gebhart/patrepeval huggingface dataset:
DNA-Templated Silver Nanoclusters for Fluorescence Turn-on Assay of Acetylcholinesterase Activity (2013)

We have developed a fluorescence turn-on assay using DNA-templated silver nanoclusters (Ag NCs) (i.e., 12 polycytosine-templated silver nanoclusters, dC12-Ag NCs), which is amenable to rapid, ultrasensitive assay of acetylcholinesterase (AChE). The detection mechanism is based on the concept, that is, AChE hydrolyzes the acetylthiocholine (ATCh) chloride to produce thiocholine (TCh). Subsequently, TCh sensitively and rapidly reacts with dC12-Ag NCs via Ag-S bond forming and enhances the fluorescence of dC12-Ag NCs. Using dC12-Ag NCs, detection of TCh has a linear concentration range of 2.0 nM to 16.0 nM and a detection limit of 0.3 nM. Due to the sensitive and rapid fluorescence turn-on response of dC12-Ag NCs to TCh, AChE with activity as low as 0.5 × 10(-4) U/mL (signal/noise = 3) can be analyzed with a dynamic range of 0.1 to 1.25 × 10(-3) U/mL. The promising application of the proposed method in AChE inhibitor screening was demonstrated. AChE concentrations were determined in human blood red cell (RBC) membranes from clinical specimens using dC12-Ag NCs, and the quantitative results were validated with Ellman's method. Aside from the ease of manufacture, reduction of matrix effect, and low background noise, the continuous detection format and detection sensitivity can open up to wider applications to AChE activity assay in neurobiology, toxicology, and pharmacology, among other fields.
Frequency tracking and variable bandwidth for line noise filtering without a reference (2011)

This paper presents a method for filtering line noise using an adaptive noise canceling (ANC) technique. This method effectively eliminates the sinusoidal contamination while achieving a narrower bandwidth than typical notch filters and without relying on the availability of a noise reference signal as ANC methods normally do. A sinusoidal reference is instead digitally generated and the filter efficiently tracks the power line frequency, which drifts around a known value. The filter's learning rate is also automatically adjusted to achieve faster and more accurate convergence and to control the filter's bandwidth. In this paper the focus of the discussion and the data will be electrocorticographic (ECoG) neural signals, but the presented technique is applicable to other recordings.
Suboptimal Inspiratory Flow Rates Are Associated with Chronic Obstructive Pulmonary Disease and All-Cause Readmissions (2017)

sPIF is common during AECOPD and predicts all-cause and COPD readmissions. Patients with sPIF may benefit from nebulized therapies. We recommend checking PIF in patients hospitalized for AECOPD for selection of delivery devices.
Lessons learnt on the analysis of large sequence data in animal genomics (2018)

The 'omics revolution has made a large amount of sequence data available to researchers and the industry. This has had a profound impact in the field of bioinformatics, stimulating unprecedented advancements in this discipline. Mostly, this is usually looked at from the perspective of human 'omics, in particular human genomics. Plant and animal genomics, however, have also been deeply influenced by next-generation sequencing technologies, with several genomics applications now popular among researchers and the breeding industry. Genomics tends to generate huge amounts of data, and genomic sequence data account for an increasing proportion of big data in biological sciences, due largely to decreasing sequencing and genotyping costs and to large-scale sequencing and resequencing projects. The analysis of big data poses a challenge to scientists, as data gathering currently takes place at a faster pace than does data processing and analysis, and the associated computational burden is increasingly taxing, making even simple manipulation, visualization and transferring of data a cumbersome operation. The time consumed by the processing and analysing of huge data sets may be at the expense of data quality assessment and critical interpretation. Additionally, when analysing lots of data, something is likely to go awry-the software may crash or stop-and it can be very frustrating to track the error. We herein review the most relevant issues related to tackling these challenges and problems, from the perspective of animal genomics, and provide researchers that lack extensive computing experience with guidelines that will help when processing large genomic data sets.
Crystallographic study of the structure of colipase and of the interaction with pancreatic lipase (1995)

