gebhart/patrepeval huggingface dataset:
Strategies for mining fungal natural products (2013)

Fungi are well known for their ability to produce a multitude of natural products. On the one hand their potential to provide beneficial antibiotics and immunosuppressants has been maximized by the pharmaceutical industry to service the market with cost-efficient drugs. On the other hand identification of trace amounts of known mycotoxins in food and feed samples is of major importance to ensure consumer health and safety. Although several fungal natural products, their biosynthesis and regulation are known today, recent genome sequences of hundreds of fungal species illustrate that the secondary metabolite potential of fungi has been substantially underestimated. Since expression of genes and subsequent production of the encoded metabolites are frequently cryptic or silent under standard laboratory conditions, strategies for activating these hidden new compounds are essential. This review will cover the latest advances in fungal genome mining undertaken to unlock novel products.
Structured Low-Rank Matrix Factorization: Global Optimality, Algorithms,\n and Applications (2017)

Recently, convex formulations of low-rank matrix factorization problems have\nreceived considerable attention in machine learning. However, such formulations\noften require solving for a matrix of the size of the data matrix, making it\nchallenging to apply them to large scale datasets. Moreover, in many\napplications the data can display structures beyond simply being low-rank,\ne.g., images and videos present complex spatio-temporal structures that are\nlargely ignored by standard low-rank methods. In this paper we study a matrix\nfactorization technique that is suitable for large datasets and captures\nadditional structure in the factors by using a particular form of\nregularization that includes well-known regularizers such as total variation\nand the nuclear norm as particular cases. Although the resulting optimization\nproblem is non-convex, we show that if the size of the factors is large enough,\nunder certain conditions, any local minimizer for the factors yields a global\nminimizer. A few practical algorithms are also provided to solve the matrix\nfactorization problem, and bounds on the distance from a given approximate\nsolution of the optimization problem to the global optimum are derived.\nExamples in neural calcium imaging video segmentation and hyperspectral\ncompressed recovery show the advantages of our approach on high-dimensional\ndatasets.\n
Electrochemical half-cell potential measurements for the detection of reinforcement corrosion (2014)

This specification describes the application of electrochemical half‐cell potential measurements (frequently also called potential mapping) for the detection of reinforcement corrosion in reinforced concrete structures. Areas of corroding reinforcement steel can be located in a nondestructive manner by means of this procedure. Half‐cell potential measurements are used in order to detect chloride‐induced corrosion. However, it is not recommended in order to assess the risk of carbonation‐induced corrosion. For this purpose the determination of the carbonation depth and the concrete cover appear to be more appropriate.
The content of this specification exclusively refers to the application of mobile, local variable reference electrodes, which are only placed on the concrete surface while measuring. The technique distinguishes itself thereby from the range of corrosion monitoring systems with stationary installed reference electrodes and sensor systems, respectively, whereby it is possible to continuously track measurements within the area of the installed electrodes. However, these methods are not dealt with in this specification.
Backplane interconnect test in a boundary-scan environment (2002)

We present algorithms for generating and applying backplane interconnect test in a boundary-scan environment. Several unique characteristics distinguish backplane interconnect test from intra-board interconnect test. We address these special characteristics and provide a solution that reduces test data volume, accommodates dynamic backplane configuration, resolve test synchronization issue and supports uses of different board technologies. We propose a walking-enable test algorithm that guarantees high fault coverage and fine diagnosis resolution. The simplicity of the walking-enable test algorithm enables straightforward implementations. Other algorithms are also presented to provide trade-offs between test application time,fault coverage and diagnosis resolution. The proposed algorithms can also be used for testing cables that connect boards or backplanes.
The RObust Header Compression (ROHC) Framework (2010)

