gebhart/patrepeval huggingface dataset:
T cell receptor signal strength in Treg and iNKT cell development demonstrated by a novel fluorescent reporter mouse (2011)

The ability of antigen receptors to engage self-ligands with varying affinity is crucial for lymphocyte development. To further explore this concept, we generated transgenic mice expressing GFP from the immediate early gene Nr4a1 (Nur77) locus. GFP was up-regulated in lymphocytes by antigen receptor stimulation but not by inflammatory stimuli. In T cells, GFP was induced during positive selection, required major histocompatibility complex for maintenance, and directly correlated with the strength of T cell receptor (TCR) stimulus. Thus, our results define a novel tool for studying antigen receptor activation in vivo. Using this model, we show that regulatory T cells (T(reg) cells) and invariant NKT cells (iNKT cells) perceived stronger TCR signals than conventional T cells during development. However, although T(reg) cells continued to perceive strong TCR signals in the periphery, iNKT cells did not. Finally, we show that T(reg) cell progenitors compete for recognition of rare stimulatory TCR self-ligands.
On the cardinality of systematic authentication codes via error-correcting codes (1996)

In both open and private communication the participants face potential threats from a malicious enemy who has access to the communication channel and can insert messages (impersonation attack) or alter already transmitted messages (substitution attack). Authentication codes (A-codes) have been developed to provide protection against these threats. In this paper we introduce a new distance, called the authentication distance (A-distance), and show that an A-code can be described as a code for the A-distance. The A-distance is directly related to the probability P/sub S/ of success in a substitution attack. We show how to transform an error-correcting code into an A-code and vice versa. We further use these transformations to provide both upper and lower bounds on the size of the information to be authenticated, and study their asymptotic behavior. As examples of obtained results, we prove that the cardinality of the source state space grows exponentially with the number of keys provided P/sub S/>P/sub I/, we generalize the square-root bound given by Gilbert, MacWilliams, and Sloane in 1979, and we provide very efficient constructions using concatenated Reed-Solomon codes.
A Versatile Nanotrap for Biochemical and Functional Studies with Fluorescent Fusion Proteins (2007)

Green fluorescent proteins (GFPs) and variants thereof are widely used to study protein localization and dynamics. We engineered a specific binder for fluorescent proteins based on a 13-kDa GFP binding fragment derived from a llama single chain antibody. This GFP-binding protein (GBP) can easily be produced in bacteria and coupled to a monovalent matrix. The GBP allows a fast and efficient (one-step) isolation of GFP fusion proteins and their interacting factors for biochemical analyses including mass spectroscopy and enzyme activity measurements. Moreover GBP is also suitable for chromatin immunoprecipitations from cells expressing fluorescent DNA-binding proteins. Most importantly, GBP can be fused with cellular proteins to ectopically recruit GFP fusion proteins allowing targeted manipulation of cellular structures and processes in living cells. Because of the high affinity capture of GFP fusion proteins in vitro and in vivo and a size in the lower nanometer range we refer to the immobilized GFP-binding protein as GFP-nanotrap. This versatile GFP-nanotrap enables a unique combination of microscopic, biochemical, and functional analyses with one and the same protein.
Self-reduction of a copper complex MOD ink for inkjet printing conductive patterns on plastics (2014)

Highly conductive copper patterns on low-cost flexible substrates are obtained by inkjet printing a metal complex based ink. Upon heating the ink, the soluble complex, which is composed of copper formate and 2-amino-2-methyl-1-propanol, decomposes under nitrogen at 140 °C and is converted to pure metallic copper. The decomposition process of the complex is investigated and a suggested mechanism is presented. The ink is stable in air for prolonged periods, with no sedimentation or oxidation problems, which are usually encountered in copper nanoparticle based inks.
Prostate-Specific Antigen Changes As Surrogate for Overall Survival in Men With Metastatic Castration-Resistant Prostate Cancer Treated With Second-Line Chemotherapy (2013)

Surrogacy for any PSA-based end point could not be demonstrated in this analysis. Thus, the benefits of cabazitaxel in mediating a survival benefit are not fully captured by early PSA changes.
Bruton Tyrosine Kinase–Dependent Immune Cell Cross-talk Drives Pancreas Cancer (2015)

