gebhart/patrepeval huggingface dataset:
Thioamide Hydroxypyrothiones Supersede Amide Hydroxypyrothiones in Potency against Anthrax Lethal Factor (2009)

Anthrax lethal factor (LF) is a critical virulence factor in the pathogenesis of anthrax. A structure-activity relationship (SAR) of potential lethal factor inhibitors (LFi) is presented in which the zinc-binding group (ZBG), linker, and backbone moieties for a series of hydroxypyrone-based compounds were systematically varied. It was found that hydroxypyrothione ZBGs generate more potent inhibitors than hydroxypyrone ZBGs. Furthermore, coupling the hydroxypyrothione to a backbone group via a thioamide bond improves potency when compared to an amide linker. QM/MM studies show that the thioamide bond in these inhibitors allows for the formation of two additional hydrogen bonds with the protein active site. In both types of hydroxypyrothione compounds, ligand efficiencies of 0.29-0.54 kcal mol(-1) per heavy atom were achieved. The results highlight the need for a better understanding to optimize the interplay between the ZBG, linker, and backbone to get improved LFi.
Electrochemical reductive biomass conversion: direct conversion of 5-hydroxymethylfurfural (HMF) to 2,5-hexanedione (HD) via reductive ring-opening (2016)

Direct electrochemical conversion of 5-hydroxymethylfurfural (HMF) to 2,5-hexanedione (HD) was achieved using water as the hydrogen source at ambient conditions.
Assessment of cardiovascular function from multi-Gaussian fitting of a finger photoplethysmogram (2015)

Monitoring of cardiovascular function on a beat-to-beat basis is fundamental for protecting patients in different settings including emergency medicine and interventional cardiology, but still faces technical challenges and several limitations. In the present study, we propose a new method for the extraction of cardiovascular performance surrogates from analysis of the photoplethysmographic (PPG) signal alone.We propose using a multi-Gaussian (MG) model consisting of five Gaussian functions to decompose the PPG pulses into its main physiological components. From the analysis of these components, we aim to extract estimators of the left ventricular ejection time, blood pressure and vascular tone changes. Using a multi-derivative analysis of the components related with the systolic ejection, we investigate which are the characteristic points that best define the left ventricular ejection time (LVET). Six LVET estimates were compared with the echocardiographic LVET in a database comprising 68 healthy and cardiovascular diseased volunteers. The best LVET estimate achieved a low absolute error (15.41 ± 13.66 ms), and a high correlation (ρ = 0.78) with the echocardiographic reference.To assess the potential use of the temporal and morphological characteristics of the proposed MG model components as surrogates for blood pressure and vascular tone, six parameters have been investigated: the stiffness index (SI), the T1_d and T1_2 (defined as the time span between the MG model forward and reflected waves), the reflection index (RI), the R1_d and the R1_2 (defined as their amplitude ratio). Their association to reference values of blood pressure and total peripheral resistance was investigated in 43 volunteers exhibiting hemodynamic instability. A good correlation was found between the majority of the extracted and reference parameters, with an exception to R1_2 (amplitude ratio between the main forward wave and the first reflection wave), which correlated low with all the reference parameters. The highest correlation ([Formula: see text] = 0.45) was found between T1_2 and the total peripheral resistance index (TPRI); while in the patients that experienced syncope, the highest agreement ([Formula: see text] = 0.57) was found between SI and systolic blood pressure (SBP) and mean blood pressure (MBP).In conclusion, the presented method for the extraction of surrogates of cardiovascular performance might improve patient monitoring and warrants further investigation.
Bionanotechnology based on silica nanoparticles (2004)

We have developed uniform core/shell nanoparticles, consisting of a silica layer coating and pigments or magnetite core, using a water-in-oil microemulsion method. The nanoparticles are highly luminescent and photostable with the size ranging from 5 nm to 400 nm. Bioconjugation of these silica nanoparticles adds unique biofunctions with various molecules such as enzymes, antibodies, and DNA molecules. Significant advantages have been shown in using bioconjugated nanoparticles for biosensing and bioimaging, such as cell staining, DNA detection and separation, rapid single bacterium detection, and biotechnological application in DNA protection.
AlGaInP/GaP Light-Emitting Diodes Fabricated by Wafer Direct Bonding Technology (1996)