The Robust Header Compression (ROHC) protocol provides an efficient,
flexible, and future-proof header compression concept. It is designed
to operate efficiently and robustly over various link technologies
with different characteristics. The ROHC framework, along with a set
of compression profiles, was initially defined in RFC 3095. To improve
and simplify the ROHC specifications, this document explicitly defines
the ROHC framework and the profile for uncompressed separately. More
specifically, the definition of the framework does not modify or
update the definition of the framework specified by RFC 3095.
[STANDARDS-TRACK]
Pathophysiology of Diabetic Retinopathy: Contribution and Limitations of Laboratory Research (2019)

Preclinical models of diabetic retinopathy are indispensable in the drug discovery and development of new therapies. They are, however, imperfect facsimiles of diabetic retinopathy in humans. This chapter discusses the advantages, limitations, and physiological and pathological relevance of preclinical models of diabetic retinopathy. The judicious interpretation and extrapolation of data derived from these models to humans and a correspondingly greater emphasis placed on translational medical research in early-stage clinical trials are essential to more successfully inhibit the development and progression of diabetic retinopathy in the future.
Design of wideband RFID tag antenna for metallic surfaces (2006)

A low-cost wideband antenna for radio frequency identification (RFID) tags mountable on metallic surfaces is presented. A novel proximity-coupled feed structure, in which the direction of the microstrip feedline is orthogonal to that of the resonant length of the radiating patch, is explored to perform simple and wideband impedance matching between an antenna and a tag chip without any additional matching networks. The proposed design is verified by simulation and measurement, which show good agreement.
Protocol pruning (1995)

A communication system uses a precise set of rules called a protocol, to define interactions among its entities. With advancing computer transmission and switching technology, communication systems are providing sophisticated services demanded by users over a wide area. Protocol standards include a very, large number of options to take care of different service possibilities and to please all the people involved in the Standards Committees. Consequently, protocols have become large and complex, and, therefore their design and analysis have become a formidable task. To cope with this problem, a variety of approaches to simplify the protocols have been proposed in the published literature, such as protocol projection, homomorphism, selective resolution, and many others. We have recently developed a new technique called protocol pruning. It reduces the complexity of the protocols by pruning them to keep only that part which is required for a specified subset of services. More importantly, it takes polynomial (rather than exponential) time and space in the size of the protocol specification. This makes the algorithm feasible for engineers to use for practical problems involving large and complex protocols. We describe the technique and discuss applications to synthesis of protocol converters/gateways, protocol conformance testing, and thinning for lightweight and high performance protocols. The technique could also be useful for protocol implementation, synthesis, validation, and verification.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Stability improvements of integral equation models (2002)

The partial element equivalent circuit (PEEC) technique is a circuit based formulation which is numerically equivalent to a full wave method of moments solution with Galerkin matching. In this paper, the PEEC formulation is used to illustrate how the high frequency model behavior can be improved for integral equation formulations. These improvements are important for both model reduction and time domain applications. The effectiveness of the method is illustrated with an example (center fed patch dipole antenna), and our results are compared with a conventional method of moments code.
A 2D image body measurement system developed with neural networks and a color-coded measurement garment (2022)

Purpose Two-dimensional (2D) measurement technology has become more popular than before, thanks to the widespread availability of smartphones and smart devices. However, most existing 2D body measurement systems have background constraints and may raise privacy concerns. The purpose of this research was to test the idea of designing a 2D measurement system that works with a color-coded measurement garment for background removal and privacy protection. Clothing consumers can use the proposed system for daily apparel shopping purposes. Design/methodology/approach A 2D body measurement system was designed and tested. The system adopted a close-fitted color-coded measurement garment and used neural network models to detect the color-code in the garment area and remove backgrounds. In total, 78 participants were recruited, and the collected data were split into training and testing sets. The training dataset was used to train the neural network and statistical prediction models for the 2D system. The testing dataset was used to compare the performance of the 2D system with a commercial three-dimensional (3D) body scanner. Findings The results showed that the color-coded measurement garment worked well with the neural network models to process the images for measurement extraction. The 2D measurement system worked better at close-fitted areas than loose-fitted areas. Originality/value This research combined a color-coded measurement garment with neural network models to solve the privacy and background challenges of the 2D body measurement system. Other researchers have never studied this approach.
Synthesis of oligonucleotides possessing versatile probes for PET labelling and their rapid ligand-free click reaction (2011)

