gebhart/patrepeval huggingface dataset:
The JAK2 617V>F mutation triggers erythropoietin hypersensitivity and terminal erythroid amplification in primary cells from patients with polycythemia vera (2007)

The JAK2 617V>F mutation is frequent in polycythemia vera (PV) and essential thrombocythemia (ET). Using quantitative polymerase chain reaction (PCR), we found that high levels of JAK2 617V>F in PV correlate with increased granulocytes and high levels of hemoglobin and endogenous erythroid colony formation. We detected normal progenitors and those that were heterozygous or homozygous for the mutation by genotyping ET and PV clonal immature and committed progenitors. In PV patients, we distinguished homozygous profiles with normal, heterozygous, and homozygous progenitors from heterozygous profiles with only heterozygous and normal progenitors. PV patients with a heterozygous profile had more mutated, committed progenitors than did other PV and ET patients, suggesting a selective amplification of mutated cells in the early phases of hematopoiesis. We demonstrated that mutated erythroid progenitors were more sensitive to erythropoietin than normal progenitors, and that most homozygous erythroid progenitors were erythropoietin independent. Moreover, we observed a greater in vitro erythroid amplification and a selective advantage in vivo for mutated cells in late stages of hematopoiesis. These results suggest that, for PV, erythrocytosis can occur through two mechanisms: terminal erythroid amplification triggered by JAK2 617V>F homozygosity, and a 2-step process including the upstream amplification of heterozygous cells that may involve additional molecular events.
The ‘sixth sense’ of ultrasound: probing nonlinear elasticity with acoustic radiation force (2015)

Prompted by a recent finding that the magnitude of the acoustic radiation force (ARF) in isotropic tissue-like solids depends linearly on a particular third-order modulus of elasticity-hereon denoted by C, this study investigates the possibility of estimating C from the amplitude of the ARF-generated shear waves. The featured coefficient of nonlinear elasticity, which captures the incipient nonlinear interaction between the volumetric and deviatoric modes of deformation, has so far received only a limited attention in the context of soft tissues due to the fact that the latter are often approximated as (i) fluid-like when considering ultrasound waves, and (ii) incompressible under static deformations. On establishing the analytical and computational platform for the proposed sensing methodology, the study proceeds with applying the prototype technique toward estimating via ARF the third-order modulus C in a series of tissue-mimicking phantoms. To help validate the concept and its implementation, the germane third-order modulus is independently estimated in each phantom via an established technique known as acoustoelasticity. The C-estimates obtained respectively via acoustoelasticity and the new theory of ARF show a significant degree of consistency. The key features of the new sensing methodology are that: (a) it requires no external deformation of a material other than that produced by the ARF, and (b) it estimates the nonlinear C-modulus locally, over the focal region of an ultrasound beam-where the shear waves are being generated.
Quantitative 3D magnetic resonance elastography: Comparison with dynamic mechanical analysis (2016)

3D MRE and DMA showed excellent consistency over a wide range of frequencies and stiffnesses. Magn Reson Med 77:1184-1192, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
Organic electro-optic modulator using transparent conducting oxides as electrodes (2005)

A novel organic electro-optic (EO) modulator using transparent conducting oxides (ZnO and In2O3) as electrodes is demonstrated for the first time. The modulator employs the poled guest-host chromophore/polymer material AJL8/APC having r33=35pm/V and is able to achieve a low Vpi=2.8 V switching voltage for an 8mm-long device at a wavelength of 1.31ìm. This corresponds to a Vpi=1.1 V switching voltage for a 1cm-long device in a push-pull configuration. The push-pull VpiL figure of merit normalized for the EO coefficient is thus 1.1V-cm/(35pm/V), which is 3-4x lower than that can be achieved with a convetional modulator structure. The bottom electrode is ZnO grown by Metal-Organic Vapor Deposition (MOCVD) and top electrode In2O3 deposited using ionbeam assisted deposition. The top electrode is directly deposited on the guest-host organic material. The design and fabrication considerations for the modulator are also discussed.
A General Method for the Formation of Aryl—Sulfur Bonds Using Copper(I) Catalysts. (2002)

