gebhart/patrepeval huggingface dataset:
Picoinjection-Enabled Multitarget Loop-Mediated Isothermal Amplification for Detection of Foodborne Pathogens (2018)

In this study, we develop a method to detect multiple DNAs of foodborne pathogens by encapsulating emulsion droplets for loop-mediated isothermal amplification (LAMP). In contrast to the traditional bulk-phase LAMP, which involves a labor-intensive mixing process, with our method, different primers are automatically mixed with DNA samples and LAMP buffers after picoinjection. By directly observing and analyzing the fluorescence intensity of the resultant droplets, one can detect DNA from different pathogens, with a detection limit 500 times lower than that obtained by bulk-phase LAMP. We further demonstrate the ability to quantify bacteria concentration by detecting bacterial DNA in practical samples, showing great potential in monitoring water resources and their contamination by pathogenic bacteria.
Supplementary Text from Phase I Safety, Pharmacokinetic and Pharmacodynamic Evaluation of the Vascular Disrupting Agent Ombrabulin (AVE8062) in Patients with Advanced Solid Tumors (2023)

&lt;p&gt;Supplementary Text - PDF file 76K, DCE methodology and results&lt;/p&gt;
Ionization Non-Equilibrium and Ablation Phenomena in a Micro-Pulsed Plasma Thruster (2002)

In this paper, plasma-surface interactions are considered in a micro-Pulsed Plasma Thruster (micro-PPT).Two inter-related problems are addressed here, namely propellant ablation and formation of the ionization layer.The ablation mode is determined by the conditions of the plasma flow outside of the Knudsen layer.We found smooth transition between two ablation modes with small velocity at the edge of the Knudsen layer and limited (sound) velocity at the Knudsen layer edge.In the first case the fraction of backflux is very large, while in the second case it is about 18% of the primary flux.It is concluded that the transition between these two modes occurs as current density increases.A non-equilibrium ionization model is also developed.It is shown that both equilibrium and nonequilibrium ionization can be realized in a micro-PPT dependent on the discharge parameters.Based on the nonequilibrium ionization model, plasma generation and near-plume expansion is calculated for a micro-PPT.Good agreement with experimental measurements of the electron and neutral densities is found.
Adhesion of coagulase-negative staphylococci grouped according to Physico-chemical surface properties (1997)

Physico-chemical cell surface properties of 23 coagulase-negative staphylococcal strains, including contact angles, zeta potentials and elemental cell surface composition were measured, together with the adhesion of all strains to hexadecane. The data were employed in a hierarchical cluster analysis, revealing that the 23 strains comprised essentially four different groups. Groups I-III were somewhat similar to each other, but group IV was markedly distinguished from the other strains, predominantly through an elevated acidity of the cell surface. These group distinctions were not related to the presence of a capsule or slime on the strains. Adhesion of the strains to hexadecane depended critically on electrostatic interactions between the hexadecane and the staphylococci, and adhesion only occurred when the electrostatic repulsion between hexadecane and the micro-organisms was less than 500 kT at closest approach. Adhesion of six representative strains from all four groups in a parallel plate flow chamber to silicone rubber, an implant material with similar hydrophobicity to hexadecane, did not show such a critical dependence, nor did it relate with the group distinction. Possibly, microbial adhesion to substratum surfaces like silicone rubber is more complicated than adhesion to an ideally smooth and homogeneous hexadecane surface in an aqueous solution. Adhesion of all six strains to silicone rubber with an adsorbed conditioning film of plasma proteins was less than that to bare silicone rubber: initial deposition rates dropped from 2000-3000 cm-2 s-1 to 100-300 cm-2 s-1 after adsorption of plasma proteins, while the stationary end-point adhesion decreased from 10 x 10(6)-15 x 10(6) cm-2 to 1 x 10(6)-5 x 10(6) cm-2. The adhering staphylococci poorly withstood the passage of an air-bubble through the parallel plate flow chamber, regardless of the presence of a conditioning film, indicating a low affinity of these relatively hydrophilic strains for hydrophobic substratum surfaces.
Surface Co-Presentation of BMP-2 and Integrin Selective Ligands at the Nanoscale Favors β1 Integrin Adhesion (2019)

