gebhart/patrepeval huggingface dataset:
Generation of Soluble Human Tumor Necrosis Factor-α Receptor 1-Fc Transgenic Pig (2011)

Background. Acute humoral xenograft rejection (AHXR) is an important barrier to xenograft survival. Human tumor necrosis factor-α (hTNF-α) is one of the essential mediators of AHXR and induces activation of porcine endothelial cells (PECs), resulting in upregulation of major histocompatibility complex molecules, adhesion molecules, and proinflammatory chemokines. We investigated whether introduction of a soluble human tumor necrosis factor receptor I-Fc (shTNFRI-Fc) fusion gene can suppress activation of PECs and, more importantly, produced shTNFRI-Fc transgenic pigs. Methods. The shTNFRI-Fc gene expression vector was constructed and inserted into PECs. The inhibitory effects of shTNFRI-Fc were tested by luciferase assay, reverse-transcriptase polymerase chain reaction, and flow cytometry. A shTNFRI-Fc transgenic pig was generated by somatic cell nuclear transfer. The expression of shTNFRI-Fc in the transgenic pig was evaluated by PCR, western blot, enzyme-linked immunosorbent assay, and immunohistochemistry. The inhibitory effects of shTNFRI-Fc in the serum obtained from the transgenic pig were also tested. Results. In comparison with control green fluorescent protein, shTNFRI-Fc protein showed much stronger inhibitory effects on NF-κB activation in the HEK293-NF-κB-luciferase reporting cell line, expression of chemokines and adhesion molecules in PECs, and TNF-α-mediated cytotoxicity. We successfully generated shTNFRI-Fc transgenic pig. Sera obtained from the transgenic pig inhibited induction of chemokines, and E-selectin in PECs stimulated with Human TNF-α. Conclusions. We have generated transgenic pigs producing shTNFRI-Fc protein that can inhibit TNF-α-mediated activation of PECs. Because TNF-α is an important mediator of xenograft rejection, the use of xenografts that can produce shTNFRI-Fc proteins de novo could be an effective approach in overcoming a considerable component of the xenograft rejection process, especially AHXR.
A memory built-in self-diagnosis design with syndrome compression (2005)

We present a memory built-in self-diagnosis (BISD) design that incorporates a fault syndrome compression scheme. We also have developed efficient faulty-word, faulty-row, and faulty-column identification methods, which have been incorporated in our new BISD design. Our approach reduces the amount of data that need to be transmitted from the chip under test to the automatic test equipment (ATE). It therefore reduces the ATE occupation time and the required ATE capture memory space. It also simplifies the analysis that has to be performed on the ATE. Simulation results for memories under various fault pattern distributions show that in most cases the data can be compressed to less than 6% of its original size.
Cross Disability Access to Touch Screen Kiosks and ATMs (1997)

The current study highlights a novel strategy of cervical cancer screening by incorporating the role of telemedicine in training ASHA workers and their role in improving the screening by home-based delivery of HPV kits with promising results.
Cliplets (2012)

We explore creating ""cliplets"", a form of visual media that juxtaposes still image and video segments, both spatially and temporally, to expressively abstract a moment. Much as in ""cinemagraphs"", the tension between static and dynamic elements in a cliplet reinforces both aspects, strongly focusing the viewer's attention. Creating this type of imagery is challenging without professional tools and training. We develop a set of idioms, essentially spatiotemporal mappings, that characterize cliplet elements, and use these idioms in an interactive system to quickly compose a cliplet from ordinary handheld video. One difficulty is to avoid artifacts in the cliplet composition without resorting to extensive manual input. We address this with automatic alignment, looping optimization and feathering, simultaneous matting and compositing, and Laplacian blending. A key user-interface challenge is to provide affordances to define the parameters of the mappings from input time to output time while maintaining a focus on the cliplet being created. We demonstrate the creation of a variety of cliplet types. We also report on informal feedback as well as a more structured survey of users.
<title>High-resolution decoding of multianode microchannel array detectors</title> (1991)

