gebhart/patrepeval huggingface dataset:
Identification of the genes encoding NAD(P)H-flavin oxidoreductases that are similar in sequence to Escherichia coli Fre in four species of luminous bacteria: Photorhabdus luminescens, Vibrio fischeri, Vibrio harveyi, and Vibrio orientalis (1994)

Genes encoding NAD(P)H-flavin oxidoreductases (flavin reductases) similar in both size and sequence to Fre, the most abundant flavin reductase in Escherichia coli, were identified in four species of luminous bacteria, Photorhabdus luminescens (ATCC 29999), Vibrio fischeri (ATCC 7744), Vibrio harveyi (ATCC 33843), and Vibrio orientalis (ATCC 33934). Nucleotide sequence analysis showed Fre-like flavin reductases in P. luminescens and V. fischeri to consist of 233 and 236 amino acids, respectively. As in E. coli Fre, Fre-like enzymes in luminous bacteria preferably used riboflavin as an electron acceptor when NADPH was used as an electron donor. These enzymes also were good suppliers of reduced flavin mononucleotide (FMNH2) to the bioluminescence reaction. In V. fischeri, the Fre-like enzyme is a minor flavin reductase representing < 10% of the total FMN reductase. That the V. fischeri Fre-like enzyme has no appreciable homology in amino acid sequence to the major flavin reductase in V. fischeri, FRase I, indicates that at least two different types of flavin reductases supply FMNH2 to the luminescence system in V. fischeri. Although Fre-like flavin reductases are highly similar in sequence to luxG gene products (LuxGs), Fre-like flavin reductases and LuxGs appear to constitute two separate groups of flavin-associated proteins.
Hologon Deflectors Incorporating Dispersive Optical Elements For Scan Line Bow Correction (1988)

Theoretical and experimental data will be presented that show how the bow in a scan-line generated by a hologon deflector can be minimized by incorporating either a prism or grating element into the deflector geometry. In addition to minimizing scan-line bow, these dispersive optical elements permit lower wavelength to grating periodic values to be used for the hologon which results in improved cross-scan and radiometric system performance.
Large‐Scale Energy Storage: A Stable Vanadium Redox‐Flow Battery with High Energy Density for Large‐Scale Energy Storage (Adv. Energy Mater. 3/2011) (2011)

Though considered a promising large-scale storage device for regulating renewable energy supply during calm and cloudy weather, the vana-dium redox battery's use has been limited by its inability to work well in a wide range of temperatures and its low energy density. Adding hydro-chloric acid to the sulfuric acid electrolyte typically used in vanadium redox flow batteries increased the batteries' energy storage capacity by 70% and expanded the operational temperature range, report Liyu Li, Zhenguo Yang, and co-workers on p. 394.
Upgrading of wastewater treatment plants for nitrogen removal: industrial application of an automated aeration management based on ORP evolution analysis (1998)

Upgrading conventional wastewater treatment plants for nitrogen removal involves total control of nitrification, denitrification and carbon removal. On low-load activated sludge processes, a comprehensive survey on fast and low kinetic biological reactions has been carried out, which describes the short-term and long-term requirements on the aeration sequences in a single tank. Although soluble and adsorbed pollution have to be treated in routine conditions, soluble pollution treatment becomes a priority during limited overloads, indicated by a slow ORP evolution. The treatment of adsorbed material is hence delayed. In order to implement the appropriate strategy, an automated aeration management system has been developed. This system is based on the analysis of both the real time signal and time evolution of the Redox potential signal. This information is used for command and control purposes. The application of this logic-based approach at full scale has been fruitful in evaluating its adaptability to the industrial environment and its potential results. The operation of seven plants under the control of the automated management system has enabled the nitrogen removal performance to be increased. Most of the nitrification and denitrification yields reach 90%, whereas previous results were far lower and more erratic. In addition, the present work determines limiting conditions for a guaranteed long-term result and a successful upgrading.
The fragile X mental retardation protein, FMRP, recognizes G‐quartets (2004)

