gebhart/patrepeval huggingface dataset:
Peptide vaccine strategy for immunotherapy of HER-2/neu overexpressing cancers (2006)

HER-2 is a member of epidermal growth factor receptors (EGFR) and preferentially heterodimerizes with other members of EGFR family (EGFR, HER-3, and HER-4) signaling cells for division. In humans, HER-2 is expressed in fetal tissues and is weakly detectable in normal tissues of adults. HER-2 is overexpressed in unmutated form in 3040% of breast and ovarian cancers and to a lesser extent in adenocarcinoma of uterus, cervix, fallopian tube and endometrium [1]. HER-2 overexpression is associated with poor prognosis, aggressive disease and resistance to chemotherapy [2]. Monoclonal antibodies directed against the extracellular domain (ECD) of HER-2 confer inhibitory effects on tumor growth in vitro and in animal models. Phase II and III clinical trials with humanized MAb to HER-2 ECD (HerceptinTM) in patients with HER-2 overexpressing breast cancers were promising. Although HER-2 is a self-protein, HER-2 specific immune responses were detectable in patients with HER-2 positive breast cancer [3]. Therefore, active specific immunotherapy offers the possibility of sustained anti-HER-2 immune responses and is potentially more applicable than passive approaches. We have identified B-cell epitopes in HER-2 ECD by computer aided analyses of protein antigenicity [4]. Four high ranking B-cell epitopes (amino acid sequences 115136, 376-395, 410-429, and 628-647) were synthesized co-linearly with a promiscuous T helper cell epitope from measles virus (sequence 288-302, designated MVF) to enhance immunogenicity and circumvent MHC restriction. High titered antibodies were raised in rabbits by immunization with chimeric B-cell epitopes. These peptide antibodies recognized the native HER-2 receptor and had tumor inhibitory effects on HER-2 overexpressing breast cancer cells in vitro and in xenografted nude mice [5]. To validate a proposed phase Ib vaccine trial in humans, we immunized transgenic mice bearing rat neu gene overexpressing mammary tumors with HER-2 B-cell epitope constructs. At least 50% of these female transgenic mice (Jackson Labs, ME) develop focal mammary tumors by twenty five weeks of age. Rat neu is a human homolog of HER-2 and has 89% amino acid sequence similarity.
<i>rpoB</i> Sequence Analysis of Cultured <i>Tropheryma whippelii</i> (2001)

Until recently no isolate of Tropheryma whippelii was available, and therefore genetic studies were limited to those based on PCR amplification of conserved genes. In this study we determined the nucleotide sequence of rpoB (encoding the beta-subunit of RNA polymerase) from a cultured strain of T. whippelii using degenerate consensus PCR and genome walking. The T. whippelii rpoB consists of 3,657 bp with a 50.4% GC content and encodes 1,218 amino acids with a calculated molecular mass of 138 kDa. Comparison of T. whippelii RpoB with other eubacterial RpoB proteins indicated sequence similarity ranging from 57.19 (Mycoplasma pneumoniae) to 74.63% (Mycobacterium tuberculosis). Phylogenetic analysis of T. whippelii based on comparison of its RpoB sequence with sequences available for other bacteria was consistent with that previously derived from the 16S ribosomal DNA (rDNA) sequence, indicating that it belongs to the actinomyces clade. The sequence comparison allowed the design of a primer pair, TwrpoB.F and TwrpoB.R, specific for T. whippelii rpoB. When incorporated into a PCR, this primer pair allowed the detection of T. whippelii rpoB in three of three 16S rDNA PCR-positive biopsy specimens and zero of seven negative controls. rpoB could therefore be targeted in PCR-mediated detection and identification of this emerging bacterial species. This approach has previously been shown useful for the identification of related mycobacteria. This study underscores that a method involving isolation and then propagation of emerging bacteria is a useful way to quickly achieve extensive molecular knowledge of these pathogens.
Support for fully interactive playout in disk-array-based video server (1994)

