gebhart/patrepeval huggingface dataset:
Galectin-1 promotes the invasion of bladder cancer urothelia through their matrix milieu (2018)

Abstract The progression of carcinoma of the urinary bladder involves migration of cancer epithelia through their surrounding tissue matrix microenvironment. This was experimentally confirmed when a gender- and grade-diverse set of bladder cancer cell lines were cultured in pathomimetic three-dimensional laminin-rich environments. The high-grade cells, particularly female, formed multicellular invasive morphologies in 3D. In comparison, low- and intermediate-grade counterparts showed growth-restricted phenotypes. A proteomic approach combining mass spectrometry and bioinformatics analysis identified the estrogen-driven lactose-binding lectin Galectin-1 (GAL-1) as a putative candidate that could drive this invasion. Expression of LGALS1 , the gene encoding GAL-1 showed an association with tumor grade progression in bladder cell lines. Immunohisto- and cyto-chemical experiments suggested greater extracellular levels of GAL-1 in 3D cultures of high-grade bladder cells and cancer tissues. High levels of GAL-1 associated with increased proliferation- and adhesion- of bladder cancer cells when grown on laminin-rich matrices. Pharmacological inhibition and Gal-1 knockdown in high-grade female cells decreased their adhesion to, and viability on, laminin-rich substrata. Higher GAL-1 also correlated with reduced E-cadherin and increased N-cadherin levels in consonance with a mesenchymal-like phenotype that we observed in 3D culture. The inhibition of GAL-1 reversed the stellate invasive phenotype to a more growth-restricted one in high-grade cells embedded within both basement-membrane-like and stromal collagenous matrix scaffolds. Finally, inhibition of GAL-1 specifically altered cell surface sialic acids, suggesting the mechanism by which the levels of GAL-1 may underlie the aggression and poor prognosis of invasive bladder cancer, especially in women.
A Systems Engineering Analysis of Image Quality: from PSD to MTF (2017)

Recent advances in optical metrology, surface scatter theory, and the effect of scattered light upon the MTF allows image degradation from diffraction effects, geometrical aberrations and residual optical fabrication errors to be calculated for multi-element optical systems.
IRMOF-74(<i>n</i>)–Mg: a novel catalyst series for hydrogen activation and hydrogenolysis of C–O bonds (2019)

Metal-Organic Frameworks (MOFs) that catalyze hydrogenolysis reactions are rare and there is little understanding of how the MOF, hydrogen, and substrate molecules interact. In this regard, the isoreticular IRMOF-74 series, two of which are known catalysts for hydrogenolysis of aromatic C-O bonds, provides an unusual opportunity for systematic probing of these reactions. The diameter of the 1D open channels can be varied within a common topology owing to the common secondary building unit (SBU) and controllable length of the hydroxy-carboxylate struts. We show that the first four members of the IRMOF-74(Mg) series are inherently catalytic for aromatic C-O bond hydrogenolysis and that the conversion varies non-monotonically with pore size. These catalysts are recyclable and reusable, retaining their crystallinity and framework structure after the hydrogenolysis reaction. The hydrogenolysis conversion of phenylethylphenyl ether (PPE), benzylphenyl ether (BPE), and diphenyl ether (DPE) varies as PPE > BPE > DPE, consistent with the strength of the C-O bond. Counterintuitively, however, the conversion also follows the trend IRMOF-74(III) > IRMOF-74(IV) > IRMOF-74(II) > IRMOF-74(I), with little variation in the corresponding selectivity. DFT calculations suggest the unexpected behavior is due to much stronger ether and phenol binding to the Mg(ii) open metal sites (OMS) of IRMOF-74(III), resulting from a structural distortion that moves the Mg<sup>2+</sup> ions toward the interior of the pore. Solid-state <sup>25</sup>Mg NMR data indicate that both H<sub>2</sub> and ether molecules interact with the Mg(ii) OMS and hydrogen-deuterium exchange reactions show that these MOFs activate dihydrogen bonds. The results suggest that both confinement and the presence of reactive metals are essential for achieving the high catalytic activity, but that subtle variations in pore structure can significantly affect the catalysis. Moreover, they challenge the notion that simply increasing MOF pore size within a constant topology will lead to higher conversions.
Antisense inhibition of group II phospholipase A2 expression blocks the production of prostaglandin E2 by P388D1 cells. (1993)

