gebhart/patrepeval huggingface dataset:
Abstract PO-117: CHD1-loss promotes tumor heterogeneity and therapy resistance in prostate cancer (2020)

Abstract Targeted therapies for driver oncogenes have transformed the management of many cancers but the magnitude and duration of response remains variable. One potential explanation for the various response is the presence of additional genomic alterations which modify the degree of dependence on the targeted driver mutation. Metastatic castration resistant prostate cancer (mCRPC) serves as an example, where the target is the androgen receptor (AR). Compared to primary disease, mCRPC is characterized by extensive heterogeneity at both genomic and transcriptional levels, including genomic copy number alterations (CNAs), which are presumed to contribute to the resistance to AR targeted therapies. To gain functional insight into the genes impacted by the copy number alterations in mCRPC, we screened 730 genes often deleted in prostate cancer for CNAs that confer in vivo resistance and identified the chromodomain helicase DNA-binding protein 1 (CHD1) as a top candidate modifying resistance, a finding supported by patient data showing that CHD1 expression is inversely correlated with clinical benefit from therapy. Depletion of CHD1 in multiple human prostate cancer cell lines confers significant resistance to enzalutamide both in vitro and in vivo. Furthermore, we observed global changes in open and closed chromatin after the depletion of CHD1, indicative of an altered chromatin state, with associated changes in gene expression. Integrative analysis of ATAC-seq and RNA-seq, combining with CRISPR-based screen, identified four heterogenous resistance drivers (GR, BRN2, NR2F1, TBX2), which are elevated in different independently derived, enzalutamide-resistant, CHD1-deleted subclones. Importantly, significantly increased transcriptional heterogeneity was observed in these CHD1-depleted resistant tumors and in the tumor samples from a large mCRPC patients’ cohort. Finally, GR inhibition restored the enzalutamide sensitiivty in resistant tumors with elevated GR signaling. These results suggest CHD1-loss, through global effects on chromatin, establishes a state of plasticity that accelerates the development of AR targeted therapy resistance through activation of heterogeneous downstream effectors, which mediated the transition away from luminal lineage identity and AR dependency. This model not only provides an innovative explanation for the significantly increased transcriptional heterogeneity observed in mCRPC patients, but also suggests that proper clinical interventions targeting these heterogenous resistance drivers may be a novel avenue to prevent or even reverse resistance towards AR targeted therapies. Citation Format: Zeda Zhang, Chuanli Zhou, Xiaoling Li, Charles Sawyers, Ping Mu. CHD1-loss promotes tumor heterogeneity and therapy resistance in prostate cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-117.
Investigating the Compatibility of Enzyme with Chelating Agents for Calcium Carbonate-Filter Cake Removal (2017)

Abstract Removal of water-based filter cake that formed either during drilling or hydraulic fracture operations is a difficult task. Chelating agents were introduced in the oil industry to solve the common problems associated with the conventional acids (hydrochloric acid, an organic acid, or a mixture of these acids), such as rapid and uncontrolled reaction rate and corrosion to well tubulars, especially in horizontal and deep wells. The objectives of this study are to (1) assess the reaction of starch with different chelating agents (GLDA, EDTA, DTPA) at different conditions of pH and temperature, (2) evaluate the compatibility of chelating agents with HTA enzyme (a-amylase enzymes), (3) assess the reaction of enzyme with starch and xanthan gum, and (4) design the best scenario for calcium carbonate filter cake removal. The obtained results showed that EDTA (20 Wt%, pH 7, and 12), DTPA (20 Wt%, pH 7, and 12), and GLDA (20 wt%, pH = 4, 7, and 12) were not able to break the starch after hot rolling for different time period (12 hrs) at 200°F. These chelating agents were incompatible with α-amylase enzyme (HTA enzyme), which was able to completely break the starch in 6 hrs at 200°F. The best scenario to remove the calcium carbonate filter cake is to soak the filter cake with use α-amylase enzyme for 6 hrs and after that soak the filter cake with GLDA (20 Wt%, pH 4) for 16 hrs.
CONCENTRATION GRADIENTS INSIDE MICRODROPLETS. (2020)