In a video-on-demand (VOD) system, it is desirable to provide the user with interactive browsing functions such as “fast forward” and “fast backward.” However, these functions usually require a significant amount of additional resources from the VOD system in terms of storage space, retrieval throughput, network bandwidth, etc. Moreover, prevalent video compression techniques such as MPEG impose additional constraints on the process since they introduce inter-frame dependencies. In this paper, we devise methods to support variable rate browsing for MPEG-like video steams and minimize the additional resources required. Specifically, we consider retrieval for a disk-array-based video server and address the problem of distributing the retrieval requests across the disks.Our overall approach for interactive browsing comprises (1) a storage method, (2) placement and sampling methods, and (3) a playout method, where the placement and sampling methods are two alternatives for video segment selection. The segment sampling scheme supports browsing at any desired speed, while minimizing the variation on the number of video segments skipped between samplings. On the other hand, the segment placement scheme supports completely uniform segment sampling across the disk array for some specific speedup rates. Experiments for the visual effect of the proposed segment skipping approach have been conducted on MPEG data. It is shown that the proposed method is a viable approach to video browsing.
Managing the availability of VNFs with the availability management framework (2017)

A Virtualized Network Function (VNF) is deployed as a cluster of VMs in the Network Functions Virtualization Infrastructure (NFVI). As in traditional telecom, VNFs are expected to provide the required functions at the requested level of availability. For this, one has to incorporate proper redundancy, and appropriate recovery and coordination mechanisms among the redundant entities. The Service Availability Forum (SA Forum) has standardized such mechanisms into a set of middleware services. Among them, the Availability Management Framework (AMF) has the responsibility of managing the availability of application services based on a configuration, called AMF configuration. We propose the use of AMF to manage the availability of the services provided by VNFs. For this, we map the AMF concepts to the Network Function Virtualization (NFV) domain and propose a method for the generation of AMF configurations for AMF managed VNFs. The approach generates an AMF configuration that meets the required level of availability of the requested service workload while aims at maximizing the resource utilization.
Development of a Continuous Process to Produce Ti via Metallothermic Reduction of TiCl<sub>4</sub> in Molten Salt (2013)

After evaluating many different routes to produce titanium, the CSIR of South Africa selected a process to produce titanium powder continuously via metallothermic reduction of TiCl 4 in molten salt. The project risks are being managed using the well-known STAGE/GATE method. The first two stages, viz, Route Selection and Preliminary Assessment have been completed and the next stage entailing campaigns extending over several days of uninterrupted operation, producing titanium at a rate of about 2 kg/h has recently begun. The rationale for selecting the process route is briefly reviewed and key process problems that had to be solved before embarking on scale-up and measures to do so are explained. Specific problems are: • Feed line blockages, • Titanium product formation and adherence to reactor internals, • Agglomerate formation; and • Production of very fine particles. Lastly the planned schedule and current status of the project are discussed.
Stabilizing the integrin αM inserted domain in alternative conformations with a range of engineered disulfide bonds (2002)

Conformational movement of the C-terminal alpha7 helix in the integrin inserted (I) domain, a major ligand-binding domain that adopts an alpha/beta Rossmann fold, has been proposed to allosterically regulate ligand-binding activity. Disulfide bonds were engineered here to reversibly lock the position of the alpha7 helix in one of two alternative conformations seen in crystal structures, termed open and closed. Our results show that pairs of residues with Cbeta atoms farther apart than optimal for disulfide bond stereochemistry can be successfully replaced by cysteine, suggesting that backbone movement accommodates disulfide formation. We also find more success with substituting partially exposed than buried residues. Disulfides stabilizing the open conformation resulted in constitutively active alphaMbeta2 heterodimers and isolated alphaM inserted domains, which were reverted to an inactive form by dithiothreitol reduction. By contrast, a disulfide stabilizing the closed conformation resulted in inactive alphaMbeta2 that was resistant to activation but became activatable after dithiothreitol treatment.
Concentrated autologous plasma protein: A biochemically neutral solder for tissue welding (2001)

These studies demonstrate that the CAPPS system provides acceptable acute and chronic properties for laser welding.
Efficient Channel Search Algorithms for Cognitive Radio in a Multichannel System (2010)

