gebhart/patrepeval huggingface dataset:
Abstract B03: Control of pancreatic cancer metabolism and histone acetylation by the tumor microenvironment (2016)

Abstract Though the significance of reciprocal interactions between genetically altered tumor cells and adjacent stroma is increasingly appreciated, this complex crosstalk remains poorly understood. Pancreatic ductal adenocarcinoma (PDAC) has a particularly prominent stromal compartment, shown to exert both tumor-supportive and tumor-suppressive or homeostatic functions in the context of the wound-like tumor microenvironment. To investigate the paracrine effects of PDAC stromal elements on pancreatic cancer cells, we developed a “stromal” culture system, which incorporates structural and diffusible stroma-derived elements into homotypic PDAC cell cultures amenable to functional genomics and metabolomics. These analyses revealed that microenvironmental cues co-regulate cancer metabolism and gene expression. Stromal inputs broadly influenced histone acetylation in the PDAC epigenome, which coincided with induction of genes implicated in anabolic metabolism and inflammation. The gene expression and metabolic changes induced by stromal factors overlap with those previously identified following oncogenic Kras, suggesting functional complementarity between cell-autonomous and microenvironmental pathways characteristic of PDAC. As epigenome modification results in changes in gene expression through the functions of readers, such as the bromodomain-containing BET proteins, we tested JQ1, a small molecule inhibitor of BET family bromodomain-containing proteins, for the capacity to inhibit gene expression changes downstream of stromal factors. Paracrine induction of pro-growth and inflammatory genes was inhibited by JQ1, suggesting that the BET family serves as a key transducer of stromal inputs to drive alterations in gene expression. Inhibition of acetyl-lysine sensing by the BET family reduced pancreatic tumor growth and associated inflammation in vivo, with significant reduction in expression of genes implicated in macromolecule biosynthesis and tumor-permissive immune regulation. This work suggests paracrine epigenome regulation as a conduit through which stromal signals drive metabolic and immune adaptation to a challenging tumor microenvironment. Citation Format: Mara H. Sherman, Ronald M. Evans. Control of pancreatic cancer metabolism and histone acetylation by the tumor microenvironment. [abstract]. In: Proceedings of the AACR Special Conference: Function of Tumor Microenvironment in Cancer Progression; 2016 Jan 7–10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2016;76(15 Suppl):Abstract nr B03.
Fostering Nursing Staff Competence in Personal Protective Equipment Education during COVID-19: A Mobile-Video Online Learning Approach (2022)

Nursing staff who are competent to use personal protective equipment (PPE) correctly can protect themselves while providing safe, high-quality care to patients. Under pandemic conditions, the ability to wear PPE correctly is essential in clinical practice, but the acquisition of correct PPE-wearing procedures is difficult for most staff in the absence of live practice drills. This study aimed to test the mobile video online learning approach by integrating PPE contexts into a digital learning system. We conducted an experiment to verify whether the mobile video online learning approach could effectively improve nursing staff's learning achievement, learning anxiety, critical thinking skills, and learning self-efficacy. The study used a quasi-experimental design and was conducted with 47 nursing staff, divided into one group using a mobile video online learning approach and one group with a conventional learning approach. We used pre-and post-test examinations of learning achievements, learning anxiety, critical thinking, and learning self-efficacy. Results showed a significant effect of using the mobile video online learning method in helping nursing staff to decrease learning anxiety and improve knowledge about COVID-19 protection, increase learning achievement, critical thinking skills, and learning self-efficacy. These benefits are of interest to nursing workplace managers wishing to maintain professional standards during epidemics by improving the nursing staff's PPE knowledge and self-efficacy concerning PPE.
A Simple and Inexpensive Electrochemical Assay for the Identification of Nitrogen Containing Explosives in the Field (2017)

We report a simple and inexpensive electrochemical assay using a custom built hand-held potentiostat for the identification of explosives. The assay is based on a wipe test and is specifically designed for use in the field. The prototype instrument designed to run the assay is capable of performing time-resolved electrochemical measurements including cyclic square wave voltammetry using an embedded microcontroller with parts costing roughly $250 USD. We generated an example library of cyclic square wave voltammograms of 12 compounds including 10 nitroaromatics, a nitramine (RDX), and a nitrate ester (nitroglycine), and designed a simple discrimination algorithm based on this library data for identification.
Field-induced Acceptor Ionization in Enhancement-mode GaN p-MOSFETs (2020)