We synthesised aryl acetylene derivatives as versatile probes for labelling of oligonucleotides. RNA oligomers bearing an aryl acetylene molecule rapidly reacted with benzylazide derivatives under ligand-free click reaction conditions.
An LCOS‐based digital‐cinema projector (2006)

Abstract— A digital cinema projector that utilizes three JVC QXGALCDs, and provides 12,000 lumens, 2000:1 contrast, and 3‐Mpixel resolution was developed. This system, which was described in a prior paper (see Ref. 10), has a novel optical configuration based on the use of intermediate imaging optics and wire‐grid polarizers and is described in greater detail in this paper. The polarization optics, including the polarization compensators, contribute to a system that provides high contrast at a low f /#, with a wide color gamut and minimal color shading at high power.
Impacts of precipitation and potential evapotranspiration patterns on downscaling soil moisture in regions with large topographic relief (2017)

Abstract Soil moisture can be estimated at coarse resolutions (>1 km) using satellite remote sensing, but that resolution is poorly suited for many applications. The Equilibrium Moisture from Topography, Vegetation, and Soil (EMT+VS) model downscales coarse‐resolution soil moisture using fine‐resolution topographic, vegetation, and soil data to produce fine‐resolution (10–30 m) estimates of soil moisture. The EMT+VS model performs well at catchments with low topographic relief (≤124 m), but it has not been applied to regions with larger ranges of elevation. Large relief can produce substantial variations in precipitation and potential evapotranspiration (PET), which might affect the fine‐resolution patterns of soil moisture. In this research, simple methods to downscale temporal average precipitation and PET are developed and included in the EMT+VS model, and the effects of spatial variations in these variables on the surface soil moisture estimates are investigated. The methods are tested against ground truth data at the 239 km 2 Reynolds Creek watershed in southern Idaho, which has 1145 m of relief. The precipitation and PET downscaling methods are able to capture the main features in the spatial patterns of both variables. The space‐time Nash‐Sutcliffe coefficients of efficiency of the fine‐resolution soil moisture estimates improve from 0.33 to 0.36 and 0.41 when the precipitation and PET downscaling methods are included, respectively. PET downscaling provides a larger improvement in the soil moisture estimates than precipitation downscaling likely because the PET pattern is more persistent through time, and thus more predictable, than the precipitation pattern.
<title>Nanometer-scale ionic reservoir based on ion-responsive hydrogels</title> (2002)

The applicability of the concept of ionic reservoir for the description of hydrogel behavior was demonstrated by potentiometric titration of poly(N-isopropylacrylamide-co-1- vinylimidazole) hydrogel suspension. Four different regions of pH-changes of the microgel suspensions were identified on the titration curve in comparison with pure water. Particularly, at 10.5>pH>6.5 a hydrogel accumulates or releases H<SUP>+</SUP> and Cl<SUP>-</SUP> ions without significant swelling/deswelling whereas at 6.5>pH>4 the storage of the ions occurs both due to their binding with ionizable groups on polymer network and due to strong swelling. The mechanical response of hydrogel (swelling/deswelling) is assumed to be a faster process than the electrochemical response (equilibration of ion concentrations interior and exterior to the hydrogel). The size of hydrogel spheres should be diminished to fasten an ionic reservoir response of the hydrogel. A novel protocol for preparation of polymer hydrogel spherical particles on a nanometer scale (nanogels) has been developed. Temperature- and pH-sensitive nanogels were detected and characterized by the dynamic light scattering technique and atomic force microscopy. Ptoentiometric titration of the obtained nanogels shows that the decrease in the ionic reservoir size gains the efficiency and, presumably, the rate of the electrochemical response. These findings indicate the necessity of time-resolved pH-measurements of the hydrogel suspensions for the characterization of the rate of the solute diffusion through the gel/water surface.
Biophysical Mimicry of Lung Surfactant Protein B by Random Nylon-3 Copolymers (2010)

