gebhart/patrepeval huggingface dataset:
Abstract PR003: Multiplexed immune phenotyping and miRNA-ISH in bronchial premalignant lesions reveals a mechanism of immune suppression (2023)

Abstract Bronchial premalignant lesions (PMLs) are precursors of lung squamous cell carcinoma. Prior work has shown that among proliferative subtype PMLs, progression to or persistence of a high-grade histology is associated with downregulation of an immune-related gene module. Furthermore, microRNA-149 (miR-149) was identified as a candidate negative regulator of this expression program. In this study, we aim to investigate the spatial distribution of miR-149 and its association with the immune environment and PML progression/persistence in PMLs. We identified 19 paraffin embedded bronchial biopsies transcriptionally defined as belonging to the proliferative subtype obtained from 9 subjects. Three consecutive sections were stained with H&amp;E for histology annotation, chromogenic miRNA in situ hybridization (miRNA-ISH) for miR-149 abundance and localization, and with 30 antibodies targeted to epithelial and immune populations using imaging mass cytometry (IMC) to perform phenotyping. We trained a robust pixel classifier to detect foci of miR-149 signal in miRNA-ISH and quantified the density of miR-149 signal. For the IMC data, we used Mesmer for cell segmentation. PhenoGraph clustering based on quantification of each antibody in each cell was used for cell population identification. Ten recurrent cellular neighborhoods were identified by K-means clustering. miR-149 density was greater in the epithelium compared with stromal tissue. The miR-149 density in dysplastic epithelium normalized to miR-149 in normal epithelium is higher in the progressive/persistent PMLs than regressive PMLs. Additionally, in progressive/persistent PMLs, we find lower average epithelial staining for the miR-149 target NLRC5 associated with a cellular neighborhood that is enriched for goblet cells and PDL1+MUC5B+ secretory cells. Cell composition analysis showed that progressive/persistent PMLs have lower CD8 T cell infiltrate in both the stroma and epithelium. These results suggest that increased miR-149 expression in progressive/persistent PMLs contributes to an immune suppressive environment characterized by a shift in secretory cell populations and T cells within the bronchial epithelium. Interventions targeting miR-149 expression may be a potential interception strategy for high-grade PMLs. Citation Format: Darren J. Chiu, Roxana Pfefferkorn, Emily Green, Boting Ning, Myrtha Constant, Marc Lenburg, Eric Burks, Sarah Mazzilli, Jennifer Beane. Multiplexed immune phenotyping and miRNA-ISH in bronchial premalignant lesions reveals a mechanism of immune suppression. [abstract]. In: Proceedings of the AACR Special Conference: Precision Prevention, Early Detection, and Interception of Cancer; 2022 Nov 17-19; Austin, TX. Philadelphia (PA): AACR; Can Prev Res 2023;16(1 Suppl): Abstract nr PR003.
Extracting fre uency dependent velocities from full waveform sonic data (2010)

In porous, fluid‐filled rock formations, compressional seismic wave velocities show a strong dependence on frequency. The potential linkage between P‐wave velocity dispersion and permeability would make the use of broadband sonic waveform data suitable for determining reservoir parameters. Automatic velocity analysis of multi‐channel sonic data can be tailored to detect and measure frequency dependent velocities.This seismic data processing strategy enables the creation of velocity dispersion logs for fluid‐filled porous media.
Role of Macromolecular Hydration in the Binding of theEscherichia coliCyclic AMP Receptor to DNA (1997)

The osmotic stress technique was used to measure the changes in macromolecular hydration that accompany binding of the Escherichia coli CAP protein to its transcription-regulatory site (C1) in the lactose promoter and that accompany the transfer of CAP from site C1 to nonspecific genomic DNA. Formation of the C1 complex is accompanied by the net release of 79 +/- 11 water molecules. If all water molecules were released from macromolecular surfaces, this result would be consistent with a net reduction of solvent-accessible surface area of 711 +/- 189 A2. This area is only slightly smaller than the solvent-inaccessible macromolecular interface in crystalline CAP-DNA complexes. The transfer of CAP from site C1 to nonspecific sites is accompanied by the net uptake of 56 +/- 10 water molecules. Taken with the water stoichiometry of sequence-specific binding, this value implies that formation of a nonspecific complex is accompanied by the net release of 2-44 water molecules. The enhanced stabilities of CAP-DNA complexes with increased osmolality (decreased water activity) may contribute to the ability of E.coli cells to tolerate dehydration and/or high external salt concentrations.
Writing‐to‐learn assignments: The journal and the microtheme (1991)