Small water microdroplets in microfluidic systems have a high surface charge density resulting from charged surfactants. As a result, an electric double layer forms inside the droplet. Depletion of ions from the center of the droplet to form the double layer can shift the concentration of ions dramatically from that of the microdroplet precursor solution. Here we show numerical solutions to the Gouy-Chapman model in spherical coordinates. Some notable effects include: 1) large percentages of the microdroplet volume experience very large DC electric fields; 2) many ions get forced into a Stern layer giving dramatically different conditions from the bulk.
18F-FAZA PET Imaging Response Tracks the Reoxygenation of Tumors in Mice upon Treatment with the Mitochondrial Complex I Inhibitor BAY 87-2243 (2014)

Our studies suggest suitability of (18)F-FAZA-PET as an early pharmacodynamic monitor on the efficacy of anticancer agents that target the mitochondrial complex I and intratumor oxygen levels (e.g., BAY 87-2243).
UCSD Biomass to Power Economic Feasibility Study - eScholarship (2009)

This report examines the economic and technical feasibility of using separated biomass feedstock from the Miramar Landfill, located in San Diego County, to generate 3 MW of power. The process will utilize gasification technology provided by West Biofuels, LLC. The objective of the study is to determine the economics of the proposed biomass power system in terms of the potential revenue streams and operational costs. The goal of this study is to determine whether this project has a positive net present value (NPV) based on the site specific parameters associated with the Miramar Landfill.
Field Accident Data Analysis of 2nd Row Children and Individual Case Reviews (2008)

&lt;div class="htmlview paragraph"&gt;Child safety is an important issue. The objective of this study was to analyze field accident data for 0-7 year old children in the 2&lt;sup&gt;nd&lt;/sup&gt; row by vehicle and crash type, irrespective of restraint use. The data was obtained from NASS-CDS for calendar years 1991-2005. Accidents were selected based on 2&lt;sup&gt;nd&lt;/sup&gt; row occupancy in towaway light vehicles with model year 1990 or newer. Side impacts caused 30.9% of serious-to-fatal injury (MAIS 3+F) to 2&lt;sup&gt;nd&lt;/sup&gt; row children followed by frontal impacts (29.8%), rollovers (24.4%) and rear crashes (15.0%). The highest risk for MAIS 3+F was in rollovers (2.8 ± 0.7%) followed by rear (1.4 ± 0.4%), side (1.0 ± 0.2%) and frontal (0.46 ± 0.10%) crashes. The differences are statistically significant (p &amp;lt;0.01).&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Individual rear and frontal impact cases were also reviewed to better understand injury mechanisms of children in the 2&lt;sup&gt;nd&lt;/sup&gt; row. The cases were obtained from the 1997-2005 NASS-CDS electronic database. Rear impact cases were chosen based on serious-to-fatal injury (MAIS 3+F). There were 19 injured children involved in 16 rear impact crashes. 13 (68.4%) injuries were associated with ≥12″ intrusion of their seating area, which pushed the child forward. There was only one child (5.3%) who was injured by rearward rotation of the front seatback. Frontal impact cases were selected by MAIS 3+F injury to the head or spine. There were 28 injured children in 26 frontal impact crashes. Children were most commonly injured by contact with the seatback, B-pillar or other structures in front of them (46.4%) or the child seat (21.4%).&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The results of this study suggest that stiffening front seats is not a reasonable approach to improving safety of 2&lt;sup&gt;nd&lt;/sup&gt; row seated children. Limiting head excursion and shielding the upper body from forces on the child seems more appropriate. The idea of a wrap-around shield integrated with the child seat may have merit in the most severe crashes where the 2&lt;sup&gt;nd&lt;/sup&gt; row child is injured by intrusion pushing the child forward into the front seatback in rear impacts or the child displacing forward contacting the front seatback or B-pillar in frontal crashes.&lt;/div&gt;
A multicenter clinical trial investigating the use of a fluoroscopically controlled cutting balloon catheter for the management of ureteral and ureteropelvic junction obstruction. (1997)

A cutting balloon endoscopic incision is effective in the majority of cases, with patency rates for endopyelotomies and endoureterotomies that mirror current endourological reports using other, albeit more time intensive and more invasive, incisional techniques.
SSCB Protection for DC Shipboard Power Systems: Breaker Design, Protection Scheme, Validation Testing (2019)

