gebhart/patrepeval huggingface dataset:
Colour Difference Metrics and Image Sharpness (2000)

We describe experiments to assess differences in the perceived sharpness of images, in which a Gaussian filter of variable width was convolved with a set of test images. Differences between the original and filtered images were computed pixel by pixel using three colour metrics: (a) mean square error (MSE) computed in RGB values; (b) CIELAB colour difference; and (c) s-CIELAB spatial colour difference. A psychophysical experiment was performed in which observers assessed the sharpness of the filtered images on a numerical category scale. The modulation transfer function (MTF) for the display was measured and the square root integral (SQRI) was evaluated as a predictor of perceived image sharpness. The results showed good agreement between the mean observer judgements and the prediction of both the colour difference metrics and the image quality metric across the full range of widths of the Gaussian filter.
Biomimetic Accommodating Intraocular Lens Using a Valved Deformable Liquid Balloon (2015)

A deformable liquid-filled lens can significantly improve accommodation over the presbyopic natural lens.
Learning to Invert: Signal Recovery via Deep Convolutional Networks (2017)

The promise of compressive sensing (CS) has been offset by two significant challenges. First, real-world data is not exactly sparse in a fixed basis. Second, current high-performance recovery algorithms are slow to converge, which limits CS to either non-real-time applications or scenarios where massive back-end computing is available. In this paper, we attack both of these challenges head-on by developing a new signal recovery framework we call {\em DeepInverse} that learns the inverse transformation from measurement vectors to signals using a {\em deep convolutional network}. When trained on a set of representative images, the network learns both a representation for the signals (addressing challenge one) and an inverse map approximating a greedy or convex recovery algorithm (addressing challenge two). Our experiments indicate that the DeepInverse network closely approximates the solution produced by state-of-the-art CS recovery algorithms yet is hundreds of times faster in run time. The tradeoff for the ultrafast run time is a computationally intensive, off-line training procedure typical to deep networks. However, the training needs to be completed only once, which makes the approach attractive for a host of sparse recovery problems.
CXC Chemokine Ligand 13 Plays a Role in Experimental Autoimmune Encephalomyelitis (2006)

Experimental autoimmune encephalomyelitis (EAE) is a Tcell-mediated autoimmune disease of the CNS that is widely used as an animal model of multiple sclerosis. In this study, we investigate the role of CXCL13, a chemokine involved in the development and organization of secondary lymphoid tissues, in the pathogenesis of EAE. We detected CXCL13 mRNA and protein in spinal cords of mice with EAE. CXCL13-deficient mice exhibited a mild, self-limited form of disease. CXCL13 appeared to be important for the establishment of chronic white matter lesions. Furthermore, adoptive transfer experiments with CXCL13-deficient hosts indicate that the chemokine plays a distinct role during the effector phase. Our findings raise the possibility that reagents that antagonize or inhibit CXCL13 might be useful for the treatment of neuroinflammatory diseases such as multiple sclerosis.
Observation of optical gain in solutions of CdS quantum dots at room temperature in the blue region (2006)

The optical gain dynamics has been studied for two CdS quantum dot samples dispersed in toluene at room temperature. This was carried out by using femtosecond transient absorption technique with an excitation at 400nm and gain measurement was studied at the fluorescence maxima (440 and 460nm). The optical gain lifetime was found to be as long as 20ps under pump fluence as low as 0.77mJ∕cm2. The low threshold is the result of long lifetime of electrons and holes and narrow emission bandwidth. These results suggest that CdS quantum dots in solution are excellent gain media for optically pumped high power blue lasers.
Complete genome sequence of a newly isolated lytic bacteriophage, EFAP-1 of<i>Enterococcus faecalis</i>, and antibacterial activity of its endolysin EFAL-1 (2009)

Bacteriophage EFAP-1 and its lytic protein, EFAL-1, can be utilized as potent antimicrobial agents against Enterococcus spp. strains resistant to conventional antibiotics in hospital infections and also as environmental disinfectants to control disease-causing Enterococcus spp. in dairy farms.
Utrophin actin binding domain: analysis of actin binding and cellular targeting (1995)

