gebhart/patrepeval huggingface dataset:
Photosensitizer dosimetry controlled PDT treatment planning reduces inter-individual variability in response to PDT (2006)

Effective Photodynamic therapy (PDT) treatment depends on the amount of active photosensitizer and the delivered light in the targeting tissue. For the same PDT treatment protocol, variation in photosensitizer uptake between animals induces variation in the treatment response between animals. This variation can be compensated via control of delivered light dose through photodynamic dose escalation based on online dosimetry of photosensitizer in the animal. The subcutaneous MAT-LyLu Dunning prostate tumor model was used in this study. Photosensitizer BPD-MA uptake was quantified by multiple fluorescence micro-probe measurements at 3 hours after verteporfin administration. PDT irradiation was carried out after photosensitizer uptake measurement with a total light dose of 75 J/cm2 and a light dose rate of 50 mW/cm2. Therapeutic response of PDT treatments was evaluated by the tumor regrowth assay. Verteporfin uptake varied considerably among tumors (inter-tumor variation 56% standard deviation) and within a tumor (largest intra-tumor variation 64%). An inverse correlation was found between mean photosensitizer intensity and PDT treatment effectiveness (R2 = 37.3%, p < 0.005). In order to compensate individual PDT treatments, photodynamic doses were calculated on an individual animal basis, by matching the light delivered to provide an equal photosensitizer dose multiplied by light dose. This was completed for the lower-quartile, mean and upper-quartile of the photosensitizer distribution. The coefficient of variance in the surviving fraction decreased from 24.9% in non-compensated PDT (NC-PDT) treatments to 16.0%, 14.0% and 15.9% in groups compensated to the lower-quartile (CL-PDT), the median (CM-PDT) and the upper-quartile (CU-PDT), respectively. In terms of treatment efficacy, the CL-PDT group was significantly less effective compared with NC-PDT, CM-PDT and CU-PDT treatments (p < 0.005). No significant difference in effectiveness was observed between NC-PDT, CM-PDT and CU-PDT. The results indicate that by measuring the mean photosensitizer concentration prior to light treatment, and then adjusting the light dose appropriately, a more uniform treatment can be applied to different animals thereby reducing the inter-individual variation in the treatment outcome.
Magnetic coupling between Sm3+and the canted spin in an antiferromagnetic SmFeO3single crystal (2012)

The perovskite SmFeO${}_{3}$ exhibits type-$G$ antiferromagnetic ordering at ${T}_{\mathrm{N}}$ \ensuremath{\approx} 670 K and an easy axis rotation transition at ${T}_{\mathrm{SR}}$ \ensuremath{\approx} 480 K. Owing to the peculiar site anisotropy of rare-earth Sm${}^{3+}$, the moment on Sm${}^{3+}$ is oriented antiparallel to the canted spin from the Fe${}^{+}$ sublattice along the $a$ axis at $T$ ${T}_{\mathrm{SR}}$. The development of the magnetic moment on Sm${}^{3+}$ as temperature decreases makes it possible to balance the two magnetic moments at ${T}_{\mathrm{comp}}$. The application of a moderate external magnetic field along the $a$ axis can trigger an abrupt reversal of the moment on Sm${}^{3+}$ and the canted spin relative to the external field at a temperature around ${T}_{\mathrm{comp}}$. We report here a study of the field-induced magnetic-moment reversal in a single crystal SmFeO${}_{3}$ by measuring the magnetization and specific heat with the external field along different crystallographic axes.
Sentiment Bias in Predictive Text Recommendations Results in Biased Writing (2018)

Prior research has demonstrated that intelligent systems make biased decisions because they are trained on biased data. As people increasingly leverage intelligent systems to enhance their productivity and creativity, could system biases affect what people create? We demonstrate that in at least one domain (writing restaurant reviews), biased system behavior leads to biased human behavior: People presented with phrasal text entry shortcuts that were skewed positive wrote more positive reviews than they did when presented with negative-skewed shortcuts. This result contributes to the pertinent debate about the role of intelligent systems in our society.
Palladium/Copper Alloy Composite Membranes for High Temperature Hydrogen Separation (2006)