An AlGaInP/GaP light-emitting diode was fabricated by wafer direct bonding technique. The device was grown on GaAs substrate by metalorganic vapor phase epitaxy (MOVPE). After bonding the n-GaP substrate on top of the epitaxial layers, the original GaAs substrate was removed. The luminous intensity of this wafer-bonded device is around 60 mcd/S r at an operation current of 20 mA. It is about two times brighter than the conventional device with absorbing GaAs substrate. The large lattice constant mismatch (3.6%) between wafer-bonded GaP substrate and GaInP did not degrade the device characteristics.
Consequences of Total and Subtotal Myeloperoxidase Deficiency: Risk or Benefit ? (2000)

A group of 100 totally or subtotally myeloperoxidase (MPO)-deficient individuals was compared to a reference population of 118 probands selected at random. Data for a protective effect of the deficiency against cardiovascular damage are presented. On the other hand, a significantly higher occurrence of severe infections and chronic inflammatory processes was noted among the deficient patients. An increased incidence of cancer among the MPO-deficient individuals was not demonstrated.
Differences in Anti-Protein a Activity among IgG Subgroups (1969)

Abstract The reaction between staphylococcal protein A and human γG globulin, which is known to be mediated by structures on the Fc part of the heavy chains, was studied qualitatively using 68 isolated γG myeloma globulins. Twenty-one myeloma globulins of subgroups γG-1, γG-2 and γG-4 gave a precipitin reaction with protein A. The 35 remaining meyloma globulins of these subgroups all inhibited this reaction, indicating the presence of protein A-reactive sites. Twelve γG-3 myeloma globulins did not precipitate or inhibit the precipitation; two showed slight inhibition that could be attributed to background γG. It thus appears that anti-protein A reactivity is confined to γG-1, γG-2 and γG-4 molecules.
Site-restricted persistent cytomegalovirus infection after selective long-term depletion of CD4+ T lymphocytes. (1989)

We have established a murine model system for exploring the ability of a CD4 subset-deficient host to cope with cytomegalovirus infection, and reported three findings. First, an antiviral response of the CD8 subset of T lymphocytes could be not only initiated but also maintained for a long period of time despite a continued absence of the CD4 subset, whereas the production of antiviral antibody proved strictly dependent upon help provided by the CD4 subset. Second, no function in the defense against infection could be ascribed as yet to CD4-CD8- T lymphocytes, which were seen to accumulate to a new subset as a result of depletion of the CD4 subset. This newly arising subset did not substitute for CD4+ T lymphocytes in providing help to B lymphocytes, and was also not effective in controlling the spread of virus in host tissues. As long as a function of these cells in the generation and maintenance of a CD8 subset-mediated response is not disproved, caution is indicated with concern to an autonomy of the CD8 subset. Third, even though with delay, the CD8+ effector cells raised in the CD4 subset-deficient host were able of clear vital tissues from productive infection and to restrict asymptomatic, persistent infection to acinar glandular epithelial cells in salivary gland tissue.
Clindamycin-induced enterocolitis in hamsters as a model of pseudomembranous colitis in patients (1978)

Stools from a patient with antibiotic-associated colitis and cecal contents from a hamster with clindamycin-induced enterocolitis were compared in a cytotoxicity assay to determine common properties. Both specimens produced actinomorphic changes in human amnion cells at 10(-7) dilutions. The toxin was acid labile, heat labile, nonether extractable, non-dialyzable, and produced maximum activity at 60% with ammonium sulfate precipitation. Cytotoxicity was neutralized with clostridial antitoxin but not with equine serum. Clostridium difficile was recovered in high concentrations in specimens from both the hamster and patients. The supernatants of these C. difficile strains produced cytoxic effects which were also neutralized by clostridial antitoxins. These results indicate that clindamycin-induced enterocolitis in hamsters is a model of human disease and implicate toxin-producing clostridia as responsible agents.
Distinct roles for IP-10/C XC L10 in three animal models, Theiler’s virus infection, EA E, and MHV infection, for multiple sclerosis: implication of differing roles for IP-10 (2004)