Colipase (Mr 10 kDa) confers catalytic activity to pancreatic lipase under physiological conditions (high bile salt concentrations). Previously determined 3-A-resolution X-ray structures of lipase-colipase complexes have shown that, in the absence of substrate, colipase binds to the noncatalytic C-terminal domain of pancreatic lipase (van Tilbeurgh H, Sarda L, Verger R, Cambillau C, 1992, Nature 359:159-162; van Tilbeurgh et al., 1993a, Nature 362:814-820). Upon lipid binding, conformational changes at the active site of pancreatic lipase bring a surface loop (the lid) in contact with colipase, creating a second binding site for this cofactor. Covalent inhibition of the pancreatic lipase by a phosphonate inhibitor yields better diffracting crystals of the lipase-colipase complex. From the 2.4-A-resolution structure of this complex, we give an accurate description of the colipase. It confirms the previous proposed disulfide connections (van Tilbeurgh H, Sarda L, Verger R, Cambillau C, 1992, Nature 359:159-162; van Tilbeurgh et al., 1993a, Nature 362:814-820) that were in disagreement with the biochemical assignment (Chaillan C, Kerfelec B, Foglizzo E, Chapus C, 1992, Biochem Biophys Res Commun 184:206-211). Colipase lacks well-defined secondary structure elements. This small protein seems to be stabilized mainly by an extended network of five disulfide bridges that runs throughout the flatly shaped molecule, reticulating its four finger-like loops. The colipase surface can be divided into a rather hydrophilic part, interacting with lipase, and a more hydrophobic part, formed by the tips of the fingers. The interaction between colipase and the C-terminal domain of lipase is stabilized by eight hydrogen bonds and about 80 van der Waals contacts. Upon opening of the lid, three more hydrogen bonds and about 28 van der Waals contacts are added, explaining the higher apparent affinity in the presence of a lipid/water interface. The tips of the fingers are very mobile and constitute the lipid interaction surface. Two detergent molecules that interact with colipase were observed in the crystal, covering part of the hydrophobic surface.
Computational On-Chip Imaging of Nanoparticles and Biomolecules using Ultraviolet Light (2017)

Significant progress in characterization of nanoparticles and biomolecules was enabled by the development of advanced imaging equipment with extreme spatial-resolution and sensitivity. To perform some of these analyses outside of well-resourced laboratories, it is necessary to create robust and cost-effective alternatives to existing high-end laboratory-bound imaging and sensing equipment. Towards this aim, we have designed a holographic on-chip microscope operating at an ultraviolet illumination wavelength (UV) of 266 nm. The increased forward scattering from nanoscale objects at this short wavelength has enabled us to detect individual sub-30 nm nanoparticles over a large field-of-view of >16 mm<sup>2</sup> using an on-chip imaging platform, where the sample is placed at ≤0.5 mm away from the active area of an opto-electronic sensor-array, without any lenses in between. The strong absorption of this UV wavelength by biomolecules including nucleic acids and proteins has further enabled high-contrast imaging of nanoscopic aggregates of biomolecules, e.g., of enzyme Cu/Zn-superoxide dismutase, abnormal aggregation of which is linked to amyotrophic lateral sclerosis (ALS) - a fatal neurodegenerative disease. This UV-based wide-field computational imaging platform could be valuable for numerous applications in biomedical sciences and environmental monitoring, including disease diagnostics, viral load measurements as well as air- and water-quality assessment.
Phosphatidylserine Is Required for the Normal Progression of Cell Plate Formation in Arabidopsis Root Meristems (2021)