The ultrafast protection speed requirement motivates the adoption of Solid-State Circuit Breakers (SSCBs) for DC shipboard power systems. A 1kV and 1.5kA SSCB based on Reverse Blocking IGCT (RB-IGCT) semiconductor technology was designed, built, and tested for DC fault protection of naval DC shipboard power systems. This paper presents different aspects and challenges in designing an RB-IGCT based SSCB, the selection and design of a selected protection coordination scheme, and the validation test setup and experimental testing results of a single SSCB and protection coordination. The developed SSCB can also be applied for fault protection of other DC distribution system applications.
Combining message switching with circuit switching in the Interconnection Cached Multiprocessor Network (2002)

In distributed memory parallel machines, data access times can vary greatly depending on data location. This makes locality considerations important for improving performance. Switching locality is a special kind of locality which conventional networks fail to exploit fully. It refers to the phenomenon in which each computation entity in a parallel application switches most of its communication between a small set of other entities. Furthermore, the membership of these sets changes infrequently. Switching locality arises naturally in many parallel applications. The Interconnection Cached Network (ICN) is a reconfigurable network especially well suited to exploiting this locality. For applications with sufficient switching locality, appropriate choices of topology and mapping in the ICN ensure that no communication request passes through more than two switches. Short communication paths reduce propagation delays and network congestion; resulting in better overall performance. In comparison, other networks are less effective in meeting these objectives. We corroborate our stand by simulating the operation of the ICN, a multi-stage interconnection network and a 2-D Mesh network on communication graphs derived from computations on unstructured grids and sparse matrices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Segmentation of compressed documents (2002)

We present a novel technique for segmentation of a JPEG-compressed document based on block activity. The activity is measured as the number of bits spent to encode each block. Each number is mapped to a pixel brightness value in an auxiliary image which is then used for segmentation. We introduce the use of such an image and show an example of a simple segmentation algorithm, which was successfully applied to test documents. The desired region can be identified and cropped (or replaced) from the compressed data without decompressing the image.
A Novel Hybrid Sequential Design Strategy for Global Surrogate Modeling of Computer Experiments (2011)

Many complex real-world systems can be accurately modeled by simulations. However, high-fidelity simulations may take hours or even days to compute. Because this can be impractical, a surrogate model is often used to approximate the dynamic behavior of the original simulator. This model can then be used as a cheap, drop-in replacement for the simulator. Because simulations can be very expensive, the data points, which are required to build the model, must be chosen as optimally as possible. Sequential design strategies offer a huge advantage over one-shot experimental designs because they can use information gathered from previous data points in order to determine the location of new data points. Each sequential design strategy must perform a trade-off between exploration and exploitation, where the former involves selecting data points in unexplored regions of the design space, while the latter suggests adding data points in regions which were previously identified to be interesting (for example, highly nonlinear regions). In this paper, a novel hybrid sequential design strategy is proposed which uses a Monte Carlo–based approximation of a Voronoi tessellation for exploration and local linear approximations of the simulator for exploitation. The advantage of this method over other sequential design methods is that it is independent of the model type, and can therefore be used in heterogeneous modeling environments, where multiple model types are used at the same time. The new method is demonstrated on a number of test problems, showing that it is a robust, competitive, and efficient sequential design strategy.
Evaluation of the Impact of Filter Shape on the Performance of SOA-Assisted SS-WDM Systems Using Parallelized Multicanonical Monte Carlo (2009)

We study the impact of the shape of optical filters on the bit error rate (BER) of a multi-channel spectrum-sliced wavelength division multiplexed (SS-WDM) system, incorporating nonlinear semiconductor optical amplifiers (SOA) to suppress the excess intensity noise, using a parallel implementation of Multicanonical Monte Carlo (MMC) algorithm. Both the slicing filter (SF) at the transmitter, and the channel selecting filter (CSF) at the receiver are allowed to be independently chosen from a reduced set of filter shapes. BER curves corresponding to a fixed SF bandwidth and bit-rate are traced for various bandwidths of the CSF. Both the single channel case, where the only impairment is the "filtering effect", and the multi-channel case, with crosstalk, are considered. We estimate the achievable spectral efficiency of SOA-assisted SS-WDM passive optical networks (PON) when both SOA-based intensity noise suppression, and forward error correction (FEC) are employed.
A Tile-Based Solution Using Cubemap for Viewport-Adaptive 360-degree Video Delivery (2019)

