gebhart/patrepeval huggingface dataset:
Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT (2015)

ZFAT is a transcriptional regulator, containing eighteen C2H2-type zinc-fingers and one AT-hook, involved in autoimmune thyroid disease, apoptosis, and immune-related cell survival. We determined the solution structures of the thirteen individual ZFAT zinc-fingers (ZF) and the tandemly arrayed zinc-fingers in the regions from ZF2 to ZF5, by NMR spectroscopy. ZFAT has eight uncommon bulged-out helix-containing zinc-fingers, and six of their structures (ZF4, ZF5, ZF6, ZF10, ZF11, and ZF13) were determined. The distribution patterns of the putative DNA-binding surface residues are different among the ZFAT zinc-fingers, suggesting the distinct DNA sequence preferences of the N-terminal and C-terminal zinc-fingers. Since ZFAT has three to five consecutive tandem zinc-fingers, which may cooperatively function as a unit, we also determined two tandemly arrayed zinc-finger structures, between ZF2 to ZF4 and ZF3 to ZF5. Our NMR spectroscopic analysis detected the interaction between ZF4 and ZF5, which are connected by an uncommon linker sequence, KKIK. The ZF4-ZF5 linker restrained the relative structural space between the two zinc-fingers in solution, unlike the other linker regions with determined structures, suggesting the involvement of the ZF4-ZF5 interfinger linker in the regulation of ZFAT function.
High-Throughput Silicon Nanophotonic Deflection Switch for On-Chip Optical Networks (2008)

We demonstrate error-free (BER<10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-12</sup> ) deflection switching of multiple 40 Gbps channels with an ultra-compact (30×10 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ), low-latency (<2ns), high throughput (over 360 Gbps), and small crosstalk (<-10 dB) optical switch based on coupled silicon microring resonators.
Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome (2020)

Abstract Background Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. Results Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Conclusions The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.
The effects of a favourable pressure gradient and of the Reynolds number on an incompressible axisymmetric turbulent boundary layer. Part 2. The boundary layer with relaminarization (1998)

This is an experimental investigation of two turbulent boundary layers (cases 2 and 4) where the streamwise negative pressure gradient changes mean properties of the flow, e.g. mean velocity profiles and skin friction, so that they display laminar-like behaviour. The maximum acceleration parameter K [les ]4×10 −6 and the starting value of the Reynolds number is 862 or 2564. Relaminarization occurs in both boundary layers as a gradual change of the turbulence properties and is not catastrophic. Retransition, however, is a fast process due to the remaining turbulence structure and may be compared with bypass transition. Together with an extensive investigation of the turbulence structure as in the companion paper, Part 1, which describes two cases (1 and 3) of boundary layers which remain turbulent, spectra and integral length scales for all four boundary layers are discussed.
Developing intelligent control from a biological perspective to examine paradigms for activation utilizing pneumatic muscle actuators (2002)

Intelligent control of a pair of actuating muscles is synthesized from a biological paradigm of controlling these muscles (agonistic and antagonist) as they work in conjunction to provide actuation to a system (exoskeleton for a human). An investigation of muscle dynamics in humans and other animals is first conducted. Using the analogies from living muscle action, a paradigm is described on how to control such a system from an energy perspective subject to the biological constraints induced via the muscle dynamics. A discussion on the use of pneumatic muscle technology to power an exoskeleton suit is then presented.
Structure-Based Design of Potent and Selective CK1γ Inhibitors (2012)

Aberrant activation of the Wnt pathway is believed to drive the development and growth of some cancers. The central role of CK1γ in Wnt signal transduction makes it an attractive target for the treatment of Wnt-pathway dependent cancers. We describe a structure-based approach that led to the discovery of a series of pyridyl pyrrolopyridinones as potent and selective CK1γ inhibitors. These compounds exhibited good enzyme and cell potency, as well as selectivity against other CK1 isoforms. A single oral dose of compound 13 resulted in significant inhibition of LRP6 phosphorylation in a mouse tumor PD model.
TU elements: a heterogeneous family of modularly structured eucaryotic transposons. (1985)

We describe here a family of foldback transposons found in the genome of the higher eucaryote, the sea urchin Strongylocentrotus purpuratus. Two major classes of TU elements have been identified by analysis of genomic DNA and TU element clones. One class consists of largely similar elements with long terminal inverted repeats (IVRs) containing outer and inner domains and sharing a common middle segment that can undergo deletions. Some of these elements contain insertions. The second class is highly heterogeneous, with many different middle segments nonhomologous to those of the first-class and variable-sized inverted repeats that contain only an outer domain. The middle and insertion segments of both classes carry sequences that also are found unassociated from the inverted repeats at many other genomic locations. We conclude that the TU elements are modular structures composed of inverted repeats plus other sequence domains that are themselves members of different families of dispersed repetitive sequences. Such modular elements may have a role in the dispersion and rearrangement of genomic DNA segments.
Proprotein convertases generate a highly functional heterodimeric form of thymic stromal lymphopoietin in chronic rhinosinusitis (2016)