We report that BTK regulates B-cell and macrophage-mediated T-cell suppression in pancreas adenocarcinomas. Inhibition of BTK with the FDA-approved inhibitor ibrutinib restores T cell-dependent antitumor immune responses to inhibit PDAC growth and improves responsiveness to chemotherapy, presenting a new therapeutic modality for pancreas cancer.
A New Air Sampler based on Electrically Charged Liquid Nanodroplets (2006)

A new pager-size air sampling device is described. Electrically charged liquid nanodroplets are produced using an electrospray source. The droplets transfer charge onto any polar or polarizable air contaminants and do not transfer charge onto non-polar species such as diatomic nitrogen and oxygen. The electrically charged contaminants are then collected and concentrated using an electric field for subsequent analysis.
Regular‐sized cell creation in microchannel emulsification by visual microprocessing method (1997)

Abstract A novel emulsification method was developed for making monodispersed regular‐sized cells. Both oil in water (O/W) and water in oil (W/O) emulsion cells were generated by permeating an internal phase into a continuous phase through a silicon microchannel, which was designed and prepared by using semiconductor technology. The microprocessing of O/W (or W/O) emulsion cells was monitored and controlled with a microscope video system. Regular‐sized O/W cells were made by a normal hydrophilic microchannel and a glass plate with use of an appropriate surfactant. On the other hand, W/O emulsion cells were made by a hydrophobic microchannel and a glass plate modified with a silane coupler reagent. Regular‐sized W/O cells were also obtained; therefore, a suitable combination of organic phase, surfactant, and electrolyte should be carefully selected. There is a possibility for creating artificial biological cells with this method. In the water/triolein and lecithin system, when the amount of oil was decreased on the permeate side, polygon or fiber cell types were created, and each cell contacted its neighbors across a thin oil layer like a biological tissue.
Fipronil insecticide: Novel photochemical desulfinylation with retention of neurotoxicity (1996)

Fipronil is an outstanding new insecticide for crop protection with good selectivity between insects and mammals. The insecticidal action involves blocking the lambda-aminobutyric acid-gated chloride channel with much greater sensitivity of this target in insects than in mammals. Fipronil contains a trifluoromethylsulfinyl moiety that is unique among the agrochemicals and therefore presumably important in its outstanding performance. We find that this substituent unexpectedly undergoes a novel and facile photoextrusion reaction on plants upon exposure to sunlight, yielding the corresponding trifluoromethylpyrazole, i.e., the desulfinyl derivative. The persistence of this photoproduct and its high neuroactivity, resulting from blocking the lambda-aminobutyric acid-gated chloride channel, suggest that it may be a significant contributor to the effectiveness of fipronil. In addition, desulfinylfipronil is not a metabolite in mammals, so the safety evaluations must take into account not only the parent compound but also this completely new environmental product.
Analyzing Shopper's Behavior through WiFi Signals (2015)

Substantial progress in WiFi-based indoor localization has proven that pervasiveness of WiFi can be exploited beyond its traditional use of internet access to enable a variety of sensing applications. Understanding shopper's behavior through physical analytics can provide crucial insights to the business owner in terms of effectiveness of promotions, arrangement of products and efficiency of services. However, analyzing shopper's behavior and browsing patterns is challenging. Since video surveillance can not used due to high cost and privacy concerns, it is necessary to design novel techniques that can provide accurate and efficient view of shopper's behavior. In this work, we propose WiFi-based sensing of shopper's behavior in a retail store. Specifically, we show that various states of a shopper such as standing near the entrance to view a promotion or walking quickly to proceed towards the intended item can be accurately classified by profiling Channel State Information (CSI) of WiFi. We recognize a few representative states of shopper's behavior at the entrance and inside the store, and show how CSI-based profile can be used to detect that a shopper is in one of the states with very high accuracy (≈ 90%). We discuss the potential and limitations of CSI-based sensing of shopper's behavior and physical analytics in general.
Controlled fission of droplet emulsion in bifurcating microfluidic channels (2004)