This work demonstrates a p-MOSFET with a GaNM.l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.2</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.8</sub> N (20 nm)/GaN heterostructure grown by metal-organic-chemical vapor deposition (MOCVD) on 6-inch Si substrate with optimized self-aligned process. Devices with source-to-drain distance, L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SD</sub> , varying from 1 μm down to 200 nm were fabricated. Significant field-induced acceptor ionization was found in these devices at high drain voltages. The device with L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SD</sub> =200 nm shows a record combination of I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON</sub> of ~45 mA/mm and ON-OFF ratio of ~10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> when compared with other p-channel transistor demonstrations. The device also exhibits Enhancement-mode operation with threshold voltage of -0.5V. The best device shows an ON-current of 100 mA/mm but at the expense of lower on-off ratio of ~10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Thiocyanate‐Free Ruthenium(II) Sensitizers for Dye‐Sensitized Solar Cells Based on the Cobalt Redox Couple (2014)

Two thiocyanate-free ruthenium(II) sensitizers, TFRS-41 and TFRS-42, with distinctive dialkoxyphenyl thienyl substituents were successfully prepared and tested for potential applications in making dye-sensitized solar cells (DSCs). Subsequent device fabrication was conducted by using a [Co(bpy)3 ](2+/3+) -based (bpy=2,2'-bipyridine) electrolyte, for which the best performance data, namely, JSC =13.11 mA cm(-2) , VOC =862 mV, fill factor=0.771, and η=8.71%, were recorded for the sensitizer TFRS-42 with a 2,6-dialkoxyphenyl substituent under AM 1.5G irradiation. The markedly higher Voc value was confirmed by the longer electron lifetime revealed in transient photovoltage (TPV) measurements versus the TFRS-1 sensitizer. In addition, DFT calculation and detailed first-principles computational analysis were conducted to provide a rationale for the observed trends in their photovoltaic performances and electron lifetimes, with reference to different performances exhibited by three thiocyanate-free sensitizers, TFRS-1, TFRS-41 and TFRS-42, versus Z907 reference. Through the proper control of peripheral substituents, the thiocyanate-free ruthenium(II)-based DSC sensitizers can positively influence the performances of DSCs, with better light-harvesting capability and suppressed charge recombination, for DSC cells fabricated by using a [Co(bpy)3 ](2+/3+) -based electrolyte.
Epitaxial Si and Gd2O3 Heterostructures - Distributed Bragg Reflectors with Stress Management Function for GaN on Si Light Emitting Devices (2013)

Tensile stress in GaN layers grown directly on Si is a serious obstacle for the implementation of this technology for electronic and photonic devices. The problem can be solved by stress engineering using epitaxial buffer layers grown on a Si-substrate. Heteroepitaxial Si and Gd2O3 multilayer structures that can be used both as a tensile strain compensating buffer for GaN epitaxial layers and an efficient reflector for light emitting devices are demonstrated in this work. A three-periods distributed Bragg reflector has been fabricated. It exhibits 82% reflectivity at the design wavelength of 450 nm. In situ curvature measurements of the 200 mm diameter wafers with the grown structure reveal compressive stress in the Gd2O3 -Si multilayer structure. The compressive stress compensates the tensile stress which arises during subsequent growth and cooling of the GaN layer.
Isoindigo, a Versatile Electron-Deficient Unit For High-Performance Organic Electronics (2013)

