude that assessing larger LDL particles in persons with atherogenic dyslipidemia may provide a mechanistic biomarker for the extent of CA.
Supplementary Figures from TIG1 Promotes the Development and Progression of Inflammatory Breast Cancer through Activation of Axl Kinase (2023)

&lt;p&gt;PDF file, 351K, Silencing endogenous TIG1 in SUM149 IBC cells inhibits cell proliferation (S1); Silencing endogenous TIG1 in KPL-4 IBC cells inhibits cell proliferation, migration, and invasion (S2); TIG1 depletion affects the growth of SUM149 cells in 3-dimensional culture (S3); Heat map of 19 selected candidates from 183 probe sets differentially expressed between SUM149 cells transfected with control siRNA and SUM149 cells transfected with siRNA targeting TIG1 (siTIG1)(S4); Representative images of crystal violet staining of migration and invasion assays for Axl-restored shTIG1-A cells (S5); TIG1 colocalized with Axl in KPL-4 cells (S6); SGI-7079 treatment inhibits the invasion of KPL-4 cells (S7).&lt;/p&gt;
Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content (2001)

In the course of evolution, genomes are shaped by processes like gene loss, gene duplication, horizontal gene transfer, and gene genesis (the de novo origin of genes). Here we reconstruct the gene content of ancestral Archaea and Proteobacteria and quantify the processes connecting them to their present day representatives based on the distribution of genes in completely sequenced genomes. We estimate that the ancestor of the Proteobacteria contained around 2500 genes, and the ancestor of the Archaea around 2050 genes. Although it is necessary to invoke horizontal gene transfer to explain the content of present day genomes, gene loss, gene genesis, and simple vertical inheritance are quantitatively the most dominant processes in shaping the genome. Together they result in a turnover of gene content such that even the lineage leading from the ancestor of the Proteobacteria to the relatively large genome of Escherichia coli has lost at least 950 genes. Gene loss, unlike the other processes, correlates fairly well with time. This clock-like behavior suggests that gene loss is under negative selection, while the processes that add genes are under positive selection.
A novel small-molecule binds to the influenza A virus RNA promoter and inhibits viral replication (2013)

Through screening by NMR spectroscopy, we discovered a novel scaffold (DPQ: 6,7-dimethoxy-2-(1-piperazinyl)-4-quinazolinamine) that binds specifically to the influenza A virus RNA promoter. The solution structure of the RNA-DPQ complex reported here demonstrates that the internal loop is the binding site of DPQ. The scaffold exhibits antiviral activity against influenza viruses.
Bridge Spatial Displacement Monitoring with Fiber Optic Deformations Sensors (2000)

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A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly ( <i>Lycorma delicatula</i> ) using the PacBio Sequel II System (2019)

Abstract A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies, however, long-read methods have historically had greater input DNA requirements and higher costs than next generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female Spotted Lanternfly ( Lycorma delicatula ) using a single PacBio SMRT Cell. The Spotted Lanternfly is an invasive species recently discovered in the northeastern United States, threatening to damage economically important crop plants in the region. The DNA from one individual was used to make one standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on one Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing approximately 36-fold coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Further, it was possible to segregate more than half of the diploid genome into the two separate haplotypes. The assembly also recovered two microbial symbiont genomes known to be associated with L. delicatula , each microbial genome being assembled into a single contig. We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.
Supplementary Figures Legend from PKCϵ Controls Mitotic Progression by Regulating Centrosome Migration and Mitotic Spindle Assembly (2023)

&lt;p&gt;Here are described the Supplementary Figures from Figure S1 to Figure S4.&lt;/p&gt;
Tuning Intrachain versus Interchain Photophysics via Control of the Threading Ratio of Conjugated Polyrotaxanes (2008)