Non-natural oligomers have recently shown promise as functional analogues of lung surfactant proteins B and C (SP-B and SP-C), two helical and amphiphilic proteins that are critical for normal respiration. The generation of non-natural mimics of SP-B and SP-C has previously been restricted to step-by-step, sequence-specific synthesis, which results in discrete oligomers that are intended to manifest specific structural attributes. Here we present an alternative approach to SP-B mimicry that is based on sequence-random copolymers containing cationic and lipophilic subunits. These materials, members of the nylon-3 family, are prepared by ring-opening polymerization of beta-lactams. The best of the nylon-3 polymers display promising in vitro surfactant activities in a mixed lipid film. Pulsating bubble surfactometry data indicate that films containing the most surface-active polymers attain adsorptive and dynamic-cycling properties that surpass those of discrete peptides intended to mimic SP-B. Attachment of an N-terminal octadecanoyl unit to the nylon-3 copolymers, inspired by the post-translational modifications found in SP-C, affords further improvements by reducing the percent surface area compression to reach low minimum surface tension. Cytotoxic effects of the copolymers are diminished relative to that of an SP-B-derived peptide and a peptoid-based mimic. The current study provides evidence that sequence-random copolymers can mimic the in vitro surface-active behavior of lung surfactant proteins in a mixed lipid film. These findings raise the possibility that random copolymers might be useful for developing a lung surfactant replacement, which is an attractive prospect given that such polymers are easier to prepare than are sequence-specific oligomers.
Screening of Brazilian families with primary dystonia reveals a novel <i>THAP1</i> mutation and a de novo <i>TOR1A</i> GAG deletion (2010)

The TOR1A and THAP1 genes were screened for mutations in a cohort of 21 Brazilian patients with Primary torsion dystonia (PTD). We identified a de novo delGAG mutation in the TOR1A gene in a patient with a typical DYT1 phenotype and a novel c.1A > G (p.Met1?) mutation in THAP1 in a patient with early onset generalized dystonia with speech involvement. Mutations in these two known PTD genes, TOR1A and THAP1, are responsible for about 10% of the PTD cases in our Brazilian cohort suggesting genetic heterogeneity and supporting the role of other genes in PTD.
The HIV transactivator TAT binds to the CDK-activating kinase and activates the phosphorylation of the carboxy-terminal domain of RNA polymerase II (1997)

The human immunodeficiency virus encodes the transcriptional transactivator Tat, which binds to the transactivation response (TAR) RNA stem-loop in the viral long terminal repeat (LTR) and increases rates of elongation rather than initiation of transcription by RNA polymerase II (Pol II). In this study, we demonstrate that Tat binds directly to the cyclin-dependent kinase 7 (CDK7), which leads to productive interactions between Tat and the CDK-activating kinase (CAK) complex and between Tat and TFIIH. Tat activates the phosphorylation of the carboxy-terminal domain (CTD) of Pol II by CAK in vitro. The ability of CAK to phosphorylate the CTD can be inhibited specifically by a CDK7 pseudosubstrate peptide that also inhibits transcriptional activation by Tat in vitro and in vivo. We conclude that the phosphorylation of the CTD by CAK is essential for Tat transactivation. Our data identify a cellular protein that interacts with the activation domain of Tat, demonstrate that this interaction is critical for the function of Tat, and provide a mechanism by which Tat increases the processivity of Pol II.
The Impact of DNA Topology and Guide Length on Target Selection by a Cytosine-Specific Cas9 (2017)