Here we present the use of surface nanopatterning of covalently immobilized BMP-2 and integrin selective ligands to determine the specificity of their interactions in regulating cell adhesion and focal adhesion assembly. Gold nanoparticle arrays carrying single BMP-2 dimersare prepared by block-copolymer micellar nanolithography and azide-functionalized integrin ligands (RGD peptides or α5β1integrin peptidomimetics) are immobilized on the surrounding polyethylene glycol alkyne by click chemistry.
High-speed X-ray phase tomography with Talbot interferometer and fringe scanning method (2012)

High-speed X-ray phase tomography based on the Fourier-transform method has been demonstrated with an X-ray Talbot interferometer using white synchrotron radiation. We report the experimental results of high-speed X-ray phase tomography with fringe-scanning method instead of Fourier-transform method to improve spatial resolution without a considerable increase of scan time. To apply fringe-scanning method to high speed tomography, we tested a scan that is a synchronous combination of one-way continuous movements of the sample rotation and the grating displacement. When this scanning method was combined with X-ray phase tomography, we were able to obtain a scan time of 5 s. A comparison of the image quality derived with the conventional approach and with the proposed approach using the fringe-scanning method showed that the latter had better spatial resolution.
A flow cytometric protocol for detection of Cryptosporidium spp. (2007)

Abstract Cryptosporidium parvum is transmitted through water and can cause severe diarrhea. The diagnosis is usually based upon observer‐dependent microscopic detection of oocysts, with rather low sensitivity and specificity. Our objective was to optimize a flow cytometric (FC) protocol for the detection of C. parvum . A specific monoclonal antibody conjugated with R‐phycoerythrin was incubated with dead oocysts to determine the optimal antibody concentration. Serial concentrations of oocysts were stained with the optimized concentration and analyzed by FC. The lower detection limit was determined, and the possibility of cross‐reaction was investigated using prokaryotic and eukaryotic microorganisms. A FC protocol was optimized to detect oocysts in spiked human stools. The optimal antibody concentration was found to be 3.0 μg/ml. The lowest number detectable was 2 × 10 3 oocysts/ml. Staining procedure was specific, as no cross‐reactions were observed. This reliable and easy FC protocol allow the specific detection of Cryptosporidium oocysts, even at very low concentrations, which is important for public health and further studies of treatment efficacy. © 2007 International Society for Analytical Cytology.
Late mortality and morbidity after liver transplantation. (1987)

Since the introduction of cyclosporine (Cs)-steroid therapy in 1980, 665 patients received orthotopic liver transplantation by the end of June 1986 at the University Health Sciences Center of Colorado (in 1980), the University Health Center of Pittsburgh (since 1981), and the Pittsburgh-affiliated Baylor University Medical Center of Dallas (since 1985). One- to 5-year actuarial survival rates of these patients were 70%, 65%, 62%, 61%, and 61%, respectively, as of July 31, 1986. With these good survival rates, liver transplantation has been accepted as a therapeutic modality for end-stage liver disease, and >50 medical centers worldwide have started liver transplantation in the last few years. This report summarizes the long-term mortality and morbidity after liver transplantation to provide some useful guides in managing liver recipients after the first posttransplant year.
Chemical Modifications of Histidyl and Tyrosyl Residues of Inorganic Pyrophosphatase from Escherichia coli (1988)

Chemical modifications by photooxidation in the presence of rose bengal (RB) and with tetranitromethane (TNM) were carried out to elucidate the amino acid residues involved in the active site of inorganic pyrophosphatase (pyrophosphate phosphohydrolase) [EC 3.6.1.1] from Escherichia coli Q13. The photooxidation caused almost complete inactivation, which followed pseudo-first-order kinetics depending on pH and concentration of RB. The presence of Mg2+ or complex between Mg2+ and substrate or substrate analogues, imidodiphosphate and sodium methylenediphosphate, gave partial protection against the photoinactivation, whereas the substrate alone showed no protective effect. The enzyme was almost completely inactivated by chemical modification with TNM, depending upon the concentration of TNM. The amino acid analyses and enzyme activity measurements revealed that 2 histidyl residues among 5 photooxidized residues and 2 tyrosyl residues per subunit were essential for the enzyme activity. The circular dichroism (CD) spectra in the far ultraviolet region showed no significant alteration during these two modifications, indicating that the polypeptide chain backbone of the enzyme remained unaltered. However, the modifications altered considerably the CD bands in the near ultraviolet region and the fluorescence spectra, indicating that subtle change in conformation had occurred in the vicinity of the active site in the enzyme molecule. These results strongly suggest that histidyl and tyrosyl residues may be involved in the active site or be located in the vicinity of the active site and seem to participate in the mechanism of stability against heat inactivation.
Query processing for moving objects with space-time grid storage model (2003)