Effective nanoscale control of intermolecular interactions in conjugated polymers is needed for the optimal development and exploitation of the latter in low-cost, large-area consumer electronics items, such as light-emitting and photovoltaic diodes, or transistors. Here we report our investigations on insulated molecular wires constituted by conjugated polymers threaded into cyclodextrin rings. Until now, there has been no detailed quantitative understanding of the role of progressive cyclodextrin encapsulation (quantifiable by the so-called "threading ratio", TR, or number of cyclodextrins per repeat unit) in tailoring the photophysics of the conjugated polymeric wires. We combine spectroscopic, electrical and surface analysis techniques to elucidate how the TR of cyclodextrin-threaded molecular wires controls formation of interchain species and related physical properties (0 < TR < or = 2.3; the maximum theoretical TR for close-packed CDs is 2.8). Increasing TR enhances the solid-state photoluminescence (PL) and electroluminescence quantum efficiency. To unravel the effect of progressive encapsulation on the intrachain decay kinetics of the polymer backbone, we added an electron-accepting quenching agent, methyl viologen (MV), to the polymer solutions. MV predominantly quenches the aggregate PL, thus enabling measurement of the decay kinetics of the intrinsic exciton even for low-TR polyrotaxanes, for which the different contributions are otherwise difficult to disentangle.
Modeling of variables in cellular infection reveals CXCL10 levels are regulated by human genetic variation and the Chlamydia-encoded CPAF protease (2020)

Susceptibility to infectious diseases is determined by a complex interaction between host and pathogen. For infections with the obligate intracellular bacterium Chlamydia trachomatis, variation in immune activation and disease presentation are regulated by both host genetic diversity and pathogen immune evasion. Previously, we discovered a single nucleotide polymorphism (rs2869462) associated with absolute abundance of CXCL10, a pro-inflammatory T-cell chemokine. Here, we report that levels of CXCL10 change during C. trachomatis infection of cultured cells in a manner dependent on both host and pathogen. Linear modeling of cellular traits associated with CXCL10 levels identified a strong, negative correlation with bacterial burden, suggesting that C. trachomatis actively suppresses CXCL10. We identified the pathogen-encoded factor responsible for this suppression as the chlamydial protease- or proteasome-like activity factor, CPAF. Further, we applied our modeling approach to other host cytokines in response to C. trachomatis and found evidence that RANTES, another T-cell chemoattractant, is actively suppressed by Chlamydia. However, this observed suppression of RANTES is not mediated by CPAF. Overall, our results demonstrate that CPAF suppresses CXCL10 to evade the host cytokine response and that modeling of cellular infection parameters can reveal previously unrecognized facets of host-pathogen interactions.
Discrete meso-element dynamic simulation of shock response of reactive porous solids (1996)

A new computer program, Discrete Meso-dynamics Method (DM2) is being developed to describe heterogeneous flow of reactive porous solids under high rates of loading. A simulated sample of Ni/Al powder mixture shows that the chemical reaction occurs for impact velocity above 1 Km/s. Fragmentation and pore collapse generate mechanical mass mixing and hot spots which appear to be the principle mechanisms for chemical reactions in porous solids.
Accelerating Image Feature Comparisons using CUDA on Commodity Hardware (2010)

Given multiple images of the same scene, image registration is the process of determining the correct transformation to bring the images into a common coordinate system—i.e., how the images fit together. Feature based registration applies a transformation function to the input images before performing the correlation step. The result of that transformation, also called feature extraction, is a list of significant points in the images, and the registration process will attempt to correlate these points, rather than directly comparing the input images.
Abstract 1850: Evaluation of Pim-1 kinase inhibition in a preclinical model of mouse prostate cancer (2015)