Abstract The journal and the microtheme, two versatile writing‐to‐learn strategies, are easily adapted to math, biology, electrical technology, and college‐life courses.
TerraSAR-X Antenna Calibration and Monitoring Based on a Precise Antenna Model (2009)

The high flexibility and tight accuracy requirements of modern spaceborne synthetic aperture radar (SAR) systems require innovative technologies to calibrate and process SAR images. To perform accurate pattern correction during SAR processing, an antenna model can be used to derive the multitude of different antenna beams generated by active antenna steering. The application of such an antenna model could be successfully demonstrated for the TerraSAR-X mission, launched in 2007. The methodology and the results of the in-orbit verification with an achieved accuracy of better than ±0.2 dB are reviewed in this paper in detail, showing its outstanding accuracy. Additionally, the results of the antenna pattern long-term monitoring are described, pointing out the high stability of the system.
Security and performance evaluation platform of biometric match on card (2013)

In order to verify the identity of a cardholder user, the typing of a PIN code is usually required, but this method does not guarantee the verification result. Only biometrics is able to authenticate an user as this information is strongly related to the user. To ensure security and privacy issues (such as the protection of the biometric data), Match On Card (MOC) solutions have been proposed. This approach consists in storing the biometric user's reference and computing the verification decision in a Secure Element (SE). The purpose of this paper is to propose an evaluation platform on biometric MOC for testing its performance and security. This platform allows to perform tests given scenarios and benchmarks for comparing MOCs. We illustrate the usefulness of this platform on a commercial MOC.
Increased cardiovascular risk in thyroid cancer patients taking levothyroxine: a nationwide cohort study in Korea (2018)

Objective Many thyroid cancer patients are exposed to long-term thyroid-stimulating hormone (TSH) suppression, often as lifetime treatment, and are consequently at risk for cardiovascular disease. We investigated the incidence of coronary heart disease (CHD) and ischemic stroke among thyroid cancer patients compared with matched control subjects. Design Retrospective cohort study. Methods A total of 182 419 subjects who received thyroidectomy for thyroid cancer during 2004–2012 were selected from the Korean National Health Insurance data, which cover approximately 97% of the entire Korean population. Propensity score matching was used to select non-cancer controls. Cox proportional hazards regression analysis was used to determine relative risk of coronary heart disease and ischemic stroke. Mean follow-up was 4.32 years. Results Thyroid cancer patients had elevated risk for CHD and ischemic stroke with hazard ratio (HR) of 1.15 (95% confidence interval (CI): 1.10–1.22) and 1.15 (1.09–1.22), respectively. This risk was increased in those who took a higher dosage of levothyroxine (HR: 1.47, 95% CI: 1.34–1.60 for CHD and HR: 1.56, 95% CI: 1.42–1.72 for ischemic stroke among those who took ≥170 μg/day levothyroxine). Although risk of atrial fibrillation was dose-dependently associated with levothyroxine dosage, it represents only a small proportion of ischemic stroke incidence (4.4%, 128/2914). Conclusions The risk for CHD and ischemic stroke was higher in thyroid cancer patients who received thyroidectomy, and the dosage of levothyroxine administered appears to play a major role. Greater caution is suggested for the screening and treatment of thyroid cancer and subsequent TSH suppression therapy, as well as proper management for cardiovascular disease prevention.
Transactional prefetching (2012)

