gebhart/patrepeval huggingface dataset:
Fluorescently labeled circular DNA molecules for DNA topology and topoisomerases (2016)

DNA topology plays essential roles in several fundamental biological processes, such as DNA replication, recombination, and transcription. Typically agarose gel electrophoresis is employed to study DNA topology. Since gel electrophoresis is time-consuming and labor intensive, it is desirable to develop other methods, such as fluorescence-based methods, for such studies. In this paper we report the synthesis of a type of unique fluorescence-labeled DNA molecules that can be used to study DNA topology and topoisomerases by fluorescence resonance energy transfer (FRET). Specifically, we inserted an 82 nt. synthetic DNA oligomer FL905 carrying a 42 nt. AT sequence with fluorescein and dabcyl labels into a gapped DNA molecule to generate relaxed and supercoiled pAB1_FL905. Since the fluorescence intensity of pAB1_FL905 is dependent on its supercoiling status, pAB1_FL905 is a powerful tool to study DNA topology and topoisomerases by FRET. pAB1_FL905 can also be developed into rapid and efficient high-throughput screening assays to identify inhibitors that target various DNA topoisomerases.
Investigating the feasibility of extracting tool demonstrations from in-situ video content (2014)

Short video demonstrations are effective resources for helping users to learn tools in feature-rich software. However manually creating demonstrations for the hundreds (or thousands) of individual features in these programs would be impractical. In this paper, we investigate the potential for identifying good tool demonstrations from within screen recordings of users performing real-world tasks. Using an instrumented image-editing application, we collected workflow video content and log data from actual end users. We then developed a heuristic for identifying demonstration clips, and had the quality of a sample set of clips evaluated by both domain experts and end users. This multi-step approach allowed us to characterize the quality of 'naturally occurring' tool demonstrations, and to derive a list of good and bad features of these videos. Finally, we conducted an initial investigation into using machine learning techniques to distinguish between good and bad demonstrations.
MULITILAYER NEURAlL NETWORK CONTROLLER FOR A CLASS OF NONLINEAR SYSTEMS (1995)

A family of novel multilayer discrete-time neural net (NN) controller is presented for the control of a class of multi-input multi-output (MIMO) dynamical systems. The NN controller includes modified delta rule weight tuning and exhibits a learning-whilefunctioning-features instead of learning-then-control so that control action is immediale with no explicit learning phase needed. The structure of the neural net controller is derived using a fdtered error/passivity approach. Linearity in the parameters is not required and certainty equivalence is not used, which overcomes several limitations in adaptive control. For guiaranteed stability, the upper bound on the constant learning rate parameter for the developed weight tuning mechanisms is shown to decrease with the number of hidden-layer neurons so that learning must slotw down: this a major draw back often documented in the literature. This major draw back is shown to be overcome easily by using a projection algorithm at each layer. The notion of persistency of excitation (PE) for multilayer NN is explored. An extension of these weight tuning updates to NN with an arbitrary number of hidden layers is discussed. The notions of discretetime passive NN and dissipative NN is introduced. Though the original system may not have any sort of passivity properties or it may be extremely difficult to demonstrate the passivity properties, the NN nnakes the closed-loop system passive. Simulation results show the theoretical conclusions.
Bending sensors based on fiber Bragg gratings: The key role of the mean effective index (2017)

In this article we show that the Bragg wavelength variation induced by a curvature in the fiber Bragg grating is related to both the variation of the effective index and the variation of the coupling coefficient of counter-propagating modes. The weighting coefficient between the two variables is the mean effective index of the grating. The two effects act in opposition as proved both by our model and by our experimental observations. This work can be used to design strain sensors insensitive to bending, or, on the contrary, bending sensors insensitive to strain.
Deformable Capsules for Object Detection (2021)