Macrophage-like P388D1 cells release [3H]arachidonic acid and produce prostaglandin E2 (PGE2) upon stimulation with bacterial lipopolysaccharide (LPS) and platelet-activating factor (PAF). To determine whether group II phospholipase A2 (PLA2) is involved in this release, we treated P388D1 cells with antisense inhibitors specific for group II PLA2 RNA. Treatment with oligonucleotide ASGII decreased PLA2 activity in P388D1 cell homogenates by approximately 60% and reduced the release of [3H]arachidonic acid and PGE2 from activated cells to nearly resting cell levels. The inhibition by antisense oligonucleotide ASGII was blocked when its sense complement, SGII, was included in the incubation mixture. Stably transfected P388D1 cells expressing an antisense construct for group II PLA2 also produced reduced quantities of PGE2 in response to LPS and PAF. These data suggest that prostaglandin production by activated P388D1 cells involves phospholipid hydrolysis by group II PLA2. Oligonucleotide ASGII also blocked the appearance of a heparin-releasable group II PLA2 in the culture supernatants of P388D1 cells. The disappearance of this protein correlated with reduced PGE2 production by activated cells, indicating that an extracellular heparin-associated pool of group II PLA2 is involved in prostaglandin production by P388D1 cells.
A Comparison of Mesenchymal Precursor Cells and Amnion Epithelial Cells for Enhancing Cervical Interbody Fusion in an Ovine Model (2011)

Implantation of allogeneic MPCs in combination with HA/TCP within an interbody spacer facilitates interbody fusion after diskectomy. The earlier, more robust fusion observed with MPCs relative to autograft and HA/TCP bone substitute indicates that this approach may offer a therapeutic benefit.
A Time To Event Framework For Multi-touch Attribution (2020)

Multi-touch attribution (MTA) estimates the relative contributions of the multiple ads a user may see prior to any observed conversions. Increasingly, advertisers also want to base budget and bidding decisions on these attributions, spending more on ads that drive more conversions. We describe two requirements for an MTA system to be suitable for this application: First, it must be able to handle continuously updated and incomplete data. Second, it must be sufficiently flexible to capture that an ad's effect will change over time. We describe an MTA system, consisting of a model for user conversion behavior and a credit assignment algorithm, that satisfies these requirements. Our model for user conversion behavior treats conversions as occurrences in an inhomogeneous Poisson process, while our attribution algorithm is based on iteratively removing the last ad in the path.
Comparison of Proprioception in Arthritic and Age-Matched Normal Knees* (2000)

Knee proprioception in middle-aged and elderly persons with advanced knee arthritis is reduced in comparison with that in middle-aged and elderly persons without arthritis. Such loss of proprioception is independent of the severity of knee arthritis and may foretell the development of arthritis. When a patient has reduced proprioception with regard to one knee affected by arthritis, he or she also has reduced proprioception with regard to the contralateral knee, independent of the presence or severity of degenerative arthritis. When an investigator is evaluating changes in proprioception after knee arthroplasty, it is best to compare the knee with the patient's untreated knee rather than with age-matched controls.
A novel sensitive detection method for DNA methylation in circulating free DNA of pancreatic cancer (2020)

Despite recent advances in clinical treatment, pancreatic cancer remains a highly lethal malignancy. In order to improve the survival rate of patients with pancreatic cancer, the development of non-invasive diagnostic methods using effective biomarkers is urgently needed. Here, we developed a highly sensitive method to detect DNA methylation in cell-free (cf)DNA samples based on the enrichment of methyl-CpG binding (MBD) protein coupled with a digital PCR method (MBD-ddPCR). Five DNA methylation markers for the diagnosis of pancreatic cancer were identified through DNA methylation microarray analysis in 37 pancreatic cancers. The sensitivity and specificity of the five markers were validated in another independent cohort of pancreatic cancers (100% and 100%, respectively; n = 46) as well as in The Cancer Genome Atlas data set (96% and 90%, respectively; n = 137). MBD-ddPCR analysis revealed that DNA methylation in at least one of the five markers was detected in 23 (49%) samples of cfDNA from 47 patients with pancreatic cancer. Further, a combination of DNA methylation markers and the KRAS mutation status improved the diagnostic capability of this method (sensitivity and specificity, 68% and 86%, respectively). Genome-wide MBD-sequencing analysis in cancer tissues and corresponding cfDNA revealed that more than 80% of methylated regions were overlapping; DNA methylation profiles of cancerous tissues and cfDNA significantly correlated with each other (R = 0.97). Our data indicate that newly developed MBD-ddPCR is a sensitive method to detect cfDNA methylation and that using five marker genes plus KRAS mutations may be useful for the detection of pancreatic cancers.
Descriptive Subgroup Mining of Folk Music (2009)