Isoindigo (iI) has proven successful as an electron-accepting building block for the preparation of electroactive materials for organic electronics. Its high yielding and scalable synthesis has enabled the rapid development of a large number of molecular and polymeric iI-based materials with remarkable physical properties. This perspective provides an overview of the fundamental properties of isoindigo and summarizes the progress in the development of new materials for varied electronic applications during the last 3 years, focusing in particular on organic photovoltaics (OPVs) and organic field effect transistors (OFETs). The fundamental electronic properties of isoindigo are discussed in the context of the substitution pattern effect (5,5′ vs 6,6′) on the frontier orbitals energies and optical properties. The development of molecular systems in the 6,6′-iI configuration for OPVs is examined with an emphasis on molecular design for improved electronic properties thanks to fine-tuning of the active layer morphology via crystallization control. Numerous copolymers of iI have been reported, with both electron-rich and electron-poor comonomers. The homopolymer of isoindigo displays electron-accepting and electrochromic properties and serves as a polymeric surrogate for fullerenes in all-polymer solar cells. The copolymers’ absorption profiles span the entire visible spectrum into the near-infrared, up to 900 nm. Bulk-heterojunction solar cells based on iI copolymers have reached up to 6.3% efficiency. While the effect of processing additives and cell architecture are important, the unique electronic properties of iI polymers also provide useful insight on energetic losses within blends with fullerenes. Selected copolymers also perform highly in air-stable field effect transistors, with p-type mobilities exceeding 3 cm2/(V s). New concepts concerning the effect of backbone curvature and side-chain branching or polarity have been investigated using iI copolymers. Additionally, some all-acceptor copolymers display n-type mobility. As the design of iI materials evolves, structural modifications of the iI core emerge, targeting ambipolar charge transport and enhanced backbone planarity. Overall, isoindigo provides the field of organic electronics with impressive performance as well as a valuable platform for structure–property relationship investigation.
Proximally Coated Cementless Bipolar Hemiarthroplasty in Dorr Type C Bone (2014)

The current study was conducted to examine the clinical and radiographic outcomes of cementless bipolar arthroplasty in patients who had type C bone at the time of the procedure. A total of 87 patients (105 hips) who had type C femora and had undergone cementless bipolar hemiarthroplasty with a proximally coated cementless prosthesis for the treatment of displaced femoral neck fractures at a single institution were reviewed. Patients included 83 women and 4 men who had a mean age of 84 years (range, 72-100 years) and were followed for a mean of 6 years (range, 2-11 years). Outcomes evaluated included aseptic implant survivorship, surgical complications, Harris Hip scores, and radiographic findings. At final follow-up, there were no revisions for aseptic implant loosening. The overall aseptic implant survivorship was 95%, with 5 patients undergoing revision surgery for aseptic reasons. Three revisions were because of periprosthetic fractures after falls, 1 revision was because of intractable groin pain, and 1 revision was because of recurrent dislocations. The surgical complication rate was 8.5%, which included 3 septic revisions, 2 avulsion fractures of the greater trochanter after falls, 2 superficial wound infections, 1 recurrent dislocation, and 1 wound hematoma. The mean Harris Hip score had improved to 80 points (range, 30-97 points) at final follow-up. Despite generally poor bone quality and medical comorbidities, elderly patients with displaced femoral neck fractures achieved excellent clinical outcomes, with few perioperative complications, through the use of proximally coated cementless bipolar hemiarthroplasty.
Ultrasound and Microbubble-Mediated Targeted Delivery of Drug Loaded Nanoparticles to Porcine Liver (2018)

In this paper, we adapt and validate a platform for ultrasound (US)and microbubble (MB)-mediated delivery of drug-loaded poly lactic-co-glycolic acid nanoparticles (NPs)to liver cancer in a large animal model as a further step toward clinical translation. A single-probe ultrasound setup was used for image-guided NP delivery using clinically approved MBs. Acoustic parameters were optimized in a phantom study. Experiments were conducted in a healthy pig model to validate the platform and test the delivery efficacy in vivo. The US/MB treatment resulted in 1.9-fold increase in expression of exogenous anticancer microRNA with respect to an untreated liver region and 1884-fold increase relative to a control animal.
Using Compliant Implants to Reduce Post-Operative Pain in Pectus Excavatum Correction (2022)