Fragile X mental retardation is a disease caused by the loss of function of a single RNA-binding protein, FMRP. Identifying the RNA targets recognized by FMRP is likely to reveal much about its functions in controlling some aspects of memory and behavior. Recent evidence suggests that one of the predominant RNA motifs recognized by the FMRP protein is an intramolecular G-quartet and that the RGG box of FMRP mediates this interaction. Searching databases of mRNA sequence information, as well as compiled sequences of predicted FMRP targets based on biochemical identification, has revealed that many of these predicted FMRP targets contain intramolecular G-quartets. Interestingly, many of the G-quartet containing RNA targets encode proteins involved in neuronal development and synaptic function. Defects in the metabolism of this set of RNAs, presumably in the translation of their protein products, is likely to underlie the behavioral and cognitive changes seen in the disease.
Concentration of Cryptosporidium, microsporidia and other water-borne pathogens by continuous separation channel centrifugation (2002)

Methods are needed for detecting pathogens in drinking water to ensure public health. The first step for any pathogen detection procedure is concentration. However, this step has been problematic because recovery efficiencies of conventional methods, like filtration, are often low and variable, which may lead to false negatives. Continuous separation channel centrifugation can simultaneously concentrate multiple pathogens as small as 1 microm with high and reproducible efficiency in a variety of water matrices.
All-Quantum-Dot Infrared Light-Emitting Diodes (2015)

Colloidal quantum dots (CQDs) are promising candidates for infrared electroluminescent devices. To date, CQD-based light-emitting diodes (LEDs) have employed a CQD emission layer sandwiched between carrier transport layers built using organic materials and inorganic oxides. Herein, we report the infrared LEDs that use quantum-tuned materials for each of the hole-transporting, the electron-transporting, and the light-emitting layers. We successfully tailor the bandgap and band position of each CQD-based component to produce electroluminescent devices that exhibit emission that we tune from 1220 to 1622 nm. Devices emitting at 1350 nm achieve peak external quantum efficiency up to 1.6% with a low turn-on voltage of 1.2 V, surpassing previously reported all-inorganic CQD LEDs.
Lysis of Autologous Melanoma Cells by Tumor*Infiltrating Lymphocytes: Association With Clinical Response (1991)

Tumor–infiltrating lymphocytes (TILs) can be grown in vitro in medium containing interleukin–2 (IL–2). In clinical trials at the Surgery Branch of the National Cancer Institute, patients with metastatic malignant melanomas were treated with IL–2 plus the adoptive transfer of autologous TILs. At the time of treatment, TILs were assayed for in vitro lysis of fresh autologous and allogeneic melanoma cells and Daudi cells. Patients were evaluated for clinical response 4–8 weeks later. Lysis of autologous tumor cells by TILs was significantly higher for responding than for non responding patients. Tumor cells from responding and non–responding patients were equally sensitive to lysis by allogeneic lymphokine–activated killer (LAK) cells. There was no difference between TILs from responding and non–responding patients for lysis of LAK sensitive Daudi cells, which was low in most cases and demonstrated that TIL lysis of autologous tumor cells was not due to LAK cells. The observed association of autologous tumors cell lysis by TILs with clinical response suggests that the development of culture methods to optimize lysis of autologous tumors may lead to increased response rates using this TIL treatment regimen.[J Natl Cancer Inst 83: 932–937, 1991]
Synthesis of [123I]N?,N?-dimethyl-6-methyl-(-4?-iodophenyl)imidazo[1,2-a]pyridine-3-acetamide for the study of peripheral benzodiazepine receptors using SPECT (2000)

The [123I]labelled imidazo[1,2-a]pyridine [123I]ioddozolpidem 4 was found to exhibit preferential activity towards Peripheral rather than Central Benzodiazepine receptors in vivo and was synthesised for the potential study of the Peripheral Benzodiazepine Receptors (PBR) using SPECT. [123I]Iodozolpidem was prepared from the corresponding tributyl tin precursor by iododestannylation with Na[123I] in the presence of peracetic acid or chloramine-T. Purification by semipreparative C-18 RP HPLC gave the product in radiochemical yields of 60–85%. The product was obtained in >97% chemical and radiochemical purity with a specific activity >80 GBq/μmol. Copyright © 2000 John Wiley & Sons, Ltd.
Purification, structure and partial characterization of the major sperm activating protein complex in human serum (1993)

