gebhart/patrepeval huggingface dataset:
A phase II, dose-optimization trial of autologous T cells genetically engineered to express anti-CD19 chimeric antigen receptor (CART-19) in patients with relapsed or refractory (r/r) CD19+ chronic lymphocytic leukemia (CLL). (2013)

TPS7132 Background: The poor prognosis and lack of effective treatment options for patients with r/r CLL highlight the need for novel therapies in this setting. CD19 is a promising anticancer target because it is broadly expressed on normal and malignant B cells through several stages of maturation but absent on pluripotent stem cells. CART-19 (CTL019) therapy involves adoptive transfer of autologous T cells genetically modified via lentiviral transduction to express chimeric antigen receptors (CAR) designed to target CD19+ cells. CART-19 cells express a CD19 antigen recognition domain combined with intracellular signaling domains, CD137 (4-1BB) and CD3-zeta, which mediate cytolytic T-cell activity. In patients with r/r CLL, CART-19 therapy showed potent antileukemic activity with long-term persistence of transduced cells at doses from 1.4 × 10 7 to 1.1 × 10 9 CART-19 cells. As of August 2012, 3 of 8 evaluable CLL patients achieved CR (two &gt; 24 months and one &gt; 5 months) and remain in CR with detectable CART-19 cells. Two patients had PR lasting 3 and 5 months, and 3 patients did not respond (Porter et al. NEJM. 2011; Kalos et al. Sci Transl Med. 2011; Porter et al. ASH 2012). Here, we describe a study to determine the optimal dose of CART-19 cells (NCT01747486). Methods: Adults with relapsed or persistent CLL or SLL after ≥ 2 previous therapies will undergo leukapheresis to obtain T cells, which will be stimulated, expanded, and lentivirus transduced ex vivo to express the CD19/4-1BB/CD3-zeta CAR. Patients will undergo lymphodepletion chemotherapy prior to infusion of CART-19 cells. In stage I of the II-stage trial, 30 patients will be randomized 1:1 and receive either 1-5 × 10 8 or 1-5 × 10 7 CART-19 T cells. The optimal dose in stage I will be selected based on clinical responses, feasibility, and tolerability. In stage II, 8 additional patients will be enrolled into the selected dose cohort. Study objectives are to determine the efficacy (CR rate within 3 months) and safety (CTCAE v 4.0) of each dose, in vivo CART-19 expansion, and manufacturing feasibility. Three patients have been enrolled as of January 2013. Clinical trial information: NCT01747486.
Noninvasive Imaging of Colitis Using Multispectral Optoacoustic Tomography (2016)

Currently, several noninvasive modalities, including MRI and PET, are being investigated to identify early intestinal inflammation, longitudinally monitor disease status, or detect dysplastic changes in patients with inflammatory bowel disease. Here, we assess the applicability and utility of multispectral optoacoustic tomography (MSOT) in evaluating the presence and severity of colitis. <b>Methods:</b> C57B/6 mice were untreated or treated with <i>Bacteroides fragilis</i> and antibiotic-mediated depletion of intestinal flora to initiate colitis. Mice were imaged using MSOT to detect intestinal inflammation. Intestinal inflammation identified with MSOT was also confirmed using both colonoscopy and histology. <b>Results:</b> Mice with bacterial colitis demonstrated a temporally associated increase in mesenteric and colonic vascularity with an increase in mean signal intensity of oxygenated hemoglobin (<i>P</i> = 0.004) by MSOT 2 d after inoculation. These findings were significantly more prominent 7 d after inoculation, with increased mean signal intensity of oxygenated hemoglobin (<i>P</i> = 0.0002) and the development of punctate vascular lesions on the colonic surface, which corresponded to changes observed on colonoscopy as well as histology. <b>Conclusion:</b> With improvements in depth of tissue penetration, MSOT may hold potential as a sensitive, accurate, noninvasive imaging tool in the evaluation of patients with inflammatory bowel disease.
Damage Caused by Dynamic/Cyclic Loading of Detonation Chamber (2011)