Abstract Pim-1 is a serine/threonine kinase that is in involved in the transcription of genes that regulate apoptosis and cell cycle progression. Pim-1 has been shown to be overexpressed in a variety of cancers and has been implicated in human prostate tumorigenesis. The aim of our study was to clarify the role of Pim-1 during the prostate tumorigenesis and determine its potential as a molecular target for therapy. To accomplish this goal, we carried out a series of experiments using a genetically engineered mouse model of prostate cancer driven by the conditional inactivation of PTEN. High levels of Pim-1 were observed during the early stages of the tumorigenesis process which decreased as tumors progressed. Expression of Pim-1 was localized in the nucleus and cytoplasm of prostatic intraepithelial neoplasia (PIN), well-differentiated, and moderately-differentiated tumors. In poorly-differentiated tumors, Pim-1expression was heterogeneously expressed at lower levels and was predominantly localized to the cytoplasm of cancer cells. Levels of Pim-1 expression were increased in tumors from mice after surgical castration. To evaluate the therapeutic potential of Pim-1as a target for prostate cancer, we tested the antitumor effects of AZD1208, a highly potent Pim kinase inhibitor, on a panel of cell lines derived from castration-naïve and castration-resistant mouse prostate cancer. AZD1208 inhibited the tumor cell growth of several cell lines and demonstrated higher sensitivity to those derived from castration resistant tumors. In vivo, drug intervention studies show that treatment with AZD1208 reduced tumor growth of castration-naïve and castration-resistant prostate tumors by 12.1 (P = 0.162) and 24.3% (P&amp;lt;0.001), respectively. These findings provide further support for a role of Pim-1 during prostate tumorigenesis and could thus serve as a rational target for the development of novel combination strategies. Citation Format: Marco A. De Velasco, Takashi Oki, Yurie Kura, Naomi Ando, Emiko Fukushima, Barry R. Davies, Dennis Huszar, Yutaka Yamamoto, Yuji Hatanaka, Nobutaka Shimizu, Kazuhiro Yoshimura, Masahiro Nozawa, Kazuhiro Yoshikawa, Kazuto Nishio, Hirotsugu Uemura. Evaluation of Pim-1 kinase inhibition in a preclinical model of mouse prostate cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1850. doi:10.1158/1538-7445.AM2015-1850
[Increased heart rate as a risk factor and treatment target in patients with heart failure]. (2017)

Numerous epidemiological studies have shown that a high resting heart rate is associated with an increased cardiovascular morbidity and mortality, particularly in heart failure. The resting heart rate is not only a risk marker in heart failure, but it is also a risk factor, i.e., modifying heart rate also modifies the risk. Chronotropic drugs have shown benefits in terms of morbidity and mortality. Nevertheless, there is a major difference between the recommended heart rate and the patientsâ€™ everyday life heart rate. Indeed, even if the proportion of heart failure patients on beta-blockers is satisfactory, the number of patients with an optimal heart rate remains insufficient. The aim of this article is to examine the deleterious effect of an elevated resting heart rate in heart failure with systolic dysfunction, in order to overcome the therapeutic inertia and to improve the outcome in this patient group.
MCSS functionality maps for a flexible protein (1999)

The Multiple Copy Simultaneous Search (MCSS) methodology for finding energetically favorable positions and orientations of small functional groups in a binding site is extended to include flexibility of the target. This makes possible the finding of novel minima not present in a fixed structure and so extends the diversity of inhibitors that can be constructed starting with the MCSS procedure. Quenched molecular dynamics is used to generate energetically favorable positions and orientations of the functional groups in the field of a flexible protein. The method is applied to the viral protein HIV-1 protease with methanol and methyl ammonium as a test case. If the protein is quenched with many copies of functional groups randomly distributed in the binding site, the resulting minima have ligand-protein interaction energies that are, on average, less favorable than those obtained with standard MCSS. This is a consequence of the renormalized potential function employed in the Locally Enhanced Sampling (LES) approximation. However, local optimizations of existing MCSS minima with a flexible protein results in lower energy minima in regions of the protein that are of particular interest. Their use in constructing a consensus protein model for ligand design is discussed.
Protease‐Activated Receptor‐2 (PAR‐2) Is Present in the Rat Hippocampus and Is Associated with Neurodegeneration (1997)