Descriptive analysis of music corpora is important to musi- cologists who are interested in identifying the properties that characterize specific genres of music. In this study we present such an analysis of a large corpus of folk tunes, all labeled by their origin. Subgroup Discovery (SD) is a rule learning technique located at the intersection of predictive and descriptive induction. One of the advantages of using this technique is the intuitive and interpretable result in the form of a collection of sim- ple rules. Classification accuracy is not the goal of this study. Instead, we discuss some of the highest scoring rules with respect to their descriptive power.
Supplementary Figure Text from T-cell Responses to Oncogenic Merkel Cell Polyomavirus Proteins Distinguish Patients with Merkel Cell Carcinoma from Healthy Donors (2023)

&lt;p&gt;PDF file 100K, Supplementary figure legend&lt;/p&gt;
Modeling cadmium and sulfate adsorption by mixed oxides (1996)

Adsorption of cadmium and sulfate in a mixed Fe(OH)3SiO2 system was studied using the triple-layer model. The uptake of H4SiO4 dissolved from the SiO2 particles was considered in modeling the cation and anion adsorption. The mixed oxides were formed with a range of Fe(OH)3:SiO2 ratios by controling the precipitation of ferric hydroxide in a suspension of fumed silica (Cab-O-Sil). Observation of the micromorphology of the mixed oxides by transmission electron microscopy showed that Fe(OH)3 formed separately from the SiO2 particles, therefore, an independent oxide model was used to simulate cation and anion adsorption. In this model Cd adsorption occurred on separate Fe(OH)3 and SiO2 surfaces. When the pH was lower than 8, Fe(OH)3 dominated Cd adsorption in the mixed system. Sulfate adsorption on the independent Fe(OH)3 surface was modeled for the mixed oxide system because no sulfate was adsorbed by the SiO2 surface at pH > 4. The uptake of H4SiO4 reduced sulfate adsorption, but it had a negligible effect on cadmium absorption due to a combination of sorbate competition and electrostatic interactions.
Macrophages are required for neonatal heart regeneration (2014)

Myocardial infarction (MI) leads to cardiomyocyte death, which triggers an immune response that clears debris and restores tissue integrity. In the adult heart, the immune system facilitates scar formation, which repairs the damaged myocardium but compromises cardiac function. In neonatal mice, the heart can regenerate fully without scarring following MI; however, this regenerative capacity is lost by P7. The signals that govern neonatal heart regeneration are unknown. By comparing the immune response to MI in mice at P1 and P14, we identified differences in the magnitude and kinetics of monocyte and macrophage responses to injury. Using a cell-depletion model, we determined that heart regeneration and neoangiogenesis following MI depends on neonatal macrophages. Neonates depleted of macrophages were unable to regenerate myocardia and formed fibrotic scars, resulting in reduced cardiac function and angiogenesis. Immunophenotyping and gene expression profiling of cardiac macrophages from regenerating and nonregenerating hearts indicated that regenerative macrophages have a unique polarization phenotype and secrete numerous soluble factors that may facilitate the formation of new myocardium. Our findings suggest that macrophages provide necessary signals to drive angiogenesis and regeneration of the neonatal mouse heart. Modulating inflammation may provide a key therapeutic strategy to support heart regeneration.
Adaptive routing in RS/6000 SP-like bidirectional multistage interconnection networks (2002)