The plastic damage caused by multiple dynamic loading and its influence on the ductility and toughness of 3.5%Ni-steel (SA203E) and C-steel (SA516M) were examined for the discussion of integrity design of detonation chambers. V-notched specimens and hourglass specimens were welded on 1/7-scale model of a 1-ton explosive class detonation chamber and subjected to 30 detonation shots. It has been indicated that 30 detonation shots caused pre-strain in the specimens. The ductility was reduced by the pre-strain. The Charpy impact toughness was affected as well in a lower temperature. It has been noted that the damage is developed with fatigue crack growth at notch root of the V-notched specimen.
Creating touch-screens anywhere with interactive projected displays (2003)

We demonstrate a system that combines steerable projection and computer vision technologies to create "touch-screen" style interactive displays on any flat surface in a space. A high-end version of the system -- the Everywhere Display (ED) -- combines an LCD projector with motorized focus and zoom, a computer controlled pan-tilt mirror, and a pan-tilt zoom camera to enable steering of interactive projections around space. A low-end version (ED-lite) enables creation of interactive displays using a portable projector and camera attached to a laptop computer. Unlike traditional augmented reality systems, the ED systems enable delivery of interactive multimedia content on ordinary objects without requiring users to wear head mounted displays or carry special input devices.
University–utility partnerships: Best practices for water innovation and collaboration (2019)

University-utility partnerships (UUPs) are mutually beneficial collaborations that promote and accelerate innovation in the water sector. The Leaders Innovation Forum for Technology (LIFT) program worked with representatives from universities and utilities to define successful methods and strategies for establishing strong university-utility collaborative partnerships. Overall, partners in a successful university-utility collaboration need to be honest and realistic to match university capabilities and utility needs. In order to manage expectations at both organizations, utilities and universities must understand their respective points of view. Building and maintaining strong relationships should be a primary concern. Successful UUPs are built upon strong relationships between organizations rather than just strong research ideas. Different implementation structures should be considered for UUPs depending on what works best for both organizations. Common hurdles to overcome when implementing UUPs include working across distances and managing risks related to financing, intellectual property, and public outreach. PRACTITIONER POINTS: University-utility collaborative partnerships are mutually beneficial and promote innovation throughout the water sector as a whole Establishing successful partnerships can be challenging, but difficulties can be mitigated by following the described best practices Partnerships can be structured and implemented in a variety of ways depending on the specific needs of each organization involved.
High Density Interconnect Standards for Next Generation Broadcast Networks (2010)

HD-BNC is a high density interconnect standard which satisfies space constraints in next generation system architectures. The configuration maintains expectations relative to user experience, mechanical robustness and low loss at extended frequencies to support higher data rates. BNC connectors per IEC 169–8, having been deployed in systems for over 50 years, offers robust performance and user friendly quarter turn bayonet style coupling. HD-BNC is therefore proposed as an open standard solution preserving all of the benefits of BNC with a fourfold footprint reduction. HD-BNC was developed from inception as a 75 Ohm interface with extensive simulation and test validation to optimize signal transmission per SMPTE-292M and 424M standards in both analog and digital video and audio signals. This paper will detail the development process and contrast this interconnect solution to others in the industry in key areas such as mechanical robustness and electrical performance of real world applications.
Viral Aerosol Concentration Characterization and Detection in Bounded Environments (2021)

Viral spread has been intermittently threatening human life over time. Characterizing the viral concentration and modelling the viral transmission are, therefore, considered major milestones for enhancing viral detection capabilities. This paper addresses the problem of viral aerosol detection from the exhaled breath in a bounded environment, e.g., a bounded room. The paper models the exhaled breath as a cloud which is emitted through the room, and analyzes the temporal-spatial virus-laden aerosol concentration by accounting for partial absorption and reflection at each side of the room. The paper first derives a closed form expression of the temporal-spatial virus-laden aerosol concentration. It then considers the deployment of a receiver composed of an air sampler and a bio-sensor to detect the viral existence of a specific virus. We, therefore, assess the detection capabilities of the proposed system via evaluating the viral miss-detection probability as a function of the sampling volume and the detection time-instance at the receiver side. Our numerical simulations verify the validity of the analytical results, and illustrate the ability of the proposed system to detect viruses in indoor environments. The results further characterize the impacts of several system parameters on the miss-detection probability.
Oncogene-Selective Sensitivity to Synchronous Cell Death following Modulation of the Amino Acid Nutrient Cystine (2017)