In a cognitive radio (CR) network, secondary users (SUs) are allowed to opportunistically access a licensed spectrum that is not currently being occupied by primary users. This paper is concerned with the problem of how to quickly and accurately locate an unoccupied channel or determine that there is no unoccupied channel, from multiple (yet finite) candidate channels for a SU with a single detector. To design channel search algorithms, we propose a design criterion that minimizes average searching time subject to constraints on the error probabilities for a multichannel system. Relying on the proposed design criterion, we develop two efficient channel search algorithms that are based on a sequential application of the sequential probability ratio test and energy detection to the candidate channels.
Surface‐enhanced Raman scattering‐active photonic crystal fiber probe: Towards next generation liquid biopsy sensor with ultra high sensitivity (2019)

The tremendous enhancement factors that surface-enhanced Raman scattering (SERS) possesses coupled with the flexibility of photonic crystal fibers (PCFs) pave the way to a new generation of ultrasensitive biosensors. Thanks to the unique structure of PCFs, which allows direct incorporation of an analyte into the axially aligned air channels, interaction between the analyte and excitation light could be increased many folds leading to flexible, reliable and sensitive probes that can be used in preclinical or clinical biosensing. SERS-active PCF probes provide unique opportunity to develop an opto-fluidic liquid biopsy needle sensor that enables one-step integrated sample collection and testing for disease diagnosis. Specificity being a key parameter to biosensors, the PCF inside the biopsy needle could be functionalized with targeting moieties to detect specific biomarkers. In this review article, we present some of the most promising recent biosensors based on PCFs including hollow-core PCFs, suspended-core PCFs and side-channel PCFs. We provide a wide range of applications of such platform using Raman spectroscopy, label free SERS or labeled SERS detection and analyze some of the main challenges to be addressed for translating it to a clinically viable next generation sensitive biopsy needle sensing probe.
Widely tunable fractional vortex laser (2015)

Fractional optical vortex with a non-integer topological charge, l, which shows a low-intensity gap (radial opening) on its spatial form, has been widely investigated in many fields such as optical manipulating of microscopic particles and quantum information of entangled photons [1,2]. However, there are few reports concerning the direct generation of a fractional vortex, expressed as a coherent superposition of optical vortices with different topological charges, from laser resonators except our previous work based on a vortex-pumped KTiOPO4 optical parametric oscillator (OPO) at a lasing wavelength of 2.128 µm [3].
Efficient and Accurate Testing of Analog-to-Di Using Oscillation-Test Method (1997)

This paper describes a practical test approach for analog-to-digital converters (ADCs) based on the oscillation-test strategy. The oscillation-test is applied to convert the ADC under test to an oscillator. The oscillation frequencies are able to monitor the ADC conversion rate, differential nonlinearity (DNL) and integral nonlinearity (INL) at each quantization band edge (QBE). Using this method, no analog stimulus should be supplied and therefore the need for a costly precision signal generator is eliminated. Besides, as the oscillation frequency is evaluated using pure digital circuitry, test accuracy is increased. This test approach is not limited to a special kind of ADC. Simulations and practical implementation prove the efficiency of the proposed test approach for ADCs.
Abstract 1631: Sequencing the circulating and infiltrating T-cell repertoire on the Ion S5TM (2017)