Abstract In this work, we propose a medical device to be used for correcting pectus excavatum. Pectus excavatum is the most common chest wall deformity, resulting in exercise intolerance, shortness of breath, and chest pain. The current correction method uses a rigid bar that causes moderate to severe pain in patients. The device presented in this paper (termed the Elastic Bar) utilizes the phenomenon seen in pectus carinatum patients in which the patient’s chest wall becomes less stiff after a force is applied for an extended period of time; the device leverages this phenomenon to create gradual correction of the deformity. The elastic bar is a compliant solution to pectus excavatum. We present a set of requirements that determine the success of the compliant solution to correcting pectus excavatum. To analyze the performance of the device against these requirements, two models are developed, one using a fixed-guided modeling approach and the other using an initially curved beam modeling approach. We then use analytical models (developed following the Pseudo-Rigid-Body modeling technique), finite element analysis simulations, and a physical prototype to verify the feasibility of this new device. We find that the three different verification methods agree within approximately 10%. We conclude that this device has the potential to provide improved care to patients with pectus excavatum.
Deep RL-Based Spectrum Occupancy Prediction Exploiting Time and Frequency Correlations (2022)

In cognitive radio systems, predicting spectrum occupancies is a convenient alternative way to continuous spectrum sensing. It can provide information on spectrum usage and so empty spectrum bands can be used by secondary users. The usage of the spectrum bands is highly correlated over both time and frequency. Recently, machine learning algorithms are used to predict spectrum occupancy by exploiting such correlations. However, this approach primarily assumes a supervised learning setting. Despite its outstanding performance, this setting requires the availability of sufficiently large datasets (of labeled data) and is not adaptive to environment changes. In this paper, different from the existing literature, a deep reinforcement learning (RL) algorithm is used to alleviate those shortcomings. In this algorithm, we define the reward functions of the deep RL setting and its state and action spaces such that it is applicable to work dynamically, in an online fashion, in real world settings. Extensive experiments validate the capability of the proposed algorithm in predicting spectrum occupancies as examined over real world spectrum measurements. These are carried out in the 832-862 megahertz frequency bands, which are used by the leading Turkish telecom providers as private uplink bands. This is a significant step towards realizing a standalone spectrum occupancy prediction operation without any control from the operator and minimizing memory requirements while alleviating the need for the labeled dataset.
Abstract PO077: BT7480, a novel fully synthetic tumor-targeted immune cell agonist (TICA™) induces tumor localized 4-1BB agonism (2021)

Abstract Harnessing costimulatory molecules expressed on T and NK cells namely 4-1BB (CD137/TNFRSF9) is ideal for cancer immunotherapy. Despite promise preclinically, 4-1BB agonistic antibodies, were unable to demarcate hepatoxicity from efficacy in the clinic. Bispecific approaches promote target-mediated clustering of 4-1BB while limiting systemic and liver toxicity. Bicycles® are novel, fully synthetic, constrained bicyclic peptides with high affinity and selectivity to their targets. Their small size (~2kDa) and tunable pharmacokinetic parameters allow Bicycles to have superior tumor penetration and de-risk hepatoxicity concerns due to a renal clearance mechanism. We hypothesized that clustering and activation of 4-1BB could be attained by conjugating a 4-1BB binding Bicycle to a tumor antigen targeting Bicycle promoting a potent tumor-localized immune response. BT7480 is a tumor-targeted immune cell agonist (TICA™) targeting Nectin-4 and agonizing 4-1BB. Nectin-4 (PVRL4) is highly expressed in numerous tumor indications with unmet clinical needs. In an engineered 4-1BB reporter system, we found BT7480 induced potent 4-1BB agonism correlating to target antigen surface expression on the co-cultured tumor cells. Moreover, BT7480 induces cytokine secretion, including interleukin-2 and interferon gamma, in immune cell co-culture in the presence of tumor antigen. This activity is strictly dependent on Nectin-4 expression on tumor cells and the ability of the TICA to bind to both Nectin-4 and 4-1BB. In a MC38 (Nectin-4-expressing) syngeneic mouse model, intermittent dosing of BT7480 led to robust anti-tumor efficacy (22 out of 24 complete responders (CRs)). Importantly, a memory response was established in CR mice as resistance to a re-challenge with MC38 tumors was observed. Additionally, BT7480 led to increased intratumoral T cell infiltration without elevation of liver enzymes in a CT26 (Nectin-4-expressing) syngeneic mouse model. In non-human primates (NHPs), BT7480 exhibits dose linear exposure and is well tolerated up to 10mpk. BT7480 represents a new generation of chemically synthetic tumor antigen targeted 4-1BB agonists with potent efficacy and a favorable safety profile. Citation Format: Elizabeth M. Repash, Punit Upadhyaya, Johanna Lahdenranta, Jessica Kublin, Jun Ma, Marianna Kleyman, Liuhong Chen, Eric Haines, Sailaja Battula, Kevin McDonnell, Kristen Hurov, Philip Brandish, Nicholas Keen. BT7480, a novel fully synthetic tumor-targeted immune cell agonist (TICA™) induces tumor localized 4-1BB agonism [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr PO077.
Cell‐Cell Cross Talk: Volatile Compounds Are Involved in Cellular Crosstalk and Upregulation (Adv. Biosys. 10/2019) (2019)