Abstract Thymic stromal lymphopoietin (TSLP) is known to be elevated and truncated in nasal polyps (NPs) of chronic rhinosinusitis and might play a significant role in type 2 inflammation in this disease. However, neither the structure nor the role of the truncated products of TSLP has been studied. We investigated the mechanisms of truncation of TSLP in NPs and the function of the truncated products. We incubated recombinant full-length 15.1 KDa human TSLP (methionine + residues 29–159, referred to as M29–159) with NP extracts. SDS-PAGE revealed two major truncated products of TSLP in NP extracts. Edman sequencing and MALDI-TOF MS results indicated that the longer truncation product was TSLP (M29–124) and the smaller product was TSLP (131–159). We found that PCSK (proprotein convertase subtilisin/kexin) family proteases were rate-limiting enzymes in the truncation and generation of TSLP (M29–130) and TSLP (131–159). Carboxypeptidases further digested 6 amino acids from the C-terminus of TSLP (M29–130) to generate TSLP (M29–124) in NPs. Interestingly, recombinant TSLP (M29–124) and TSLP (131–159) did not manifest TSLP activity, but PCSK-digested TSLP had significantly higher activity than full-length TSLP on myeloid dendritic cells and group 2 innate lymphoid cells. Finally, we identified a 14.2 KDa TSLP from incubation of TSLP with NP extracts under non-reducing conditions that was significantly reduced in the presence of DTT. This indicates that the two cleaved products are dimerized with disulfide bonds and the dimerized form, TSLP (29–124 + 131–159), is an active metabolite and may contribute to the amplification of type 2 inflammation in NPs.
<title>Texture-based image enhancement for segmentation performance</title> (1997)

This paper describes a hierarchical algorithm for multi- resolution texture-based image enhancement for segmentation performance. The proposed algorithm is a modification of the steerable pyramid algorithm that has been successfully implemented for research in texture synthesis. We investigate in this paper the application of such a multiscale approach for image analysis to the problem of image enhancement for segmentation. We present the application of the proposed algorithm to two medical images as a first exploration of the potential benefits of the approach. While some quantitative measure of assessment needs ultimately to be developed for performance assessment, some subjective evaluation at this early stage of the research can provide early feedback on the magnitude of a potential benefit. While the early results presented in this paper are encouraging, it is yet to be demonstrated that the proposed algorithm or an optimized version of the algorithm yields increased performance compared to other techniques.
Immunization with Lentivirus-Like Particles Elicits a Potent SIV-Specific Recall Cytotoxic T-Lymphocyte Response in Rhesus Monkeys (1993)

An effective acquired immunodeficiency syndrome (AIDS) vaccine should be capable of eliciting human immunodeficiency virus (HIV)-specific cytotoxic T-lymphocyte (CTL) responses. We have explored the use of lentivirus-like particles produced in mammalian cells infected with a recombinant vaccinia virus to immunize for the induction of CTL in the simian immunodeficiency virus (SIV)/rhesus monkey model for AIDS. SIV-like particles in a threonyl-MDP-based adjuvant did not elicit a high frequency of SIV gag-specific effector cells in naive rhesus monkeys. However, immunization with these particles elicited a potent recall CTL response in monkeys previously vaccinated with a recombinant vaccinia-SIV virus. These observations suggest that poxvirus-produced virus-like particles may represent a safe immunogen for use in periodic boosting to maintain viable cell-mediated immunity to the AIDS virus.
Possible sympatry between kenngoor (Phascogale calura) and wambenger (Phascogale tapoatafa wambenger) (2018)

We report the capture of individuals of two species of phascogale (Phascogale tapoatafa wambenger and P. calura) at the same locations within the same habitat and during the same survey event, something that has not been reported previously. This would suggest that these species may occur in sympatry where their distributions overlap. Further investigations are required to confirm the extent of sympatry as this could have implications for the conservation and management of both species.
Tightness Characteristics of Packings (2005)