With the growing popularity of mobile computing devices and wireless communications, managing dynamically changing information about moving objects is becoming feasible. In this paper we implement a system that manages such information and propose an efficient range query algorithm with a filtering step which efficiently determines if a polyline corresponding to the trajectory of a moving object intersects with a given range. We study the performance of the system, which shows that despite the filtering step, for moderately large ranges, the range query algorithm we propose outperforms the algorithm without filtering.
A Highly Active and Tolerable Neoadjuvant Regimen Combining Paclitaxel, Carboplatin, 5-FU, and Radiation Therapy in Patients with Stage II and III Esophageal Cancer (2007)

This novel neoadjuvant chemoradiation regimen for treatment of patients with stage II-III esophageal cancer is feasible. Results are encouraging with a high pathologic complete tumor regression and R0 resection rate and an acceptable morbidity and mortality. Preliminary survival data are very promising.
Fast algorithm for restoration of foggy images (2013)

This paper describes a new fast method for foggy images restoration derived from the dark channel prior methodology. Based on a physical foggy image formation model, the parameters of the restoration algorithm are estimated from the saturation channel of a single colour image without any prior knowledge of the scene. The performance of the proposed method is evaluated on a set of real-world images and compared with other state-of-art fog removal and contrast enhancement methods. It is shown that the new method outperforms other tested techniques in terms of the execution speed and perceptual quality of the restored images.
Surface changes of corona-discharge-treated polyethylene films (2000)

Morphological and chemical changes of the surface of low-density polyethylene (LDPE), linear middle-density polyethylene (L-MDPE), and their 80/20 blend were studied by different techniques after corona-discharge treatment in air and subsequent annealing. The surface tension was determined by wetting; the roughness was measured by atomic force microscope (AFM), and the surface chemical composition was analyzed by X-ray photoelectron spectroscopy (XPS), whereas the low-molecular-mass fraction washed off by chloroform by FTIR. The surface tension of the films increases with the electrode current. The surface roughness depends primarily on the polymer type and is less affected by the corona treatment. At the initial stage of annealing, posttreatment-type oxidation and hydrophobic recovery are competing. The former is more pronounced in L-MDPE, the latter in LDPE. After annealing at 50°C for 160 days, hydrophobic recovery becomes predominant in each film studied, which is accompanied by significant smoothening of the surface. According to XPS and FTIR results, this is due to the migration of low-molecular-mass components (oligomers, oxidized polymer fractions, and additives) to the surface. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 76: 1529–1541, 2000
Metallobiology and therapeutic chelation of biometals (copper, zinc and iron) in Alzheimer’s disease: Limitations, and current and future perspectives (2021)

Several multidirectional and multifaceted studies on metal chelation therapeutics show the need for improved synthesis, screening, and analysis of compounds to be able to effectively present chelating anti-AD drugs. Most drug candidates studied have limitations in their physicochemical properties; some enhance redistribution of metal ions, while others indirectly activate signaling pathways in AD. The metal chelation process in vivo still needs to be established and the design of potential anti-AD compounds that bi-functionally sequester metal ions as well as inhibit the Aβ aggregation by competing with the metal ions and reducing metal-induced oxidative damage and neurotoxicity may signal a bright end in chelation-based therapeutics of AD.
Voraussetzungen und Installation (1989)

Es genügt leider nicht, einen PC und das PageMaker-Programm zu besitzen, um sich stolz unter die Desktop-Publisher zu zählen. Sie müssen zumindest Zugang zu einem Ausgabegerät haben, am besten zu einem Laserdrucker. Um die Texte zu erstellen, brauchen Sie auch ein Textverarbeitungsprogramm. Wenn Sie zudem noch Bilder oder Grafiken verarbeiten wollen, benötigen Sie auch dazu ein entsprechendes Programm, evtl. auch einen Scanner.
Ups and downs in alfalfa: Proteomic and metabolic changes occurring in the growing stem (2015)