Phosphatidylserine (PS) is involved in various cellular processes in yeast and animals. However, PS functions in plants remain unclear. In Arabidopsis, PS is relatively enriched in flower and root tissues, and the genetic disturbance of PS biosynthesis in phosphatidylserine synthase1 (PSS1)/ pss1 heterozygotes induces sporophytic and gametophytic defects during pollen maturation. This study functionally characterized PS in Arabidopsis roots and observed that pss1 seedlings exhibited a short-root phenotype by reducing the meristem size and cell elongation capacity. Confocal microscopy imaging analyses of PS with GFP-LactC2 and the endocytic activity with FM 4-64 revealed that although GFP-LactC2 (or PS) was localized in the plasma membrane and endocytic membranes, the lack of PS in pss1 roots did not affect the constitutive endocytosis. Instead, a fluorescence imaging analysis of the cytokinetic phases in the dividing zone of pss1-2 roots revealed a significant delay in telophase progression, requiring active cargo vesicle trafficking for cell plate formation. Confocal microscopy imaging analysis of transgenic GFP-LactC2 root cells with developing cell plates indicated that GFP-LactC2 was localized at the cell plate. Moreover, confocal microscopy images of transgenic pss1-2 and PSS1 roots expressing the cell plate-specific syntaxin construct ProKNOLLE:eGFP-KNOLLE showed abnormal cell plate development in pss1-2ProKNOLLE:eGFP-KNOLLE roots. These results suggested that PS is required for root cytokinesis, possibly because it helps mediate the cargo vesicular trafficking required for cell plate formation.
Non-invasively determined cardiovascular actions and plasma concentrations of theophylline in man (1982)

In a group of 8 volunteers systolic time intervals (STIs), thoracic impedance stroke volume, blood pressure and plasma concentrations were simultaneously determined up to 90 min after an iv. dose of 208 mg of theophylline. In spite of a decrease in stroke volume index (SVI), cardiac index (CI) and systolic blood pressure, possibly induced by a decrease in preload, heart rate also decreased. No positive inotropic effect could be observed from changes in STIs. The mean concentration time course in the 2nd compartment (hypothetical tissue compartment) calculated from kinetic parameters in 7 subjects, showed a significant linear correlation with the decrease in SVI (r = 0.49) and CI (r = 0.47) when theophylline concentrations were increasing. The peripheral effects of theophylline are compatible with a selective phosphodiesterase inhibition of venous smooth muscle.
Driver Intent Prediction with Barrier Functions (2021)

Path planning and collision avoidance algorithms for driver assist systems and autonomous vehicles require predictions of the future locations of other vehicles. In the absence of V2X communication, driver intent prediction algorithms provide this information. Intent prediction algorithms generally fall into two categories: those based on vehicle dynamics models and filtering, and machine learning based approaches. Both approaches have advantages and drawbacks, but two disadvantages both approaches share is the relative computational complexity and the likelihood of false positives and negatives. In the literature, barrier functions (BF) are used to enhance safety by providing forward invariance of an admissible set. In this paper, BFs are used to determine driver intent in a comparatively efficient manner with quick detection particularly at high speeds, in a way where the chance of false positives and negatives can be significantly reduced.
Application of diffusive gradients in thin-films technique for speciation, bioavailability, modeling and mapping of nutrients and contaminants in soils (2021)

Soil plays an important role in controlling the biogeochemical cycling of nutrients and contaminants in the environment. Reliable analytical techniques are critical to better understand their transformation in soils. Diffusive Gradients in Thin-films technique (DGT) is one of such techniques, which has become increasingly popular in soil research since 1998. Undeniably, DGT attracts increasing attentions from multidisciplinary researchers worldwide. This is mainly due to its inherent merits, including ease of use, in situ measurement, and biomimetic applications. Further, four important aspects of DGT applications in soil research were summarized. They include: 1) chemical speciation, 2) bioavailability measurement, 3) desorption kinetic modeling, and 4) interfacial process mapping of nutrients and contaminants, with main focus on the progresses achieved during the past five years. In short, DGT is effective in studying the biochemical behaviors of nutrients (e.g., phosphate and nitrate), trace elements (e.g., Cd, Ni, Zn, Cu, Pb, and As), and polar organic compounds (e.g., antibiotics, pesticides, and bisphenols) in soils. Toward the end, we proposed several aspects of applying DGT as a versatile tool in soil research.
Functional characterization of probiotic surface layer protein-carrying Lactobacillus amylovorus strains (2014)

We demonstrated adhesive and significant pathogen inhibitory efficacies among the swine intestinal L. amylovorus strains studied, pointing to their potential use as probiotic feed supplements, but no independent role could be demonstrated for the major S-layer proteins in adherence to epithelial cells. The results indicate that many intestinal bacteria may coexist with and confer benefits to the host by mechanisms not attributable to adhesion to epithelial cells or mucus.
<title>Excimer laser damage testing of optical materials</title> (1993)