The Multi-Anode Microchannel Array (MAMA) is a photon counting detector which utilizes a photocathode for photon to electron conversion, a microchannel plate (MCP) for signal amplification and a proximity focused anode array for position sensitivity. The detector electronics decode the position of an event through coincidence discrimination. The decoding algorithm which associates a given event with the appropriate pixel is determined by the geometry of the array. A new algorithm incorporated into a CMOS Application Specific Integrated Circuit (ASIC) decoder which improves the pixel spatial resolution is described. The new algorithm does not degrade the detector throughput and does not require any modifications to the detector tube. The standard MAMA detector has a pixel size of 25 x 25 square microns, but with the new decoder circuit the pixel size is reduced to 12.5 x 12.5 square microns. We have built the first set of decode electronics utilizing the new ASIC chips and report here on the first imaging tests of this system.
Ablation of Myocardial Tissue With Nanosecond Pulsed Electric Fields (2015)

Ablation with nsPEFs is a promising alternative to radiofrequency (RF) ablation of AF. It may dramatically reduce procedure times and produce more consistent lesion thickness than RF ablation.
Feature Selection Methods for Text ClassiÞcation (2007)

We consider feature selection for text classification both the- oretically and empirically. Our main result is an unsuper- vised feature selection strategy for which we give worst-case theoretical guarantees on the generalization power of the resultant classification function ˜ f with respect to the classi- fication function f obtained when keeping all the features. To the best of our knowledge, this is the first feature selec- tion method with such guarantees. In addition, the anal- ysis leads to insights as to when and why this feature se- lection strategy will perform well in practice. We then use the TechTC-100, 20-Newsgroups, and Reuters-RCV2 data sets to evaluate empirically the performance of this and two simpler but related feature selection strategies against two commonly-used strategies. Our empirical evaluation shows that the strategy with provable performance guarantees per- forms well in comparison with other commonly-used feature selection strategies. In addition, it performs better on cer- tain datasets under very aggressive feature selection.
Detection of Far-Field Radio-Frequency Signals by Niobium Superconducting Quantum Interference Device Arrays (2015)

The capability of an all-niobium superconducting quantum interference device (SQUID) array to operate as an electrically small antenna capable of detecting radio frequency from distant sources was demonstrated. The measurements were performed in three different arrays, with each array consisting of 2400 identical cells. The intrinsic broadband characteristics of the device were confirmed by the flat frequency response of the ratio of the output and input voltages (the S21 parameter) of the array between 300 kHz and 1 GHz. Setting the device to its optimal operating parameters allowed the detection of signals from local frequency-modulation stations.
Optically Active Polyelectrolyte Multilayers as Membranes for Chiral Separations (2003)

Ultrathin films of chiral polyelectrolyte complex, prepared by the multilayering process, exhibit selectivity in the membrane separations of optically active compounds, such as l- and d-ascorbic acid. The flux through these polyelectrolyte multilayers, PEMUs, is exceptionally high and may be controlled by the concentration of salt present in the permeating solutions. Both in-situ ATR-FTIR and chiral capillary electrochromatography indicate that flux selectivity is mainly kinetically controlled, stemming from a difference in diffusion rates of various enantiomers through PEMUs, rather than a difference in partitioning.
A Model of Storage I/O Performance Interference in Virtualized Systems (2011)

In this paper, we propose simple performance models to predict the impact of consolidation on the storage I/O performance of virtualized applications. We use a measurement-based approach based on tools such as blktrace and tshark for storage workload characterization in a commercial virtualized solution, namely VMware ESX server. Our approach allows a distinct characterization of read/write performance attributes on a per request level and provides valuable information for parameterization of storage I/O performance models. In particular, based on measures of quantities such as the mean queue-length seen upon arrival by requests, we define simple linear prediction models for the throughput, response times, and mix of read/write requests in consolidation based only on information collected in isolation experiments for the individual virtual machines.
Invertible Amphiphilic Homopolymers (2004)

Stimuli-responsive polymers and assemblies are viable candidates for the so-called "smart" materials. In this communication, we report a new class of amphiphilic homopolymers that forms micelle-like structures in polar solvents and inverted micelle-like structures in apolar solvents. We demonstrate that these superstructures are the result of the changes in the molecular-level conformations in the monomer.
Abstract 2667: In vitro properties and pre-clinical activity of PF-06801591, a high-affinity engineered anti-human PD-1 (2017)