Capsule networks promise significant benefits over convolutional networks by storing stronger internal representations, and routing information based on the agreement between intermediate representations' projections. Despite this, their success has been limited to small-scale classification datasets due to their computationally expensive nature. Though memory efficient, convolutional capsules impose geometric constraints that fundamentally limit the ability of capsules to model the pose/deformation of objects. Further, they do not address the bigger memory concern of class-capsules scaling up to bigger tasks such as detection or large-scale classification. In this study, we introduce a new family of capsule networks, deformable capsules (\textit{DeformCaps}), to address a very important problem in computer vision: object detection. We propose two new algorithms associated with our \textit{DeformCaps}: a novel capsule structure (\textit{SplitCaps}), and a novel dynamic routing algorithm (\textit{SE-Routing}), which balance computational efficiency with the need for modeling a large number of objects and classes, which have never been achieved with capsule networks before. We demonstrate that the proposed methods efficiently scale up to create the first-ever capsule network for object detection in the literature. Our proposed architecture is a one-stage detection framework and it obtains results on MS COCO which are on par with state-of-the-art one-stage CNN-based methods, while producing fewer false positive detection, generalizing to unusual poses/viewpoints of objects.
Reconstruction of Munsell color space by a five-layer neural network (1992)

We have constructed a wine-glass-type five-layer neural network and generated an identity mapping of the surface spectral-reflectance data of 1280 Munsell color chips, using a backpropagation learning algorithm. To achieve an identity mapping, the same data set is used for the input and for the teacher. After the learning was completed, we analyzed the responses to individual chips of the three hidden units in the middle layer in order to obtain the internal representation of the color information. We found that each of the three hidden units corresponds to a psychological color attribute, that is, the Munsell value (luminance), red–green, and yellow–blue. We also examined the relationship between the internal representation and the number of hidden units and found that the network with three hidden units acquires optimum color representation. The five-layer neural network is shown to be an efficient method for reproducing the transformation of color information (or color coding) in the visual system.
Non-contact video-based vital sign monitoring using ambient light and auto-regressive models (2014)

Remote sensing of the reflectance photoplethysmogram using a video camera typically positioned 1 m away from the patient's face is a promising method for monitoring the vital signs of patients without attaching any electrodes or sensors to them. Most of the papers in the literature on non-contact vital sign monitoring report results on human volunteers in controlled environments. We have been able to obtain estimates of heart rate and respiratory rate and preliminary results on changes in oxygen saturation from double-monitored patients undergoing haemodialysis in the Oxford Kidney Unit. To achieve this, we have devised a novel method of cancelling out aliased frequency components caused by artificial light flicker, using auto-regressive (AR) modelling and pole cancellation. Secondly, we have been able to construct accurate maps of the spatial distribution of heart rate and respiratory rate information from the coefficients of the AR model. In stable sections with minimal patient motion, the mean absolute error between the camera-derived estimate of heart rate and the reference value from a pulse oximeter is similar to the mean absolute error between two pulse oximeter measurements at different sites (finger and earlobe). The activities of daily living affect the respiratory rate, but the camera-derived estimates of this parameter are at least as accurate as those derived from a thoracic expansion sensor (chest belt). During a period of obstructive sleep apnoea, we tracked changes in oxygen saturation using the ratio of normalized reflectance changes in two colour channels (red and blue), but this required calibration against the reference data from a pulse oximeter.
Identification of a New Iron-Regulated Virulence Gene, <i>ireA</i> , in an Extraintestinal Pathogenic Isolate of <i>Escherichia coli</i> (2001)