The IBM RS/6000 SP is one of the most successful commercially available multicomputers. SP owes its success partially to the scalable, high bandwidth, low latency network. In this paper, we present the adaptive routing scheme used in the new SP network switch chip called the Switch2. We show that the adaptive routing methods outperform the oblivious routing methods on SP like multistage networks. It is shown that the adaptive routing increases the network throughout by up to 229% over oblivious routing in some cases. We also study the effect of output selection, functions on the network performance. We present six different output selection functions and study their performance for different system parameters and communication patterns through extensive simulation. The results show that three of these selection functions perform similar to each other and outperform the other selection functions consistently. Therefore, unlike previous research findings for meshes and tori, there is no need to use multiple (or hybrid) selection functions to obtain the best performance for the SP like bidirectional multistage interconnection networks. We also provide an analysis of the cost-effectiveness of different selection functions with respect to the complexity of their hardware implementations.
Abstract 5765: Tumor-elicited myeloid progenitors promote metastasis through induction of mesenchymal to epithelial transition (2010)

Abstract Malignant primary tumor cells colonize in target organs to form dormant micrometastasis. In some cases, the micrometastases progress to macrometastasis resulting in more than 90% of human cancer related deaths. However, the cellular and molecular regulators of metastatic initiation and progression remains poorly understood. Using a variety of metastatic tumor models we show that recruited bone marrow-derived myeloid progenitor cells comprise a significant fraction of the metastatic lung as compared to the primary tumor that predominantly have infiltrated macrophages. Specific depletion of the myeloid progenitor cells did not affect primary tumor growth but significantly impaired lung metastases. Global gene expression profiling of the CD11b+GR1+ myeloid progenitor cells identified potential pro-metastatic mediators. We have characterized one such mediator that promotes lung metastasis via promoting mesenchymal to epithelial transition (MET) of disseminated tumor cells. Our data suggests that this transition favors enhanced proliferation and survival of disseminated tumor cells so that they can successfully form functional metastases. RNAi-mediated acute suppression of this mediator in the bone marrow markedly inhibited lung metastases. Taken together, these findings illustrate the critical roles of the myeloid progenitors in metastasis and suggest the potential impact of targeting bone marrow cells and MET pathways in metastatic disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5765.
Suburothelial Bladder Contraction Detection with Implanted Pressure Sensor (2017)

This study confirms correlation between suburothelial pressure readings and intravesical bladder pressures. Due to device erosion during ambulatory studies, a wireless implant is recommended for clinical rehabilitation applications.
Exchange-correlation effects in silicon (111) inversion layers: Strain-enhanced valley-occupancy phase transition (1981)

For multivalley systems, scaling relations, which are exact in the random-phase approximation (RPA), are derived which relate the exchange-correlation energy per particle of a $v$-valley system to that of a degenerate electron gas. These potentials are used in a local density-functional calculation of the ground-state energy of a Si(111) inversion layer. The exchange-correlation effects together with a small spontaneous lattice distortion greatly reduce the magnitude of the random interfacial strain needed to account for the observed valley degeneracies seen on many Si surfaces.
Carbomethoxyfluorocarbene (2003)

Carbomethoxyfluorocarbene was studied in solution by laser flash photolysis with UV-vis and infrared detection. In contrast to expectations, carbomethoxyfluorocarbene is more reactive than carbomethoxychlorocarbene. [structure: see text]
A Comparative Proteomic Analysis of Human and Rat Embryonic Cerebrospinal Fluid (2007)

During vertebrate central nervous system development, the apical neuroepithelium is bathed with embryonic Cerebrospinal Fluid (e-CSF) which plays regulatory roles in cortical cell proliferation and maintenance. Here, we report the first proteomic analysis of human e-CSF and compare it to an extensive proteomic analysis of rat e-CSF. As expected, we identified a large collection of protease inhibitors, extracellular matrix proteins, and transport proteins in CSF. However, we also found a surprising suite of signaling and intracellular proteins not predicted by previous proteomic analysis. Some of the intracellular proteins are likely to represent the contents of microvesicles recently described within the CSF (Marzesco, A. M., et al. J. Cell Sci. 2005, 118 (Pt. 13), 2849-2858). Defining the rich composition of e-CSF will enable a greater understanding of its concerted actions during critical stages of brain development.
Test-TSV estimation during 3D-IC partitioning (2013)