360-degree video delivery in Virtual Reality is very challenging due to the fact that 360-degree videos require much higher bandwidth than conventional videos. To overcome this problem, viewport-adaptive streaming has been introduced. In this study, we propose a new adaptation method for tiling-based viewport-adaptive streaming of 360-degree videos. For content preparation, the Cubemap projection format is used, where faces or parts of a face are encoded as tiles. Also, the problem is formulated as an optimization problem, in which each visible tile is weighted based on how that tile overlaps with the viewport. To solve the problem, an approximation algorithm is proposed in this study. An evaluation of the proposed method and reference methods is carried out under different tiling schemes and bandwidths. Experiments show that the Cubemap format with tiling provides a lot of benefits in terms of storage, viewport quality across different viewing directions and bandwidths, and tolerance to prediction errors.
Investigation of a Bicyclo[1.1.1]pentane as a Phenyl Replacement within an LpPLA 2 Inhibitor (2016)

We describe the incorporation of a bicyclo[1.1.1]pentane moiety within two known LpPLA<sub>2</sub> inhibitors to act as bioisosteric phenyl replacements. An efficient synthesis to the target compounds was enabled with a dichlorocarbene insertion into a bicyclo[1.1.0]butane system being the key transformation. Potency, physicochemical, and X-ray crystallographic data were obtained to compare the known inhibitors to their bioisosteric counterparts, which showed the isostere was well tolerated and positively impacted on the physicochemical profile.
Mitigating Nonlinear Crosstalk from In-service Line Monitoring Equipment for Undersea Communication Systems (2017)

We demonstrate a novel technique that provides a monitoring gain (relative to launch power) of up to 10 dB for in-service supervisory channels. Fast polarization spinning mitigates NL crosstalk which would otherwise instigate uncorrectable block errors in FEC-supported PolMux signals. The method simplifies interoperability of terminal equipment in Open Cable Systems.
EXTH-99. SYSTEMIC AND BRAIN PHARMACOKINETICS OF A GABAA RECEPTOR AGONIST, AMLAL-101, AS AN INVESTIGATIONAL THERAPEUTIC FOR THE TREATMENT OF PRIMARY AND METASTATIC BRAIN CANCERS (2022)

Abstract PURPOSE AMLAL-101 is a novel agent which preferentially targets α3, α5 subtypes of ɣ-amino butyric acid receptors and shows anti-tumor activity against disparate cancer types. AMLAL-101 is being advanced as an ‘add-on’ to potentiate treatment of primary and metastatic brain cancers. However, AMLAL-101 must penetrate the blood-brain barrier (BBB) and show sufficient brain retention. The primary purpose of this study was to determine the plasma pharmacokinetics (PK) and quantitative estimate of the BBB permeability of AMLAL-101. METHODS We performed intracranial microdialysis, employing jugular vein cannulated Sprague-Dawley rats which facilitated simultaneous serial blood and brain extracellular fluid (ECF) sampling. AMLAL-101 was injected i.p. at 5 mg/kg and serial blood and brain ECF samples collected up to 10 h post-dosing. Plasma and ECF samples were analyzed by LC/MS-MS and plasma and ECF concentration vs time PK profiles determined. In vivo recovery analysis was performed using retrodialysis and rapid equilibrium dialysis employed to determine the extent of protein binding. RESULTS AMLAL-101 plasma protein binding was 85% and in vivo recovery from ECF was 25%. AMLAL-101 peak concentration (Cmax) in plasma and brain ECF were 15 µM and 13.8 µM, respectively. The plasma and brain ECF area under the concentration (AUC0-10) were 27.5 h.µg/mL and 24.10 h.µg/mL, respectively. The brain partitioning of unbound AMLAL-101 (Kp,uu; determined either as a ratio of brain ECF Cmax:unbound plasma Cmax or brain ECF AUC: unbound plasma AUC), were 6.13 and 4.13, respectively. The elimination half-life of AMLAL-101 was 3 h for both brain ECF and plasma. CONCLUSIONS These results suggest that AMLAL-101 has the requisite BBB permeability required for brain cancer therapeutics. AMLAL-101 shows significant brain retention when compared to a chemically similar agent that does not show anti-cancer activity, which may contribute to efficacy of AMLAL-101 as an anti-tumor agent for treatment of brain cancers.
Figure S5 from TEM8/ANTXR1-Specific CAR T Cells as a Targeted Therapy for Triple-Negative Breast Cancer (2023)