Serum has long been known to enhance sperm motility, and the major factor that mediates this activation has been shown to be a macromolecule complex with a MW of about 250 kD. This macromolecule, named Sperm Activating Protein (SPAP) has now been purified by a four step protocol. Starting with 100 mL of serum 20 to 200 micrograms of purified SPAP was recovered (N = 40). Studies on the identification and structure of SPAP revealed that the macromolecule is formed by an IgG molecule to which an apolipoprotein A-I molecule is bound. Further studies on the structure of the complex was performed by partial proteolytic cleavage of SPAP by pepsin and papain and interaction with poly- and monoclonal antibodies. Based on these results the most plausible structure of SPAP places one molecule of apo A-I between the two arms of the Fab portion of an IgG4 molecule. Human spermatozoa incubated with polyclonal anti-SPAP serum and a second FITC-labelled antiserum showed fluorescence at a distinct band at the lower part of the sperm head, indicating that SPAP acts by direct interaction with the spermatozoa. The SPAP molecule shows a new mechanism mediated by the immunoglobulins, that may be very important for male fecundity.
Differentiation of breast lesions based on viscoelasticity response at sub-Hertz frequencies (2016)

There is an urgent need for a noninvasive but more accurate method to assess breast masses before referring the patient to biopsy. In this study, we use the slow viscoelastic creep response to evaluate breast masses at low (&lt;1 Hz) frequencies. This method uses an automated ramp-and-hold compression device and a high-frame-rate ultrasound imaging to track tissue strain. The study cohort included 30 pre-biopsy patients with suspicious masses. Sequential high-frame-rate images were recorded during the ramp-and-hold process. The data were used to calculate the creep response at each point. Then, using a classic linear model, the retardation-time map was created within the field of view. The resulting retardation-time maps exhibited clear distinction of the mass margins. The results showed that benign breast lesions appear with an increase in creep retardation-time compared to surrounding breast glandular tissue, and the opposite trend was true for the malignant lesions. Statistical analysis of the viscoelasticity features revealed that a contrast feature based on the retardation-time is an accurate classifier of malignant and benign masses (P&lt;0.0003). It is concluded that the retardation time is a promising biomarker for differentiation of breast masses. [Work supported by NIH Grant CA168575.]
Robust and Efficient Algorithms for Separating Latent Overlapped Fingerprints (2012)

Overlapped fingerprints are frequently encountered in latent fingerprints lifted from crime scenes. It is necessary to separate such overlapped fingerprints into component fingerprints so that existing fingerprint matchers can recognize them. The most crucial step in separating overlapped fingerprints is estimation of component orientation fields, which is a challenging problem for existing orientation field estimation algorithms. We propose a robust orientation field estimation algorithm (called the basic algorithm) for latent overlapped fingerprints whose core is the constrained relaxation labeling algorithm. We also propose improved versions of the basic algorithm for two special but frequent cases: 1) the mated template fingerprint of one component fingerprint is known and 2) the two component fingerprints are from the same finger. In both cases, further constraints are used to reduce ambiguity in relaxation labeling. Experimental results on both real and simulated overlapped fingerprints show that the proposed algorithm outperforms the state-of-the-art algorithm in both accuracy and efficiency. The two improved versions also perform better than the basic algorithm in respective cases. The latent overlapped fingerprint database collected for this study is made publicly available for performance evaluation.
Packetscore: statistics-based overload control against distributed denial-of-service attacks (2005)