We report a mild, palladium-free synthetic protocol for the cross-coupling reaction of aryl iodides and thiols using 10 mol % CuI and 10 mol\n% neocuproine, with NaO<i>t-</i>Bu as the base, in toluene at 110 °C. Using this protocol, we have shown that a variety of aryl sulfides can be\nsynthesized in excellent yields from readily available iodides and thiols.
[POSTER] Halo3D: A Technique for Visualizing Off-Screen Points of Interest in Mobile Augmented Reality (2017)

When working with mobile Augmented Reality (AR) applications, users need to be aware of relevant points of interest (POIs) that are located off-screen. These POIs belong to the context since they are not observable in the 3D first-person AR view on screen. The context in mobile AR can include a large number of POIs including locally dense clusters as in mobile AR applications for production plant machine maintenance. Existing solutions display 3D arrows or an area on the edges of the screen to represent the POIs of the context. These techniques display the direction but not the distance of each POI. We present Halo3D, a visualization technique that conveys the 3D direction and distance of off-screen POIs while avoiding overlap and clutter in a high-POI-density AR environment.
ENKI (2015)

A data owner outsourcing the database of a multi user application wants to prevent information leaks caused by outside attackers exploiting software vulnerabilities or by curious personnel. Query processing over encrypted data solves this problem for a single user, but provides only limited functionality in the face of access restrictions for multiple users and keys. ENKI is a system for securely executing queries over sensitive, access restricted data on an outsourced database. It introduces an encryption based access control model and techniques for query execution over encrypted, access restricted data on the database with only a few cases requiring computations on the client. A prototype of ENKI supports all queries seen in three real world use cases and executes queries from TPC-C benchmark with a modest overhead compared to the single user mode.
Synthesis and characterization of oligocyclosiloxanes via the hydrosilation of vinylsilanes and vinylsiloxanes with heptamethylcyclotetrasiloxane (1993)

Abstract The preparation of oligocyclosiloxanes via hydrosilation reactions has been investigated. Hydrosilation reactions employing heptamethylcyclotetrasiloxane and vinyl‐containing silanes and siloxanes yielded a variety of oligocyclosiloxanes with various numbers of cyclosiloxane rings connected through tri‐, tetra‐, penta‐, hexa‐, hepta‐, or octafunctional junctions. The oligocyclosiloxanes were characterized by gas chromatography, IR spectroscopy, 29 Si‐, 1 H‐, and 13 C‐NMR spectroscopy, elemental analysis, and vapor phase osmometry. The polycyclics were redistributed with hexamethyldisiloxane and the resulting fragments analyzed by gas chromatography. All results were consistent with the formation of isomeric oligocyclosiloxanes due to a lack of absolute regioselectivity of the hydrosilation reaction. © 1993 John Wiley & Sons, Inc.
Ultra-Compact and Robust Physically Unclonable Function Based on Voltage-Compensated Proportional-to-Absolute-Temperature Voltage Generators (2016)

This paper presents a technique for designing an ultra-compact and robust physically unclonable function for security-oriented applications. The circuits are based on pairs of analog circuits whose output voltage is supply voltage compensated and proportional to absolute temperature (PTAT). The difference between two outputs of a PTAT pair is digitized to produce 1 b output which is sensitive mostly only to random transistor threshold voltage variations. Fabricated in a 65 nm, the proposed 256 b PUF array takes an area of 3.07 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /bit, consumes 0.548 pJ/bit at a throughput of 10 Mb/s, while showing desirable robustness against temperature and supply voltage variations with 3.5% and 1.004% bit-instability across 0 to 80°C and 0.6 to 1.2 V, respectively. The unpredictability and uniqueness of the 256 b PUF output are verified by NIST randomness test and Hamming Distance between keys. As compared with the state of the art, the proposed design has an 8.3× smaller area/bit or 2× better robustness against noise and environmental variations.
A neutral glycoprotease of Pasteurella haemolytica A1 specifically cleaves O-sialoglycoproteins (1992)