The demands on industry to reduce fugitive emissions are increasing, steadily /1/, /2/. On this background it is necessary to improve function and tightness of tightening joints like flanged joints and stuffing box packings. Function and tightness can only be guaranteed if the entire chain of parameters involved is taken in to account (design criteria, gasket factors, calculation, mounting procedure). On the field of flanged joints there are standardization projects on the way that address the topics of the new regulatory demands. Only few work is done regarding stuffing box packings, however. Similar to flanged joints a reliable function and tightness of stuffing box packings can only be achieved if the behaviour of the parts (bolts, gland, stuffing box) is known and their interaction is understood. Regarding the behaviour of stuffing box packing materials it is necessary to determine characteristics like deformation capability, relaxation, friction and leak rate. These characteristics have to be used to prove function and tightness. Some attempts to define these characteristic values have already been made; test procedures and test rigs to determine these values have been developed. Parallel to that, gasket manufacturers are developing new packing materials and entire packing sets in order to meet the more stringent requirements on tightness. One of these newly developed products are nonwoven packing sets which should be applicable up to temperatures of 280 °C in the processing and chemical industry. In the paper the most relevant packing material characteristics and the necessary tests to determine these characteristics are reviewed, first. Then the results of extensive tests with new nonwoven packing sets regarding tightness characteristics, friction, wear and gap extrusion are presented.
Suboptimal control via numeric saturation in linear digital compensators (1987)

Saturation arithmetic is often used in finite precision digital compensators to circumvent instability due to radix overflow. The saturation limits in the digital structure lead to nonlinear behavior during large state transients. It is shown that if all recursive loops in a compensator are interrupted by at least one saturation limit, then there exists a bounded external scaling rule which assures against overflow at all nodes in the structure. Design methods are proposed based on the generalized second method of Lyanpunov, which take the internal saturation limits into account to implement a robust dual-mode suboptimal control for bounded input plants. The saturating digital compensator provides linear regulation for small disturbances, and near-time-optimal control for large disturbances or changes in the operating point. Computer aided design tools are developed to facilitate the analysis and design of this class of digital compensators.
ChemInform Abstract: The Heck Reaction with Unprotected Allylic Amidines and Guanidines. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
FDMA-FSK noncoherent network operated at 600 Mbit/s using two-electrode DFB lasers and fibre optical filter demultiplexer (1989)

We demonstrate a two-channel FDMA-FSK star network using frequency-tunable two-electrode DFB lasers. Channels arc demultiplexed by a tunable fibre Fabry-Perot filter, which also converts the FSK signal to ASK format for noncoherent detection. Bit error rates of 10-13 have been measured at 600 Mbit/s transmission rate for (223-1) word lengths. High bit rate and frequency tunability have thus been combined for use in an FDMA.
Understanding and Improving Drilled-Down Information Extraction from Online Data Visualizations for Screen-Reader Users (2023)

Inaccessible online data visualizations can significantly disenfranchise screen-reader users from accessing critical online information. Current accessibility measures, such as adding alternative text to visualizations, only provide a high-level overview of data, limiting screen-reader users from exploring data visualizations in depth. In this work, we developed taxonomies of information sought by screen-reader users to interact with online data visualizations granularly through role-based and longitudinal studies with screen-reader users. Utilizing these taxonomies, we extended the functionality of VoxLens by supporting drilled-down information extraction. We assessed the performance of our VoxLens enhancements through task-based user studies.
Harnessing translational research in wheat for climate resilience (2021)

Despite being the world's most widely grown crop, research investments in wheat (Triticum aestivum and Triticum durum) fall behind those in other staple crops. Current yield gains will not meet 2050 needs, and climate stresses compound this challenge. However, there is good evidence that heat and drought resilience can be boosted through translating promising ideas into novel breeding technologies using powerful new tools in genetics and remote sensing, for example. Such technologies can also be applied to identify climate resilience traits from among the vast and largely untapped reserve of wheat genetic resources in collections worldwide. This review describes multi-pronged research opportunities at the focus of the Heat and Drought Wheat Improvement Consortium (coordinated by CIMMYT), which together create a pipeline to boost heat and drought resilience, specifically: improving crop design targets using big data approaches; developing phenomic tools for field-based screening and research; applying genomic technologies to elucidate the bases of climate resilience traits; and applying these outputs in developing next-generation breeding methods. The global impact of these outputs will be validated through the International Wheat Improvement Network, a global germplasm development and testing system that contributes key productivity traits to approximately half of the global wheat-growing area.
Synthesis of Isagarin, a New Type of Tetracyclic Naphthoquinone from Pentas longiflora (1998)

Isagarin (1) was synthesized in four steps from 1,4-dimethoxynaphthaldehyde (4). The key intermediate 2-(1,2-dihydroxyethyl)-1,4-naphthoquinone (3) was found to react with acylated pyridinium ylides to afford, after spontaneous intramolecular condensation, the desired natural product isagarin (1). Depending on the type of acylated pyridinium ylides, different types of new pyranonaphthoquinone derivatives were obtained.
Effect of incubation temperature on in vitro maturation of porcine oocytes: nuclear maturation, fertilisation and developmental competence (2001)

