gebhart/patrepeval huggingface dataset:
Rapid Detection of H5N1 Subtype Influenza Viruses by Antigen Capture Enzyme-Linked Immunosorbent Assay Using H5- and N1-Specific Monoclonal Antibodies (2009)

Highly pathogenic avian influenza (HPAI) virus of the H5N1 subtype has caused devastating damage to poultry flocks and sporadic human H5N1 infections. There is concern that this virus subtype may gain transmissibility and become pandemic. Rapid diagnosis and surveillance for H5N1 subtype viruses are critical for the control of H5N1 infection. In this study, we report a robust antigen-capture enzyme-linked immunosorbent assay (AC-ELISA) based on H5- and N1-specific monoclonal antibodies (MAbs) for the rapid detection of H5N1 subtype viruses. The H5 hemagglutinin (HA)-specific MAb (2D9) targets a conformational epitope which recognized multiple clades of H5N1 viruses, including clades 0, 1, 2.1, 2.2, 2.3, 4, 7, and 8. The N1 neuraminidase (NA)-specific MAb (8H12) recognized a linear epitope comprising the sequence AELPF. This epitope was 99% conserved in the NA of 708 analyzed H5N1 viruses, while the epitope was absent in NAs of subtypes N2 through N9. The specificity of the AC-ELISA was examined by using 41 H5N1 HPAI strains from multiple clades, 36 non-H5N1 viruses, and 4 influenza B viruses. No cross-reactivity was observed for any of the non-H5N1 viruses tested. The estimated detection limit was 1 to 2 HA titers. It is concluded that this H5N1 AC-ELISA can simultaneously detect H5 and N1 subtype antigens, eliminating the need for secondary testing for the NA subtype. Implementation of this assay in ELISA-like formats suitable for field use, such as dot ELISA, immunofiltration, or electrochemical biosensor technologies, would provide dual on-site detection of H5 and N1 in clinical or environmental specimens.
N-halamine biocidal coatings (2006)

Novel N-halamine siloxane and epoxide coatings are described. The coatings can be rendered biocidal by exposure to dilute bleach. Once the bound chlorine is lost from the coatings, it can be regenerated by further exposure to dilute bleach. Synthetic schemes and biocidal efficacy data are presented. The stabilities of the bound chlorine on the surfaces are also addressed. Substrates employed include sand, textiles, and paint. Potential uses for the technology are discussed.
A subtractive approach to molecular engineering of dimethoxybenzene-based redox materials for non-aqueous flow batteries (2015)

The development of new high capacity redox active materials is key to realizing the potential of non-aqueous redox flow batteries (RFBs).
Confocal air-coupled acoustic radiation force probe for the optical coherence elastography of tissues (2021)

We have designed and developed an air-coupled ultrasonic radiation force probe co-focused with a phase-sensitive optical coherence tomography system (ACUS-OCT). Our custom-made 1 MHz spherically focused piezo-electric transducer with a concentric circular opening of 10 mm diameter allows for the confocal micro-excitation of waves and the spatial (2D, 3D) motion measurement of tissues. Phantom studies demonstrated the capabilities of this probe to produce quasi-harmonic excitation up to 4 kHz for the generation of highly localized elastic waves. Experimental results in ocular tissues showed the highly localized 2D/3D elasticity mapping capabilities of this approach with great potential for clinical translation.
<i>In vitro</i>evolution of phi29 DNA polymerase using isothermal compartmentalized self replication technique (2016)

Compartmentalized self replication (CSR) is widely used for in vitro evolution of thermostable DNA polymerases able to perform PCR in emulsion. We have modified and adapted CSR technique for isothermal DNA amplification using mezophilic phi29 DNA polymerase and whole genome amplification (WGA) reaction. In standard CSR emulsified bacterial cells are disrupted during denaturation step (94-96°C) in the first circles of PCR. Released plasmid DNA that encodes target polymerase and the thermophilic enzyme complement the emulsified PCR reaction mixture and start polymerase gene amplification. To be able to select for mezophilic enzymes we have employed multiple freezing-thawing cycles of emulsion as a bacterial cell wall disruption step instead of high temperature incubation. Subsequently WGA like plasmid DNA amplification could be performed by phi29 DNA polymerase applying different selection pressure conditions (temperature, buffer composition, modified dNTP, time, etc.). In our case the library of random phi29 DNA polymerase mutants was subjected to seven selection rounds of isothermal CSR (iCSR). After the selection polymerase variant containing the most frequent mutations was constructed and characterized. The mutant phi29 DNA polymerase can perform WGA at elevated temperatures (40-42°C), generate two to five times more of DNA amplification products, and has significantly increased half-life at 30 and 40°C, both in the presence or the absence of DNA substrate.
A maximum entropy Chinese character-based parser (2003)