Abstract T-cell repertoire (TCR) sequencing by next-generation sequencing (NGS) is a valuable tool for building a deeper understanding of the adaptive immune system. As immunotherapies, particularly T-cell dependent therapies, show increasing potential in treating cancer, the ability to gain a detailed, unbiased view of the TCR becomes imperative for biomarker discovery, immune response to treatment, and study of tumor microenvironments. A key question the field seeks to understand is the relationship between circulating T-cells and infiltrating T-cells at the tumor site. Here, we present a novel approach for TCR sequencing using the Ion S5 ™ sequencer which leverages simplified library construction workflows and offers a more complete characterization of the entire V(D)J region of TCRB. This method can leverage mRNA as input, minimizing requirements in starting materials and focusing sequencing to productive TCRB arrangements. This approach targets the constant (C) and the FR1 regions, minimizing the potential for primer bias and greatly increasing the phylogenetic information content compared to techniques that exclusively characterize the CDR3 domain. Our results show that the observed circulating T-cell repertoire size is approximately 2 orders of magnitude higher than the infiltrating T-cell repertoire. Accordingly, while it is difficult to fully capture the complete repertoire of circulating T-cells due to its vast diversity, we show that it is possible to reliably capture the complete infiltrating T-cell repertoire with as high as 10 samples on the Ion 530 ™ chip. Replicate sequencing runs of infiltrating T-cells offers correlation of ~0.9, indicating that the results were reproducible, and the samples were sequenced to appropriate depth. In summary, we believe that this workflow will allow researchers to more routinely characterize the infiltrating T-cell repertoire and offers the field a better understanding of the impact of repertoire diversity on tumor elimination. Citation Format: Geoffrey Lowman, Elizabeth Linch, Lauren Miller, Denise Topacio-Hall, Timothy Looney, Alex Pankov, Yongming Sun, Xinzhan Peng, Mark Andersen, Fiona Hyland, Ann Mongan. Sequencing the circulating and infiltrating T-cell repertoire on the Ion S5TM [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 1631. doi:10.1158/1538-7445.AM2017-1631
Visual Analytics Law Enforcement Toolkit (2010)

We present VALET, a Visual Analytics Law Enforcement Toolkit for analyzing spatiotemporal law enforcement data. VALET provides users with a suite of analytical tools coupled with an interactive visual interface for data exploration and analysis. This system includes linked views and interactive displays that spatiotemporally model criminal, traffic and civil (CTC) incidents and allows officials to observe patterns and quickly identify regions with higher probabilities of activity. Our toolkit provides analysts with the ability to visualize different types of data sets (census data, daily weather reports, zoning tracts, prominent calendar dates, etc.) that provide an insight into correlations among CTC incidents and spatial demographics. In the spatial domain, we have implemented a kernel density estimation mapping technique that creates a color map of spatially distributed CTC events that allows analysts to quickly find and identify areas with unusually large activity levels. In the temporal domain, reports can be aggregated by day, week, month or year, allowing the analysts to visualize the CTC activities spatially over a period of time. Furthermore, we have incorporated temporal prediction algorithms to forecast future CTC incident levels within a 95% confidence interval. Such predictions aid law enforcement officials in understanding how hotspots may grow in the future in order to judiciously allocate resources and take preventive measures. Our system has been developed using actual law enforcement data and is currently being evaluated and refined by a consortium of law enforcement agencies.
In vitro micronucleus scoring by flow cytometry: Differential staining of micronuclei versus apoptotic and necrotic chromatin enhances assay reliability (2005)

The in vitro micronucleus test has received considerable attention in recent years for its use in drug safety assessment and toxicological research. The less tedious nature of the assay relative to chromosome aberration analyses is a driving force, and explains why many chemical and drug safety programs have adopted the endpoint. Development of a high-throughput micronucleus scoring system would further enhance the utility of the assay for lead optimization and other early drug development work. Although several variations of a flow cytometric (FCM) method for scoring cell-culture-derived micronuclei (MN) have been described in the literature, they have been unable to distinguish true MN from apoptotic and necrotic chromatin (Nüsse M and Marx K 1997: Mutat Res 392: 109-115). Here, we report advances to this methodology whereby a sequential staining procedure is used to differentially label these types of sub-2n particles. With the use of ethidium monoazide (EMA), the chromatin of dead and dying cells is labeled. After a photoactivation step that covalently binds EMA to chromatin, cytoplasmic membranes are digested and resulting lysates are incubated with RNase plus a pan-nucleic acid dye (SYTOX Green). This process provides a suspension of free nuclei and sub-2n particles that are labeled with either SYTOX or SYTOX and EMA. Preliminary studies with heat-shocked L5178Y mouse cells demonstrated that EMA stains necrotic and mid- through late-stage apoptotic cells. Importantly, the sequential labeling procedure provided reliable micronucleus enumeration, even when cultures contained high percentages of dead cells. Subsequently, experiments with the following diverse genotoxicants were performed: hydroxyurea, methyl methanesulfonate, benzo[a]pyrene, etoposide, cyclophosphamide, and vinblastine. Additionally, the nongenotoxicants sucrose, tributyltin methoxide, and dexamethasone were tested up to 5 mg/ml, or to cytotoxic concentrations. FCM data were found to correspond closely with microscopy-based measurements. Collectively, these data suggest that this sequential EMA/SYTOX staining procedure provides reliable, high-throughput enumeration of in vitro MN.
A second-generation liquid crystal phase-shifting point-diffraction interferometer employing structured substrates (2005)