Cas9 is an RNA-guided DNA cleavage enzyme being actively developed for genome editing and gene regulation. To be cleaved by Cas9, a double stranded DNA, or the protospacer, must be complementary to the guide region, typically 20-nucleotides in length, of the Cas9-bound guide RNA, and adjacent to a short Cas9-specific element called Protospacer Adjacent Motif (PAM). Understanding the correct juxtaposition of the protospacer- and PAM-interaction with Cas9 will enable development of versatile and safe Cas9-based technology. We report identification and biochemical characterization of Cas9 from Acidothermus cellulolyticus (AceCas9). AceCas9 depends on a 5'-NNNCC-3' PAM and is more efficient in cleaving negative supercoils than relaxed DNA. Kinetic as well as in vivo activity assays reveal that AceCas9 achieves optimal activity when combined with a guide RNA containing a 24-nucleotide complementarity region. The cytosine-specific, DNA topology-sensitive, and extended guide-dependent properties of AceCas9 may be explored for specific genome editing applications.
D2Det: Towards High Quality Object Detection and Instance Segmentation (2020)

We propose a novel two-stage detection method, D2Det, that collectively addresses both precise localization and accurate classification. For precise localization, we introduce a dense local regression that predicts multiple dense box offsets for an object proposal. Different from traditional regression and keypoint-based localization employed in two-stage detectors, our dense local regression is not limited to a quantized set of keypoints within a fixed region and has the ability to regress position-sensitive real number dense offsets, leading to more precise localization. The dense local regression is further improved by a binary overlap prediction strategy that reduces the influence of background region on the final box regression. For accurate classification, we introduce a discriminative RoI pooling scheme that samples from various sub-regions of a proposal and performs adaptive weighting to obtain discriminative features. On MS COCO test-dev, our D2Det outperforms existing two-stage methods, with a single-model performance of 45.4 AP, using ResNet101 backbone. When using multi-scale training and inference, D2Det obtains AP of 50.1. In addition to detection, we adapt D2Det for instance segmentation, achieving a mask AP of 40.2 with a two-fold speedup, compared to the state-of-the-art. We also demonstrate the effectiveness of our D2Det on airborne sensors by performing experiments for object detection in UAV images (UAVDT dataset) and instance segmentation in satellite images (iSAID dataset). Source code is available at https://github.com/JialeCao001/D2Det.
High-Molecular-Weight Surface-Exposed Proteins of Haemophilus Influenzae Mediate Binding to Macrophages (1994)

The molecular basis for direct bacteria-macrophage interactions that distinguishes nontypeable (NT) Haemophilus influenzae from type b organisms is not known. Because of similarities between filamentous hemagglutinin (FHA) adhesin of Bordetella pertussis and high-molecular-weight (HMW) proteins commonly expressed by NT H. influenzae, the role that HMW proteins play in determining NT H. influenzae-macrophage interactions was assessed. In tests with genetically engineered organisms, HMW protein-expressing bacteria bound significantly better than isogenic HMW protein-deficient bacteria to macrophages. HMW protein-dependent binding to macrophages is trypsin-sensitive, is independent of divalent cations, does not occur via the leukocyte integrin CD11b/CD18, and is not affected by galactose-containing carbohydrates. Organisms bound via HMW proteins remain largely extracellular and viable. Like FHA of Bordetella organisms, HMW proteins mediate binding of NT H. influenzae to macrophages. However, unlike the interaction determined by FHA, this interaction is characteristically one of adhesion and requires additional serum opsonization for efficient killing of bacteria by macrophages.
1.3-μm wavelength InP laterally coupled distributed feedback ridge laser (2002)

In this paper, the fabrication and characterization of 1.3-/spl mu/m wavelength GaInAsP-InP laterally coupled DFB ridge laser are presented for the first time, to our knowledge. One-step MOCVD (metal organic chemical vapor deposition) has been used for the epitaxial growth of the laser structure with a separate confinement heterostructure bulk active layer.