This report summarizes progress made during the a three year University Coal Research grant (DEFG26-03NT41792) at the Colorado School of Mines. The period of performance was September 1, 2003 through August of 2006. We made excellent progress toward our goal of contributing to the development of high productivity, sulfur tolerant composite metal membranes for hydrogen production and membrane reactors. Composite Pd and Pd alloy metal membranes with thin metal films (1-7 {micro}m) were prepared on porous stainless steel and ceramic supports that meet or exceed the DOE 2010 and 2015 pure hydrogen flux targets at differential pressure of only 20 psi. For example, a 2 {micro}m pure Pd membrane on a Pall AccuSep{reg_sign} substrate achieved an ideal H{sub 2}/N{sub 2} separation factor of over 6000, with a pure hydrogen flux of 210 SCFH/ft{sup 2} at only 20 psig feed pressure. Similar performance was achieved with a Pd{sub 80}Au{sub 20} composite membrane on a similar stainless steel substrate. Extrapolating the pure hydrogen flux of this PdAu membrane to the DOE Fossil Energy target conditions of 150 psia feed pressure and 50 psia permeate pressure gives a value of 508 SCFH/ft{sup 2}, exceeding the 2015 target. At these thicknesses, it is the support cost that will dominate the cost of a large scale module. In a direct comparison of FCC phase PdCu and PdAu alloys on identical supports, we showed that a Pd{sub 85}Au{sub 15} (mass %) alloy membrane is not inhibited by CO, CO{sub 2}, or steam present in a water-gas shift feed mixture at 400 C, has better resistance to sulfur than a Pd{sub 94}Cu{sub 6} membrane, and has over twice the hydrogen permeance.
A Human Stem Cell Model of Fabry Disease Implicates LIMP-2 Accumulation in Cardiomyocyte Pathology (2019)

Here, we have used patient-derived induced pluripotent stem cell (iPSC) and gene-editing technology to study the cardiac-related molecular and functional consequences of mutations in GLA causing the lysosomal storage disorder Fabry disease (FD), for which heart dysfunction is a major cause of mortality. Our in vitro model recapitulated clinical data with FD cardiomyocytes accumulating GL-3 and displaying an increased excitability, with altered electrophysiology and calcium handling. Quantitative proteomics enabled the identification of >5,500 proteins in the cardiomyocyte proteome and secretome, and revealed accumulation of the lysosomal protein LIMP-2 and secretion of cathepsin F and HSPA2/HSP70-2 in FD. Genetic correction reversed these changes. Overexpression of LIMP-2 directly induced the secretion of cathepsin F and HSPA2/HSP70-2, implying causative relationship, and led to massive vacuole accumulation. In summary, our study has revealed potential new cardiac biomarkers for FD, and provides valuable mechanistic insight into the earliest pathological events in FD cardiomyocytes.
Supplementary Methods, Figures, Tables, and References from Characterization of <i>KRAS</i> Rearrangements in Metastatic Prostate Cancer (2023)

Supplementary Methods, Figures, Tables, and References from Characterization of &lt;i&gt;KRAS&lt;/i&gt; Rearrangements in Metastatic Prostate Cancer
All‐Carbon Nanotube‐Based Flexible Field‐Emission Devices: From Cathode to Anode (2011)

Abstract The fabrication of a flexible field‐emission device (FED) using single‐walled carbon nanotube (SWNT) network films as the conducting electrodes (anode and cathode) and thin multi‐walled CNT/TEOS hybrid films as the emitters is reported. P‐type doping with gold ions and passivation with tetraethylorthosilicate (TEOS) made the SWNT network film highly conductive and environmentally stable, and hence a good alternative to conventional indium tin oxide electrodes. CNT/TEOS hybrid emitters showed high current density, low turn‐on field, and long‐term emission stability, compared with CNT emitters; these characteristics can be attributed to the TEOS sol, acting both as a protective layer surrounding the nanotube tip, and as an adhesive layer enhancing the nanotube adhesion to the substrate. All‐CNT‐based flexible FEDs fabricated by this approach showed high flexibility in field emission characteristics and extremely bright electron emission patterns.
Microdeletions of ELP4 are associated with language impairment, autism spectrum disorder and epilepsy (2015)