Cancer cells reprogram their metabolism, altering both uptake and utilization of extracellular nutrients. We individually depleted amino acid nutrients from isogenic cells expressing commonly activated oncogenes to identify correspondences between nutrient supply and viability. In HME (human mammary epithelial) cells, deprivation of cystine led to increased cell death in cells expressing an activated epidermal growth factor receptor (EGFR) mutant. Cell death occurred via synchronous ferroptosis, with generation of reactive oxygen species (ROS). Hydrogen peroxide promoted cell death, as both catalase and inhibition of NADPH oxidase 4 (NOX4) blocked ferroptosis. Blockade of EGFR or mitogen-activated protein kinase (MAPK) signaling similarly protected cells from ferroptosis, whereas treatment of xenografts derived from EGFR mutant non-small-cell lung cancer (NSCLC) with a cystine-depleting enzyme inhibited tumor growth in mice. Collectively, our results identify a potentially exploitable sensitization of some EGFR/MAPK-driven tumors to ferroptosis following cystine depletion.
A gesture-based american sign language game for deaf children (2005)

We present a system designed to facilitate language development in deaf children. The children interact with a computer game using American Sign Language (ASL). The system consists of three parts: an ASL (gesture) recognition engine; an interactive, game-based interface; and an evaluation system. Using interactive, user-centered design and the results of two Wizard-of-Oz studies at Atlanta Area School for the Deaf, we present some unique insights into the spatial organization of interfaces for deaf children.
ChemInform Abstract: Synthesis of the Oxygenated Bicyclo[9.3.1]pentadecane Ring System of Phomactin A Using Chromium(II)‐Mediated Macrocyclization and Ring Closure Metathesis. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Morphology and antifungal effect of nano-ZnO and nano-Pd-doped nano-ZnO against Aspergillus and Candida (2012)

The present work was aimed to study the activity of nano-particulated ZnO and nano Pd doped nano-ZnO against Aspergillus and Candida species, commonly contaminating the water supply systems. Micro-ZnO was purchased from the market (Aldrich, USA) while nano ZnO were synthesized using sole gel and precipitation methods and their morphology was determined using XRD and TEM techniques. The average grain size of nano-ZnO estimated by these techniques was 30 nm and 20 nm, respectively. The doping of nano-ZnO with 5 % Pd was achieved by a thermal decomposition method and its morphology; as characterized by XRD, TEM and FESEM techniques; gave an average grain size of 35 nm. Serial dilutions of nano-ZnO doped with 5 % Pd, pure nano-ZnO and micro-ZnO (as a control) were prepared from 10 mg/mL stock solution of each in dermasel agar (OXOID), inoculated with standard strains of Candida albicans and Aspergillus niger and incubated at 37°C for 24 and 48 hours, respectively. Their antimicrobial effect was compared by the minimal inhibitory concentration (MIC), determined as the dilution giving a negligible growth of microorganism. Nano-ZnO doped with 5 % nano-Pd, pure nano-ZnO and micro-ZnO, showed antifungal activity against Aspergilus niger with an MIC of 1.25, 2.5 and 5mg/mL, respectively. However, Candida albicans yeasts were relatively resistant to these compounds, with an MIC of 2.5, 5 and 10 mg/mL for Pd doped nano-ZnO, nano-ZnO and micro-ZnO, respectively. Thus nano-ZnO was twice as potent in killing Aspergillus, as compared to its non-nano-counterpart and loading of nano-ZnO with 5 % nano-Pd further increased its activity, four times that of micro-ZnO. Further investigations are needed to confirm the potential use of nano-ZnO and its doping with nano-Pd in the treatment of water supply systems and food preservation.
Multiparametric prostate magnetic resonance imaging in the evaluation of prostate cancer (2015)