Three dimensional integrated circuits (3D-ICs) are emerging as a viable solution to the interconnect scaling problem. During early design space exploration, a large number of possible partitioning solutions are evaluated w.r.t. performance, area, through-silicon-via (TSV) count, etc. During this evaluation process, the number of test-TSVs need to be added to the total TSV count, to prevent unexpected area overhead later on in the design flow. While a fixed test-TSV count may provide sufficient guardbanding, in this paper we show that it often overestimates the actual number of test-TSVs required. Currently, the only way to determine the pareto-optimial test-TSV count is to sweep the test-TSV constraint, and repeatedly apply 3D test architecture optimization algorithms. This process is time consuming, and is too slow to be used in automated partitioning. In this paper, we present a quick and accurate estimation of the pareto-optimal number of test-TSVs required for a given partition. This can be used as an input to the partitioner to quickly estimate the total number of TSVs used for a given partition, reducing over-design.
Effect of an Enhanced Self-Care Protocol on Lymphedema Status among People Affected by Moderate to Severe Lower-Limb Lymphedema in Bangladesh, a Cluster Randomized Controlled Trial (2020)

This study offers the first evidence for including lymphatic stimulating activities in recommended self-care for people affected by moderate and severe LF-related lymphedema.
Cooperative emission from a disordered system: a classical model (1997)

The effect of disorder on the collective emission from a system of classical oscillators is studied theoretically. Three types of disorder are considered: random orientation of dipole moments, finite spread in frequencies of the individual oscillators (diagonal disorder), and dipole- dipole interaction (off-diagonal disorder). We found that for sufficiently high concentration of oscillators the diagonal disorder does not completely destroy the collective character of the emission. We show that the eigenmodes of a cooperative system with disorder comprise a large number of oscillators and, due to cooperative character of the emission, their lifetime is much longer than the lifetime of an individual oscillator. Consequently, the cooperative emission spectrum of the system is not simply broadened by the disorder, but represents a superposition of relatively narrow peaks.
Surgical Interventions for Treating Acute Achilles Tendon Rupture: Key Findings from a Recent Cochrane Review (2012)

Jones, Matthew P. MBBS, BSc; Khan, Riaz J.K. FRCS(Tr&Orth), FRACS; Carey Smith, Richard L. FRCS(Tr&Orth), FRACS Author Information
Electrochemical Measurements of the Kinetics of Inhibition of Two FeFe Hydrogenases by O<sub>2</sub> Demonstrate That the Reaction Is Partly Reversible (2015)

The mechanism of reaction of FeFe hydrogenases with oxygen has been debated. It is complex, apparently very dependent on the details of the protein structure, and difficult to study using conventional kinetic techniques. Here we build on our recent work on the anaerobic inactivation of the enzyme [Fourmond et al. Nat. Chem. 2014, 4, 336-342] to propose and apply a new method for studying this reaction. Using electrochemical measurements of the turnover rate of hydrogenase, we could resolve the first steps of the inhibition reaction and accurately determine their rates. We show that the two most studied FeFe hydrogenases, from Chlamydomonas reinhardtii and Clostridium acetobutylicum, react with O2 according to the same mechanism, despite the fact that the former is much more O2 sensitive than the latter. Unlike often assumed, both enzymes are reversibly inhibited by a short exposure to O2. This will have to be considered to elucidate the mechanism of inhibition, before any prediction can be made regarding which mutations will improve oxygen resistance. We hope that the approach described herein will prove useful in this respect.
Efficient implementation of the multigrid preconditioned conjugate gradient method on distributed memory machines (1994)

A multigrid preconditioned conjugate gradient (MGCG) method[15], which uses the multigrid method as a preconditioner for the CG method, has a good convergence rate even for the problems on which the standard multigrid method does not converge efficiently. This paper considers a parallelization of the MGCG method and proposes an efficient parallel MGCG method on distributed memory machines. For the good convergence rate of the MGCG method, several difficulties in parallelizing the multigrid method are successfully settled. Besides, the parallel MGCG method on Fujitsu multicomputer AP1000[8] has high performance and it is more than 10 times faster than the Scaled CG (SCG) method[6].