Abstract Monoclonal-antibody-based therapies targeting the immune checkpoint receptors have become the new standard of care in many cancers. Antibodies that specifically target programmed death receptor-1 (PD-1) or its cognate ligand, programmed death receptor ligand-1 (PD-L1), alone or in combination, have yielded clinical benefits and durable responses in patient subsets with various cancers (including metastatic melanoma, NSCLC, RCC, urothelial cancer, cHL and others). Here we report on the biophysical characteristics and non-clinical antagonistic activities of PF-06801591. PF-06801591 is a humanized anti-PD-1 antibody of human IgG4 isotype, that binds selectively and with similar potency to human and cynomolgus monkey PD-1 receptor (EC50 ~50 pM) and blocks its interaction with its cognate ligands PD-L1 and PD-L2 (IC50 &lt; 1 nM) with no detectable Fc effector function. The interaction of PF-06801591 to PD-1 rescues T cell suppression and exhaustion that translates into NFAT activation, IL-2 and IFN-gamma secretion and T cell proliferation both in vitro cultures and in vivo using an acute xeno GvHD model with human PBMC transfer. Binding of PF-068001591 to human and cynomolgus PD-1 is characterized by the formation of a very stable complex (T1/2 = 2 h) as measured by SPR at 37 C, resulting in high affinity (KD ~20 pM) as measured in solution by KinExA at 23 C. In addition, we explored therapeutic potential of anti-PD-1 in combination with other immunotherapy agents using surrogate antibodies in non-clinical tumor models. The data presented here support future development of PF-06801591 as a single agent or in combination with other immunotherapies. Citation Format: Sawsan Youssef, Yasmina Abdiche, HoangKim Nguyen, Joyce Chou, Sherman Michael Chin, Cris Kamperschroer, Patricia A. Schneider, Eugenia Kraynov, Heike I. Krupka, Arvind Rajpal, John Lin. In vitro properties and pre-clinical activity of PF-06801591, a high-affinity engineered anti-human PD-1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2667. doi:10.1158/1538-7445.AM2017-2667
Computational co-optimization of design parameters and motion trajectories for robotic systems (2018)

We present a novel computational approach to optimizing the morphological design of robots. Our framework takes as input a parameterized robot design as well as a motion plan consisting of trajectories for end-effectors and, optionally, for its body. The algorithm optimizes the design parameters including link lengths and actuator placements whereas concurrently adjusting motion parameters such as joint trajectories, actuator inputs, and contact forces. Our key insight is that the complex relationship between design and motion parameters can be established via sensitivity analysis if the robot’s movements are modeled as spatiotemporal solutions to an optimal control problem. This relationship between form and function allows us to automatically optimize the robot design based on specifications expressed as a function of actuator forces or trajectories. We evaluate our model by computationally optimizing four simulated robots that employ linear actuators, four-bar linkages, or rotary servos. We further validate our framework by optimizing the design of two small quadruped robots and testing their performances using hardware implementations.
Proposal for generating new beta cells in a muted immune environment for type 1 diabetes (2013)

A randomized, double-blind prospective trial among recent onset type 1 diabetes patients has been designed using Cyclosporine A and a proton-pump inhibitor, which increases gastrin levels and has been shown to work through the Reg receptor to transform pancreatic duct cells into islets.
Refined candidate region specified by haplotype sharing for <i>Escherichia coli</i> F4ab/F4ac susceptibility alleles in pigs (2009)

Infection of the small intestine by enterotoxigenic Escherichia coli F4ab/ac is a major welfare problem and financial burden for the pig industry. Natural resistance to this infection is inherited as a Mendelian recessive trait, and a polymorphism in the MUC4 gene segregating for susceptibility/resistance is presently used in a selection programme by the Danish pig breeding industry. To elucidate the genetic background involved in E. coli F4ab/ac susceptibility in pigs, a detailed haplotype map of the porcine candidate region was established. This region covers approximately 3.7 Mb. The material used for the study is a three generation family, where the founders are two Wild boars and eight Large White sows. All pigs have been phenotyped for susceptibility to F4ab/ac using an adhesion assay. Their haplotypes are known from segregation analysis using flanking markers. By a targeted approach, the candidate region was subjected to screening for polymorphisms, mainly focusing on intronic sequences. A total of 18 genes were partially sequenced, and polymorphisms were identified in GP5, CENTB2, APOD, PCYT1A, OSTalpha, ZDHHC19, TFRC, ACK1, MUC4, MUC20, KIAA0226, LRCH3 and MUC13. Overall, 227 polymorphisms were discovered in the founder generation. The analysis revealed a large haplotype block, spanning at least 1.5 Mb around MUC4, to be associated with F4ab/ac susceptibility.
Letrozole for ovulation induction (2006)