Imaging has traditionally played a minor role in the diagnosis and staging of prostate cancer. However, recent controversies generated by the use of prostate-specific antigen (PSA) screening followed by random biopsy have encouraged the development of new imaging methods for prostate cancer. Multiparametric magnetic resonance imaging (mpMRI) has emerged as the imaging method best able to detect clinically significant prostate cancers and to guide biopsies. Here, the authors explain what mpMRI is and how it is used clinically, especially with regard to high-risk populations, and we discuss the impact of mpMRI on treatment decisions for men with prostate cancer. CA Cancer J Clin 2016;66:326-336. © 2015 American Cancer Society.
Adversarial Attacks on Deep Models for Financial Transaction Records (2021)

Machine learning models using transaction records as inputs are popular among financial institutions. The most efficient models use deep-learning architectures similar to those in the NLP community, posing a challenge due to their tremendous number of parameters and limited robustness. In particular, deep-learning models are vulnerable to adversarial attacks: a little change in the input harms the model's output. In this work, we examine adversarial attacks on transaction records data and defences from these attacks. The transaction records data have a different structure than the canonical NLP or time series data, as neighbouring records are less connected than words in sentences, and each record consists of both discrete merchant code and continuous transaction amount. We consider a black-box attack scenario, where the attack doesn't know the true decision model, and pay special attention to adding transaction tokens to the end of a sequence. These limitations provide more realistic scenario, previously unexplored in NLP world. The proposed adversarial attacks and the respective defences demonstrate remarkable performance using relevant datasets from the financial industry. Our results show that a couple of generated transactions are sufficient to fool a deep-learning model. Further, we improve model robustness via adversarial training or separate adversarial examples detection. This work shows that embedding protection from adversarial attacks improves model robustness, allowing a wider adoption of deep models for transaction records in banking and finance.
Unsupervised Paraphrasing with Pretrained Language Models (2020)

Paraphrase generation has benefited extensively from recent progress in the designing of training objectives and model architectures. However, previous explorations have largely focused on supervised methods, which require a large amount of labeled data that is costly to collect. To address this drawback, we adopt a transfer learning approach and propose a training pipeline that enables pre-trained language models to generate high-quality paraphrases in an unsupervised setting. Our recipe consists of task-adaptation, self-supervision, and a novel decoding algorithm named Dynamic Blocking (DB). To enforce a surface form dissimilar from the input, whenever the language model emits a token contained in the source sequence, DB prevents the model from outputting the subsequent source token for the next generation step. We show with automatic and human evaluations that our approach achieves state-of-the-art performance on both the Quora Question Pair (QQP) and the ParaNMT datasets and is robust to domain shift between the two datasets of distinct distributions. We also demonstrate that our model transfers to paraphrasing in other languages without any additional finetuning.
Characterization and epitope mapping of four HLA class II reactive mouse monoclonal antibodies using transfected L cells and human cells transfected with mutants of DQB1*0302 (1995)

Abstract: To study epitopes of HLA class II molecules, four mouse monoclonal antibodies (mAbs) 13B6, 17F8, 19A1 and 12G6 were made using HLA‐DQ8, DP2 and DP4 expressing mouse transfectants for immunization. Three of the mAbs, 13B6, 17F8 and 19A1, bound to all DQ1, 4, 8 or 9 positive B‐lymphoblastoid cell lines (B‐LCLs) and transfectants tested, i.e. cells carrying the DQB1 genes 0302‐3, 0401‐2, 0501‐3, 0601‐4 and 0609 irrespective of the accompanying DQA1 gene. These DQB1 genes code for the shared amino acids (aa) GVY in position 45–47 of the DQ β chain. DQ1+4+8+9 specific (IIB3) and DQ3 specific (IVD12) reference mAbs inhibited binding of all three mAbs. Testing 13B6, 17F8 and 19A1 with cells made using aa substitutions in various positions of DQP1*0302 indicated involvement of aa 45 in the epitopes of all three mAbs. The last mAb (12G6) bound to all B–LCLs and all DP transfected cells. However, only some DR transfectants and a single DQ transfectant (carrying DQA1 *0201 and DQB1*0202) bound mAb 12G6. This reactivity pattern correlates with a shared sequence of aa (RFDSDVGE) in position 39–46 of DR‐and DQ‐ and 37–44 of DP p chains.
Photocatalytic CO2 reduction using visible light by metal-monocatecholato species in a metal–organic framework (2015)