Memory access latency is the primary performance bottleneck in modern computer systems. Prefetching data before it is needed by a processing core allows substantial performance gains by overlapping significant portions of memory latency with useful work. Prior work has investigated this technique and measured potential benefits in a variety of scenarios. However, its use in speeding up Hardware Transactional Memory (HTM) has remained hitherto unexplored. In several HTM designs transactions invalidate speculatively updated cache lines when they abort. Such cache lines tend to have high locality and are likely to be accessed again when the transaction re-executes. Coarse grained transactions that update several cache lines are particularly susceptible to performance degradation even under moderate contention. However, such transactions show strong locality of reference, especially when contention is high. Prefetching cache lines with high locality can, therefore, improve overall concurrency by speeding up transactions and, thereby, narrowing the window of time in which such transactions persist and can cause contention. Such transactions are important since they are likely to form a common TM use-case. We note that traditional prefetch techniques may not be able to track such lines adequately or issue prefetches quickly enough. This paper investigates the use of prefetching in HTMs, proposing a simple design to identify and request prefetch candidates, and measures performance gains to be had for several representative TM workloads.
Organorhodium(III)- and Iridium(III)-Substituted 20-Tungstobismuthates(III) and -Antimonates(III), [(MCp*)2X2W20O70]10– (M = RhIII and IrIII; X = BiIII and SbIII) (2021)

The synthesis of four organometallic RhCp*- and IrCp*-containing heteropoly-20-tungstates, [{RhCp*}<sub>2</sub>Bi<sub>2</sub>W<sub>20</sub>O<sub>70</sub>]<sup>10-</sup> (<b>1</b>), [{IrCp*}<sub>2</sub>Bi<sub>2</sub>W<sub>20</sub>O<sub>70</sub>]<sup>10-</sup> (<b>2</b>), [{RhCp*}<sub>2</sub>Sb<sub>2</sub>W<sub>20</sub>O<sub>70</sub>]<sup>10-</sup> (<b>3</b>), and [{IrCp*}<sub>2</sub>Sb<sub>2</sub>W<sub>20</sub>O<sub>70</sub>]<sup>10-</sup> (<b>4</b>) has been accomplished by reaction of (MCp*Cl<sub>2</sub>)<sub>2</sub> with [X<sub>2</sub>W<sub>22</sub>O<sub>74</sub>(OH)<sub>2</sub>]<sup>12-</sup> in aqueous solution at pH 6 and 70 °C. The four polyanions <b>1</b>-<b>4</b> were structurally characterized in the solid state by single-crystal XRD, FTIR, and TGA and in solution by <sup>183</sup>W and <sup>13</sup>C NMR. For the Rh derivatives <b>1</b> and <b>3</b> the <sup>183</sup>W-<sup>103</sup>Rh coupling (<sup>2</sup> <i>J</i> <sub>W-Rh</sub> 3.0 Hz) could be identified by <sup>183</sup>W NMR.
<title>Quasi-Conformal Remapping For Compensation Of Human Visual Field Defects: Advances In Image Remapping For Human Field Defects</title> (1989)

We are investigating image coordinate transformations possibly to be used in a low vision aid for human patients. These patients typically have field defects with localized retinal dysfunction predominately central (age related maculopathy) or peripheral (retinitis pigmentosa). Previously we have shown simple eccentricity-only remappings which do not maintain conformality. In this report we present our initial attempts on developing images which hold quasi-conformality after remapping. Although the quasi-conformal images may have less local distortion, there are discontinuities in the image which may counterindicate this type of transformation for the low vision application.
Impact Assessment of Cadmium Toxicity and Its Bioavailability in Human Cell Lines (Caco-2 and HL-7702) (2014)

Cadmium (Cd) is a widespread environmental toxic contaminant, which causes serious health-related problems. In this study, human intestinal cell line (Caco-2 cells) and normal human liver cell line (HL-7702 cells) were used to investigate the toxicity and bioavailability of Cd to both cell lines and to validate these cell lines as in vitro models for studying Cd accumulation and toxicity in human intestine and liver. Results showed that Cd uptake by both cell lines increased in a dose-dependent manner and its uptake by Caco-2 cells (720.15 µg mg(-1) cell protein) was significantly higher than HL-7702 cells (229.01 µg mg(-1) cell protein) at 10 mg L(-1). A time- and dose-dependent effect of Cd on cytotoxicity assays (LDH release, MTT assay) was observed in both Cd-treated cell lines. The activities of antioxidant enzymes and differentiation markers (SOD, GPX, and AKP) of the HL-7702 cells were higher than those of Caco-2 cells, although both of them decreased significantly with raising Cd levels. The results from the present study indicate that Cd above a certain level inhibits cellular antioxidant activities and HL-7702 cells are more sensitive to Cd exposure than Caco-2 cells. However, Cd concentrations <0.5 mg L(-1) pose no toxic effects on both cell lines.
The Use of Evoked EMG in Detecting Misplaced Thoracolumbar Pedicle Screws (2001)