The paper presents a maximum entropy Chinese character-based parser trained on the Chinese Treebank ("CTB" henceforth). Word-based parse trees in CTB are first converted into character-based trees, where word-level part-of-speech (POS) tags become constituent labels and character-level tags are derived from word-level POS tags. A maximum entropy parser is then trained on the character-based corpus. The parser does word-segmentation, POS-tagging and parsing in a unified framework. An average label F-measure 81.4% and word-segmentation F-measure 96.0% are achieved by the parser. Our results show that word-level POS tags can improve significantly word-segmentation, but higher-level syntactic strutures are of little use to word segmentation in the maximum entropy parser. A word-dictionary helps to improve both word-segmentation and parsing accuracy.
A multidimensional analysis of genes mutated in breast and colorectal cancers (2007)

A recent study of a large number of genes in a panel of breast and colorectal cancers identified somatic mutations in 1149 genes. To identify potential biological processes affected by these genes, we examined their putative roles based on sequence similarity, membership in known functional groups and pathways, and predicted interactions with other proteins. These analyses identified functional groups and pathways that were enriched for mutated genes in both tumor types. Additionally, the results pointed to differences in molecular mechanisms that underlie breast and colorectal cancers, including various intracellular signaling and metabolic pathways. These studies provide a multidimensional framework to guide further research and help identify cellular processes critical for malignant progression and therapeutic intervention.
Acceptor Specificity of ATP: Nucleoside-5′-Phosphate Pyrophosphotransferase from Streptomyces adephospholyticus (1978)

ATP: nucleoside-5′-phosphate pyrophosphotransferase [EC 2.7.6.4] of Streptomyces adephospholyticus synthesizes not only 3′-pyrophosphates of 5′-purine ribomononucleotides but also those of pyrimidine mononucleotides, some short oligonucleotides, a variety of 5′-diphosphonucleosidic coenzymes and mG-5′-ppp-5′-Am7⁠.
Generating CK19-Positive Cells with Hair-Like Structures from Wharton's Jelly Mesenchymal Stromal Cells (2012)

Wharton's jelly mesenchymal stromal cells (WJMSCs) are considered mesenchymal, multipotent, and capable of differentiating into cells of mesodermal origin. Ectodermal differentiation from mesenchymal cells has been recently reported. Herein, we show for the first time that we can generate cytokeratin 19-positive cells and hair-like structures from WJMSCs in vitro using 2 separate methodologies that utilize osteogenic media to induce WJMSCs to undergo osteogenic differentiation. In one method, WJMSCs were seeded on a matrix isolated from Wharton's jelly following decellularization. In the other method, WJMSCs were cultured to form spheroids. Our findings demonstrate that WJMSCs may have the capacity for ectodermal differentiation.
Natural Color Profile Adjustment for Professionals (2012)

While there may be no point in arguing about taste, creative professionals make a living from sharing theirs. Making specific, individual color preferences that a creative professional knows how to achieve when creating content on a display also propagate into print is a significant challenge since it lacks real-time feedback. The present paper introduces a method for allowing creative professionals to use the tools they know and love to also personalize the color behavior of their devices. This is achieved by analyzing color changes applied to images and applying them to a device's ICC profile. As a result the personalized device results in customized color behavior regardless of the workflow used. The paper describes the ICC profile transformation algorithm in detail and provides a color error analysis of its performance.
Co-activation of the diaphragm and external intercostal muscles through an adaptive closed-loop respiratory pacing controller (2023)

Our findings demonstrate that simultaneous activation of the inspiratory muscles could be used as a suitable strategy to delay stimulation-induced diaphragmatic fatigue and to induce a sigh-like behavior that could improve respiratory health.
A novel sensor for monitoring acoustic cavitation. Part II: Prototype performance evaluation (2003)