Metal-organic frameworks (MOFs) with isolated metal-monocatecholato groups have been synthesized via postsynthetic exchange (PSE) for CO2 reduction photocatalyst under visible light irradiation in the presence of 1-benzyl-1,4-dihydronicotinamide and triethanolamine. The Cr-monocatecholato species are more efficient than the Ga-monocatecholato species.
S65 Genome-wide association study of survival times after diagnosis of idiopathic pulmonary fibrosis (2021)

<h3>Introduction</h3> Idiopathic pulmonary fibrosis (IPF) is a devastating lung disease where the lungs become progressively scarred. The median survival time after diagnosis is three years, albeit disease progression varies greatly between individuals. Recently, large genome-wide association studies (GWAS) have shown there are a number of DNA regions associated with disease risk, however these variants are generally not associated with disease progression. <h3>Aim</h3> To identify genetic variants associated with disease progression. <h3>Methods</h3> We performed a two-stage GWAS of transplant-free survival times after diagnosis of IPF. In stage 1, genome-wide analyses were performed in three separate studies using a Cox proportional hazards models adjusting for age, sex, study centre and genetic principal components and the results were meta-analysed across the studies. In stage 2, variants with p&lt;5×10<sup>−5</sup> in the stage 1 meta-analysis and p&lt;0.05 in each separate study with consistent direction of effects were tested for their association with IPF survival in independent samples. Variants were deemed associated with IPF survival if they were genome-wide significant in a meta-analysis of stages 1 and 2 (p&lt;5×10<sup>−8</sup>). Immunohistochemistry and transcriptomics were performed to follow-up genes implicated by the genome-wide analysis. <h3>Results</h3> A total of 1,481 IPF cases and 9 million genetic variants were included in the stage 1 analysis, and 397 individuals in stage 2. One variant, rs35647788 in an intron of <i>PCSK6</i>, was genome-wide significant in the stage 1 and 2 meta-analysis, and showed nominal significance (p&lt;0.05) in each study with consistent direction of effects across all studies. Gene-prioritisation analyses identified <i>PCSK6</i>, of which rs35647788 lies in an intron of, as the most likely gene of interest. Immunohistochemistry showed that <i>PCSK6</i> was highly expressed in lung tissue samples from IPF cases compared to controls, specifically in the lung epithelium. In IPF cases, higher levels of circulating <i>PCSK6</i> were associated with poorer survival times and increased <i>PCSK6</i> gene expression was associated with a greater annual decline in lung capacity. There was little overlap between the genetic determinants of disease risk and survival times. <h3>Conclusions</h3> This is the first GWAS of IPF survival which has identified novel important biological processes involved in the progression of IPF.
Neuroendocrine regulation of galanin gene expression (1991)

Over the past several decades, we have come to appreciate the central role of intercellular communication in the regulation of normal homeostasis. Effective communication requires a dynamic web of pathways that carry precise, and informative, messages. Several classes of molecules have been shown to carry these messages, including nucleosides, amino acids, complex amines, carbohydrates, steroids, and peptides. Our understanding of the importance of small peptides in this communications network has been expanded by the physiological and pharmacological studies of numerous investigators over the past sixty years. This understanding has led to a search for additional peptide mediators to account for the exquisite subtleties of intercellular communication. Dr. Victor Mutt, whom we honor by this volume, has led the efforts to identify and characterize such peptides and is responsible for the discovery of several of the most important of them. As described elsewhere in this volume, one of the more recent products of these investigations is galanin, an amidated peptide isolated and purified from copious quantities of porcine intestinal extracts (Tatemoto et al., 1983). Amino acid sequence and structural analysis suggest that galanin is unrelated to any of the other known families of regulatory peptides, and to date it remains the only known member of its own family.KeywordsPC12 CellNerve Growth FactorNeuroendocrine RegulationEstradiol BenzoateUpstream Flank RegionThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.