Distributed denial of service (DDoS) attack is a critical threat to the Internet. Currently, most ISPs merely rely on manual detection of DDoS attacks after which offline fine-grain traffic analysis is performed and new filtering rules are installed manually to the routers. The need of human intervention results in poor response time and fails to protect the victim before severe damages are realized. The expressiveness of existing filtering rules is also too limited and rigid when compared to the ever-evolving characteristics of the attacking packets. Recently, we have proposed a DDoS defense architecture that supports distributed detection and automated on-line attack characterization. We focus on the design and evaluation of the automated attack characterization, selective packet discarding and overload control portion of the proposed architecture. Our key idea is to prioritize packets based on a per-packet score which estimates the legitimacy of a packet given the attribute values it carries. Special considerations are made to ensure that the scheme is amenable to high-speed hardware implementation. Once the score of a packet is computed, we perform score-based selective packet discarding where the dropping threshold is dynamically adjusted based on (1) the score distribution of recent incoming packets and (2) the current level of overload of the system.
A Robot Gripper With Variable Stiffness Actuation for Enhancing Collision Safety (2019)

This article presents the design of a two-finger variable stiffness gripper and demonstrates how the adjustable compliance of the fingers can enhance manipulation safety and robustness during collisions. The compliance between actuators and fingers are generated by using repulsive magnets as preloaded nonlinear springs such that by adjusting the air-gaps between the magnets, the position and stiffness of the fingers can be controlled simultaneously. The capability of the proposed design in collision detection and reaction is demonstrated via two collision scenarios. In the first experiment, a momentum-based collision detection algorithm in the context of compliant grasping is investigated. In the second experiment, an optimal reaction strategy is developed that exploits the adjustable stiffness characteristics of the gripper to improve safety during collisions. The experimental results of the two scenarios indicate the effectiveness of the proposed gripper in enhancing collision safety.
Characterization of Subsurface Cavities using Gravity and Ground Penetrating Radar (2019)

ABSTRACT Subsurface cavities occur naturally by dissolution of carbonates and evaporites or by human action, such as the construction of tunnels and tombs. They can be filled with air, water, sediments, or a combination. Gravity and ground penetrating radar (GPR) methods have been used widely to determine the location and size of subsurface cavities. The objective of this study is to present a quantitative approach to estimate the porosity and water saturation of cavity-filling materials from GPR and gravity measurements. The approach uses appropriate rock-physics models of the dielectric permittivity and density of a shallow cavity and estimates the porosity and water saturation inside the cavity by solving the two model equations simultaneously for these two variables. We test the proposed method using synthetic GPR and gravity data sets corresponding to three spherical-cavity models: air-filled, water-filled, and a partially-saturated sand filling. Results show that the method is accurate in retrieving the correct porosity within 0.76% error and water saturation within 2.4% error. We also apply the method on three published case studies over air-filled rectangular cavities. We found that the proposed method estimated the correct porosity and water saturation in one study but failed with the other studies. However, when the procedure was repeated with gravity values calculated from parameters reported in these studies, the proposed method estimated the correct porosity and water saturation accurately.
COVER: A Cooperative Virtual Force Robot Deployment Technique (2015)

We present a Cooperative Virtual Force Robot Deployment (COVER) technique. Virtual force (VF) technique appears as one of the prominent approaches to perform multi-robot deployment autonomously. However, most of the existing VF based approaches lack purposeful deployment. Our approach modifies the original VF approach to overcome this problem and considers the mission requirements such as the number of required robots in each locality (e.g., landmarks are distributed and each needs a specific number of robots in its vicinity). In addition, COVER expedites the deployment process by establishing a cooperative relation between robots and neighboring landmarks. Extensive simulation experiments have been carried out to assess the performance of COVER along with Hungarian deployment method (a centralized approach), the basic virtual force (BVF) and other recent proposed variations. The simulation results demonstrate the effectiveness of COVER for several performance factors such as total travelled distance, total exchanged messages and total deployment time.
Modeling and simulation of time-varying delays (2012)

This paper presents the numerical methods for modeling and simulation of fundamental continuous time-varying delays. Continuous time-varying delays are categorized as variable time delay and variable transport delay. These two fundamental delays are formulated and implemented as two Simulink® built-in blocks. The difference between these two delays are discussed. With these two fundamental time varying delays, physical system such as convey belt, control system with delayed control signals, delay differential equations, can be easily modeled and simulated.
Bipolar transistors on thin SOI: concept, status and prospect (2005)