Utrophin, or dystrophin-related protein, is an autosomal homologue of dystrophin. The protein is apparently ubiquitously expressed and in muscle tissues the expression is developmentally regulated. Since utrophin has a similar domain structure to dystrophin it has been suggested that it could substitute for dystrophin in dystrophic muscle. Like dystrophin, utrophin has been shown to be associated with a membrane-bound glycoprotein complex. Here we demonstrate that expressed regions of the predicted actin binding domain in the NH2 terminus of utrophin are able to bind to F-actin in vitro, but do not interact with G-actin. The utrophin actin binding domain was also able to associate with actin-containing structures, stress fibres and focal contacts, when microinjected into chick embryo fibroblasts. The expressed NH2-terminal 261 amino acid domain of utrophin has an affinity for skeletal F-action (Kd 19 +/- 2.8 microM), midway between that of the corresponding domains of alpha-actinin (Kd 4 microM) and dystrophin (Kd 44 microM). Moreover, this utrophin domain binds to non-muscle actin with a approximately 4-fold higher affinity than to skeletal muscle actin. These data (together with those of Matsumura et al. (1992) Nature, 360, 588-591) demonstrate for the first time that utrophin is capable of performing a functionally equivalent role to that of dystrophin. The NH2 terminus of utrophin binds to actin and the COOH terminus binds to the membrane associated glycoprotein complex, thus in non-muscle and developing muscle utrophin performs the same predicted 'spacer' or 'shock absorber' role as dystrophin in mature muscle tissues. These data suggest that utrophin could replace dystrophin functionally in dystrophic muscle.
The effect of surface reflection and surrounding environment on target temperature estimation using an infrared FPA (2007)

The accuracy of infrared temperature estimation can degrade significant for enclosed objects with reflective surfaces. This paper describes a basic model of the incident radiation on a FPA sensor element considering a target object, surrounding environment, surface temperatures, surface emissivity/reflection and optics. The model is used to characterize the direct (one color method) temperature estimation error as a function of reflection, wavelength, target temperatures and the environment geometry. Temperature estimation errors based on numerical simulations with focus on near infrared are compared in this paper in a variety of scenarios assuming target temperatures between 1000 to 1600 Kelvin. In one scenario is the measured radiation corrected to minimize the error due to reflection.
Distinct antigenic subtypes of human beta interferon can be distinguished by neutralization. (1996)

Different molecular configurations of human beta interferon were titrated with the standard reference antiserum of the National Institutes of Health (NIH) which had been prepared with natural beta fibroblast interferon in order to determine to what extent differences in these configurations would influence the neutralization of the antiviral action of interferon. Neutralization tests were carried out in Vero cells by diluting both interferon and antiserum. Encephalomyocarditis virus was employed as challenge virus. The neutralization titer was considered to have been reached when the effect of eight units of interferon was reduced to one. Two natural beta interferons prepared from fibroblasts and from amniotic membranes gave similar high titers. However, titers were reduced five-fold with recombinant interferons expressed in Escherichia coli, which do not contain carbohydrate, one with the natural sequence and a mutant with a single amino acid substitution (cysteine for serine). The NIH antiserum did not neutralize the effect of a protein fraction from amniotic membranes antigenically different from the human alpha, beta or gamma interferons but having the biological activity of interferon. We conclude that the carbohydrate moieties of human beta interferons are essential for their recognition by the NIH antiserum and that antibodies specific for human recombinant beta interferon, which does not contain carbohydrate, are needed.
A method for predicting key data center temperatures by known airflow streams (2012)

We present a simplified model for predicting key data-center temperatures, such as those of rack inlets and cooler returns. If the primary airflow streams into and out of all racks and coolers are known, these airflow values can be combined with the assumption of a well-mixed room ambient volume to create a simplified, but energy-balanced, set of temperature equations. Since the temperature estimates are restricted to only a small number of data center objects, solutions can be found quickly. This temperature model can be adapted to quickly address data center design or management issues without multiple Computational Fluid Dynamics (CFD) simulations. Optimized cooler set points can be quickly found with only slight adjustments to the model. In another application, the effects of cooler capacity models are easily understood when incorporated within the temperature model. The object-averaged inlet temperature estimates generated by this temperature model compare favorably to those found by CFD.
Unboundedly parallel simulations via recurrence relations (1990)