A neutral metalloprotease with marked specificity for an O-sialoglycoprotein has been isolated from culture supernatants of Pasteurella haemolytica A1. The 35-kDa enzyme cleaves human erythrocyte glycophorin A, which is O glycosylated, but does not cleave N-glycosylated proteins or nonglycosylated proteins. Glycophorin A was cleaved when it was present in situ in erythrocyte ghost plasma membranes or when it was free in solution. The glycoprotease did not hydrolyze glycophorin A from which sialate residues had been removed by neuraminidase treatment. An immobilized preparation of the enzyme cleaved glycophorin A at several positions, with a major site of cleavage at Arg-31-Asp-32. The glycoprotease is inhibited by EDTA, citrate, and ascorbate, but inhibition appears to be due to the masking of metal ion activators rather than to their removal. The enzyme is not inhibited by phosphoramidon, an inhibitor of other bacterial neutral metalloproteases.
Directly Modulated Laser Transmitters for Scalable Multi-rate DPSK Communications§ (2018)

We present a new approach for generating multi-rate burst-mode DPSK waveforms using time and frequency-windowed directly modulated laser transmitters. Near-theoretical performance is demonstrated over a wide range of data rates using a WDM-scalable implementation.
A shear gradient-activated microfluidic device for automated monitoring of whole blood haemostasis and platelet function (2016)

Accurate assessment of blood haemostasis is essential for the management of patients who use extracorporeal devices, receive anticoagulation therapy or experience coagulopathies. However, current monitoring devices do not measure effects of haemodynamic forces that contribute significantly to platelet function and thrombus formation. Here we describe a microfluidic device that mimics a network of stenosed arteriolar vessels, permitting evaluation of blood clotting within small sample volumes under pathophysiological flow. By applying a clotting time analysis based on a phenomenological mathematical model of thrombus formation, coagulation and platelet function can be accurately measured in vitro in patient blood samples. When the device is integrated into an extracorporeal circuit in pig endotoxemia or heparin therapy models, it produces real-time readouts of alterations in coagulation ex vivo that are more reliable than standard clotting assays. Thus, this disposable device may be useful for personalized diagnostics and for real-time surveillance of antithrombotic therapy in clinic.
Click-Modified Anandamide siRNA Enables Delivery and Gene Silencing in Neuronal and Immune Cells (2012)

Click chemistry of alkyne-modified RNA with different receptor ligand azides was used to prepare 3'-folate, 3'-cholesterol, and, as a new entity, 3'-anandamide-modified RNA in high yields and excellent purity. The anandamide-modified RNA shows surprisingly high transfection properties and enables the delivery of siRNA even into difficult-to-transfect RBL-2H3 cells which model neuronal uptake. Furthermore, the system was employed in human immune cells (BJAB), demonstrating silencing effects similar to those of a cationic, benchmark transfection reagent. In addition, the anandamide conjugates were found to be nontoxic. The reported chemistry and the described properties of the anandamide siRNA extend the possibilities of using siRNA-based gene silencing in neuronal and immune cells.
Elimination of cross talk in waveguide intersections (1998)

We present general criteria for crossing perpendicular waveguides with nearly 100% throughput and 0% cross talk. Our design applies even when the waveguide width is of the order of the wavelength. The theoretical basis for this phenomenon is explained in terms of symmetry considerations and resonant tunneling and is then illustrated with numerical simulations for both a two-dimensional photonic crystal and a conventional high-index-contrast waveguide crossing. Cross-talk reduction by up to 8 orders of magnitude is achieved relative to unmodified crossings.
Characterization of in vitro and in vivo gene transfer properties of adenovirus serotype 35 vector (2003)