This paper describes a series of experimental studies to evaluate the performance of newly developed sensors for monitoring broadband acoustic emissions generated by acoustic cavitation. The prototype sensors are fabricated in the form of hollow, open-ended cylinders, whose inner surface is made from a thin film of piezoelectric polymer acting as a passive acoustic receiver of bandwidth greater than 10 MHz. A 4-mm thick coating of special acoustical absorber forms the outer surface of the sensor. The layer functions as a shield to cavitation events occurring outside the hollow sensor body, allowing megahertz acoustic emissions emanating from within the liquid contained in the sensor to be monitored. Testing of the new sensor concept has been carried out within the cavitating field provided by a commercial ultrasonic cleaning vessel operating at 40 kHz whose power output is rated at 1 kW. It is demonstrated that the prototype cavitation sensors are able to record a systematic increase in the level of the high-frequency acoustic spectrum (> 1 MHz) as electrical power to the cleaning vessel is increased. Through careful control of the experimental conditions, reproducibility of the high frequency "energy" associated with the cavitation spectrum was found to be typically +25%.
17.2: Compensation of False Contours on a PDP using a Pixel Based Motion Estimator Combined with an Efficient Coding Technique (2003)

Abstract False contours occurs on PDP since the eye tracks moving objects in a video scene. To correctly render these moving objects the definitive solution is to use the motion information and pre‐compensate the eye's tracking. Such a solution will be presented using a pixel‐based motion estimator combined to an efficient video coding technique.
Survey of Approaches for Handling Static Analysis Alarms (2016)

Static analysis tools have showcased their importance and usefulness in automated detection of code anomalies and defects. However, the large number of alarms reported and cost incurred in their manual inspections have been the major concerns with the usage of static analysis tools. Existing studies addressing these concerns differ greatly in their approaches to handle the alarms, varying from automatic postprocessing of alarms, supporting the tool-users during manual inspections of the alarms, to designing of light-weight static analysis tools. A comprehensive study of approaches for handling alarms is, however, not found. In this paper, we review 79 alarms handling studies collected through a systematic literature search and classify the approaches proposed into seven categories. The literature search is performed by combining the keywords-based database search and snowballing. Our review is intended to provide an overview of various alarms handling approaches, their merits and shortcomings, and different techniques used in their implementations. Our findings include that the categorized alarms handling approaches are complementary and they can be combined together in different ways. The categorized approaches and techniques employed in them can help the designers and developers of static analysis tools to make informed choices.
A technology compensated current reference in standard CMOS (2007)

An accurate current reference that compensates also for process variations is presented and realized in a 0.18 mum technology. This new concept allows tracking of oxide thickness in integrated MOS capacitors. The circuit uses SC-technique and adaptive biasing, together with inherent compensation. It is shown that 2-3% of accuracy over full process and temperature range can be achieved. Results for a different foundry are presented, too. The resistorless design is simple and suitable for low voltage. Power consumption is only 7.7 muA.
Scheduling parallelizable tasks to minimize average response time (1994)

A parallelizable (or malleable) task is one which can be run on an arbitrary number of processors, with a task execution time that depends on the number of processors allotted to it. Consider a system of M independent parallelizable tasks which are to be scheduled without preemption on a parallel computer consisting of P identical processors. For each task, the execution time is a known function of the number of processors allotted to it. The goal is to find (1) for each task i, an allotment of processors β, and (2) overall, a non-preemptive schedule assigning the tasks to the processors which minimizes the average response time of the tasks. Equivalently, we can minimize the flow time which is the sum of the completion times of each of the tasks.
Design of Cascaded Continuous-Time Sigma-Delta Modulators (2006)

Cascaded sigma-delta modulators implemented with continuous-time circuits are becoming popular due to its high potential to build high resolution, high bandwidth A/D converters. This paper shows a survey of the recent advances in this field. Architecture selection together with some design aspects are discussed for low oversampling ratio applications. The design of noise cancellation logic and the influence of integrator gain errors are also discussed. Finally some new challenges are proposed for next designs.
Image-sourced fingerprinting for LED-based indoor tracking (2017)

