gebhart/patrepeval huggingface dataset:
ISOLATION OF HUMAN ZONULIN, A NEW FAMILY OF TISSUE-SPECIFIC PHYSIOLOGIC MODULATORS OF TIGHT JUNCTIONS (1998)

32 We have recently demonstrated that Zonula Occludens Toxin (Zot) interacts with a specific intestinal epithelial surface receptor, with subsequent activation of a complex intracellular cascade of events that regulate tight junctions (tj) permeability. Based on this observation, we postulated that Zot may mimic the effect of a functionally and immunologically related physiological modulator of epithelial tj. Therefore, affinity-purified anti-Zot antibodies and the Ussing chamber assay were used in combination to search for the Zot analogue (that we named zonulin) in various human tissues, including intestine, heart, and brain. Both human fetal and adult tissues were used. The tissues were disrupted by homogenization, centrifuged at 40,000 rpm for 30 min, and the supernatant collected and lyophilized. The resulting lyophilized product was subsequently reconstituted in PBS, loaded onto a Sephadex G-50 chromatographic column, and Western immunoblotting positive fractions were subjected to a salt gradient chromatography through a Q-Sepharose column. Western immunoblotting positive fractions were subjected to N-terminal sequencing and tested for biological activity on both rabbit and monkey intestine mounted in Ussing chambers. Western immunoblotting of fraction 1 (20% (w/v) NaCl) isolated from human brain, heart, and intestine showed a single band of 50 kDa in size. The N-terminal sequences of these bands revealed that zonulin purified from adult human intestine was identical to the zonulin purified from human heart and fetal intestine, but different from zonulin purified from human brain. Mucosal addition of 100 μl of fraction 1 of zonulin purified from either human intestine or heart induced a significant reduction of rabbit and monkey intestinal resistance (Rt), both in the jejunum and ileum, but not in the colon. No significant effect was observed when zonulin purified from human brain was tested. Zonulin from human heart also increased the intestinal absorption of insulin both in the jejunum(0.058±0.003 vs 0.12±0.005 fmol/cm2.min, untreated vs. Zonulin-treated tissues, respectively, p=0.001) and in the ileum(0.006±0.0002 vs. 0.018±0.005 fmol/cm2.min, untreated vs. zonulin-treated tissues, respectively, p=0.05) in a time-dependent manner. These results demonstrate that: 1. Zonulin represents a family of related eukaryotic proteins that modulate tj; 2. There are different isoforms of the molecule with common, active C-terminal sequences, and variable N-terminal sequences; 3. Probably the N-terminal part of zonulin interacts with specific surface receptors and determines the tissue-specificity of the molecule.
Near-Infrared Spectroscopy for the Evaluation of Anesthetic Depth (2015)

The standard-of-care guidelines published by the American Society of Anesthesiologists (ASA) recommend monitoring of pulse oximetry, blood pressure, heart rate, and end tidal CO2 during the use of anesthesia and sedation. This information can help to identify adverse events that may occur during procedures. However, these parameters are not specific to the effects of anesthetics or sedatives, and therefore they offer little, to no, real time information regarding the effects of those agents and do not give the clinician the lead-time necessary to prevent patient "awareness." Since no "gold-standard" method is available to continuously, reliably, and effectively monitor the effects of sedatives and anesthetics, such a method is greatly needed. Investigation of the use of functional near-infrared spectroscopy (fNIRS) as a method for anesthesia or sedation monitoring and for the assessment of the effects of various anesthetic drugs on cerebral oxygenation has started to be conducted. The objective of this paper is to provide a thorough review of the currently available published scientific studies regarding the use of fNIRS in the fields of anesthesia and sedation monitoring, comment on their findings, and discuss the future work required for the translation of this technology to the clinical setting.
Clinical implementation of target tracking by breathing synchronized delivery (2006)