New methods are presented for parallel simulation of discrete event systems that, when applicable, can usefully employ a number of processors much larger than the number of objects in the system being simulated. Abandoning the distributed event list approach, the simulation problem is posed using recurrence relations. We bring three algorithmic ideas to bear on parallel simulation: parallel prefix computation, parallel merging , and iterative folding . Efficient parallel simulations are given for (in turn) the G/G/1 queue, a variety of queueing networks having a global first come first served structure (e.g., a series of queues with finite buffers), acyclic networks of queues, and networks of queues with feedbacks and cycles. In particular, the problem of simulating the arrival and departure times for the first N jobs to a single G/G/1 queue is solved in time proportional to N/P + log P using P processors.
Mapping metabolic changes by noninvasive, multiparametric, high-resolution imaging using endogenous contrast (2018)

Monitoring subcellular functional and structural changes associated with metabolism is essential for understanding healthy tissue development and the progression of numerous diseases, including cancer, diabetes, and cardiovascular and neurodegenerative disorders. Unfortunately, established methods for this purpose either are destructive or require the use of exogenous agents. Recent work has highlighted the potential of endogenous two-photon excited fluorescence (TPEF) as a method to monitor subtle metabolic changes; however, mechanistic understanding of the connections between the detected optical signal and the underlying metabolic pathways has been lacking. We present a quantitative approach to detecting both functional and structural metabolic biomarkers noninvasively, relying on endogenous TPEF from two coenzymes, NADH (reduced form of nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide). We perform multiparametric analysis of three optical biomarkers within intact, living cells and three-dimensional tissues: cellular redox state, NADH fluorescence lifetime, and mitochondrial clustering. We monitor the biomarkers in cells and tissues subjected to metabolic perturbations that trigger changes in distinct metabolic processes, including glycolysis and glutaminolysis, extrinsic and intrinsic mitochondrial uncoupling, and fatty acid oxidation and synthesis. We demonstrate that these optical biomarkers provide complementary insights into the underlying biological mechanisms. Thus, when used in combination, these biomarkers can serve as a valuable tool for sensitive, label-free identification of changes in specific metabolic pathways and characterization of the heterogeneity of the elicited responses with single-cell resolution.
BLISS: Using Robot in Learning Intervention to Promote Social Skills for Autism Therapy (2016)

Robots have been introduced for autism therapy. However, most robotics studies focused on providing means of practice with dyadic interaction activities. To live in the society, autistic children need social interaction skills. In this study, we developed a mobile robot with non-threatening facial expression and investigated the potential of using this robot in triadic interaction activity for autism therapy to promote social interaction in children with autism. From the experiment that subjects play a picture matching game, it can be indicated that the robot can attract children with autism. Subjects can learn and understand the rule with their parents' participation. They could learn the name of the object in the picture that they do not know before as well. Some parents found that the robot could aid them in training their children. Autism specialists discovered some capabilities that they have never observed from the subjects in their therapeutic sessions. Therefore, this robot could be useful for autism specialists in finding aptitudes of children with autism in order to provide suitable intervention for effective therapy. This robot could be helpful for parents/caregivers in conducting therapeutic activities at home (continuing after therapeutic session with specialists) for even more effective therapy.
New control of PV solar farm as STATCOM (PV-STATCOM) for increasing grid power transmission limits during night and day (2014)