Two available groups of medications for ovulation induction are the oral selective estrogen receptor modulators, including clomiphene citrate and gonadotropins. Clomiphene is a well-tolerated, effective oral agent, but is known to have relatively common antiestrogenic endometrial and cervical mucus side effects that could prevent pregnancy despite successful ovulation. The available alternative after clomiphene citrate treatment failure usually includes gonadotropins, which are associated with several problems, including high cost, parenteral administration, necessity for sophisticated treatment monitoring to minimize the risk of severe ovarian hyperstimulation syndrome, and multiple pregnancy. Because of these problems, we proposed aromatase inhibition as a new method of ovulation induction. Others, as well as ourselves, have reported the success of letrozole, one of the third-generation aromatase inhibitors, in inducing and augmenting ovulation, in addition to other benefits associated with reducing the dose of gonadotropins required for ovarian stimulation, particularly in poor responders. The major advantages of letrozole, and possibly other aromatase inhibitors, include absence of persistent antiestrogenic effect owing to the short half-life (approximately 2 days) and lack of estrogen receptor depletion. This ensures a higher physiological estrogen concentration around the time of ovulation, with preservation of the hypothalamo–pituitary–ovarian axis leading to mono-follicular ovulation, which reduces the risk of multiple pregnancy. The current evidence suggests that aromatase inhibitors may replace clomiphene citrate and will become an integral part of other infertility treatments, in particular assisted reproduction. However, definitive studies, in the form of randomized controlled trials, are needed.
Effects of Commercial Anthocyanin-Rich Extracts on Colonic Cancer and Nontumorigenic Colonic Cell Growth (2004)

Commercially prepared grape (Vitis vinifera), bilberry (Vaccinium myrtillus L.), and chokeberry (Aronia meloncarpa E.) anthocyanin-rich extracts (AREs) were investigated for their potential chemopreventive activity against colon cancer. The growth of colon-cancer-derived HT-29 and nontumorigenic colonic NCM460 cells exposed to semipurified AREs (10-75 microg of monomeric anthocyanin/mL) was monitored for up to 72 h using a sulforhodamine B assay. All extracts inhibited the growth of HT-29 cells, with chokeberry ARE being the most potent inhibitor. HT-29 cell growth was inhibited approximately 50% after 48 h of exposure to 25 microg/mL chokeberry ARE. Most importantly, the growth of NCM460 cells was not inhibited at lower concentrations of all three AREs, illustrating greater growth inhibition of colon cancer, as compared to nontumorigenic colon cells. Extracts were semipurified and characterized by high-pressure liquid chromatography, spectrophotometry, and colorimetry. Grape anthocyanins were the glucosylated derivatives of five different anthocyanidin molecules, with or without p-coumaric acid acylation. Bilberry contained five different anthocyanidins glycosylated with galactose, glucose, and arabinose. Chokeberry anthocyanins were cyanidin derivatives, monoglycosylated mostly with galactose and arabinose. The varying compositions and degrees of growth inhibition suggest that the anthocyanin chemical structure may play an important role in the growth inhibitory activity of commercially available AREs.
Targeting of the BclA and BclB proteins to the <i>Bacillus anthracis</i> spore surface (2008)

The exosporium is the outermost layer of the Bacillus anthracis spore. The predominant protein on the exosporium surface is BclA, a collagen-like glycoprotein. BclA is incorporated on the spore surface late in the B. anthracis sporulation pathway. A second collagen-like protein, BclB, has been shown to be surface-exposed on B. anthracis spores. We have identified sequences near the N-terminus of the BclA and BclB glycoproteins responsible for the incorporation of these proteins into the exosporium layer of the spore and used these targeting domains to incorporate reporter fluorescent proteins onto the spore surface. The BclA and BclB proteins are expressed in the mother cell cytoplasm and become spore-associated in a two-step process involving first association of the protein with the spore surface followed by attachment of the protein in a process that involves a proteolytic cleavage event. Protein domains associated with each of these events have been identified. This novel targeting system can be exploited to incorporate foreign proteins into the exosporium of inactivated, spores resulting in the surface display of recombinant immunogens for use as a potential vaccine delivery system.
Multimechanistic Monoclonal Antibodies (MAbs) Targeting Staphylococcus aureus Alpha-Toxin and Clumping Factor A: Activity and Efficacy Comparisons of a MAb Combination and an Engineered Bispecific Antibody Approach (2017)