Target‐tracking techniques can be categorized based on the mechanism of the feedback loop. In real time tracking, breathing‐delivery phase correlation is provided to the treatment delivery hardware. Clinical implementation of target tracking in real time requires major hardware modifications. In breathing synchronized delivery (BSD), the patient is guided to breathe in accordance with target motion derived from four‐dimensional computed tomography (4D‐CT). Violations of mechanical limitations of hardware are to be avoided at the treatment planning stage. Hardware modifications are not required. In this article, using sliding window IMRT delivery as an example, we have described step‐by‐step the implementation of target tracking by the BSD technique: (1) A breathing guide is developed from patient's normal breathing pattern. The patient tries to reproduce this guiding cycle by following the display in the goggles; (2) 4D‐CT scans are acquired at all the phases of the breathing cycle; (3) The average tumor trajectory is obtained by deformable image registration of 4D‐CT datasets and is smoothed by Fourier filtering; (4) Conventional IMRT planning is performed using the images at reference phase (full exhalation phase) and a leaf sequence based on optimized fluence map is generated; (5) Assuming the patient breathes with a reproducible breathing pattern and the machine maintains a constant dose rate, the treatment process is correlated with the breathing phase; (6) The instantaneous average tumor displacement is overlaid on the dMLC position at corresponding phase; and (7) DMLC leaf speed and acceleration are evaluated to ensure treatment delivery. A custom‐built mobile phantom driven by a computer‐controlled stepper motor was used in the dosimetry verification. A stepper motor was programmed such that the phantom moved according to the linear component of tumor motion used in BSD treatment planning. A conventional plan was delivered on the phantom with and without motion. The BSD plan was also delivered on the phantom that moved with the prescheduled pattern and synchronized with the delivery of each beam. Film dosimetry showed underdose and overdose in the superior and inferior regions of the target, respectively, if the tumor motion is not compensated during the delivery. BSD delivery resulted in a dose distribution very similar to the planned treatments.
Capacity-Approaching TQC-LDPC Convolutional Codes Enabling Power-Efficient Decoders (2016)

In this paper, we develop a new capacity-approaching code, namely, parallel-concatenated (PC)-Low Density Parity Check (LDPC) convolutional code that is based on the parallel concatenation of trellis-based quasi-cyclic LDPC (TQC-LDPC) convolutional codes. The proposed PC-LDPC convolutional code can be derived from any QC-LDPC block code by introducing the trellis-based convolutional dependency to the code. The capacity-approaching PC-LDPC convolutional codes are encoded through parallel concatenated trellis-based QC recursive systematic convolutional (RSC) encoder (namely, QC-RSC encoder) that is also proposed in this paper. The proposed PC-LDPC convolutional code and the associated encoder retain a fine input granularity on the order of the lifting factor of the underlying block code. We also describe the corresponding trellis-based QC maximum a posteriori probability (namely, QC-MAP) decoder that efficiently decodes the PC-LDPC convolutional code. Performance and hardware implementation results show that the PC-LDPC convolutional codes with the QC-MAP decoder have two times lower complexity for a given bit-error-rate (BER), signal-to-noise ratio, and data rate, than conventional QC-LDPC block codes and LDPC convolutional codes. Moreover, the PC-LDPC convolutional code with the QC-MAP decoder outperforms the conventional QC-LDPC block codes by more than 0.5 dB for a given BER, complexity, and data rate and approaches Shannon capacity limit with a gap smaller than 1.25 dB. This low decoding complexity and the fine granularity make it feasible to efficiently implement the proposed capacity-approaching PC-LDPC convolutional code and the associated trellis-based QC-MAP decoder in next generation ultra-high data rate mobile systems.
A new green approach to Fenton’s chemistry using tea dregs and coffee grounds as raw material (2014)

Abstract Fenton’s chemistry has long been useful in industry because of the power of hydrogen peroxide (HP), in the presence of ferrous iron (Fe 2+ ), to produce a highly reactive free radical species capable of oxidizing aqueous materials. However, its application has been limited due to the rapid oxidation of ferrous iron. The rapid oxidation of ferrous iron limits the production of free radicals necessary for a powerful reaction. We developed two ‘green’ iron catalysts using used tea leaves (tea dregs) or coffee grounds as raw material. The new ‘green’ iron catalysts contained iron in a reductive stable status for a Fenton catalyst. The study showed that the developed ‘green’ iron catalysts can be used as iron fertilizer and for the Fenton’s reaction on the degradation of methylene blue (MB), and in the disinfection of Escherichia coli . The tea and coffee polyphenols were estimated to be responsible for the reductive stable state of the iron in the developed catalysts, due to their reducing power and chelating iron ability. The developed new ‘green’ iron catalysts are expected to diffuse in wide fields such as food, medicine, public health, agriculture, the environment, etc.
GRL-0519, a Novel Oxatricyclic Ligand-Containing Nonpeptidic HIV-1 Protease Inhibitor (PI), Potently Suppresses Replication of a Wide Spectrum of Multi-PI-Resistant HIV-1 Variants <i>In Vitro</i> (2013)