We have recently developed a replication-defective, recombinant adenovirus (Ad) vector composed of the whole Ad serotype 35 (Ad35), a member of subgroup B. We describe herein the in vitro and in vivo gene transfer properties of Ad35 vector in comparison with Ad serotype 5 (Ad5) and the Ad5F35 vector, which is a fiber-substituted Ad5 vector containing Ad35 fiber proteins. In vitro, Ad35 vector efficiently transduced not only human CAR-positive cells but also CAR-negative cells. Following intravenous administration into mice, both Ad5 and Ad35 vectors were rapidly cleared from the bloodstream with a half-life of approximately 3 min. Ad5 vector-mediated transgene expression predominantly occurred in liver parenchymal cells, although the Ad5 vector was delivered to both liver parenchymal and nonparenchymal cells. In contrast, Ad35 vector was efficiently taken up by liver nonparenchymal cells and mediated transduction efficiency in the liver on a level 4 log orders lower than the Ad5 vector. These findings demonstrate that Ad35 vector is an attractive vehicle for gene transfer into human cells, while the biodistribution profile of Ad35 vector in mice is much different from that of the Ad5 vector.
Speaker identification and verification using eigenvoices (2000)

Gaussian Mixture Models (GMMs) have been successfully applied to the tasks of speaker ID and verification when a large amount of enrolment data is available to characterize client speakers ([1],[10],[11]). However, there are many applications where it is unreasonable to expect clients to spend this much time training the system. Thus, we have been exploring the performance of various methods when only a sparse amount of enrolment data is available. Under such conditions, the performance of GMMs deteriorates drastically. A possible solution is the “eigenvoice” approach, in which client and test speaker models are confined to a low-dimensional linear subspace obtained previously from a different set of training data. One advantage of the approach is that it does away with the need for impostor models for speaker verification. After giving a detailed description of the eigenvoice approach, the paper compares the performance of conventional GMMs on speaker ID and verification with that of GMMs obtained by means of the eigenvoice approach. Experimental results are presented to show that conventional GMMs perform better if there are abundant enrolment data, while eigenvoice GMMs perform better if enrolment data are sparse. The paper also gives experimental results for the case where the eigenspace is trained on one database (TIMIT), but client enrolment and testing involve another (YOHO). For this case, we show that performance improves if an environment adaptation technique is applied to the eigenspace. Finally, we discuss priorities for future work.
RETINAL VESSEL ANALYSIS - NEW POSSIBILITIES (2002)

Retinal Vessel Analysis is a new technique to assess behavior of large retinal vessels based on diameter measurements. The Retinal Vessel Analyzer (RVA) measures continuously on-line obtaining data in relation to time and local position. Possible analysis tools include (a) Time Course Analysis of physiological, pathological, or therapy induced changes; (b) Local Course Analysis to recognize local narrow or wide vessel segments along the vessel; (c) Vasomotoric Analysis to determine vasomotions and blood pressure related diameter changes; (d) Functional Analysis to examine dynamic behavior e.g. the ability to autoregulate and (e) Functional Imaging to visualize functional parameters of vessels in single vessel segments. RVA is thus able to recognize and study different autoregulation mechanisms.
On the LDPC-Coded Modulation for Ultra-High-Speed Optical Transport in the Presence of Phase Noise (2013)

A Monte Carlo integration based method to calculate symbol log-likelihood ratios for soft iterative decoding in the presence of imperfect carrier phase estimation (CPE) is proposed. The proposed method shows good robustness when CPE is imperfect, in particular for optimum modulation schemes.
A scalable single-photon imager using a single superconducting nanowire (2016)

Detecting spatial and temporal information of individual photons by using single-photon-detector (SPD) arrays is critical to applications in spectroscopy, communication, biological imaging, astronomical observation, and quantum-information processing. Among the current SPDs1,detectors based on superconducting nanowires have outstanding performance2, but are limited in their ability to be integrated into large scale arrays due to the engineering difficulty of high-bandwidth cryogenic electronic readout3-8. Here, we address this problem by demonstrating a scalable single-photon imager using a single continuous photon-sensitive superconducting nanowire microwave-plasmon transmission line. By appropriately designing the nanowire's local electromagnetic environment so that the nanowire guides microwave plasmons, the propagating voltages signals generated by a photon-detection event were slowed down to ~ 2% of the speed of light. As a result, the time difference between arrivals of the signals at the two ends of the nanowire naturally encoded the position and time of absorption of the photon. Thus, with only two readout lines, we demonstrated that a 19.7-mm-long nanowire meandered across an area of 286 {\mu}m * 193 {\mu}m was capable of resolving ~590 effective pixels while simultaneously recording the arrival times of photons with a temporal resolution of 50 ps. The nanowire imager presents a scalable approach to realizing high-resolution photon imaging in time and space.
Abstract 2543: Concurrent chemotherapy and temozolomide-resistant CAR-T immunotherapy enhances glioblastoma clearance in experimental animals (2018)