Copy number variations (CNV) are important in the aetiology of neurodevelopmental disorders and show broad phenotypic manifestations. We compared the presence of small CNVs disrupting the ELP4-PAX6 locus in 4,092 U.K. individuals with a range of neurodevelopmental conditions, clinically referred for array comparative genomic hybridisation (aCGH), with WTCCC controls (n=4,783). The phenotypic analysis was then extended using the DECIPHER database. We followed up association using an autism patient cohort (n=3,143) compared with six additional control groups (n=6,469). In the clinical discovery series we identified eight cases with ELP4 deletions, and one with a partial duplication of ELP4 and PAX6. These cases were referred for neurological phenotypes including language impairment, developmental delay, autism and epilepsy. Six further cases with a primary diagnosis of ASD and similar secondary phenotypes were identified with ELP4 deletions, as well as another six (out of 9) with neurodevelopmental phenotypes from DECIPHER. CNVs at ELP4 were only present in 1/11,252 controls. We found a significant excess of CNVs in discovery cases compared with controls, p=7.5x10-3; as well as for autism, p=2.7x10-3. Our results suggest ELP4 deletions are highly likely to be pathogenic, predisposing to a range of neurodevelopmental phenotypes from ASD to language impairment and epilepsy.
Applying artificial neural networks to predict the dissolution profile of silica-calcium phosphate composite (SCPC) particles in vitro (2016)

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Abstract 5496: A predictive model for selective targeting of the Warburg effect through GAPDH inhibition with a natural product (2018)

Abstract Cancer cells undergo numerous adaptive processes to sustain growth and survival. One notable mechanism is by rewiring metabolism, most prominently through a phenomenon known as the Warburg effect (WE). The WE is defined by increased glucose consumption and lactate excretion in the presence or absence of oxygen. Although the WE has been extensively studied, efforts to develop successful glycolytic inhibitors have been largely unsuccessful. Targeting cancer metabolism has remained a challenge due to the lack of obvious metabolic biomarkers and difficulties achieving full enzyme inhibition without inducing toxicity in normal tissue. Although targeted cancer therapies that use genetics have been largely successful, principles for selectively targeting tumor metabolism that also depend on the environment remain unknown. In the present study, we employ metabolic control analysis to reveal that glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the sixth enzyme in glycolysis, exhibits differential control properties during the WE and can be used to predict response to targeting glucose metabolism. Using high-performance liquid chromatography coupled to high-resolution mass spectrometry (HPLC-HRMS), we conducted comparative metabolomics to establish a natural product produced by Trichoderma fungi, koningic acid (KA), as a selective inhibitor of GAPDH. We expressed a fungal-derived resistant-GAPDH allele in human cells to show that KA is highly specific for GAPDH. With machine learning, integrated pharmacogenomics, and metabolomics, we demonstrate that KA efficacy is not determined by the status of individual genes, but by the quantitative extent of the WE, leading to a therapeutic window in vivo. Thus, the basis of targeting the WE can be encoded by molecular principles that extend beyond genetic status. Current work focuses on elucidating acquired resistance mechanisms of KA in cancer cells undergoing the WE. Together, these data importantly demonstrate that a complete understanding of pharmacogenomics for cancer therapy likely requires information encoded at the metabolic level. Citation Format: Maria V. Liberti, Ziwei Dai, Suzanne E. Wardell, Joshua A. Baccile, Xiaojing Liu, Xia Gao, Robert Baldi, Mahya Mehrmohamadi, Marc O. Johnson, Neel S. Madhukar, Alexander Shestov, Iok I. C. Chio, Olivier Elemento, Jeffrey C. Rathmell, Frank C. Schroeder, Donald P. McDonnell, Jason W. Locasale. A predictive model for selective targeting of the Warburg effect through GAPDH inhibition with a natural product [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5496.
Enhancing a biomedical information extraction system with dictionary mining and context disambiguation (2004)

Journals and conference proceedings represent the dominant mechanisms for reporting new biomedical results. The unstructured nature of such publications makes it difficult to utilize data mining or automated knowledge discovery techniques. Annotation (or markup) of these unstructured documents represents the first step in making these documents machine-analyzable. Often, however, the use of similar (or the same) labels for different entities and the use of different labels for the same entity makes entity extraction difficult in biomedical literature. In this paper we present a system called BioAnnotator for identifying and classifying biological terms in documents. BioAnnotator uses domain-based dictionary lookup for recognizing known terms and a rule engine for discovering new terms. We explain how the system uses a biomedical dictionary to learn extraction patterns for the rule engine and how it disambiguates biological terms that belong to multiple semantic classes.
Groundbased Infrared Imaging of Comet Giacobini-Zinner: The Distribution of Dust During the Ice Flyby (2011)