We report that GRL-0519, a novel nonpeptidic human immunodeficiency virus type 1 (HIV-1) protease inhibitor (PI) containing tris-tetrahydrofuranylurethane (tris-THF) and a sulfonamide isostere, is highly potent against laboratory HIV-1 strains and primary clinical isolates (50% effective concentration [EC50], 0.0005 to 0.0007 μM) with minimal cytotoxicity (50% cytotoxic concentration [CC50], 44.6 μM). GRL-0519 blocked the infectivity and replication of HIV-1NL4-3 variants selected by up to a 5 μM concentration of ritonavir, lopinavir, or atazanavir (EC50, 0.0028 to 0.0033 μM). GRL-0519 was also potent against multi-PI-resistant clinical HIV-1 variants isolated from patients who no longer responded to existing antiviral regimens after long-term antiretroviral therapy, highly darunavir (DRV)-resistant variants, and HIV-2ROD. The development of resistance against GRL-0519 was substantially delayed compared to other PIs, including amprenavir (APV) and DRV. The effects of nonspecific binding of human serum proteins on GRL-0519's antiviral activity were insignificant. Our analysis of the crystal structures of GRL-0519 (3OK9) and DRV (2IEN) with protease suggested that the tris-THF moiety, compared to the bis-THF moiety present in DRV, has greater water-mediated polar interactions with key active-site residues of protease and that the tris-THF moiety and paramethoxy group effectively fill the S2 and S2' binding pockets, respectively, of the protease. The present data demonstrate that GRL-0519 has highly favorable features as a potential therapeutic agent for treating patients infected with wild-type and/or multi-PI-resistant variants and that the tris-THF moiety is critical for strong binding of GRL-0519 to the HIV protease substrate binding site and appears to be responsible for its favorable antiretroviral characteristics.
Dietary Supplements of Two Doses of Calcium Salts of Conjugated Linoleic Acid During the Transition Period and Early Lactation (2005)

Reduction of milk fat secretion by the use of conjugated linoleic acid (CLA) supplements may alleviate energy demands during early lactation. The objective of the present study was to evaluate lactational performance, net energy balance, and reproductive response of dairy cows supplemented with 2 doses of CLA from 2 wk before predicted calving until 9 wk postpartum. Holstein cows (n = 48) were divided into 3 treatment groups: 1) control, 2) low dose CLA treatment (CLA-1), and 3) high dose CLA treatment (CLA-2). Supplements for all treatments provided 230 g/d of fat; the control group received Ca salts of palm fatty acid distillate and the CLA groups received a mixture of Ca salts of CLA isomers and Ca salts of palm fatty acid distillate (31.6 and 63.2 g/d of CLA isomers for CLA-1 and CLA-2, respectively). Supplementation with CLA resulted in an 11 and 21% decrease in milk fat yield for CLA-1 and CLA-2, respectively. Milk production and secretion of other milk components did not differ among treatments. Milk energy output was significantly reduced with CLA-2, but net energy balance, body weight, and body condition scores were unaffected. Treatment had no effect on hepatic triglyceride concentration or plasma glucose and insulin, but nonesterified fatty acids tended to be lower for CLA-1. There were no consistent dose-related effects on reproduction variables, and no adverse effects were observed during the treatment or posttreatment period. Supplemental CLA was effective in reducing milk fat content, but it did not have a significant effect on milk yield or net energy balance.
Top-K aggregation queries over large networks (2010)

Searching and mining large graphs today is critical to a variety of application domains, ranging from personalized recommendation in social networks, to searches for functional associations in biological pathways. In these domains, there is a need to perform aggregation operations on large-scale networks. Unfortunately the existing implementation of aggregation operations on relational databases does not guarantee superior performance in network space, especially when it involves edge traversals and joins of gigantic tables. In this paper, we investigate the neighborhood aggregation queries: Find nodes that have top-k highest aggregate values over their h-hop neighbors. While these basic queries are common in a wide range of search and recommendation tasks, surprisingly they have not been studied systematically. We developed a Local Neighborhood Aggregation framework, called LONA, to answer them efficiently. LONA exploits two properties unique in network space: First, the aggregate value for the neighboring nodes should be similar in most cases; Second, given the distribution of attribute values, it is possible to estimate the upper-bound value of aggregates. These two properties inspire the development of novel pruning techniques, forward pruning using differential index and backward pruning using partial distribution. Empirical results show that LONA could outperform the baseline algorithm up to 10 times in real-life large networks.
A Machine-Learning Approach to Automatic Detection of Delimiters in Tabular Data Files (2016)

Detection of string and column delimiters is a critical first step in the automated ingestion of files containing tabular data. In this paper we present an algorithm that uses a logistic-regression classifier to evaluate whether a particular choice of delimiters is correct. The delimiter choice that is given the highest score by the classifier is chosen as the one most likely to be correct. The algorithm makes the correct choice over 90% of the time on a test data set of files with a variety of different delimiters.
Optimal wavelengths for vein‐selective photothermolysis (2012)

Preferential photocoagulation of venous blood is possible at wavelengths with a high Hb/HbO(2) absorption coefficient ratio. Laser-induced metHb may also affect wavelength-dependent selective photothermolysis. Venular malformations such as port wine stains could potentially be treated more selectively with ~630-780 nm sources. Nd:YAG laser pulses at 1,064 nm tend to affect arterial more than venous blood.
Highly Specific and Sensitive Target Binding by the Humanized pS396-Tau Antibody hC10.2 Across a Wide Spectrum of Alzheimer’s Disease and Primary Tauopathy Postmortem Brains (2022)

S396 hyperphosphorylation is a feature of the formation of seeding-competent tau across different tauopathies and it is present both in intra- and extracellular pathological tau. hC10.2 represents an excellent candidate for a hyperphosphorylation-selective therapeutic tau antibody for the treatment of AD and primary tauopathies.
Development of a replication‐deficient adenoviral vector‐based vaccine candidate for the interception of HPV16‐ and HPV18‐induced infections and disease (2017)

High-risk Human papilloma virus (HPV) types are the causative agents of cervical cancer and several other anogenital malignancies. The viral proteins expressed in the (pre)malignant cells are considered ideal targets for immunological intervention. Many approaches have been evaluated for this purpose, mostly aiming at the induction of HPV16 E7- and/or E6-specific cellular immunogenicity. As clinical success has so far been limited, novel approaches are required. We describe the development and pre-clinical testing of a vaccine candidate consisting of replication-deficient adenovirus type 26 and 35 based vectors for the interception of HPV16- and HPV18-related disease. We developed HPV16- and HPV18-specific antigens consisting of fusion proteins of E2, E6 and E7. The vaccine will be suitable for every disease stage, from incident and persistent infections where E2 is predominantly expressed up to late stages where E6 and E7 expression are upregulated. Importantly E6 and E7 are present as reordered fragments to abrogate the transforming activity of these two proteins. Loss of transforming activity was demonstrated in different in vitro models. Robust T-cell immunogenicity was induced upon immunization of mice with the vaccine candidate. Finally, the developed vaccine vectors showed considerable therapeutic efficacy in the TC-1 mouse model. The absence of transforming activity of the antigens and the favorable immunogenicity profile of the adenovirus based vectors along with the fact that these vectors can be readily produced on a large scale makes this approach attractive for clinical evaluation.
Using family history information to promote healthy lifestyles and prevent diseases; a discussion of the evidence (2010)

In addition to risk assessment, family history information can be used to personalize health messages, which are potentially more effective in promoting healthy lifestyles than standardized health messages. More research is needed on the evidence for the effectiveness of such a tool.
Development of magneto-plasmonic nanoparticles for multimodal image-guided therapy to the brain (2016)

Magneto-plasmonic nanoparticles are one of the emerging multi-functional materials in the field of nanomedicine. Their potential for targeting and multi-modal imaging is highly attractive. In this study, magnetic core/gold shell (MNP@Au) magneto-plasmonic nanoparticles were synthesized by citrate reduction of Au ions on magnetic nanoparticle seeds. Hydrodynamic size and optical properties of magneto-plasmonic nanoparticles synthesized with the variation of Au ions and reducing agent concentrations were evaluated. The synthesized magneto-plasmonic nanoparticles exhibited superparamagnetic properties, and their magnetic properties contributed to the concentration-dependent contrast in magnetic resonance imaging (MRI). The imaging contrast from the gold shell part of the magneto-plasmonic nanoparticles was also confirmed by X-ray computed tomography (CT). The transmigration study of the magneto-plasmonic nanoparticles using an in vitro blood-brain barrier (BBB) model proved enhanced transmigration efficiency without disrupting the integrity of the BBB, and showed potential to be used for brain diseases and neurological disorders.
The Adaptive Gain Integrating Pixel Detector at the European XFEL (2018)

The Adaptive Gain Integrating Pixel Detector (AGIPD) is an X-ray imager, custom designed for the European X-ray Free-Electron Laser (XFEL). It is a fast, low-noise integrating detector, with an adaptive gain amplifier per pixel. This has an equivalent noise of less than 1 keV when detecting single photons and, when switched into another gain state, a dynamic range of more than 10<sup>4</sup> photons of 12 keV. In burst mode the system is able to store 352 images while running at up to 6.5 MHz, which is compatible with the 4.5 MHz frame rate at the European XFEL. The AGIPD system was installed and commissioned in August 2017, and successfully used for the first experiments at the Single Particles, Clusters and Biomolecules (SPB) experimental station at the European XFEL since September 2017. This paper describes the principal components and performance parameters of the system.
Using Nanosecond Shocks for Cardiac Defibrillation (2019)

The purpose of this review article is to summarize our current understanding of the efficacy and safety of cardiac defibrillation with nanosecond shocks. Experiments in isolated hearts, using optical mapping of the electrical activity, have demonstrated that nanosecond shocks can defibrillate with lower energies than conventional millisecond shocks. Single defibrillation strength nanosecond shocks do not cause obvious damage, but repeated stimulation leads to deterioration of the hearts. In isolated myocytes, nanosecond pulses can also stimulate at lower energies than at longer pulses and cause less electroporation (propidium uptake). The mechanism is likely electroporation of the plasma membrane. Repeated stimulation leads to distorted calcium gradients.
Bubble-Induced Color Doppler Feedback for Histotripsy Tissue Fractionation (2016)

Histotripsy therapy produces cavitating bubble clouds to increasingly fractionate and eventually liquefy tissue using high-intensity ultrasound pulses. Following cavitation generated by each pulse, coherent motion of the cavitation residual nuclei can be detected using metrics formed from ultrasound color Doppler acquisitions. In this paper, three experiments were performed to investigate the characteristics of this motion as real-time feedback on histotripsy tissue fractionation. In the first experiment, bubble-induced color Doppler (BCD) and particle image velocimetry (PIV) analysis monitored the residual cavitation nuclei in the treatment region in an agarose tissue phantom treated with two-cycle histotripsy pulses at [Formula: see text] using a 500-kHz transducer. Both BCD and PIV results showed brief chaotic motion of the residual nuclei followed by coherent motion first moving away from the transducer and then rebounding back. Velocity measurements from both PIV and BCD agreed well, showing a monotonic increase in rebound time up to a saturation point for increased therapy dose. In a second experiment, a thin layer of red blood cells (RBC) was added to the phantom to allow quantification of the fractionation of the RBC layer to compare with BCD metrics. A strong linear correlation was observed between the fractionation level and the time to BCD peak rebound velocity over histotripsy treatment. Finally, the correlation between BCD feedback and histotripsy tissue fractionation was validated in ex vivo porcine liver evaluated histologically. BCD metrics showed strong linear correlation with fractionation progression, suggesting that BCD provides useful quantitative real-time feedback on histotripsy treatment progression.
3D global windings hybrid excitation switching flux machine (2014)

In this paper a new structure of a hybrid excitation flux-switching synchronous machine is presented. A 3D finite elements analysis and a comparison with experimental results are exposed. This model makes possible to show the flux path of the excitation flux and to explore the flux regulation capability of this new structure. The on-load performances of this machine, in DC generator, are also analyzed.