Theiler's murine encephalomyelitis virus (TMEV) causes demyelination with inflammation of the central nervous system (CNS) in mice and is used as an animal model for multiple sclerosis (MS). Interferon-gamma inducible protein-10 kDa (IP-10) is a CXC chemokine and a chemoattractant for CXCR3+ T cells. IP-10 mRNA is expressed in the CNS during TMEV infection. However, administration of anti-IP-10 serum caused no difference in clinical signs, inflammation, demyelination, virus persistence or anti-virus antibody response in TMEV infection, while levels of virus specific and autoreactive lymphoproliferation increased. This likely reflects a difference in the pathogenesis of TMEV infection from that of two other animal models for MS, mouse hepatitis virus infection and experimental allergic encephalomyelitis (EAE), where blocking of IP-10 resulted in clinical and histological improvement with suppression of antigen specific lymphoproliferation. In this review, we compare and contrast the roles of IP-10 between the three animal models for MS, and discuss the relevance to MS patients with different clinical courses.
Phonon effects in molecular transistors: Quantal and classical treatment (2004)

We present a comprehensive theoretical treatment of the effect of electron-phonon interactions on molecular transistors, including both quantal and classical limits. We study both equilibrated and out of equilibrium phonons. We present detailed results for conductance, noise, and phonon distribution in two regimes. One involves temperatures large as compared to the rate of electronic transitions on and off the dot; in this limit our approach yields classical rate equations, which are solved numerically for a wide range of parameters. The other regime is that of low temperatures and weak electron-phonon coupling where a perturbative approximation in the Keldysh formulation can be applied. The interplay between the phonon-induced renormalization of the density of states on the quantum dot and the phonon-induced renormalization of the dot-lead coupling is found to be important. Whether or not the phonons are able to equilibrate in a time rapid compared to the transit time of an electron through the dot is found to affect the conductance. Observable signatures of phonon equilibration are presented. We also discuss the nature of the low-$T$ to high-$T$ crossover.
Some rheological aspects of fracture in thermoforming (1982)

Abstract This paper focuses on several aspects of drawability, including the interactions between material parameters, operating temperatures, and frictional properties of the material. The deep draw process for a molten plastic sheet can be described by a simplified model using the characteristics of the normal stress as a lumped parameter. A rapid evaluation of the draw ratio and mold closing speed can be obtained by systematically drawing a series of three draw ratios. The fracture mode should then be examined to determine the appropriateness of molding temperatures. Therefore the maximum attainable draw ratio can be calculated from the elongational viscosity data. To support the analysis, data is provided on the formation of a cup with polystyrene sheets and using Maxwell extensional model as an example.
Dermal mast cells in scleroderma: their skin density, tryptase/chymase phenotypes and degranulation (1998)