A thermal-infrared image of comet Giacobini-Zinner has been used to determine the spatial distribution of dust grains in the Comet's coma. In the present paper we emphasize the results of this imaging which bear on the expected impact rate of dust grains on the International Cometary Explorer (ICE). The expected impact rate is calculated for a range of grain radii. For particle sizes comparable to those inferred for most comets, the impact rate is on the order of several hundred per second. This rate is in agreement with the predictions by Divine (1985), but it is more than two orders of magnitude larger than the rate observed by ICE if the observed impacts were on the spacecraft body. However, the observed impact rate is roughly comparable to that inferred from our infrared imaging if, as suggested by Gurnett et al. (this issue), the impacts were on the ICE antennae, which had a much smaller cross-sectional area than the spacecraft body.
Correlation of on‐wafer 400 V dynamic behavior and trap characteristics of GaN‐HEMTs (2014)

A method for identifying the critical traps for the dynamic behavior of gallium nitride high electron mobility transistors (GaN‐HEMTs) is described. This method provides information on where the critical traps are located in the horizontal direction. At first, the on‐wafer 400 V dynamic behavior of a GaN‐HEMT was measured. Acceptor‐like trap behavior with 0.14 eV activation energy was observed using conductance analysis. Next, trap characterization was achieved using the capacitance and series conductance transients of a comb‐style Schottky barrier diode after electrical stress. Several different biases were applied to determine the locations of the detected traps, because depletion area edges can change upon imposition of different biases. Notably, 0.18 eV acceptor‐like trap behavior below the Schottky electrode, 0.44 eV donor‐like trap behavior in the access region, and 0.5eV acceptor‐like trap behavior in access region were observed. By correlating these diode results with HEMT results, it was concluded that the critical trap behavior likely occurs below the gate electrode in HEMT. As a conclusion, the information obtained with this method should provide useful information for the improvement of device processes.
The Impact of Clinical Information on the Assessment of Endoscopic Activity: Characteristics of the Ulcerative Colitis Endoscopic Index Of Severity [UCEIS] (2015)

The UCEIS is minimally affected by knowledge of clinical details, strongly correlates with patient-reported symptoms, and is a suitable instrument for trials. CRGs performed better than individuals.
Fabrication of 3D Photonic Crystals toward Arbitrary Manipulation of Photons in Three Dimensions (2016)

The creation of large-area, unintentional-defect-free three-dimensional (3D) photonic crystals in the optical regime is a key challenge toward the realization of the arbitrary 3D manipulation of photons. In this article, we discuss an advanced fabrication method of 3D silicon photonic crystals based on the highly accurate alignment and wafer bonding of silicon-on-insulator (SOI) wafers. We introduce an advanced alignment system, in which the alignment process is automated by image recognition and feed-back control of stages, and show that it achieves an alignment accuracy better than ~50 nm. The bonding of SOI wafers is also investigated to obtain 3D crystals composed of highly pure crystalline silicon. We show the fabrication results of large-area 3D photonic crystals based on such considerations and demonstrate the successful introduction of artificial defects as functional components, such as coupled waveguide pairs or waveguides/nanocavities. We expect that these will be pioneering results toward the arbitrary 3D control of photons using 3D photonic crystals.
Discography Causes End Plate Deflection (1993)

Thoracolumbar cadaver spine segments were studied by biplane radiography techniques during intradiscal injection of radiographic contrast agent. In these radiographically nondegenerated discs, significant deformation of the end plate accompanied these in vitro discograms. End plate deflections averaged 0.3 mm. The intervertebral disc bulges averaged 0.5 mm. These results suggest that the end plate itself, or events within the bone, are possible pain sources during clinical discography.
Video S1 from ICOS Is an Indicator of T-cell–Mediated Response to Cancer Immunotherapy (2023)

&lt;p&gt;Video S1: Combo group Day 2 PET image&lt;/p&gt;
Iterative reconstruction for few-view grating-based phase-contrast CT —An in vitro mouse model (2013)