Secreted alpha-toxin and surface-localized clumping factor A (ClfA) are key virulence determinants in <i>Staphylococcus aureus</i> bloodstream infections. We previously demonstrated that prophylaxis with a multimechanistic monoclonal antibody (MAb) combination against alpha-toxin (MEDI4893*) and ClfA (11H10) provided greater strain coverage and improved efficacy in an <i>S. aureus</i> lethal bacteremia model. Subsequently, 11H10 was found to exhibit reduced affinity and impaired inhibition of fibrinogen binding to ClfA002 expressed by members of a predominant hospital-associated methicillin-resistant <i>S. aureus</i> (MRSA) clone, ST5. Consequently, we identified another anti-ClfA MAb (SAR114) from human tonsillar B cells with >100-fold increased affinity for three prominent ClfA variants, including ClfA002, and potent inhibition of bacterial agglutination by 112 diverse clinical isolates. We next constructed bispecific Abs (BiSAbs) comprised of 11H10 or SAR114 as IgG scaffolds and grafted anti-alpha-toxin (MEDI4893*) single-chain variable fragment to the amino or carboxy terminus of the anti-ClfA heavy chains. Although the BiSAbs exhibited <i>in vitro</i> potencies similar to those of the parental MAbs, only 11H10-BiSAb, but not SAR114-BiSAb, showed protective activity in murine infection models comparable to the respective MAb combination. <i>In vivo</i> activity with SAR114-BiSAb was observed in infection models with <i>S. aureus</i> lacking ClfA. Our data suggest that high-affinity binding to ClfA sequesters the SAR114-BiSAb to the bacterial surface, thereby reducing both alpha-toxin neutralization and protection <i>in vivo</i> These results indicate that a MAb combination targeting ClfA and alpha-toxin is more promising for future development than the corresponding BiSAb.
Terahertz imaging and quantum cascade laser based devices (2010)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010.
Characterization of human antibody responses to four corners hantavirus infections among patients with hantavirus pulmonary syndrome (1994)

Hantavirus pulmonary syndrome (HPS) is a human disease caused by a newly identified hantavirus, which we will refer to as Four Corners virus (FCV). FCV is related most closely to Puumala virus (PUU) and to Prospect Hill virus (PHV). Twenty-five acute HPS serum samples were tested for immunoglobulin G (IgG) and IgM antibody reactivities to FCV-encoded recombinant proteins in Western blot (immunoblot) assays. All HPS serum samples contained both IgG and IgM antibodies to the FCV nucleocapsid (N) protein. FCV N antibodies cross-reacted with PUU N and PHV N proteins. A dominant FCV N epitope was mapped to the segment between amino acids 17 and 59 (QLVTARQKLKDAERAVELDPDDVNKSTLQSRRAAVSALETKLG). All HPS serum samples contained IgG antibodies to the FCV glycoprotein-1 (G1) protein, and 21 of 25 serum samples contained FCV G1 IgM antibodies. The FCV G1 antibodies did not cross-react with PUU G1 and PHV G1 proteins. The FCV G1 type-specific antibody reactivity mapped to a segment between amino acids 59 and 89 (LKIESSCNFDLHVPATTTQKYNQVDWTKKSS). One hundred twenty-eight control serum samples were tested for IgG reactivities to the FCV N and G1 proteins. Nine (7.0%) contained FCV N reactivities, 3 (2.3%) contained FCV G1 reactivities, and one (0.8%) contained both FCV N and FCV G1 reactivities. The epitopes recognized by antibodies present in control serum samples were different from the epitopes recognized by HPS antibodies, suggesting that the control antibody reactivities were unrelated to FCV infections. These reagents constitute a type-specific assay for FCV antibodies.