Our laboratory is studying an extraintestinal pathogenic isolate of Escherichia coli (CP9) as a model pathogen. We have been using human urine, ascites, and blood ex vivo to identify genes with increased expression in these media relative to expression in Luria-Bertani (LB) broth. Such genes may represent new or unrecognized virulence traits. In this study, we report the identification of a new gene, ireA (iron-responsive element). This gene has an open reading frame of 2,049 nucleotides, and its peptide has a molecular mass of 75.3 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Its expression is increased a mean of 3.6-fold in human urine, 16.2-fold in human ascites, and 6.6-fold in human blood relative to expression in LB medium, and it is Fe repressible. IreA also exhibits peptide similarities (48 to 56%) to previously identified proteins that function as siderophore receptors, suggesting that IreA is involved in iron acquisition. PCR-based analysis of ireA's phylogenetic distribution detected ireA in none (0%) of 14 fecal isolates that represented probable commensal strains, but in 13 (26%) of 50 random urine and blood clinical isolates (P = 0.05) and in 5 (100%) of 5 representatives of the J96-like, clonal group of which CP9 is a member (P < 0.001). In a mouse urinary tract infection model, the presence of ireA contributed significantly to CP9's ability to colonize the bladder (P < 0.02), evidence that IreA is a urovirulence factor. Taken together, these findings demonstrate that ireA encodes a new virulence factor, which is likely involved in Fe acquisition.
A simple novel device for air sampling by electrokinetic capture (2015)

This work introduces a very simple plug-and-play device that can sample air at a high-volume flow rate with no moving parts and collect particles down to the sub-micron range. The performance of the device is substantially equivalent to capture by pumping through a filter for microbiome analysis by quantitative PCR and amplicon sequencing.
Data from A Clinical PET Imaging Tracer ([<sup>18</sup>F]DASA-23) to Monitor Pyruvate Kinase M2–Induced Glycolytic Reprogramming in Glioblastoma (2023)

<div>AbstractPurpose:<p>Pyruvate kinase M2 (PKM2) catalyzes the final step in glycolysis, a key process of cancer metabolism. PKM2 is preferentially expressed by glioblastoma (GBM) cells with minimal expression in healthy brain. We describe the development, validation, and translation of a novel PET tracer to study PKM2 in GBM. We evaluated 1-((2-fluoro-6-[<sup>18</sup>F]fluorophenyl)sulfonyl)-4-((4-methoxyphenyl)sulfonyl)piperazine ([<sup>18</sup>F]DASA-23) in cell culture, mouse models of GBM, healthy human volunteers, and patients with GBM.</p>Experimental Design:<p>[<sup>18</sup>F]DASA-23 was synthesized with a molar activity of 100.47 ± 29.58 GBq/μmol and radiochemical purity >95%. We performed initial testing of [<sup>18</sup>F]DASA-23 in GBM cell culture and human GBM xenografts implanted orthotopically into mice. Next, we produced [<sup>18</sup>F]DASA-23 under FDA oversight, and evaluated it in healthy volunteers and a pilot cohort of patients with glioma.</p>Results:<p>In mouse imaging studies, [<sup>18</sup>F]DASA-23 clearly delineated the U87 GBM from surrounding healthy brain tissue and had a tumor-to-brain ratio of 3.6 ± 0.5. In human volunteers, [<sup>18</sup>F]DASA-23 crossed the intact blood–brain barrier and was rapidly cleared. In patients with GBM, [<sup>18</sup>F]DASA-23 successfully outlined tumors visible on contrast-enhanced MRI. The uptake of [<sup>18</sup>F]DASA-23 was markedly elevated in GBMs compared with normal brain, and it identified a metabolic nonresponder within 1 week of treatment initiation.</p>Conclusions:<p>We developed and translated [<sup>18</sup>F]DASA-23 as a new tracer that demonstrated the visualization of aberrantly expressed PKM2 for the first time in human subjects. These results warrant further clinical evaluation of [<sup>18</sup>F]DASA-23 to assess its utility for imaging therapy–induced normalization of aberrant cancer metabolism.</p></div>
Recent advances in the production of recombinant glycoconjugate vaccines (2019)