An integrated micro fluidic system for controlled fission of water-in-oil droplet emulsions has been designed, fabricated, and analyzed. The system consists of a droplet generator connected to a divergent channel. The fission of water droplets is achieved through bifurcating the flow of the continuous phase surrounding the droplet to generate pressure gradients that deform the droplet until it breaks. The sizes of the splitted droplets are controlled through varying the channel widths and the angle of the bifurcating junction. The fission phenomenon matches with simulation results at defined conditions.
The therapeutic potential of nicotinic acetylcholine receptor agonists for pain control (2001)

Due to the limitations of currently available analgesics, a number of novel alternatives are currently under investigation, including neuronal nicotinic acetylcholine receptor (nAChR) agonists. During the 1990s, the discovery of the antinociceptive properties of the potent nAChR agonist epibatidine in rodents sparked interest in the analgesic potential of this class of compounds. Although epibatidine also has several mechanism-related toxicities, the identification of considerable nAChR diversity suggested that the toxicities and therapeutic actions of the compound might be mediated by distinct receptor subtypes. Consistent with this view, a number of novel nAChR agonists with antinociceptive activity and improved safety profiles in preclinical models have now been identified, including A-85380, ABT-594, DBO-83, SIB-1663 and RJR-2403. Of these, ABT-594 is the most advanced and is currently in Phase II clinical evaluation. Nicotinically-mediated antinociception has been demonstrated in a variety of rodent pain models and is likely mediated by the activation of descending inhibitory pathways originating in the brainstem with the predominant high-affinity nicotine site in brain, the alpha4beta2 subtype, playing a critical role. Thus, preclinical findings suggest that nAChR agonists have the potential to be highly efficacious treatments in a variety of pain states. However, clinical proof-of-principle studies will be required to determine if nAChR agonists are active in pathological pain.
Electrostatic Current Generator Having a Disk Electret as an Active Element (1978)

An electrostatic current generator having a disk electret as the active element is described. The electret consists of two oppositely polarized half-disks producing an electric field normal to the plane of the electret. The electret constitutes the rotor of the generator and is located between two pairs of conducting half-disks which constitute the stator of the generator. The field of the electret induces charges on each half-disk of the stator. The magnitude and polarity of these charges at any given time are determined by the angle formed at this particular time between the plane separating the two halves of the electret and the plane separating the half-disks of the stator. When the half-disks of the stator are appropriately connected through an external circuit, an ac current is produced. The order of magnitude of the peak value of the current is given by I ≈ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> ωS where ae is the effective surface charge density of the electret, S is the total area of the flat surfaces of the electret, and w is the angular velocity of rotation of the electret.
Efficient Algorithms for Protein Sequence Design and the Analysis of Certain Evolutionary Fitness Landscapes (1999)

Protein sequence design is a natural inverse problem to protein structure prediction: given a target structure in three dimensions, we wish to design an amino acid sequence that is likely fold to it. A model of Sun, Brem, Chan, and Dill casts this problem as an optimization on a space of sequences of hydrophobic (H) and polar (P) monomers; the goal is to find a sequence that achieves a dense hydrophobic core with few solvent-exposed hydrophobic residues. Sun et al. developed a heuristic method to search the space of sequences, without a guarantee of optimality or near-optimality; Hart subsequently raised the computational tractability of constructing an optimal sequence in this model as an open question. Here we resolve this question by providing an efficient algorithm to construct optimal sequences; our algorithm has a polynomial running time, and performs very efficiently in practice. We illustrate the implementation of our method on structures drawn from the Protein Data Bank. We also consider extensions of the model to larger amino acid alphabets, as a way to overcome the limitations of the binary H/P alphabet. We show that for a natural class of arbitrarily large alphabets, it remains possible to design optimal sequences efficiently. Finally, we analyze some of the consequences of this sequence design model for the study of evolutionary fitness landscapes. A given target structure may have many sequences that are optimal in the model of Sun et al.; following a notion raised by the work of J. Maynard Smith, we can ask whether these optimal sequences are "connected" by successive point mutations. We provide a polynomial-time algorithm to decide this connectedness property, relative to a given target structure. We develop the algorithm by first solving an analogous problem expressed in terms of submodular functions, a fundamental object of study in combinatorial optimization.
Renoprotective effects of olmesartan medoxomil on diabetic nephropathy in streptozotocin-induced diabetes in rats (2013)