Traditional high speed bipolar transistors are not compatible with the thin silicon-on-insulator substrates that are used for low power-delay product CMOS manufacturing. This paper discusses an SOI-CMOS compatible vertical bipolar transistor, from its inception to experimental verification on 120 nm SOI. Unique electrical characteristics, such as breakdown behavior and substrate bias dependency, are examined in detail and correlated to simple theory. Future directions and prospects of complementary SOI-BiCMOS are outlined.
Multi-Scale People Detection and Motion Analysis for Video Surveillance (2010)

Visual processing of people, including detection, tracking, recognition, and behavior interpretation, is a key component of intelligent video surveillance systems. Computer vision algorithms with the capability of “looking at people” at multiple scales can be applied in different surveillance scenarios, such as farfield people detection for wide-area perimeter protection, mid-field people detection for retail/banking applications or parking lot monitoring, and near-field people/face detection for facility security and access. In this chapter, we address the people detection problem in different scales as well as human tracking and motion analysis for real video surveillance applications including people search, retail loss prevention, people counting, and display effectiveness.
Genetic Control of Tolerance to Type II Collagen and Development of Arthritis in an Autologous Collagen-Induced Arthritis Model (2003)

T cell recognition of the type II collagen (CII) 260-270 peptide is a bottleneck for the development of collagen-induced arthritis (CIA), an animal model of rheumatoid arthritis. We have earlier made C3H.Q mice expressing CII with glutamic acid instead of aspartic acid at position 266 (the MMC-C3H.Q mouse), similar to the rat and human CII epitope, which increases binding to MHC class II and leads to effective presentation of the peptide in vivo. These mice show T cell tolerance to CII, but also develop severe arthritis. The present investigation shows that non-MHC genes play a decisive role in determining tolerance and arthritis susceptibility. We bred MMC into B10.Q mice, which display similar susceptibility to CIA induced with rat CII as the C3H.Q mice. In contrast to MMC-C3H.Q mice, MMC-B10.Q mice were completely resistant to arthritis. Nontransgenic (B10.Q x C3H.Q)F(1) mice were more susceptible to CIA than either of the parental strains, but introduction of the MMC transgene leads to CIA resistance, showing that the protection is dominantly inherited from B10.Q. In an attempt to break the B10-mediated CIA protection in MMC-transgenic mice, we introduced a transgenic, CII-specific, TCR beta-chain specific for the CII(260-270) glycopeptide, in the highly CIA-susceptible (B10.Q x DBA/1)F(1) mice. The magnification of the autoreactive CII-specific T cell repertoire led to increased CIA susceptibility, but the disease was less severe than in mice lacking the MMC transgene. This finding is important for understanding CIA and perhaps also rheumatoid arthritis, as in both diseases MHC class II-restricted T cell recognition of the glycosylated CII peptide occurs.
Speech Separation Using Speaker Inventory (2019)

Overlapped speech is one of the main challenges in conversational speech applications such as meeting transcription. Blind speech separation and speech extraction are two common approaches to this problem. Both of them, however, suffer from limitations resulting from the lack of abilities to either leverage additional information or process multiple speakers simultaneously. In this work, we propose a novel method called speech separation using speaker inventory (SSUSI), which combines the advantages of both approaches and thus solves their problems. SSUSI makes use of a speaker inventory, i.e. a pool of pre-enrolled speaker signals, and jointly separates all participating speakers. This is achieved by a specially designed attention mechanism, eliminating the need for accurate speaker identities. Experimental results show that SSUSI outperforms permutation invariant training based blind speech separation by up to 48% relatively in word error rate (WER). Compared with speech extraction, SSUSI reduces computation time by up to 70% and improves the WER by more than 13% relatively.
Serotyping of Cryptococcus neoformans by dot enzyme assay (1996)

A method is described for the serotyping of Cryptococcus neoformans based on direct analysis of culture supernatants for the major type-specific capsular antigen, glucuronoxylomannan. Factor sera prepared by absorption of polyclonal rabbit antisera (Iatron Laboratories, Inc., Tokyo, Japan) or selected anti-C. neoformans monoclonal antibodies were used in a dot enzyme assay to detect the presence of antigen.