Glycoconjugate vaccines against bacteria are one of the success stories of modern medicine and have led to a significant reduction in the global occurrence of bacterial meningitis and pneumonia. Glycoconjugate vaccines are produced by covalently linking a bacterial polysaccharide (usually capsule, or more recently O-antigen), to a carrier protein. Given the success of glycoconjugate vaccines, it is surprising that to date only vaccines against <i>Haemophilus influenzae</i> type b, <i>Neisseria meningitis</i> and <i>Streptococcus pneumoniae</i> have been fully licenced. This is set to change through the glycoengineering of recombinant vaccines in bacteria, such as <i>Escherichia coli</i>, that act as mini factories for the production of an inexhaustible and renewable supply of pure vaccine product. The recombinant process, termed Protein Glycan Coupling Technology (PGCT) or bioconjugation, offers a low-cost option for the production of pure glycoconjugate vaccines, with the in-built flexibility of adding different glycan/protein combinations for custom made vaccines. Numerous vaccine candidates have now been made using PGCT, which include those improving existing licenced vaccines (e.g., pneumococcal), entirely new vaccines for both Gram-positive and Gram-negative bacteria, and (because of the low production costs) veterinary pathogens. Given the continued threat of antimicrobial resistance and the potential peril of bioterrorist agents, the production of new glycoconjugate vaccines against old and new bacterial foes is particularly timely. In this review, we will outline the component parts of bacterial PGCT, including recent advances, the advantages and limitations of the technology, and future applications and perspectives.
Catalytic Asymmetric Synthesis of Optically Active Allenes from Terminal Alkynes (2012)

CuBr and ZnI(2) have been developed as catalysts or subcatalysts for the efficient asymmetric synthesis of axially chiral allenols with up to 97% ee from readily available propargylic alcohols, aliphatic or aromatic aldehyde, pyrrolidine, and commerically available ligands. The alcohol unit in the terminal alkynes plays a very important role for ensuring high enantioselectivity via coordination.
Multispectral enhancement towards digital staining. (2012)

We have presented a multispectral enhancement method that can be adjusted to produce digitally stained-images. The current experimental results show the viability of the method. However, to achieve robust enhancement performance issues that arise from variations in staining conditions has to be addressed as well. This would be part of our future work.
Fuzzy finite-state automata can be deterministically encoded into recurrent neural networks (1998)

There has been an increased interest in combining fuzzy systems with neural networks because fuzzy neural systems merge the advantages of both paradigms. On the one hand, parameters in fuzzy systems have clear physical meanings and rule-based and linguistic information can be incorporated into adaptive fuzzy systems in a systematic way. On the other hand, there exist powerful algorithms for training various neural network models. However, most of the proposed combined architectures are only able to process static input-output relationships; they are not able to process temporal input sequences of arbitrary length. Fuzzy finite-state automats (FFAs) can model dynamical processes whose current state depends on the current input and previous states. Unlike in the case of deterministic finite-state automats (DFAs), FFAs are not in one particular state, rather each state is occupied to some degree defined by a membership function. Based on previous work on encoding DFAs in discrete-time second-order recurrent neural networks, we propose an algorithm that constructs an augmented recurrent neural network that encodes a FFA and recognizes a given fuzzy regular language with arbitrary accuracy. We then empirically verify the encoding methodology by correct string recognition of randomly generated FFAs. In particular, we examine how the networks' performance varies as a function of synaptic weight strengths.
Protein Crystal Staining for Second Harmonic Generation Imaging (2014)