In article number 1900131, Hossam Haick and co-workers report a new route for cross talk between cancer cells that occurs, even when they are far away from each other. The cross talk relies on volatile organic compounds (VOCs) that are generated by the cancer cell and exchanged with the cells that are found in their vicinity or at long distances.
PILOT STUDY ON THE SAFETY AND EFFICACY OF GRANULOCYTE/MONOCYTE ADSORPTION APHERESIS WITH ADACOLUMN IN PATIENTS WITH INFLAMMATORY BOWEL DISEASE (2004)

Purpose: Two open, multicenter, pilot studies evaluated the efficacy and safety of selective granulocyte/monocyte adsorption apheresis with Adacolumn, an immunomodulatory device, in the treatment of ulcerative colitis (UC) and Crohn's disease (CD). Methods: Patients who were intolerant or refractory to other IBD therapies underwent 5 sessions ((60 minutes/wk). Assessments occurred at baseline, Wks 1, 3, 5, 7, 12, and 16 using the Mayo disease activity index (DAI) for UC (range 0–12) or the CD activity index (CDAI; range 0–600). Primary endpoint was change in scores from Wk 1 to Wk 7. Quality of life (QOL) was measured using the Inflammatory Bowel Disease Questionnaire (IBDQ) and SF-36. Higher IBDQ scores indicate improved QOL. Results: Fifteen patients were enrolled in each of the 2 studies. All 5 treatments were completed by 11 of the 15 UC patients. Mean DAI scores fell from 5.9 ± 1.4 at Wk 1 to 5.2 ± 2.9 at Wk 7. Four patients (27%) responded to therapy (defined as DAI reduction of ≥3 points). Remission (defined as DAI score ≤2; rectal bleeding ≤ 1; endoscopic evaluation ≤ 1) was observed in 1 of 11 patients. Mean IBDQ scores improved (127 ± 23 at Wk 1 to 155 ± 28 at Wk 7). Mean scores on the SF-36 physical and emotional subdomains improved by a mean of 10 (13%) and 26.8 points (57.5%), respectively. Of the CD patients, 14 of 15 completed all 5 treatments. CDAI mean scores fell from 292 ± 59 at Wk 1 to 225 ± 124 at Wk 7. Eight CD patients (57%) responded (defined as CDAI reduced by >70 points). Remission (defined as CDAI score ≤150) was observed in 5 patients. Mean IBDQ scores improved (133 ± 28 before treatment to 161 ± 45 at Wk 7). Mean scores on the SF-36 physical and emotional subdomains improved by 4.6 (8%) and 12.8 points (24%), respectively. Adverse effects were infrequent. No device-related SAEs were observed. Conclusions: Adacolumn is well tolerated and shows clinical benefits in patients with refractory IBD. Patients with UC may experience further benefits from a longer regimen. Sham-controlled studies are underway.
Synthesis of Indolines via a Domino Cu-Catalyzed Amidation/Cyclization Reaction (2008)

A highly efficient one-pot procedure for the synthesis of indolines and their homologues based on a domino Cu-catalyzed amidation/nucleophilic substitution reaction has been developed. Substituted 2-iodophenethyl mesylates and related compounds afforded the corresponding products in excellent yields. No erosion of optical purity was observed when transforming enantiomerically pure mesylates under the reaction conditions.