Electrical stimulation of pedicle screws and EMG recording in abdominal and leg muscles in sheep provide a reliable indication of pedicle screw position. This technique can be directly applied to human thoracolumbar surgery, but differences in pedicle size would mean that new threshold voltage criteria would need to be established.
Current Situation of the Pandemic COVID-19 and Measures (2020)

This novel corona virus infectious disease has been rapidly transmitted to six continents compared to previous pandemic diseases, and hospital-centered, patient-centered approaches are not effective in controlling this disease.
Image Density and Fragility of Urinary Calculi Part II: A Clinical Correlation (1990)

Clinically, we definded the image density (ID) of a urinary calculus as ”the dif-ference of the radiopacity of the stone and the average radiopacity of the background surrounding it on a KUB film. ”From Nov. 1, 1988 to Feb. 28, 1989, there were 51 solitary ureteral stones initally treated by ESWL at the Department of Urology of NTUH. Of them, 35 were upper ureteral stones, 11 middle ureteral stones and 5 lower ureteral stones. Ten upper ureteral stones were manually repositioned back to renal pelvis and 90% of them were completely crushed by one session of ESWl (Dornier HM-3, maxium 2400 pulses, 18-22KV), the rest of them were treated in situ. 23 (68%) out of 34 ureteral stones treated in situ, with and ID≦3.0, were completely disinter-grated by one session of ESWL. There were 7 stones bearing an ID＞3.0 treated in situ, one received only one session of ESWL and resulted in residual fragments. Image density of calculi is a new clinical distinction to be included with stone size and posi-tion to make ESWL a more informed treatment. (J Urol R.O.C., 1:289-295, 1990)
Simultaneous Second and Third Harmonic Generation in Gallium Phosphide Microdisk Resonators (2021)

Gallium phosphide is a nonlinear crystal of growing importance for integrated photonics. We observe and characterize a simultaneous second harmonic generation and third harmonic generation in a gallium phosphide microdisk for the first time.
Development of a flexible tactile sensor system for a humanoid robot (2004)

The application of robots in the same workspace with humans results, intended or unintended, in direct mechanical interaction. This requires additional sensory abilities of the robots. Besides sensor systems that help the robots to structure their environment, like cameras, radar sensors, etc., a sensor system on the robot's surface is needed that is able to detect mechanical contacts of the robot with its environment. Because of shadings it is not possible to exclude potential collisions in spite of the "structuring" sensor systems. Therefore a tactile sensor system is essential for reasons of security but also as support of the robot control system and additional communication channel. In this paper we propose the requirements to such a system related to its application on an autonomous humanoid robot. According to these postulated requirements a prototypal system was built and integrated in an existing experimental setup which consists of a redundant robot arm with 7 degrees of freedom in a human-similar kinematics. The sensor and its technical specifications as well as the experimental setup are described in the second part of this paper.
An IonStar Experimental Strategy for MS1 Ion Current-Based Quantification Using Ultrahigh-Field Orbitrap: Reproducible, In-Depth, and Accurate Protein Measurement in Large Cohorts (2017)