This paper presents a novel concept of utilizing PV solar farm inverter as STATCOM, termed PV-STATCOM, for improving stable power transfer limits of the interconnected transmission system. The entire inverter rating of PV solar farm which remains dormant in the nighttime is utilized with voltage and damping controls to enhance stable power transmission limits. During daytime, the inverter capacity left after real power production is used to accomplish the above objective. Transient stability studies are conducted on a realistic single machine infinite bus power system having a midpoint located PV-STATCOM using EMTDC/PSCAD simulation software. The PV-STATCOM improves the stable transmission limits substantially in the night and also in the day even while generating large amounts of real power. Power transfer increases are also demonstrated in the same power system for i) two solar farms operating as PV-STATCOMs, and ii) a solar farm as PV-STATCOM and an inverter based wind farm with similar STATCOM controls. This novel utilization of PV solar farm asset can thus improve power transmission limits which would have otherwise required expensive additional equipment such as, series/shunt capacitors, or separate Flexible AC Transmission System (FACTS) Controllers.
Treatment of a landfill leachate in powdered activated carbon enhanced sequencing batch bioreactors (1987)

Abstract Addition of powdered activated carbon (PAC) significantly improved treatment of a chemical waste landfill leachate in sequencing batch bioreactors (SBRs). Concentrations for many of the monitored halogenated organic compounds in the effluent were below their respective detection limits. Excellent treatment efficiency was achieved under a variety of operating conditions: wastewater composition, feed rate, hydraulic retention time, organic loading, PAC dosages, biomass and PAC concentrations in the bioreactors. The PAC‐SBR performance was unaffected when wastewater feeding was suspended during weekends and holidays. The PAC‐SBR treatment cost is much lower than either that of the conventional granular activated carbon adsorption technology or the two‐stage process of biodegradation and carbon treatment.
Prospects for Thermophilic Microorganisms in Microbial Enhanced Oil Recovery (MEOR) (1991)

Abstract Microbial activity in crude oils under reservoir and storage conditions has been known to exist for a long time. Such activity can cause deleterious effects in the quality and subsequent processing of crudes. In the past ten to fifteen years, however, a considerable research effort has shown that there are beneficial microbial systems which can be used in microbial enhanced oil recovery (MEOR), a promising process and the resulting biotechnology may be deliverable. In this laboratory, systematic studies are being conducted which deal with the effects of thermophilic, temperature adapted, acidophilic and chemotrophic microorganisms on the chemical and physical properties of selected types of crude oils over a wide range of temperatures, pressures and salt concentrations. Current studies indicate that during the biotreatment several properties of crude oils are affected. The oils are (1) emulsified, (2) acidified, (3) there is a qualitative and quantitative change in light and heavy fraction of crudes, (4) there are chemical changes in fractions containing sulfur compounds, (5) there is an apparent solubilization of trace metals and (6) the qualitative and quantitative chemical and physical changes appear to be microbial species dependent. In this paper, recent work with Boscan crude, a high sulfur, heavy crude oil from Venezuela will be discussed.
Cloning and Recombinant Expression of a Novel Mouse-secreted Phospholipase A2 (1999)

Secreted phospholipases A2 (sPLA2s) form a class of structurally related enzymes that are involved in a variety of physiological and pathological effects including inflammation and associated diseases, cell proliferation, cell adhesion, and cancer, and are now known to bind to specific membrane receptors. Here, we report the cloning and expression of a novel sPLA2 isolated from mouse thymus. Based on its structural features, this sPLA2 is most similar to the previously cloned mouse group IIA sPLA2 (mGIIA sPLA2). As for mGIIA sPLA2, the novel sPLA2 is made up of 125 amino acids with 14 cysteines, is basic (pI = 8.71) and its gene has been mapped to mouse chromosome 4. However, the novel sPLA2 has only 48% identity with mGIIA and displays similar levels of identity with the other mouse group IIC and V sPLA2s, indicating that the novel sPLA2 is not an isoform of mGIIA sPLA2. This novel sPLA2 has thus been called mouse group IID (mGIID) sPLA2. In further contrast with mGIIA, which is found mainly in intestine, transcripts coding for mGIID sPLA2 are found in several tissues including pancreas, spleen, thymus, skin, lung, and ovary, suggesting distinct functions for the two enzymes. Recombinant expression of mGIID sPLA2 in Escherichia coli indicates that the cloned sPLA2 is an active enzyme that has much lower specific activity than mGIIA and displays a distinct specificity for binding to various phospholipid vesicles. Finally, recombinant mGIID sPLA2 did not bind to the mouse M-type sPLA2 receptor, while mGIIA was previously found to bind to this receptor with high affinity.
Measurement of particulate densities in air (2001)