The advent of location-based services has created a necessity for indoor positioning and tracking. We propose an automated fingerprinting-based algorithm for an indoor tracking system that uses light-emitting diodes (LED) equipped with imaging sensors. The fingerprint collection part requires a calibration step that consists of the following: (i) a theoretic light power distribution is calculated using the visible light communication channel model; (ii) the imaging sensors mounted on the LED arrays capture the grayscale images; (iii) the captured images and the theoretically calculated light power distribution are used to estimate the light power map. Linear and non-linear regression, and artificial neural networks are used for mapping from the grayscale pixel values to the light power levels. A photodetector on the user equipment measures the light power in real-time. The estimated fingerprint map and the real-time power measurements are used in an extended Kalman filter. The results show that we can reach an accuracy on the order of the degree of granularity of the fingerprint map.
Pulsed gate dielectric breakdown in a 32 nm technology under different ESD stress configurations (2010)

We report pulsed high-k gate dielectric breakdown in various configurations emulating ESD stress in real input/output circuits. The stress on the receiver is of greater concern than is stress on the driver due to different gate oxide areas under stress. Methods to improve pad voltage tolerance for gate oxide breakdown are proposed.
Pressure sensor apparatus. [for sensing fluid pressure in body cavities using radioactive fluids] (1977)

A pressure sensor apparatus primarily for sensing pressure in a body cavity such as the cranium, bladder or vena cava of an animal or human comprising a housing having non-radioactive fluids contained in two spaced apart regions of the housing is described. A radioactive fluid immiscible with at least one of the non-radioactive fluids is also contained within the housing between the nonradioactive fluids. The interface between the radioactive fluid and one of the non-radioactive fluids is optionally formed by a resilient member such as an elastomeric diaphragm. A flexible member is connected to the housing and communicates with one of the two spaced apart regions in the housing. The other spaced apart region in the housing is closed by a resilient member such as a metallic diaphragm. With this arrangement, the movement of the radioactive fluid is proportional to the pressure sensed by the flexible member and is sensed by a radiation detector. 9 claims, 5 figures.
Orthogonal Polynomials based Hybrid Coded-Modulation for Multi-Tb/s Optical Transport (2013)

Orthogonal polynomials based single-carrier hybrid coded-modulation is proposed as multi-Tb/s enabling technology while employing the commercially available electronics. The proposed scheme can simultaneously solve the problems related to limited bandwidth and high energy consumption of information infrastructure.
Molecular cloning of a cDNA encoding the “61-kDa” calmodulin-stimulated cyclic nucleotide phosphodiesterase. Tissue-specific expression of structurally related isoforms. (1993)

We have isolated a 2287-bp cDNA encoding the 61-kDa calmodulin-stimulated cyclic nucleotide phosphodiesterase (CaM PDE) from a bovine brain library. A large open reading frame within the cDNA encodes a 530-residue polypeptide which is identical to the sequence of the purified protein previously determined by direct amino acid sequencing. Moreover, COS cells transfected with the cDNA express a cAMP and cGMP hydrolytic activity that is stimulated by calcium and calmodulin, confirming that the cDNA represents a mRNA species encoding a CaM PDE isozyme. RNase protection analyses indicate that either 61-kDa CaM PDE mRNA or structurally related transcripts encoding different CaM PDE isoforms are expressed in a tissue-specific manner. Total RNA isolated from brain (cerebral cortex, basal ganglia, hippocampus, cerebellum, and medulla/spinal cord), heart, aorta, liver, kidney outer medulla, kidney papilla, trachea, and lung completely protected a 410-base antisense riboprobe corresponding to sequence encoding a portion of the catalytic domain. Little or no protection was detected using adrenal cortex, adrenal medulla, liver, kidney cortex, spleen, or T-lymphocyte total RNA. Only brain RNA completely protected a 240-base antisense riboprobe corresponding to the 61-kDa CaM PDE amino terminus encompassing a putative calmodulin-binding domain. However, heart, aorta, liver, kidney, trachea, and lung RNA protected 150 bases of this riboprobe suggesting that these tissues express an isoform structurally related to the 61-kDa CaM PDE. Northern analysis of mRNA isolated from brain, heart, aorta, liver, kidney, lung, and trachea revealed that the cDNA hybridizes with a 3.8- and a 4.4-kb (kilobase) mRNA species. Interestingly, Northern blots of bovine cerebral cortex and heart mRNA probed under stringent conditions with antisense transcripts corresponding to either the 5'- or 3'-untranslated sequence of the 61-kDa CaM PDE cDNA hybridized with only the 4.4-kb mRNA from both tissues. Since different, yet structurally similar CaM PDE isoforms are expressed in brain and in heart, this result, in addition to the RNase protection data, is consistent with the idea that the mRNAs encoding these two CaM PDE isoforms are products of an alternately spliced gene.
Packet Scheduling for Multiple‐Switch Software‐Defined Networking in Edge Computing Environment (2018)