By design, point-diffraction interferometers are much less sensitive to environmental disturbances than dual-path interferometers, but, until very recently, have not been capable of phase shifting. The liquid crystal point-diffraction interferometer (LCPDI) utilizes a dye-doped, liquid crystal (LC) electro-optical device that functions as both the point-diffraction source and the phase-shifting element, yielding a phase-shifting diagnostic device that is significantly more compact and robust while using fewer optical elements than conventional dual-path interferometers. These attributes make the LCPDI of special interest for diagnostic applications in the scientific, commercial, military, and industrial sectors, where vibration insensitivity, power requirements, size, weight, and cost are critical issues. Until very recently, LCPDI devices have used a plastic microsphere embedded in the LC fluid layer as the point-diffraction source. The process for fabricating microsphere-based LCPDI devices is low-yield, labor-intensive, and very "hands-on"; great care and skill are required to produce devices with adequate interference fringe contrast for diagnostic measurements. With the goal of evolving the LCPDI beyond the level of a laboratory prototype in mind, we have developed "second-generation" LCPDI devices in which the reference-diffracting elements are an <i>integral part of the substrates</i> by depositing a suitable optical material (vapor-deposited thin films or photoresist) directly onto the substrate surface. These "structured" substrates eliminate many of the assembly difficulties and performance limitations of current LCPDI devices as well as open the possibility of mass-producing LCPDI devices at low cost by the same processes used to manufacture commercial LC displays.
Signal classification using global dynamical models, Part I: Theory (1996)

Detection and classification of signals is one of the principal areas of signal processing, and the utilization of nonlinear information has long been considered as a way of improving performance beyond standard linear (e.g. spectral) techniques. Here, we develop a method for using global models of chaotic dynamical systems theory to define a signal classification processing chain, which is sensitive to nonlinear correlations in the data. We use it to demonstrate classification in high noise regimes (negative SNR), and argue that classification probabilities can be directly computed from ensemble statistics in the model coefficient space. We also develop a modification for non‐stationary signals (i.e. transients) using non‐autonomous ODEs. In Part II of this paper, we demonstrate the analysis on actual open ocean acoustic data from marine biologics.
Enzymatic pre-treatment as a means of enhancing the antibacterial activity and stability of ZnO nanoparticles sonochemically coated on cotton fabrics (2012)

Zinc oxide nanoparticles (ZnO NP's) are known for their excellent antibacterial properties. This paper describes a method for enhancing the stability and the antibacterial activity of ZnO NPs synthesized and embedded sonochemically on cotton fabrics, by pre-treating the fabric surface with cellulase enzyme. The enzymatic pre-treatment resulted in the deposition of smaller sized NPs with improved adhesion. The reduction in particle size brought about better antibacterial performance against several types of bacteria. The sonochemically produced ZnO coating withstood 10 laundry cycles at 92 °C retaining its antibacterial activity.
Installing Guest Molecules at Specific Sites within Scaffold Protein Crystals (2017)

Protein crystals are porous self-assembling materials that can be rapidly evolved by mutagenesis. We aimed to develop scaffold assisted crystallography techniques in an engineered protein crystal with large pores (>13 nm). Guest molecules were installed via a single covalent bond to attempt to reduce the conformational freedom and achieve high-occupancy structures. We used four different conjugation strategies to attach guest molecules to three different cysteine sites within pre-existing protein crystals. In all but one case, the presence of the adduct was obvious in the electron density. Structure determination of larger guest molecules may be feasible due to the large pores of the engineered scaffold crystals.