Protease-activated receptor-2 (PAR-2) is a seven-transmembrane G protein-coupled receptor that possesses a structure and activation mechanism similar to those of the thrombin receptor. It is activated by low concentrations of trypsin (300 pM) and a synthetic hexapeptide [sequence of serine, leucine, isoleucine, glycine, arginine, leucine (SLIGRL), the rodent PAR-2 "tethered ligand"] representing the first six amino acids following the putative PAR-2 cleavage site. Previous studies have indicated that alpha-thrombin and SFLLRN (synthetic hexapeptide sequence of serine, phenylalanine, leucine, leucine, arginine, asparagine; the human thrombin receptor "tethered ligand") induce neurite retraction and neurotoxicity. Because of the strong similarities between thrombin receptor and PAR-2, we have proposed that PAR-2 may also participate in neurodegeneration. In the present study, we used reverse transcriptase polymerase chain reaction and immunocytochemistry to provide the first evidence that PAR-2 is present in the rat hippocampus. Moreover, we found SLIGRL to be toxic to hippocampal neurons in a concentration-dependent manner (> or = 100 microM). Calcium signaling studies were performed to aid in determining the mechanism by which PAR-2 activation is neurotoxic.
Phonetic Classification Using Hierarchical, Feed-forward, Spectro-temporal Patch-based Architectures (2007)

... object recognition was applied to the task of phonetic classification. During learning, the system processed 2-D wideband magnitude spectrograms directly as images, producing a set of 2-D spectrotemporal patch dictionaries at different spectro-temporal positions, orientations, scales, and of varying complexity. During testing, features were computed by comparing the stored patches with patches from novel spectrograms. Classification was performed using a regularized least squares classifier (Rifkin, Yeo et al. 2003; Rifkin, Schutte et al. 2007) trained on the features computed by the system. On a 20-class TIMIT vowel classification task, the model features achieved a best result of 58.74 % error, compared to 48.57 % error using state-of-the-art MFCC-based features trained using the same classifier. This suggests that hierarchical, feed-forward, spectro-temporal patch-based architectures may be useful for phonetic analysis.
Clinicopathologic Study of Conjunctivochalasis (2004)

Based on our histopathologic findings, we hypothesize that mechanical forces between the lower lid and conjunctiva gradually interfered with lymphatic flow. Chronic, prolonged mechanical obstruction of lymphatic flow may result in lymphatic dilation and eventually give rise to clinical conjunctivochalasis.
No radiographic wrist damage after treatment to target in recent-onset juvenile idiopathic arthritis (2019)

NTR, NL1504 (NTR1574). Registered 01-06-2009.
73.4: Reflective LCD with High Reflectance and Color Reproductivity for Reduced Eye Strain (2015)

We fabricated prototypes of a 434‐ppi 5.9‐in reflective liquid crystal display for use as an e‐book reader. With high‐level optical characteristics with a reflectance of 25.1% and an NTSC ratio of 37%, we achieved eye‐friendly reflective LCD.
Stent thrombosis: a poor man's disease? (2009)

The incidence rate of stent thrombosis is at least 0.85% in our population. It appears in patients with significantly lower socioeconomic status and with certain clinical predictors. These results warrant stricter follow-up and support the policy of healthcare providers regarding patients at risk for stent thrombosis.
Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes (2018)

Our microbial composition analysis pipeline for single-molecule real-time 16S rRNA gene sequencing (MCSMRT, https://github.com/jpearl01/mcsmrt ) overcomes deficits of standard marker gene-based microbiome analyses by using CCS of entire 16S rRNA genes to provide increased taxonomic and phylogenetic resolution. Extensions of this approach to other marker genes could help refine taxonomic assignments of microbial species and improve reference databases, as well as strengthen the specificity of associations between microbial communities and dysbiotic states.