The expanding interest for using lignocellulosic biomass in industry spurred the study of the mechanisms underlying plant cell-wall synthesis. Efforts using genetic approaches allowed the disentanglement of major steps governing stem fibre synthesis. Nonetheless, little is known about the relations between the stem maturation and the evolution of its proteome. During Medicago sativa L. maturation, the different internodes grow asynchronously allowing the discrimination of various developmental stages on a same stem. In this study, the proteome of three selected regions of the stem of alfalfa (apical, intermediate and basal) was analyzed and combined with a compositional analysis of the different stem parts. Interestingly, the apical and the median regions share many similarities: high abundance of chloroplast- and mitochondrial-related proteins together with the accumulation of proteins acting in the early steps of fibre production. In the mature basal region, forisomes and stress-related proteins accumulate. The RT-qPCR assessment of the expression of genes coding for members of the cellulose synthase family likewise indicates that fibres and the machinery responsible for the deposition of secondary cell walls are predominantly formed in the apical section. Altogether, this study reflects the metabolic change from the fibre production in the upper stem regions to the acquisition of defence-related functions in the fibrous basal part.
Crossreactivity to vinculin and microbes provides a molecular basis for HLA-based protection against rheumatoid arthritis (2015)

The HLA locus is the strongest risk factor for anti-citrullinated protein antibody (ACPA)(+) rheumatoid arthritis (RA). Despite considerable efforts in the last 35 years, this association is poorly understood. Here we identify (citrullinated) vinculin, present in the joints of ACPA(+) RA patients, as an autoantigen targeted by ACPA and CD4(+) T cells. These T cells recognize an epitope with the core sequence DERAA, which is also found in many microbes and in protective HLA-DRB1*13 molecules, presented by predisposing HLA-DQ molecules. Moreover, these T cells crossreact with vinculin-derived and microbial-derived DERAA epitopes. Intriguingly, DERAA-directed T cells are not detected in HLA-DRB1*13(+) donors, indicating that the DERAA epitope from HLA-DRB1*13 mediates (thymic) tolerance in these donors and explaining the protective effects associated with HLA-DRB1*13. Together our data indicate the involvement of pathogen-induced DERAA-directed T cells in the HLA-RA association and provide a molecular basis for the contribution of protective/predisposing HLA alleles.
Strain-induced band modulation of thermal phonons in carbon nanotubes (2021)

We show that carbon nanopeapods are an ideal artificial superlattice to induce band modulation of thermal phonons. Based on spectral energy density analysis, we found that a periodic deformation in carbon nanotubes induced by fullerene encapsulation leads to zone folding of phonon dispersions up to near the maximum frequency. The zone-folding effect gives rise to phonon band gaps caused either by Bragg reflection or mode hybridization, and this reduces group velocity. This was quantified to play the leading role in reduction of thermal conductivity by the fullerene encapsulation. The strain modulation of thermal phonon bands opens a possibility to control material thermal conductivity.
Multivoxel Pattern of Blood Oxygen Level Dependent Activity can be sensitive to stimulus specific fine scale responses (2020)

At ultra-high field, fMRI voxels can span the sub-millimeter range, allowing the recording of blood oxygenation level dependent (BOLD) responses at the level of fundamental units of neural computation, such as cortical columns and layers. This sub-millimeter resolution, however, is only nominal in nature as a number of factors limit the spatial acuity of functional voxels. Multivoxel Pattern Analysis (MVPA) may provide a means to detect information at finer spatial scales that may otherwise not be visible at the single voxel level due to limitations in sensitivity and specificity. Here, we evaluate the spatial scale of stimuli specific BOLD responses in multivoxel patterns exploited by linear Support Vector Machine, Linear Discriminant Analysis and Naïve Bayesian classifiers across cortical depths in V1. To this end, we artificially misaligned the testing relative to the training portion of the data in increasing spatial steps, then investigated the breakdown of the classifiers' performances. A one voxel shift led to a significant decrease in decoding accuracy (p < 0.05) across all cortical depths, indicating that stimulus specific responses in a multivoxel pattern of BOLD activity exploited by multivariate decoders can be as precise as the nominal resolution of single voxels (here 0.8 mm isotropic). Our results further indicate that large draining vessels, prominently residing in proximity of the pial surface, do not, in this case, hinder the ability of MVPA to exploit fine scale patterns of BOLD signals. We argue that tailored analytical approaches can help overcoming limitations in high-resolution fMRI and permit studying the mesoscale organization of the human brain with higher sensitivities.
Analysis of a Personalized Provision of Service Level Agreement (SLA) Algorithm (2023)