Clean air is one of the most important issues that govern the health of all live forms. However, presently there are not many quick and simple methods for measuring impurities like particulates in air. These impurities have an enormous diversity in their physical and chemical structure. They may be unburned carbon particles from a diesel engine exhaust and chimney, pollen grains in the spring air, or asbestos in a factory. This paper shows that changes in the composition of the air cause a change in the speed of sound. Therefore by measuring the change in the speed of sound, it is possible to monitor the density of particulates in the air. Preliminary tests are conducted on various smoke–air mixtures. The results demonstrate that this methodology is very sensitive to any changes in the composition of the air. Its implementation is very simple and efficient, and costs much less than the conventional method currently used in the auto industry. This technique will be used to calculate the mass density of the particulates resulting from a diesel engine, and results thus obtained will be compared with those calculated using other methods.
Double-Chambered Ferritin Platform: Dual-Function Payloads of Cytotoxic Peptides and Fluorescent Protein (2015)

Ferritin cage nanoparticles are promising platforms for targeted delivery of imaging and therapeutic agents. One of the main advantages of cage nanoparticles is the ability to display multiple functionalities through genetic modification so as to achieve desired therapeutic or diagnostic functions. Ferritin complexes formed from short ferritin (sFt) lacking the fifth helix can accommodate dual peptide and protein functionalities on N- and C-terminal sites in sFt monomers. The resulting double-chambered NanoCage (DCNC) offers the potential of dual activities; these activities are augmented by the avidity of the ligands, which do not impede each other's function. Here we demonstrated proof-of-concept of DCNCs, loading the tumor-targeting proapoptotic peptide CGKRK(KLAKLAK)2 onto the N-terminal chamber and green fluorescent protein (GFP) onto the C-terminal chamber. The resulting KLAK-sFt-GFP DCNCs were internalized into the human breast adenocarcinoma cell line MDA-MB-231 and induced apoptosis. These findings suggest that DCNCs containing various combinations of peptides and proteins could be applied as therapeutics in different diseases.
Elucidating the Importance of DOT1L Recruitment in MLL-AF9 Leukemia and Hematopoiesis (2021)

<i>MLL1 (KMT2a)</i> gene rearrangements underlie the pathogenesis of aggressive MLL-driven acute leukemia. AF9, one of the most common MLL-fusion partners, recruits the histone H3K79 methyltransferase DOT1L to MLL target genes, constitutively activating transcription of pro-leukemic targets. DOT1L has emerged as a therapeutic target in patients with MLL-driven leukemia. However, global DOT1L enzymatic inhibition may lead to off-target toxicities in non-leukemic cells that could decrease the therapeutic index of DOT1L inhibitors. To bypass this problem, we developed a novel approach targeting specific protein-protein interactions (PPIs) that mediate DOT1L recruitment to MLL target genes, and compared the effects of enzymatic and PPIs inhibition on leukemic and non-leukemic hematopoiesis. MLL-AF9 cell lines were engineered to carry mutant <i>DOT1L</i> constructs with a defective AF9 interaction site or lacking enzymatic activity. In cell lines expressing a <i>DOT1L</i> mutant with defective AF9 binding, we observed complete disruption of DOT1L recruitment to critical target genes and inhibition of leukemic cell growth. To evaluate the overall impact of DOT1L loss in non-leukemic hematopoiesis, we first assessed the impact of acute <i>Dot1l</i> inactivation in adult mouse bone marrow. We observed a rapid reduction in myeloid progenitor cell numbers within 7 days, followed by a loss of long-term hematopoietic stem cells. Furthermore, WT and PPI-deficient DOT1L mutants but not an enzymatically inactive DOT1L mutant were able to rescue sustained hematopoiesis. These data show that the AF9-DOT1L interaction is dispensable in non-leukemic hematopoiesis. Our findings support targeting of the MLL-AF9-DOT1L interaction as a promising therapeutic strategy that is selectively toxic to MLL-driven leukemic cells.