Recently, second harmonic generation (SHG) microscopy has become a useful tool in the field of structural biology for the detection of protein crystals. SHG, or the frequency doubling of light, is a process specific to crystalline media lacking inversion centers. Through theoretical models and experimental data, it is estimated that ~84% of the known protein crystal structures give detectable SHG signal using current SHG microscopy instrumentation. Extending this coverage could be extremely useful to structural biologists who routinely screen entire 96 well plates, with hundreds of crystallization conditions, in search of diffraction-quality protein crystals. A series of SHG active dyes, including Malachite Green (MG) and trans-4-[4-(dimethylamino)styryl]-1-methylpyridinium iodide (DMI) were investigated to assess their ability to enhance the nonlinear optical (NLO) response across a broad range of protein crystals with varying degrees of inherent SHG activity. MG and DMI were shown to enhance the SHG activity of tetragonal (P43212) lysozyme crystals, a protein that typically generates little to no SHG signal. SHG enhancements for lysozyme of approximately 16000x and 20x were achieved by intercalation of MG and DMI, respectively. These results are consistent with predictions based on the differences in symmetry and structure for the two dyes. The kinetics of the dye intercalation and uptake were investigated with SHG time-lapse images taken of a lysozyme crystal after the addition of MG dye into the crystallization well. Kinetic results indicate that an increase in SHG activity becomes easily noticeable within minutes of exposure to the dyes. These results show a significant progress towards increasing the coverage of SHG microscopy for protein crystal detection.
New polymer electrolyte membranes for fuel cells operating above 100 degrees C. Approaches and recent progress (2003)

The state-of-the-art of PEMFC technology is based on per-fluoro-sulfonic acid (PFSA) polymer membranes operating at a typical temperature of 80 C. The newest development in the field is alternative polymer electrolytes for operation above 100 C. This paper is devoted to a review on the development, which is classified into three groups: modified PFSA membranes, alternative sulfonated polymer and their inorganic composite membranes and acid-base complex membranes. High temperature PEMFC has been demonstrated with advanced features such as fast electrode kinetics, high CO tolerance, simple thermal and water management and possible integration with the fuel processing unit. (authors)
Super-Thin Leaky Coaxial Cable ZLCX-2.5D (2013)

Recently, demand for leaky coaxial cables (abbreviated as LCX hereinafter) as a thin and lightweight antenna for small area networks in meeting rooms or instruments is increasing. We have developed ZLCX-2.5D that is the thinnest and the lightest LCX, whose diameter is 4 mm and weight is 20 g/m. The measured coupling loss and transmission loss at 2.4 GHz are 57 dB and 1.3 dB/m, respectively. As this new LCX has superior performance, it is applicable to an antenna for 2.4GHz wireless LAN system in a small space.
Leptospiral Proteins Recognized during the Humoral Immune Response to Leptospirosis in Humans (2001)

Leptospirosis is an emerging zoonosis caused by pathogenic spirochetes belonging to the genus Leptospira. An understanding of leptospiral protein expression regulation is needed to develop new immunoprotective and serodiagnostic strategies. We used the humoral immune response during human leptospirosis as a reporter of protein antigens expressed during infection. Qualitative and quantitative immunoblot analysis was performed using sera from 105 patients from Brazil and Barbados. Sera from patients with other diseases and healthy individuals were evaluated as controls. Seven proteins, p76, p62, p48, p45, p41, p37, and p32, were identified as targets of the humoral response during natural infection. In both acute and convalescent phases of illness, antibodies to lipopolysaccharide were predominantly immunoglobulin M (IgM) while antibodies to proteins were exclusively IgG. Anti-p32 reactivity had the greatest sensitivity and specificity: positive reactions were observed in 37 and 84% of acute- and convalescent-phase sera, respectively, while only 5% of community control individuals demonstrated positive reactions. Six immunodominant antigens were expressed by all pathogenic leptospiral strains tested; only p37 was inconsistently expressed. Two-dimensional immunoblots identified four of the seven infection-associated antigens as being previously characterized proteins: LipL32 (the major outer membrane lipoprotein), LipL41 (a surface-exposed outer membrane lipoprotein), and heat shock proteins GroEL and DnaK. Fractionation studies demonstrated LipL32 and LipL41 reactivity in the outer membrane fraction and GroEL and DnaK in the cytoplasmic fraction, while p37 appeared to be a soluble periplasmic protein. Most of the other immunodominant proteins, including p48 and p45, were localized to the inner membrane. These findings indicate that leptospiral proteins recognized during natural infection are potentially useful for serodiagnosis and may serve as targets for vaccine design.