Olmesartan medoxomil (OM) is one of the newest members of the angiotensin receptor blocker (ARB) family. The renoprotective effects of the angiotensin II type 1 receptor antagonist OM was investigated in a streptozotocin (STZ)-induced diabetic rat model. In this study, we investigated whether OM was able to ameliorate diabetic nephropathy (DN). Thirty male Sprague Dawley rats were assigned to 3 groups: the non-diabetic (group A, n=10), the untreated STZ-induced DN control (group B, n=10) and the STZ-induced DN treated with OM (group C, n=10). Blood pressure (BP) and glucose, creatinine (Cr), blood urea nitrogen (BUN), superoxide dismutase (SOD), malondialdehyde (MDA) microalbumin and urinary protein concentrations were measured. In STZ diabetic rats, BP, glucose, Cr, BUN, MDA and urinary protein levels were significantly increased compared to the non-diabetic control group. OM significantly improved the biological indices in the DN rats. The renal pathological changes were also observed under a light microscope. Our results suggested that OM exerted renoprotective effects on rats with STZ-induced diabetes.
Selective interpretation as a technique for debugging computationally intensive programs (1987)

As part of Rice University's project to build a programming environment for scientific software, we have built a facility for program execution that solves some of the problems inherent in debugging large, computationally intensive programs. By their very nature such programs do not lend themselves to full-scale interpretation. In moderation however, interpretation can be extremely useful during the debugging process. In addition to discussing the particular benefits that we expect from interpretation, this paper addresses how interpretive techniques can be effectively used in conjunction with the execution of compiled code. The same implementation technique that permits interpretation to be incorporated as part of execution will also permit the execution facility to be used for debugging parallel programs running on a remote machine.
Implication of the Mosquito Midgut Microbiota in the Defense against Malaria Parasites (2009)

Malaria-transmitting mosquitoes are continuously exposed to microbes, including their midgut microbiota. This naturally acquired microbial flora can modulate the mosquito's vectorial capacity by inhibiting the development of Plasmodium and other human pathogens through an unknown mechanism. We have undertaken a comprehensive functional genomic approach to elucidate the molecular interplay between the bacterial co-infection and the development of the human malaria parasite Plasmodium falciparum in its natural vector Anopheles gambiae. Global transcription profiling of septic and aseptic mosquitoes identified a significant subset of immune genes that were mostly up-regulated by the mosquito's microbial flora, including several anti-Plasmodium factors. Microbe-free aseptic mosquitoes displayed an increased susceptibility to Plasmodium infection while co-feeding mosquitoes with bacteria and P. falciparum gametocytes resulted in lower than normal infection levels. Infection analyses suggest the bacteria-mediated anti-Plasmodium effect is mediated by the mosquitoes' antimicrobial immune responses, plausibly through activation of basal immunity. We show that the microbiota can modulate the anti-Plasmodium effects of some immune genes. In sum, the microbiota plays an essential role in modulating the mosquito's capacity to sustain Plasmodium infection.
Human apolipoprotein AI mimetic peptides for the treatment of atherosclerosis. (2003)