To determine the distribution, tryptase/chymase phenotypes and degranulation of mast cells (MCs) in the dermis of patients with scleroderma, we examined MC density in the skin of 22 patients with systemic sclerosis (SSc) and 11 with localized scleroderma (LSc). We used antitryptase and antichymase antibodies after Carnoy's fixation. Detailed reports of two representative patients with SSc and LSc are included. In the scleroedematous stage (grade 1) showing oedema in both papillary and reticular dermis with variable homogenization of collagen bundles in the reticular dermis, MC skin density was variable in each specimen although MC skin density, as a whole, was significantly increased as compared with normal skin (P < 0.05). In the sclerotic stage (grade 2) characterized by homogenization of collagen bundles in the entire dermis, MC skin density was significantly decreased as compared with normal skin (P < 0.005). LSc showed changes similar to those in SSc. The ratio of MCTC cells (both tryptase- and chymase-positive MC) to MCT cells (tryptase-positive but chymase-negative MC) was variable in SSc and LSc. MCT cells were exclusively dominant in three patients with SSc and two with LSc. In a patient with SSc (patient 1) showing remarkable perivascular and interstitial oedema in the upper dermis, MC skin density was increased in the oedematous portion and tryptase-positive granules were distributed in extracellular locations. In another patient with LSc (patient 2), tryptase positivity increased and chymase positivity decreased in both number and intensity as the skin sclerosis progressed. MCs must have variable interactions with the lesional skin in SSc and LSc. The present study suggests that MCs are involved in the development of interstitial oedema.
Mapping Stress-Induced Changes in Autoinducer AI-2 Production in Chemostat-Cultivated Escherichia coli K-12 (2001)

Numerous gram-negative bacteria employ a cell-to-cell signaling mechanism, termed quorum sensing, for controlling gene expression in response to population density. Recently, this phenomenon has been discovered in Escherichia coli, and while pathogenic E. coli utilize quorum sensing to regulate pathogenesis (i.e., expression of virulence genes), the role of quorum sensing in nonpathogenic E. coli is less clear, and in particular, there is no information regarding the role of quorum sensing during the overexpression of recombinant proteins. The production of autoinducer AI-2, a signaling molecule employed by E. coli for intercellular communication, was studied in E. coli W3110 chemostat cultures using a Vibrio harveyi AI-2 reporter assay (M. G. Surrette and B. L. Bassler, Proc. Natl. Acad. Sci. USA 95:7046-7050, 1998). Chemostat cultures enabled a study of AI-2 regulation through steady-state and transient responses to a variety of environmental stimuli. Results demonstrated that AI-2 levels increased with the steady-state culture growth rate. In addition, AI-2 increased following pulsed addition of glucose, Fe(III), NaCl, and dithiothreitol and decreased following aerobiosis, amino acid starvation, and isopropyl-beta-D-thiogalactopyranoside-induced expression of human interleukin-2 (hIL-2). In general, the AI-2 responses to several perturbations were indicative of a shift in metabolic activity or state of the cells induced by the individual stress. Because of our interest in the expression of heterologous proteins in E. coli, the transcription of four quorum-regulated genes and 20 stress genes was mapped during the transient response to induced expression of hIL-2. Significant regulatory overlap was revealed among several stress and starvation genes and known quorum-sensing genes.
Mobility modeling in wireless networks (2001)

The movement pattern of mobile users plays an important role in performance analysis of wireless computer and communication networks. In this paper, we first give an overview and classification of mobility models used for simulation-based studies. Then, we present an enhanced random mobility model, which makes the movement trace of mobile stations more realistic than common approaches for random mobility. Our movement concept is based on random processes for speed and direction control in which the new values are correlated to previous ones. Upon a speed change event, a new target speed is chosen, and an acceleration is set to achieve this target speed. The principles for direction changes are similar. Finally, we discuss strategies for the stations' border behavior (i.e., what happens when nodes move out of the simulation area) and show the effects of certain border behaviors and mobility models on the spatial user distribution.
Changes in chemical composition of burley tobacco during senescence and curing. 3. Tobacco-specific nitrosamines (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChanges in chemical composition of burley tobacco during senescence and curing. 3. Tobacco-specific nitrosaminesHarold R. Burton, George H. Childs Jr., Roger A. Andersen, and Pierce D. FlemingCite this: J. Agric. Food Chem. 1989, 37, 2, 426–430Publication Date (Print):March 1, 1989Publication History Published online1 May 2002Published inissue 1 March 1989https://pubs.acs.org/doi/10.1021/jf00086a034https://doi.org/10.1021/jf00086a034research-articleACS PublicationsRequest reuse permissionsArticle Views340Altmetric-Citations30LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The commensal microbiome is associated with anti–PD-1 efficacy in metastatic melanoma patients (2018)