The present study examined the effect of low culture temperature during in vitro maturation (IVM) of pig oocytes on their nuclear maturation, fertilisation and subsequent embryo development. In experiment 1, oocytes were cultured at 35 or 39 degrees C for 44 h in modified tissue culture medium 199 supplemented with 10 ng/ml epidermal growth factor, 0.57 mM cysteine, 75 microg/ml potassium penicillin G, 50 microg/ml streptomycin sulphate, 0.5 microg/ml LH and 0.5 microg/ml FSH to examine the nuclear maturation status. In experiment 2, oocytes were cultured at 35 degrees C for 44 or 68 h and nuclear maturation was examined. In experiment 3, oocytes matured for 44 or 68 h at 39 degrees C and for 68 h at 35 degrees C were co-incubated with frozen-thawed spermatozoa for 5-6 h. Putative embryos were transferred into North Carolina State University (NCSU) 23 medium containing 0.4% bovine serum albumin. At 12 h after insemination, some oocytes were fixed to examine the fertilisation rate and the remaining embryos were examined at 48 and 144 h for cleavage and blastocyst formation rate, respectively. Compared with 39 degrees C, culture of oocytes at 35 degrees C for 44 h significantly (p < 0.05) reduced the metaphase II (M II) rate (79% vs 12%). However, extension of culture time to 68 h at 35 degrees C significantly increased (p < 0.05) the M II rate (7% vs 58%). In experiment 3, compared with other groups, fewer (p < 0.05) oocytes reached M II when cultured at 35 degrees C for 68 h (69-81% vs 49%). Extension of culture duration to 68 h at 39 degrees C stimulated spontaneous activation (28%) of oocytes. No difference in cleavage rates was observed among different groups. Compared with oocytes matured for 44 h at 39 degrees C (31%), the proportion of blastocysts obtained was low (p < 0.05) for oocytes matured at 35 degrees C (13%) or 39 degrees C (3%) for 68 h. The results indicate that lower culture temperature can delay nuclear maturation of pig oocytes. However, extension of culture time can stimulate nuclear maturation and these oocytes are capable of fertilisation and development to the blastocyst stage at moderate rates.
A Surface-Enhanced Raman Spectral Library of Important Drugs Associated With Point-of-Care and Field Applications (2019)

During the past decade, the ability of surface-enhanced Raman spectroscopy (SERS) to measure extremely low concentrations, such as mg/L and below, and the availability of hand-held Raman spectrometers, has led to a significant growth in the number and variety of applications of SERS to real-world problems. Most of these applications involve the measurement of drugs, such as quantifying medication in patients, identifying illicit drugs in impaired drivers, and more recently, identifying drugs used as weapons. Similar to Raman spectroscopy, most of the point-of-care and field applications involve the identification of the drug to determine the course of action. However, unlike Raman spectroscopy, spectral libraries are not readily available to perform the necessary identification. In a large part, this is due to the uniqueness of the commercially available SERS substrates, each of which can produce different spectra for the same drug. In an effort to overcome this limitation, we have measured numerous drugs using the most common, and readily available SERS material and hand-held Raman analyzers, specifically gold colloids and analyzers using 785 nm laser excitation. Here we present the spectra of some 39 drugs of current interest, such as buprenorphine, delta-9 tetrahydrocannabinol, and fentanyl, which we hope will aid in the development of current and future SERS drug analysis applications.
Tau polarization asymmetry as a probe ofZ’ couplings (1992)

Studying the decay of a Z' to ${\mathrm{\ensuremath{\tau}}}^{+}$${\mathrm{\ensuremath{\tau}}}^{\mathrm{\ensuremath{-}}}$ at a future hadron collider will allow its polarization asymmetry to be measured, and will provide direct information about its leptonic couplings. It has not previously been appreciated that this measurement was possible. If this measurement is to be performed, detectors at the Superconducting Super Collider and Large Hadron Collider must be able to trigger on high-energy \ensuremath{\tau}'s.
Increasing the activity of monoclonal antibody therapeutics by continuous chromatography (MCSGP) (2010)

The charged monoclonal antibody (mAb) variants of the commercially available therapeutics Avastin®, Herceptin® and Erbitux® were separated by ion-exchange gradient chromatography in batch and continuous countercurrent mode (MCSGP process). Different stationary phases, buffer conditions and two MCSGP configurations were used in order to demonstrate the broad applicability of MCSGP in the field of charged protein variant separation. Batch chromatography and MCSGP were compared with respect to yield, purity, and productivity. In the case of Herceptin®, also the biological activity of the product stream was taken into account as performance indicator. The robustness of the MCSGP process against feed composition variations was confirmed experimentally and by model simulations.