The aim of this work is to investigate the improvement of image quality in few-view grating-based phase-contrast computed tomography (PCCT) applications via compressed sensing (CS) inspired iterative reconstruction on an in vitro mouse model. PCCT measurements are performed on a grating-based PCCT setup using a high-brilliance synchrotron source and a conventional tube source. The sampling density of the data is reduced by a factor of up to 20 and iteratively reconstructed. It is demonstrated that grating-based PCCT intrinsically meets the major conditions for a successful application of CS. Contrast fidelity and the reproduction of details is presented in all reconstructed objects. The feasibility of the iterative reconstruction on data generated with a conventional X-ray source is illustrated on a fluid phantom and a mouse specimen, undersampled by a factor of up to 20.
Acute toxicity of neoadjuvant bolus 5-FU/methotrexate and leucovorin rescue followed by continuous infusion 5-FU plus pre-operative radiation therapy for rectal cancer (1996)

We present an analysis of acute toxicity of 3 cycles of neoadjuvant bolus methotrexate (MTX) with leucovorin (LV) rescue plus bolus 5-FU, followed by continuous infusion 5-FU with concurrent pre-operative 5040 cGy, and post-operative bolus 5-FU/LV in patients with rectal cancer. Nine patients (1: unresectable, 6: locally advanced, 2: resectable but bulky disease) with adenocarcinoma of the rectum limited to the pelvis were enrolled. For the neoadjuvant segment, the first 4 patients received 3 successive weeks of chemotherapy followed by a 1 week break (continuous course). Due to toxicity, the remaining 5 patients received an intermittent treatment schedule consisting of 3 weekly cycles with 1 week break between cycles 1 and 2 and cycles 2 and 3 followed by a 1 week break (intermittent course). The complete response rates were clinical: 11%, pathologic: 11%, and total: 22%. The incidence of total Grade 3+ toxicity during the neoadjuvant chemotherapy segment was 56% (5/9), and during the pre-operative combined modality segment was 33% (3/9). Therefore, for the entire pre-operative period (neoadjuvant chemotherapy plus pre-operative combined modality segments) 67% (6/9) patients had grade 3+ toxicity. The incidence of total Grade 3+ toxicity during the post-operative combined modality segment was 50% (3/6). The preliminary data suggest that resectability and complete response rates with this neoadjuvant MTX/5-FU/LV plus pre-operative radiation therapy and continuous infusion 5-FU regimen are similar to our prior experience with conventional bolus 5-FU/LV and radiation therapy. However, the incidence of grade 3+ acute toxicity is higher. Additional experience is needed to determine if this approach offers a significant advantage in local control and survival. Radiat Oncol Invest 1996;4:90–97. © 1996 Wiley-Liss, Inc.
A CMOS wave-pipelined image processor for real-time morphology (2002)

This paper presents the implementation of a high-speed morphological image processor using CMOS wave-pipelining. A modular and expandable architecture, based on wave-pipelined transmission gate logic, has been developed for gray-scale and binary morphological operators. Using this architecture, 3/spl times/3 (2-dimensional) structuring element binary dilation and erosion units, and a two-stage morphological skeleton transform filter have been implemented in CMOS 1.2 /spl mu/m technology. The operating frequency is 333 MHz, which exceeds the speeds reported in literature for this functionality. Simulation results indicate a speed-up of 4-5 compared to non-pipelined processor implementations. The wave-pipelined implementation also offers a significant reduction in latency and hardware complexity compared to regular pipelined architectures.
The Impact of Nonlinear Power Amplifier Load Impedance on Notched Waveforms for Cognitive Radar Spectrum Sharing (2020)

High-bandwidth waveforms are required to obtain good range resolution in radar applications, yet contiguous bandwidth is often not readily available. To that end, there has been significant effort involved with the design of spectrally notched radar waveforms. However, maintaining the desired notch depth for these optimized waveforms is challenging in actual transmission due to third- and other odd-order nonlinearities in the transmitter power amplifier (PA) Here the effect of the PA is examined for a particular class of transmitter-compatible notched waveforms. Load-pull measurements show that the impedance needed to maximize the power-added efficiency (PAE) and range of the radar system while ensuring a desired minimum notch depth can change significantly for different notch positions and widths. This illustrates the need for reconfigurable power amplifier circuitry in radars for waveform notching applications.