The existence of restricted Service Level Agreement (SLA) choices, which typically correspond with a couple of service tiers, can result in a customer accepting a service that may not effectively respond to their needs. From a service provider perspective, it is also a less than optimum business model, with capacity being reserved for customers who will not use it and subsequently being unavailable for customers who would. We, therefore, advocate the use of personalized SLAs to avoid such situations, which can ideally be set up without the assistance of a human operator. We suggest classifying customers according to their distinguishing features, one of which includes a customer’s propensity to have online devices in their home. Through the results presented in this paper, we are confident about the accuracy of our classification results; however, we recognize that there are opportunities for latency improvements in the efficiency of the process.
Nitric Oxide (NO) in normal and hypoxic vascular regulation of the spiny dogfish,Squalus acanthias (2005)

Nitric oxide (NO) is a potent vasodilator in terrestrial vertebrates, but whether vascular endothelial-derived NO plays a role in vascular regulation in fish remains controversial. To explore this issue, a study was made of spiny dogfish sharks (Squalus acanthias) in normoxia and acute hypoxia (60 min exposure to seawater equilibrated with 3% oxygen) with various agents known to alter NO metabolism or availability. In normoxia, nitroprusside (a NO donor) reduced blood pressure by 20%, establishing that vascular smooth muscle responds to NO. L-arginine, the substrate for NO synthase, had no hemodynamic effect. Acetylcholine, which stimulates endothelial NO and prostaglandin production in mammals, reduced blood pressure, but also caused marked bradycardia. L-NAME, an inhibitor of all NO synthases, caused a small 10% rise in blood pressure, but cell-free hemoglobin (a potent NO scavenger and hypertensive agent in mammals) had no effect. Acute hypoxia caused a 15% fall in blood pressure, which was blocked by L-NAME and cell-free hemoglobin. Serum nitrite, a marker of NO production, rose with hypoxia, but not with L-NAME. Results suggest that NO is not an endothelial-derived vasodilator in the normoxic elasmobranch. The hypertensive effect of L-NAME may represent inhibition of NO production in the CNS and nerves regulating blood pressure. In acute hypoxia, there is a rapid up-regulation of vascular NO production that appears to be responsible for hypoxic vasodilation.
Recombinant peptide fusion construction for protein‐templated catalytic palladium nanoparticles (2020)

Although peptide-enabled synthesis of nanostructures has garnered considerable interest for use in catalytic applications, it has so far been achieved mostly via Fmoc based solid phase peptide synthesis. Consequently, the potential of longer peptides in nanoparticle synthesis have not been explored largely due to the complexities and economic constraints of this chemical synthesis route. This study examines the potential of a 45-amino acid long peptide expressed as fusion to green fluorescence protein (GFPuv) in Escherichia coli for use in palladium nanoparticle synthesis. Fed-batch fermentation with E. coli harboring an arabinose-inducible plasmid produced a product containing three copies of Pd4 peptide fused to N-terminus of GFPuv ((Pd4)<sub>3</sub> -GFPuv). Using the intrinsic fluorescence of GFPuv, expression and enrichment of the fusion product was easily monitored. Crude lysate, desalted lysate, and an ion-exchange enriched fraction containing (Pd4)<sub>3</sub> -GFPuv were used to test the hypothesis that high purity of the biologic material used as the nanoparticle synthesis template may not be necessary. Nanoparticles were characterized using a variety of material science techniques and used to catalyze a model Suzuki-Miyaura coupling reaction. Results demonstrated that palladium nanoparticles can be synthesized using the soluble cell extract containing (Pd4)<sub>3</sub> -GFPuv without extensive purification or cleavage steps, and as a catalyst the crude mixture is functional.