Software‐defined networking (SDN) decouples the control plane and data forwarding plane to overcome the limitations of traditional networking infrastructure. Among several communication protocols employed for SDN, OpenFlow is most widely used for the communication between the controller and switch. In this paper two packet scheduling schemes, FCFS‐Pushout (FCFS‐PO) and FCFS‐Pushout‐Priority (FCFS‐PO‐P), are proposed to effectively handle the overload issue of multiple‐switch SDN targeting the edge computing environment. Analytical models on their operations are developed, and extensive experiment based on a testbed is carried out to evaluate the schemes. They reveal that both of them are better than the typical FCFS‐Block (FCFS‐BL) scheduling algorithm in terms of packet wait time. Furthermore, FCFS‐PO‐P is found to be more effective than FCFS‐PO in the edge computing environment.
Abstract #LB-154: Identification of novel helper epitopes of MAGE-A4 and Survivin tumor antigen: Useful tool for the propagation of Th1 cells (2009)

AACR Annual Meeting-- Apr 18-22, 2009; Denver, CO

MAGE-A4 has been considered as an attractive cancer-testis (CT) antigen for tumor immunotherapy. It has been well accepted that T helper type 1 (Th1)-dominant immunity is critical for the successful induction of antitumor immunity in a tumor-bearing host. The adoptive Th1 cell therapy has been demonstrated to be an attractive strategy for inducing tumor eradication in mouse systems. However, no clinical trial of Th1 cell therapy has carried out. Here, we first identified MAGE-A4-derived promiscuous helper epitope peptide bound to both HLA-DPB1*0501 and DRB1*1403. Using the peptide, we established a suitable protocol for the propagation of MAGE-A4-specific Th1 cells in vitro. Culture of CD4+ T cells with IFN-\#947;-treated peripheral blood mononuclear cells (PBMC)-derived adherent cells in the presence of helper epitope peptide resulted in a great expansion of MAGE-A4-reactive Th cells producing IFN-\#947; but not IL-4. Moreover, it was demonstrated that ligation of MAGE-A4-reactive Th1 cells with the cognate peptide caused the production of IFN-\#947; and IL-2. Using this expansion procedure, we identified two novel survivin helper peptides, SU21 and SU22. The survivin molecule is known as one of the most desired target molecules for tumor immunotherapy. Therefore, survivin-specific Th1 cells would also play a critical role for tumor immunotherapy. Among the identified peptides, SU22 is capable of binding to HLA-DR53. The other peptide was presented to Th1 cells by HLA-DRB1*1501/1502. The Th1 cells induced by SU21 or SU22 produced IFN-\#947; against autologous dendritic cells pulsed with recombinant survivin protein, suggesting that both epitopes are functional antigens, which are naturally processed and presented. When PBMC were cultured with activated survivin-reactive Th1 cells in the presence of survivin peptide, most immunoregulatory cells including CD8-, CD19-, CD56- and CD11c-positive cells increased the expression levels of early activation maker, CD69. Moreover cytotoxic activity of NK cells and CD8+ T cells increased. It is suggesting that administration of activated Th1 cells would promote activity of immune cells in patients with cancer. Thus, our identified MAGE-A4 and survivin helper epitope peptides will become good tools for the propagation of tumor-specific Th1 cells applicable to adoptive immunotherapy of human cancer. We are planning a clinical trial of Th1 cell therapy combined with helper peptides after evaluating its rationality in hu-mouse therapy model. The new challenge to the adoptive immunotherapy is now started and we believed Th1 cell therapy using tumor-specific Th1 cells expanded with helper epitope peptide will become a promising strategy for the immunotherapy of human cancer.

Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr LB-154.