Photolithography technology is moving towards deep UV wavelengths in order to obtain smaller feature sizes on integrated circuits. Optical glasses are being replaced with fused silica because of the DUV application. There are concerns that the short pulse, high instantaneous power generated with excimer lasers can cause structural changes in the fused silica materials. The damage includes: changing absorption, observed fluorescence, and induced stress birefringence. This paper will address the laser damage testing protocol for fused silica. We will discuss the setup, equipment, and procedures for laser damaging. Precision measurements of the absorption, fluorescence, and stress birefringence are required to have a good understanding of the laser damage. The paper will also address the equipment problems associated with these measurements and initial comparisons between 193 nm and 248 nm laser damage.
Visualization of navigation information in www systems with support of mobility (2000)

Navigating through an information space is an activity, which takes place in many areas of information processing especially within the emerging area of world wide hyper-media systems like the World Wide Web. In this
The Variations of Organic Fluorescent Property in the Effluents from Biotreatment Unit Followed by Constructed Wetland Process (2012)

In this study, EEFM (Excitation emission fluorescent matrix) was used to evaluate the variation of organic characteristic of both source sewages into WuYiShan wastewater treatment. Similar organic property for both source sewages was identified, having four peaks, respectively belonging to fulvic acid, humic acid, aromatic protein and soluble microbial by-product. The fluorescent intensity (FI) of dominant humic acid fraction increased after biological treatment, and decreased in constructed wetland. UV process could result the increase of FI value of humic acid. However, the ratio of FI value of peak location in soluble microbial by-product to fulvic acid, called as Fs/Ff, continuously had an ascent after the biotreatment, constructed wetland and UV process. The organic property was apparently affected by the interior microorganism activity.
Quantification of Triphenyl-2H-tetrazoliumchloride Reduction Activity in Bacterial Cells (2017)

This protocol describes the use of the 2,3,5-triphenyl-2H-tetrazolium chloride (TTC) salt to evaluate the cell redox potential of rhizobia cells. The production of brightly colored and insoluble 1,3,5-Triphenyltetrazolium formazan arising from TTC reduction is irreversible and can be easily quantified using a spectrophotometer. This protocol allows the production of reproducible results in a relatively short time for <i>Sinorhizobium meliloti</i> 1021 cells grown both in exponential and stationary phases. The results here presented show that the <i>S. meliloti</i> cells deriving from exponential-phase cultures had increased cell redox potential as compared to the ones deriving from stationary-phase cultures. This means that under exponential growth conditions the <i>S. meliloti</i> cells generate higher amount of reducing equivalents needed for TTC reduction.
Creating Student Alliances in Nutrition Medicine Education (2013)

Objective To increase medical students’ knowledge, attitudes and skills in nutrition medicine through the creation of a student partnership and inter‐professional activities across universities. Methods The Boston Medical Student Committee on Nutrition (BMSCoN) is a partnership between nutrition student leaders of 3 Boston medical schools. Its mission is to increase student awareness of nutrition's impact on health and of the roles all health care professionals play in promoting healthy lifestyles. Each school's student nutrition group elects a representative to the BMSCoN committee. The group is led by a chair elected by school representatives and members. Results BMSCoN created a yearly lecture series highlighting nutrition topics in medicine with open attendance to all students. Themes included “Eating by Example – Empowering Future Doctors to be Healthy Role Models” and “Socioeconomic Issues in Nutrition”. Participation in nutrition interest groups is rising from 78 (2011) to 86 (2012). Lecture attendance increased from 28 (Jan 2012) to 38 (Oct 2012). An average of 35 students from all 3 schools attend each lecture. Conclusion Student interest in nutrition medicine is increasing. By forming an intercollegiate alliance of students, a network to further enhance nutrition medicine education now exists. We will continue our lecture series and create more opportunities for student nutrition involvement.
Novel RF direct under-sampling technique and its application to OFDM systems (2009)

A novel RF direct under-sampling technique, which is equivalent to RF Nyquist-sampling, has been developed. The technique enables higher-order modulations such as a 16-QAM signal to be demodulated without losing vector information despite under-sampling being used. The only drawback of the technique is that it requires a precise sampling frequency to be synchronized with the input RF carrier frequency. Therefore, we also developed a new frequency comparator that makes carrier regeneration implementable even when 16-QAM signals are demodulated. To prove the validity of the new under-sampling technique, we report experimental results of the OFDM receiver fabricated using FPGA devices.
Scalable Neural Tangent Kernel of Recurrent Architectures. (2020)