&lt;p&gt;No overt toxicity detected in mice receiving TEM8 CAR T cells.&lt;/p&gt;
Fullerene-Free Polymer Solar Cells with Highly Reduced Bimolecular Recombination and Field-Independent Charge Carrier Generation (2014)

Photogeneration, recombination, and transport of free charge carriers in all-polymer bulk heterojunction solar cells incorporating poly(3-hexylthiophene) (P3HT) as donor and poly([N,N'-bis(2-octyldodecyl)-naphthelene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-alt-5,5'-(2,2'-bithiophene)) (P(NDI2OD-T2)) as acceptor polymer have been investigated by the use of time delayed collection field (TDCF) and time-of-flight (TOF) measurements. Depending on the preparation procedure used to dry the active layers, these solar cells comprise high fill factors (FFs) of up to 67%. A strongly reduced bimolecular recombination (BMR), as well as a field-independent free charge carrier generation are observed, features that are common to high performance fullerene-based solar cells. Resonant soft X-ray measurements (R-SoXS) and photoluminescence quenching experiments (PQE) reveal that the BMR is related to domain purity. Our results elucidate the similarities of this polymeric acceptor with the superior recombination properties of fullerene acceptors.
Automated feature generation from structured knowledge (2011)

The prediction accuracy of any learning algorithm highly depends on the quality of the selected features; but often, the task of feature construction and selection is tedious and nonscalable. In recent years, however, there have been numerous projects with the goal of constructing general-purpose or domain-specific knowledge bases with entity-relationship-entity triples extracted from various Web sources or collected from user communities, e.g. YAGO, DBpedia, Freebase, UMLS, etc. This paper advocates the simple and yet far-reaching idea that the structured knowledge contained in such knowledge bases can be exploited to automatically extract features for general learning tasks. We introduce an expressive graph-based language for extracting features from such knowledge bases and a theoretical framework for constructing feature vectors from the extracted features. Our experimental evaluation on different learning scenarios provides evidence that the features derived through our framework can considerably improve the prediction accuracy, especially when the labeled data at hand is sparse.
Hotspot Detection in a Service-Oriented Architecture (2014)

Large-scale websites are predominantly built as a service-oriented architecture. Here, services are specialized for a certain task, run on multiple machines, and communicate with each other to serve a user's request. Reducing latency and improving the cost to serve is quite important, but optimizing this service call graph is particularly challenging due to the volume of data and the graph's non-uniform and dynamic nature.
Germline Mutations in theCDKN2BTumor Suppressor Gene Predispose to Renal Cell Carcinoma (2015)

Germline loss-of-function CDKN2B mutations were identified in a subset of patients with features of inherited RCC. Detection of germline CDKN2B mutations will have an impact on familial cancer screening and might prove to influence the management of disseminated disease.
Smith, Hall, and Freeman Reply: (1996)

A Reply to the Comment by Hans L. Trautenberg et al.Received 26 December 1995DOI:https://doi.org/10.1103/PhysRevLett.76.4449©1996 American Physical Society
A 0.53pJK2 7000μm2 resistor-based temperature sensor with an inaccuracy of ±0.35°C (3σ) in 65nm CMOS (2018)

In microprocessors and DRAMs, on-chip temperature sensors are essential components, ensuring reliability by monitoring thermal gradients and hot spots. Such sensors must be as small as possible, since multiple sensors are required for dense thermal monitoring. However, conventional BJT-based temperature sensors are not compatible with the sub-1V supply of advanced processes. Subthreshold MOSFETs can operate from lower supplies, but at high temperatures their performance is limited by leakage [1,2]. Thermal diffusivity (TD) sensors achieve sub-1V operation and small area with moderate accuracy, but require milliwatts of power [3]. Recently, resistor-based sensors based on RC WienBridge (WB) filters have realized high resolution and energy efficiency [4,5]. Fundamentally, they are robust to process and supply-voltage scaling. However, their readout circuitry has been based on continuous-time (CT) ΔΣ ADCs or frequency-locked loops (FLLs), which require precision analog circuits and occupy considerable area (>0.7mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ).