gebhart/patrepeval huggingface dataset:
AAV-HBV mouse model replicates immune exhaustion patterns of chronic HBV patients at single-cell level (2023)

Abstract Background and Aims Unresolved hepatitis B virus (HBV) infection leads to a progressive state of immune exhaustion that impairs resolution of infection, leading to chronic infection (CHB). The immune-competent AAV-HBV mouse is a common HBV preclinical immune competent model, though a comprehensive characterization of the liver immune microenvironment and its translatability to human infection is still lacking. We investigated the intrahepatic immune profile of the AAV-HBV mouse model at a single-cell level and compared with data from CHB patients in immune tolerant (IT) and immune active (IA) clinical stages. Methods Immune exhaustion was profiled through an iterative subclustering approach for cell-typing analyses of single-cell RNA-sequencing data in CHB donors and compared to the AAV-HBV mouse model 24-weeks post-transduction to assess its translatability. This was validated using an exhaustion flow cytometry panel at 40 weeks post-transduction. Results Using single-cell RNA-sequencing, CD8 pre-exhausted T-cells with self-renewing capacity ( TCF7 +), and terminally exhausted CD8 T-cells ( TCF7 -) were detected in the AAV-HBV model. These terminally exhausted CD8 T-cells (expressing Pdcd1 , Tox , Lag3 , Tigit ) were significantly enriched versus control mice and independently identified through flow cytometry. Importantly, comparison to CHB human data showed a similar exhausted CD8 T-cell population in IT and IA donors, but not in healthy individuals. Conclusions Long term high titer AAV-HBV mouse liver transduction led to T-cell exhaustion, as evidenced by expression of classical immune checkpoint markers at mRNA and protein levels. In both IT and IA donors, a similar CD8 exhausted T-cell population was identified, with increased frequency observed in IA donors. These data support the use of the AAV-HBV mouse model to study T-cell exhaustion in HBV infection and the effect of immune-based therapeutic interventions. Lay Summary The AAV-HBV mouse model is used as a research tool to study hepatitis B infection. In this study we evaluated the translation value from mouse to human with regards to T-cell exhaustion. Highlights AAV-HBV mice transduced with a high titer vector showed presence of CD8 exhausted T-cells after 24 weeks. High titer transduced mice, but not lower titer show increased expression of LAG-3, TOX, TIM-3 and TIGIT in CD8 T-cells. PD-1 was increased in CD8 T-cells, independent of HBV transduction titer. A similar exhausted CD8 T-cell population could be found in chronic HBV donors, but not in healthy individuals. Graphical abstract
Perkin 1 Abstracts: Natural Product Synthesis (2000)

Perkin 1 Abstracts: Natural Product Synthesis aims to highlight syhtheses that have been recently published. It includes brief descriptions of biological activity and key steps. A more comprehensive list of Natural Product sytheses and isolations can be found in Natural Product Updates.
Supplementary Figure Legend from Nuclear Epidermal Growth Factor Receptor Is a Functional Molecular Target in Triple-Negative Breast Cancer (2023)

&lt;p&gt;PDF - 69K, Legend for Supplementary Figure 1.&lt;/p&gt;
Chimeric Influenza Virus Replicating Predominantly in the Murine Upper Respiratory Tract Induces Local Immune Responses against Human Immunodeficiency Virus Type 1 in the Genital Tract (1998)

Previously, a mucosal model of immunization against human immunodeficiency virus type 1 (HIV-1) was established by using influenza virus as a vector for the neutralizing gp41 epitope ELDKWA. Whether replication of this chimeric influenza virus in the upper respiratory tract of mice is sufficient for inducing mucosal immune responses in the genital tract was investigated. An immunization strategy was established that permits the virus to replicate in the murine upper respiratory tracts but not in the lungs. Intranasal application of the chimeric virus induced HIV-1-specific antibodies in sera and genital tract. In addition, chimeric virus-specific antibody-secreting cells were detected in lymphocyte populations obtained from lungs, spleens, and urogenital tracts. These results indicate that replication of the chimeric influenza/ELDKWA virus in the upper respiratory tract is sufficient to induce systemic immune responses as well as local immune responses in the genital tract.
Nonlinear silicon nanophotonics for mid-infrared applications (2011)

The silicon nanophotonic wire platform can be applied toward development of integrated optical devices for the generation and processing of mid-infrared light signals. The demonstration of a mid-infrared optical parametric amplifier will be reviewed, and recent work aimed at expanded gain bandwidth and reduced pump power requirements will be presented.
Adaptive optics with advanced phase-contrast techniques I High-resolution wave-front sensing (2001)

High-resolution phase-contrast wave-front sensors based on phase spatial light modulators and micromirror/ liquid-crystal arrays are introduced. Wave-front sensor performance is analyzed for atmospheric-turbulence-induced phase distortions described by the Kolmogorov and the Andrews models. A high-resolution phase-contrast wave-front sensor (nonlinear Zernike filter) based on an optically controlled liquid-crystal phase spatial light modulator is experimentally demonstrated. The results demonstrate high-resolution visualization of dynamically changing phase distortions within the sensor time response of approximately 10 ms.
Quantitative Study of the Applicability of Fiber-Optic Gyroscopes for MWD Borehole Surveying (2000)

Summary Horizontal drilling increases the productivity of the drilling processes, but inevitably requires a measurement-while-drilling surveying system employing three-axis accelerometers to determine the inclination and the tool face angles, and three-axis magnetometers to provide the azimuth. The magnetometer measurements are affected by drillstring magnetic interference and downhole ore deposits, which necessitates the installation of the magnetometers inside costly nonmagnetic drill collars. The aim of this article was to examine the usefulness of the fiber-optic gyroscope (FOG) to replace magnetometers for real-time monitoring of the azimuth. System analysis of the effect of the severe downhole environment on the FOG's overall performance is presented. This analysis includes modeling the effects of shock forces, vibrations due to mud pump noise, bending vibrations due to drill collar whirling and linear coupling between the axial and transverse modes of vibration. The results obtained show that the FOG has excellent immunity to shock and vibration. Moreover, since magnetic fields have only a minor effect on the FOG, it can be installed directly behind the drill bit, thus eliminating nonmagnetic drill collars. This improves the measurement accuracy and eliminates the cost associated with nonmagnetic drill collars.
Antimicrobial susceptibility of Lactobacillus species isolated from commercial ethanol plants (2007)

Bacterial contamination of commercial fermentation cultures is a common and costly problem to the fuel ethanol industry. Antimicrobials such as virginiamycin (VIR) and penicillin (PEN) are frequently used to control contamination but there are little data available on the susceptibility of bacterial contaminants to these agents. A survey of bacterial contaminants from a wet-mill ethanol plant with no history of using antibiotics and a dry-grind facility that periodically doses with VIR found that the majority of contaminants were species of Lactobacillus. Thirty-seven isolates of Lactobacillus species from the wet-mill and 42 isolates from the dry-grind facility were tested for antimicrobial susceptibility using broth dilution and agar dilution methods. In general, the Lactobacillus isolates from the dry-grind plant had higher minimum inhibitory concentrations (MICs) for the tested agents than the isolates from the wet-mill facility. The MIC(90) for VIR was 4 microg/ml for the dry-grind isolates versus 0.25 microg/ml for the wet-mill isolates; and for PEN, the MIC(90)'s were >8 and 2 microg/ml for the dry-grind and wet-mill isolates, respectively. Sixteen Lactobacillus isolates from the dry-grind plant but none from the wet-mill possessed vatE, a gene that encodes a streptogramin acetyltransferase associated with resistance to virginiamycin. Despite decreased susceptibility to virginiamycin, most dry-grind isolates had MICs lower than the maximal recommended application rate of 6 ppm.
Phenotyping cotton ovule fibre initiation with spatial statistics (2007)

Yield in cultivated cotton (Gossypium spp.) is affected by the number and distribution of fibres initiated on the seed surface but, apart from simple statistical summaries, little has been done to assess this phenotype quantitatively. Here we use two types of spatial statistics to describe and quantify differences in patterning of cotton ovule fibre initials (FI). The following five different species of Gossypium were analysed: G. hirsutum L., G. barbadense L., G. arboreum, G. raimondii Ulbrich. and G. trilobum (DC.) Skovsted. Scanning electron micrographs of FIs were taken on the day of anthesis. Cell centres for fibre and epidermal cells were digitised and analysed by spatial statistics methods appropriate for marked point processes and tessellations. Results were consistent with previously published reports of fibre number and spacing. However, it was shown that the spatial distributions of FIs in all of species examined exhibit regularity, and are not completely random as previously implied. The regular arrangement indicates FIs do not appear independently of each other and we surmise there may be some form of mutual inhibition specifying fibre-initial development. It is concluded that genetic control of FIs differs from that of stomata, another well studied plant idioblast. Since spatial statistics show clear species differences in the distribution of FIs within this genus, they provide a useful method for phenotyping cotton.
Analisi del comportamento biomeccanico di stent: un approccio agli elementi finiti (in italian) - Analysis of stent biomechanics: A finite element approach (2006)

In this paper several stent typologies (self-expandable and ballon-expandable), employed to treat coronary and intravascular stenotic arteries, are analyzed through a three-dimensional finite-element approach, based on a large strain and large displacement formulation. In detail, varying a number of&#13;\ngeometrical parameters, statical and dynamical numerical simulations are performed to evaluate stent mechanical behaviour (in terms of radial variation, foreshortening and flexibility) and&#13;\ninteraction effects between mechanical devices and treated biological tissue. Numerical simulations on stenting and&#13;\nangioplasty, obtained by considering several coupled discrete models of the stent-artery system and based on a classical friction-free contact algorithm, allow to evaluate the influence of device typology and vascular geometry on both biomechanical&#13;\ninteraction effects and effectiveness of the medical treatment.
An unexpected aromatic S N2? substitution of a 4-bromobenzopyran (1989)

Reaction of 4-bromo-6-cyano-3,4-dihydro-2,2-dimethyl-3,3-ethylenedioxy-2H-1-benzopyran (2) with secondary amide anions provides C-5 substituted products in moderate yields.
Abstract 12904: Ticagrelor Removal From Human Blood (2015)

Background: In acute coronary events, ticagrelor is recommended to be loaded prior to cardiac catheterization. In the PLATO study the rate of severe bleeding on ticagrelor in patients who needed urgent bypass graft surgery was high but similar for ticagrelor and clopidogrel. The reversible binding mode of action of ticagrelor onto the P2Y12 receptor provides an opportunity for drug removal not possible for the thienopyridines (clopidogrel and prasugrel) which are all irreversibly binding to P2Y12. Objective: Our goal was to devise an efficient method for ticagrelor removal from blood. Methods: Ticagrelor removal was measured in two sets of experiments. The first set was performed in a first-pass manner and used as drug vehicle bovine serum albumin (BSA) solution (0.4% and 4%), while the second set employed in three experiments blood either bought from BioreclamationIVT (older than 24 hours) or freshly collected from a healthy volunteer and mixed with ticagrelor at a concentration of approximately 5.1 ug/mL. BSA solution as well as blood carrying ticagrelor were passed at various velocities through columns containing two types of sorbent (Cytosorb and Porapak Q). Ticagrelor concentration was measured from the affluent and effluent solution using a liquid chromatography technique with tandem mass spectrometric detection LC/MS/MS). Results: Ticagrelor removal peaked at 99% and 100% using 40 mL Cytsorb and Porapak Q columns, respectively, during BSA experiments. The most efficient ticagrelor drug removal from blood was obtained with 260 mL sorbent (113 g of Cytosorb), with a peak removal from whole blood of 100% and 99% from blood cells during a 10-hour recirculating experiment reaching blood and plasma levels of 15 and 2 ng/mL, respectively, much below the ticagrelor platelet aggregation inhibition IC50 levels (30 ng/mL). Cytosorb has been also shown to absorb in bench experiments 99% of dabigatran in albumin solution and up to 96% of radiocontrast, creating the premises of a possible all-inclusive method of antiplatelets, anticoagulants, and radiocontrast removal. Conclusion: Sorbent adsorption demonstrates robust removal of ticagrelor from BSA solution and human blood samples.
Foldable neuromorphic memristive electronics (2014)

Neuromorphic computer will need folded architectural form factor to match brain cortex's folded pattern for ultra-compact design. In this work, we show a state-of-the-art CMOS compatible pragmatic fabrication approach of building structurally foldable and densely integrated neuromorphic devices for non-volatile memory applications. We report the first ever memristive devices with the size of a motor neuron on bulk mono-crystalline silicon (100) and then with trench-protect-release-recycle process transform the silicon wafer with devices into a flexible and semi-transparent silicon fabric while recycling the remaining wafer for further use. This process unconditionally offers the ultra-large-scale-integration opportunity - increasingly critical for ultra-compact memory.
Effects of Composition of Oligo(ethylene glycol)-Based Mixed Monolayers on Peptide Grafting and Human Immunoglobulin Detection (2014)

Alkanethiols carrying ethylene glycol units (EGn, n = 3 or 6) with amine termini (EG3NH2 or EG6NH2) were coadsorbed with a “diluent”, hydroxyl-terminated alkanethiol (EG3OH), to form mixed self-assembled monolayers (SAMs). The mixed SAMs were characterized, and hexameric peptide ligand His-Trp-Arg-Gly-Trp-Val (HWRGWV), which shows affinity binding toward the Fc (constant fragment) of human immunoglobulin (IgG), was grafted onto different dilutions of EG6NH2–EG3OH mixed SAMs for preparation of IgG detection surfaces. The specificity toward IgG was optimal for peptides grafted on SAMs prepared from 10% EG6NH2 precursor solution, even though this surface did not have the highest number of peptides per unit area. Surface plasmon resonance (SPR) experiments showed that IgG bound to the peptides on the mixed SAM with a dissociation constant Kd of 9.33 × 10–7, maximum binding capacity Qm of 3.177 mg m–2, and adsorption rate constant ka of 1.99 m3 mol–1 s–1. IgG binding from complex mixtures of Chinese Hamster Ovary supernatant (CHO) was investigated on peptides grafted to mixed and pure SAMs. Regeneration of the surfaces was achieved by treatment with 10% acetonitrile in 0.1 M NaOH solution. Overall, the use of peptides grafted on mixed SAMs improved the effectiveness of detection and had an impact on specificity and regeneration of biosensors.
Effect of Various Insecticides on Beneficial Insects and Spiders in Cotton, 1982 (1984)

Abstract Lockett 77 cotton was planted on 4 June in a randomized complete block design replicated 4 times. Plots were 12 rows wide by 100 ft long. One irrigation was applied on 22 to 23 July and plots were sidedressed with 72 lb N/acre on 8 July. Numbers of beneficials were determined semiweekly with 50 sweep net samples in each plot. Insects were taken to the laboratory, frozen and counted. Insecticides were applied with a John Deere Hi-Cycle 6000 Ground Sprayer employing drops and three nozzles per row, and at a rate of 10 gal/acre. Adults and nymphs were included in counts of insects with piercing-sucking mouthparts. An extremely heavy Heliothis spp. egg lay occurred on 5 Aug.; but 0.86 in. rain fell on 7 to 8 Aug.; and spraying was delayed until the field dried sufficiently for entry of equipment. All plots wer sampled on 11 Aug and treatments were applied early morning on 12 Aug. Heliothis spp. 3rd-to 6th-stage larvae were collected from plots on 20 Aug. Larvae could not be found in all plots, so collections from each treatment were grouped together. Larvae were fed in the laboratory on pinto bean diet and observed for parasite emergence. Dead pupae and larvae were dissected to determine if they were parasitized. Heliothis spp. larvae and damage were sampled semiweekly before and after insecticide application.
A methodology for a correct sizing of electrochemical storage devices (2015)

Electrochemical storage devices are spreading in many applications. Nevertheless, the data given by the manufacturers are often few and not homogenous. Using these data a correct sizing for a given application results very difficult and usually the designers makes a rough design in which the expected lifetime is not known and the costs are not optimized. This situation depends, mainly, on the lack of knowledge in modeling and studying electrochemical storage devices. In this paper, the authors underline the necessity of an integrated model for the definition of the nominal data of a storage device. Moreover, starting always from the solution of an integrated model, they propose a methodology for a correct sizing of a storage unit for a given application.
On expressing module interconnections in Ada (1986)

It is commonly believed that Ada lacks the facility to specify explicit import and export lists which are useful in specifying detailed interconnections of various modules. In this paper not only do we show that such requirements can be expressed in the language, but also that related issues of providing flexible linkages and enforcing precise detailed interfaces can be enforced by the use of the Ada language.
A Fast and Slippery Slope for File Systems (2016)

There is a vast number and variety of file systems currently available, each optimizing for an ever growing number of storage devices and workloads. Users have an unprecedented, and somewhat overwhelming, number of data management options. At the same time, the fastest storage devices are only getting faster, and it is unclear on how well the existing file systems will adapt. Using emulation techniques, we evaluate five popular Linux file systems across a range of storage device latencies typical to low-end hard drives, latest high-performance persistent memory block devices, and in between. Our findings are often surprising. Depending on the workload, we find that some file systems can clearly scale with faster storage devices much better than others. Further, as storage device latency decreases, we find unexpected performance inversions across file systems. Finally, file system scalability in the higher device latency range is not representative of scalability in the lower, submillisecond, latency range. We then focus on Nilfs2 as an especially alarming example of an unexpectedly poor scalability and present detailed instructions for identifying bottlenecks in the I/O stack.
High-mobility, trap-free charge transport in conjugated polymer diodes (2019)

Charge transport in conjugated polymer semiconductors has traditionally been thought to be limited to a low-mobility regime by pronounced energetic disorder. Much progress has recently been made in advancing carrier mobilities in field-effect transistors through developing low-disorder conjugated polymers. However, in diodes these polymers have to date not shown much improved mobilities, presumably reflecting the fact that in diodes lower carrier concentrations are available to fill up residual tail states in the density of states. Here, we show that the bulk charge transport in low-disorder polymers is limited by water-induced trap states and that their concentration can be dramatically reduced through incorporating small molecular additives into the polymer film. Upon incorporation of the additives we achieve space-charge limited current characteristics that resemble molecular single crystals such as rubrene with high, trap-free SCLC mobilities up to 0.2 cm<sup>2</sup>/Vs and a width of the residual tail state distribution comparable to k<sub>B</sub>T.
Time‐Constant Dispersion (2008)

This chapter contains sections titled: Constant-Phase Elements Convective Diffusion Impedance at Small Electrodes Geometry-Induced Current and Potential Distributions Porous Electrodes Oxide Layers Problems
Supplementary Figure 6 from Soluble CD200 Is Critical to Engraft Chronic Lymphocytic Leukemia Cells in Immunocompromised Mice (2023)

&lt;p&gt;PDF file - 69K, Engraftment of CD19+CD5+ CLL cells in peritoneal cavity: Absolute count (x105 cells) of CD19+CD5+ CLL cells in the peritoneal cavity of animals receiving either sCD200hi CLL plasma, or sCD200 absorbed CLL plasma in the presence or absence of T-cell depleting antibody OKT3 (infused iv)&lt;/p&gt;
[WRN gene]. (2009)

Werner's syndrome is a typical progeroid syndrome with many specific features of aging early in life. Clinical features of Werner's syndrome closely resemble accelerated aging, such as cataract, scleroderma skin, diabetes and tumorigenesis. The causative gene of this syndrome is denoted as WRN, which encodes a homolog of the E. coli RecQ DNA helicase and is located on chromosome 8p2-p11.2. WRN is not only a helicase but also an exonuclease and ATPase. WRN protein plays a key role in genome stability, particularly during DNA replication and telomere metabolism. In this review, we introduce the clinical characteristics of Werner's syndrome and recent topics concerning WRN in comparison with other progeroid syndromes.
ChemInform Abstract: Scalable Synthesis of the VEGF‐R2 Kinase Inhibitor JNJ‐17029259 Using Ultrasound‐Mediated Addition of MeLi—CeCl3 to a Nitrile. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.