The effects of apolipoprotein (Apo) AI mimetic peptide synthesized from D- and L-amino acids on atherosclerotic lesion formation were investigated in low-density lipoprotein (LDL) receptor-deficient mice on a Western diet and in apoE null mice. In addition, their effects on the inflammatory changes induced in LDL-receptor mice fed a Western diet following influenza A infection were studied. When apolipoprotein AI mimetic peptides synthesized from either D- or L-amino acids were administered to LDL-receptor null mice, only peptides synthesized from D-amino acids were stable in the circulation and enhanced the ability of high-density lipoprotein (HDL) to protect LDL against oxidation. Administration of the peptide D-4F to LDL-receptor null mice and apoE null mice decreased lesion size. Additionally, in LDL receptor null mice after influenza infection, D-4F treatment increased plasma HDL levels and paraoxonase activity, and inhibited increased in LDL-cholesterol and peak levels of interleukin-6 post-infection. Injection of female mice with male macrophages, and subsequent measurement of the male 'sry' gene, revealed a marked increase in macrophage traffic into the aortic arch after infection that was prevented by administration of D-4F. This indicates that: (i) oral D-4F has powerful anti-atherosclerotic properties, and (ii) the loss of the anti-inflammatory properties of HDL after influenza infection in mice is associated with increased arterial macrophage traffic that can be prevented by administration of D-4F.
Major features of immunesenescence, including reduced thymic output, are ameliorated by high levels of physical activity in adulthood (2018)

It is widely accepted that aging is accompanied by remodelling of the immune system including thymic atrophy and increased frequency of senescent T cells, leading to immune compromise. However, physical activity, which influences immunity but declines dramatically with age, is not considered in this literature. We assessed immune profiles in 125 adults (55-79 years) who had maintained a high level of physical activity (cycling) for much of their adult lives, 75 age-matched older adults and 55 young adults not involved in regular exercise. The frequency of naïve T cells and recent thymic emigrants (RTE) were both higher in cyclists compared with inactive elders, and RTE frequency in cyclists was no different to young adults. Compared with their less active counterparts, the cyclists had significantly higher serum levels of the thymoprotective cytokine IL-7 and lower IL-6, which promotes thymic atrophy. Cyclists also showed additional evidence of reduced immunesenescence, namely lower Th17 polarization and higher B regulatory cell frequency than inactive elders. Physical activity did not protect against all aspects of immunesenescence: CD28<sup>-ve</sup> CD57<sup>+ve</sup> senescent CD8 T-cell frequency did not differ between cyclists and inactive elders. We conclude that many features of immunesenescence may be driven by reduced physical activity with age.
Low-noise CMOS Fluorescence Sensor (2007)

This paper reports a novel integrated circuit for fluorescence sensing. The circuit implements a differential readout architecture in order to reduce the overall noise figure. The circuit has been fabricated in a commercially available 0.5 <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">μ</i> m CMOS technology. Preliminary results show that the reset noise is reduced by a factor of 1.42 and the readout noise by a factor of 9.20 when the pixel is operated in differential mode versus single-ended mode. Spectral responsivity characteristics show that the photodiodes are most sensitive at 480 nm. Using a commercially available emission filter, the sensor was able to reliably detect a concentration of Fura-2 as low as 39 nM. The sensor was used to perform ratiometric measurements and was able to reliably detect a free calcium concentration of 17 nM.
Production of metastable singlet oxygen in the reaction of nitric oxide with active oxygen (2008)

Predictive modeling of the performance of EOIL laser systems must address the kinetics of the active oxygen flow, including the production of O<sub>3</sub> from recombination of O and O<sub>2</sub>, and the effects of NO as an additive to remove O and promote O<sub>2</sub>(a) formation. This paper describes experimental measurements of the reaction kinetics for active-oxygen flows generated by microwave discharge of O<sub>2</sub>/He mixtures at 3 to 10 torr. The concentrations of O<sub>2</sub>(a<sup>1</sup>&Delta;), O, and O<sub>3</sub> were directly measured as functions of reaction time in a discharge-flow reactor. Both the O removal rate and the O<sub>3</sub> production rate were observed to be significantly lower than expected from the widely accepted three-body recombination mechanism for O<sub>3</sub> production, indicating the existence of a previously unknown O<sub>3</sub> dissociation reaction. Addition of NO to the flow well downstream of the discharge resulted in readily detectable production of O<sub>2</sub>(a) in addition to that generated by the discharge. The observed O2(a) production rates were remarkably insensitive to variations in total pressure, O<sub>2</sub> concentration, and NO concentration over the ranges investigated. The mechanism for this O<sub>2</sub>(a) production remains to be identified, however it appears to involve a hitherto undetected, metastable, energetic species produced in the active-oxygen flow.