Anti-PD-1-based immunotherapy has had a major impact on cancer treatment but has only benefited a subset of patients. Among the variables that could contribute to interpatient heterogeneity is differential composition of the patients' microbiome, which has been shown to affect antitumor immunity and immunotherapy efficacy in preclinical mouse models. We analyzed baseline stool samples from metastatic melanoma patients before immunotherapy treatment, through an integration of 16<i>S</i> ribosomal RNA gene sequencing, metagenomic shotgun sequencing, and quantitative polymerase chain reaction for selected bacteria. A significant association was observed between commensal microbial composition and clinical response. Bacterial species more abundant in responders included <i>Bifidobacterium longum</i>, <i>Collinsella aerofaciens</i>, and <i>Enterococcus faecium.</i> Reconstitution of germ-free mice with fecal material from responding patients could lead to improved tumor control, augmented T cell responses, and greater efficacy of anti-PD-L1 therapy. Our results suggest that the commensal microbiome may have a mechanistic impact on antitumor immunity in human cancer patients.
Type of Electrode Insertion and Hearing Preservation Outcomes (2011)

Objective Assess the levels of hearing preservation during cochlear implant surgery by comparing different electrode insertion techniques (standard cochleostomy, soft surgery, round window). Method Retrospective chart review looking at levels of hearing preservation after cochlear implantation in children and adults, using different electrode insertion techniques (N = 144 ears from 32 patients). Pre‐ and postoperative pure tone thresholds at 250, 500, and 1000 Hz frequencies were measured. Statistical analysis was performed using nonparametric method (Kruskal Wallis test). Results One hundred and four (72%) procedures were performed using standard cochleostomy, 25 (17 %) procedures were performed using soft surgery, and 15 (11 %) procedures were performed using round window insertion. Postoperative hearing thresholds were used as the main outcome measure. In all groups, residual hearing was preserved in different degrees (total: 30 %, moderate: 27 %, marginal: 37 %, none: 6 %). Statistically significant differences were encountered between the 3 groups. Soft surgery technique and round window insertion had better hearing preservation results compared to standard cochleostomy ( P &lt;. 008 and P &lt;. 009, respectively). No difference between round window and soft surgery techniques was encountered ( P =. 07). Conclusion Although cochlear implants are a revolutionary technology, they carry the risk of destroying residual hearing. Our study demonstrates that the use of soft surgery or round window techniques warrants better residual hearing when compared to standard cochleostomy.
Reversible multiple time scale molecular dynamics (1992)

The Trotter factorization of the Liouville propagator is used to generate new reversible molecular dynamics integrators. This strategy is applied to derive reversible reference system propagator algorithms (RESPA) that greatly accelerate simulations of systems with a separation of time scales or with long range forces. The new algorithms have all of the advantages of previous RESPA integrators but are reversible, and more stable than those methods. These methods are applied to a set of paradigmatic systems and are shown to be superior to earlier methods. It is shown how the new RESPA methods are related to predictor–corrector integrators. Finally, we show how these methods can be used to accelerate the integration of the equations of motion of systems with Nosé thermostats.
Cholinergic agonists and interleukin 1 regulate processing and secretion of the Alzheimer beta/A4 amyloid protein precursor. (1992)

Activation of protein kinase C by phorbol esters is known to accelerate the processing and secretion of the beta/A4 amyloid protein precursor. We have now examined various first messengers that increase protein kinase C activity of target cells for their ability to affect beta/A4 amyloid protein precursor metabolism. Acetylcholine and interleukin 1, which are altered in Alzheimer disease, were shown to increase processing of the beta/A4 amyloid protein precursor via the secretory cleavage pathway. Cholinergic agonists stimulated secretion in human glioma and neuroblastoma cells as well as in PC12 cells transfected with the M1 receptor, while interleukin 1 stimulated secretion in human endothelial and glioma cells.