Kernels derived from deep neural networks (DNNs) in the infinite-width provide not only high performance in a range of machine learning tasks but also new theoretical insights into DNN training dynamics and generalization. In this paper, we extend the family of kernels associated with recurrent neural networks (RNNs), which were previously derived only for simple RNNs, to more complex architectures that are bidirectional RNNs and RNNs with average pooling. We also develop a fast GPU implementation to exploit its full practical potential. While RNNs are typically only applied to time-series data, we demonstrate that classifiers using RNN-based kernels outperform a range of baseline methods on 90 non-time-series datasets from the UCI data repository.
Structural and functional characterisation of multi‐copper oxidase CueO from lignin‐degrading bacterium Ochrobactrum sp. reveal its activity towards lignin model compounds and lignosulfonate (2018)

Structural data are available in the PDB under the accession number 6EVG.
Laser blastocyst biopsy for preimplantation diagnosis in the human (1997)

A new methodology for blastocyst biopsy that uses a 1.48 microm diode laser is described. Trophectoderm cells are biopsied after laster zona drilling and culture, fixed and processed for fluorescent in situ hybridisation (FISH) analysis. Preliminary results on the efficiency of the procedure and blastocyst recovery rate are promising. Blastocyst laser biopsy is a useful tool in preimplantation genetic diagnosis (PGD) as it allows a more reliable diagnosis and widens the diagnostic possibilities on account of the higher number of cells obtained in the biopsy.
Inhibition of TGFBIp Expression by Lithium: Implications forTGFBI-Linked Corneal Dystrophy Therapy (2011)

PURPOSE. The purpose of this study was to investigate the effects and molecular mechanisms of lithium on inhibition of TGFBIp expression as a potential therapy for TGFBI-linked corneal dystrophy. METHODS. Primary culture corneal fibroblasts were isolated from the corneas of healthy subjects and patients with granular corneal dystrophy type 2 (GCD2) with a homozygous mutation in TGFBI R124H. Levels of TGFBIp and its mRNA in corneal fibroblasts treated with various lithium (LiCl) concentrations were analyzed by Western blot, RT-PCR, and quantitative real-time PCR. RESULTS. LiCl treatment reduced the expression levels of normal and mutant TGFBIp in a dose- and a time-dependent manner. Furthermore, TGF-β1-induced TGFBIp expression decreased by 35% and 67% after treatment with 5 mM and 10 mM LiCl, respectively. LiCl decreased the level of pSmad3 (S423/425) in a dose-dependent manner. Furthermore, LiCl increased the level of pGSK-3α/β (S21/9) in a dose-dependent manner. Also observed was the interaction between GSK-3β and Smad3, which was enhanced by lithium. In addition, Western blot analysis showed that the ratio of LC3-II/LC3-I in corneal fibroblasts increased after LiCl treatment. Cell viability at different doses was greater than 98%, indicating that LiCl did not induce significant corneal fibroblast death. Finally, the observed attenuating effects of LiCl on TGFBIp expression were not the results of cell death. CONCLUSIONS. The accumulation of mutant TGFBIp ultimately leads to the histopathologic and clinical manifestations associated with TGFBI-linked corneal dystrophy. These data strongly suggest that lithium may be used for the prevention or treatment of this disease.
A New Binomial Mapping and Optimization Algorithm for Reduced-Complexity Mesh-Based On-Chip Network (2007)

This paper presents an efficient binomial IP mapping and optimization algorithm (BMAP) to reduce the hardware cost of on-chip network (OCN) infrastructure. The complexity of BMAP is O(N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> log(N)). Based on our OCN system synthesis flow, the proposed algorithm provides more economic network component mapping in comparison with traditional OCN mapping algorithm. The experimental result shows total traffic on network is reduced by 37% and average network hop count is reduced by 46%. With further optimization, the hardware efficiency is enhanced therefore the total hardware cost of network infrastructure is reduced to 51%~85%