In-depth and reproducible protein measurement in many biological samples is often critical for pharmaceutical/biomedical proteomics but remains challenging. MS1-based quantification using quadrupole/ultrahigh-field Orbitrap (Q/UHF-Orbitrap) holds great promise, but the critically important experimental approaches enabling reliable large-cohort analysis have long been overlooked. Here we described an IonStar experimental strategy achieving excellent quantitative quality of MS1 quantification. Key features include: (i) an optimized, surfactant-aided sample preparation approach provides highly efficient (>75% recovery) and reproducible (<15% CV) peptide recovery across large cell/tissue cohorts; (ii) a long column with modest gradient length (2.5 h) yields the optimal balance of depth/throughput on a Q/UHF-Orbitrap; (iii) a large-ID trap not only enables highly reproducible gradient delivery as for the first time observed via real-time conductivity monitoring, but also increases quantitative loading capacity by >8-fold and quantified >25% more proteins; (iv) an optimized HCD-OT markedly outperforms HCD-IT when analyzing large cohorts with high loading amounts; (v) selective removal of hydrophobic/hydrophilic matrix components using a novel selective trapping/delivery approach enables reproducible, robust LC-MS analysis of >100 biological samples in a single set, eliminating batch effect; (vi) MS1 acquired at higher resolution (fwhm = 120 k) provides enhanced S/N and quantitative accuracy/precision for low-abundance species. We examined this pipeline by analyzing a 5 group, 20 samples biological benchmark sample set, and quantified 6273 unique proteins (≥2 peptides/protein) under stringent cutoffs without fractionation, 6234 (>99.4%) without missing data in any of the 20 samples. The strategy achieved high quantitative accuracy (3-6% media error), low intragroup variation (6-9% media intragroup CV) and low false-positive biomarker discovery rates (3-8%) across the five groups, with quantified protein abundances spanning >6.5 orders of magnitude. Finally, this strategy is straightforward, robust, and broadly applicable in pharmaceutical/biomedical investigations.
Psychometric evaluation and normative data for a Swedish version of the Patient Health Questionnaire 15‐Item Somatic Symptom Severity Scale (2013)

The lack of an available Swedish version of the Patient Health Questionnaire 15-Item Somatic Symptom Severity Scale (PHQ-15) motivated the present psychometric evaluation of such a version as well as providing normative data for the PHQ-15. Data from 3,406 individuals who took part in the Västerbotten Environmental Health Study in Sweden were used. The respondents constitute a random sample, aged 18 to 79 years, stratified for age and sex. They responded to a Swedish translation of the PHQ-15 as well as the Hospital Anxiety and Depression Scale, the Perceived Stress Scale, and the Shirom Melamed Burnout Questionnaire for assessment of convergent validity. The distribution of PHQ-15 scores was positively skewed and mesokurtic in shape, and the internal consistency of the PHQ-15 was satisfactory. Correlation coefficients between PHQ-15 score and the measures of anxiety, depression, stress and mental/physical exhaustion indicate satisfactory validity. Normative data for PHQ-15 scores as well as for categories of somatic symptom severity are provided. The favorable psychometric properties of the Swedish version of the PHQ-15 suggest use of this instrument for quantification of somatization in Swedish and similar populations, and has the advantage of available normative data.
Role of Wnt Signaling Pathways in Clear Cell Renal Cell Carcinoma Pathogenesis in Relation to VHL and HIF Status (2020)

Renal cell carcinoma (RCC) encompasses various tumor types characterized by a variety of genetic abnormalities. The genetic changes, like mutations, deletions, and epigenetic alterations, can affect the signaling components and signaling networks, causing the modification of tumor pathogenesis and prognosis of RCC. The most prevalent RCC, clear cell RCC (ccRCC), is asymptomatic in the early stages, refractory to chemotherapy and radiation therapy, and has a poorer prognosis compared with the papillary and chromophobe ccRCC types. Loss of the VHL gene and upregulation of oxygen sensors, hypoxiainducible factor alphas (HIF-α), which promote different growth factors, is a signature of sporadic ccRCC. The VHL-HIF-α and Wnt/β-catenin pathways are closely connected and contribute to the ontogeny of ccRCC. This review confines to ccRCC and the role of the Wnt/β-catenin signaling pathways and its crosstalk with VHL/HIF.
ChemInform Abstract: Dimetalation of Furans and Thiophenes. One‐Pot Procedures for Furan‐2,5‐ and Thiophene‐2,5‐dicarboxaldehyde. (1988)

Abstract The title compounds (V) and (IX) are obtained from furan (I) or thiophene (VI) by formylation of the dipotassio (III) or dilithio derivative (VIII) with DMF (IV).
Convex-Arc Drawings of Pseudolines (2016)

A weak pseudoline arrangement is a topological generalization of a line arrangement, consisting of curves topologically equivalent to lines that cross each other at most once. We consider arrangements that are outerplanar---each crossing is incident to an unbounded face---and simple---each crossing point is the crossing of only two curves. We show that these arrangements can be represented by chords of a circle, by convex polygonal chains with only two bends, or by hyperbolic lines. Simple but non-outerplanar arrangements (non-weak) can be represented by convex polygonal chains or convex smooth curves of linear complexity.