Abstract Dismal long-term progression-free survival of glioblastoma (GBM) patients, who are concurrently treated with radiation and chemotherapy, demands development of alternative strategies for management of this disease. Recent clinical success of chimeric antigen receptors expressing T cells (CAR-T) in GBM patients, interest in tumor-directed immunotherapy has been reinvigorated. However as per standard care, immunotherapy must be concurrent with or following the standard care protocol for glioma therapy, which includes Temozolomide (TMZ) chemotherapy. Concurrent chemotherapy with TMZ reduces the efficacy of adoptive T cell immunotherapy by inducing severe lymphopenia, while post-chemotherapy treatment minimizes the window of opportunity for effective immunotherapy, because of inherent tumor heterogeneity resulting in an altered antigenic profile in recurrent GBMs. To address this, we have created a TMZ-resistant CAR-T cell directed against IL13Rα2+ GBM tumors by introducing a mutated O6-methylguanine-DNA methyltransferase (MGMT) moiety in the existing IL13CAR backbone. This specific mutation in MGMT (P140KMGMT) blocks the interaction of TMZ to MGMT and therefore protects the rapidly proliferating anti-GBM CAR-T cells from TMZ-induced lymphopenia. Activated P140KMGMT-IL13CAR-T cells were protected from TMZ-induced cytotoxicity in vitro without any loss of anti-tumor effects of these modified CAR-T cells. Experimental xenograft animals treated with P140KMGMT-IL13CAR-T cells and concurrent TMZ therapy showed 2-fold increase in median survival over groups that were treated with TMZ alone, and 2.8-fold increase in overall survival over groups that were treated with TMZ-sensitive second generation IL13CAR-T cells and concurrent TMZ. These encouraging results point us strongly in the direction of developing this CAR-T technology towards a promising future of concurrent chemotherapy and immunotherapy of GBM. Citation Format: Sadhak Sengupta, Mansour Gergi, Prajna Guha, Sudarshana Sengupta, Richard P. Junghans, Prakash Sampath. Concurrent chemotherapy and temozolomide-resistant CAR-T immunotherapy enhances glioblastoma clearance in experimental animals [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 2543.
Simplified analogs of sclerophytin A as potential anticancer agents (2007)

3971 Sclerophytin A (1), a rare 2,11-cyclized cembranoid natural product of marine origin, was reported to possess potent growth inhibitory activity against the L1210 cell line. We have embarked on the synthesis of highly simplified analogs of sclerophytin A that can be synthesized in 3-5 steps in the hope of developing potential anticancer agents. For the preparation of analogs 2, aldol condensation of (S)-(+)-carvone with a halo-benzaldehyde gave aldol adducts in acceptable yield and moderate to high diastereoselectivity. Etherification of alcohols afforded glycolates. Cycloaldol reaction of keto-esters afforded isobenzofurans in good yields and as single diastereomers. For the preparation of analogs 3, oxidative rearrangement of alcohols gave enones. Compounds with different substitutions at the R (methyl, ethyl, geranyl) and X (bromide, dichloride) positions were prepared. The human KB-3 carcinoma cell line was used to assess their growth inhibitory properties using the MTT colorimetric assay. IC50 values ranged from 3 to >100 μM. The most potent compounds were those with R = ethyl and X = 3-bromide or 2,4-dichloride. Further refinement of the structures and testing of antitumor properties are ongoing. Supported by the Arkansas Biosciences Institute and the NIH (CA75577, RR15569).