gebhart/patrepeval huggingface dataset:
A new rapid resazurin-based microdilution assay for antimicrobial susceptibility testing of Neisseria gonorrhoeae (2017)

Objectives: Rapid, cost-effective and objective methods for antimicrobial susceptibility testing of Neisseria gonorrhoeae would greatly enhance surveillance of antimicrobial resistance. Etest, disc diffusion and agar dilution methods are subjective, mostly laborious for large-scale testing and take ∼24 h. We aimed to develop a rapid broth microdilution assay using resazurin (blue), which is converted into resorufin (pink fluorescence) in the presence of viable bacteria. Methods: The resazurin-based broth microdilution assay was established using 132 N. gonorrhoeae strains and the antimicrobials ceftriaxone, cefixime, azithromycin, spectinomycin, ciprofloxacin, tetracycline and penicillin. A regression model was used to estimate the MICs. Assay results were obtained in ∼7.5 h. Results: The EC50 of the dose–response curves correlated well with Etest MIC values (Pearson’s r = 0.93). Minor errors resulting from misclassifications of intermediate strains were found for 9% of the samples. Major errors (susceptible strains misclassified as resistant) occurred for ceftriaxone (4.6%), cefixime (3.3%), azithromycin (0.6%) and tetracycline (0.2%). Only one very major error was found (a ceftriaxone-resistant strain misclassified as susceptible). Overall the sensitivity of the assay was 97.1% (95% CI 95.2–98.4) and the specificity 78.5% (95% CI 74.5–82.9). Conclusions: A rapid, objective, high-throughput, quantitative and cost-effective broth microdilution assay was established for gonococci. For use in routine diagnostics without confirmatory testing, the specificity might remain suboptimal for ceftriaxone and cefixime. However, the assay is an effective low-cost method to evaluate novel antimicrobials and for high-throughput screening, and expands the currently available methodologies for surveillance of antimicrobial resistance in gonococci.
Shigellosis: Innate Mechanisms of Inflammatory Destruction of the Intestinal Epithelium, Adaptive Immune Response, and Vaccine Development (2003)

Acute infectious colitis remains a major pediatric issue of worldwide impact because it still represents a significant public health burden among the larger group of diarrheal diseases with the highest mortality rate. It is also a relevant model of inflammatory bowel diseases (IBD), such as Crohn's disease and ulcerative colitis. Among cases of acute colitis of infectious origin, shigellosis is certainly the one that has benefited the most from a significant research effort. Shigella, the causative agent, is a Gram-negative bacterium that has the capacity to invade, disrupt, and cause inflammatory destruction of the intestinal epithelial barrier. The molecular and cellular bases of this invasive phenotype essentially encompass crossing of the epithelial lining, apoptotic killing of macrophages, entry into epithelial cells, and escape into the cytoplasm, followed by cell-to-cell spread. Intracellular colonization is likely to protect the micro-organisms from killing by humoral and cellular effectors of the innate immune response. Concurrently, the capacity of Shigella to reprogram invaded epithelial cells to produce proinflammatory mediators plays a major role in the strong inflammatory profile of the disease. This profile is likely to impact on the nature and quality of the adaptive response, which is dominated by humoral protection at the mucosal level.
Capturing Single Molecules of Immunoglobulin and Ricin with an Aptamer-Encoded Glass Nanopore (2009)

Nanopore-based single-molecule biosensors have been extensively studied. Protein pores that have receptors attached to them are target-selective, but their real-time applications are limited by the fragility of the lipid membrane into which the protein pores are embedded. Synthetic nanopores are more stable and provide flexible pore sizes, but the selectivity is low when detecting in the translocation mode. In spite of modifications with probing molecules, such as antibodies, to potentiate specific targeting, these nanopores fail to bind individual target molecules. Distinguishing between binding and translocation blocks remains unsolved. Here, we propose an aptamer-encoded nanopore that overcomes these challenges. Aptamers are well-known probing oligonucleotides that have high sensitivity and selectivity. In contrast to antibodies, aptamers are much smaller than their targets, rendering target blockades in the nanopore much more distinguishable. We used aptamer-encoded nanopores to detect single molecules of immunoglobulin E and the bioterrorist agent ricin, sequentially captured by the immobilized aptamer in the sensing zone of the pore. The functional nanopore also probed sequence-dependent aptamer-protein interactions. These findings will facilitate the development of a universal nanopore for multitarget detection.
Understanding the Decline in Foreign Investor Sentiment towards Vietnam during the 1990s (2001)

(2001). Understanding the Decline in Foreign Investor Sentiment towards Vietnam during the 1990s. Asia Pacific Business Review: Vol. 8, No. 1, pp. 1-18.
A biomechanical comparison of different surgical techniques of graft fixation in anterior cruciate ligament reconstruction (1987)

Different surgical methods of graft fixation in ACL reconstruction were examined to determine the effects on mechanical properties of the reconstructed ACL. Ten human cadavers were used in this study. Six different types of grafts were studied. The tendon grafts were removed from each cadaver and fixed to femurs and tibias as ACL substitutes with different surgical fixation methods, leaving femur-reconstructed graft-tibia preparations. The surgical techniques used were staple fixation, tying sutures over buttons, and screw fixation. In the latter, the screws were introduced through femoral and tibial drill holes from the outside in order to achieve interference fit as described by Lambert. Tensile testing demonstrated that the original ACL is significantly stronger than the graft used for reconstruction in linear load, stiffness, and maximum tensile strength. All of the failures of the reconstructed ACL grafts occurred at the fixation site, indicating that the mechanically weak link of the reconstructed graft is located at the fixation site. Among the different methods of fixation, one-third of the patellar tendon secured with a cancellous screw, especially with a custom designed large diameter screw, showed significantly higher values. Although many other factors affect the success of ACL reconstruction, our study indicates that the method of surgical fixation is the major factor influencing the graft's mechanical properties in the immediate postoperative period.
Preliminary Studies of the Use of an Automated Flow‐Cell Electrodeposition System for the Formation of CdTe Thin Films by Electrochemical Atomic Layer Epitaxy (1995)

This paper is the first report of the formation of thin films, thicker than ten monolayers, using electrochemical atomic layer epitaxy (ECALE). Thin films of have been electrodeposited on polycrystalline gold substrates in an electrochemical thin‐layer flow‐cell deposition system using the ECALE methodology. Studies of the deposit morphology have been performed using scanning electron microscopy and atomic force microscope. Significant improvements in deposit morphology are reported as a result of changes to the ECALE cycle program and deposition hardware. Deposit compositions analyzed using electron probe microanalysis and inductively coupled plasma atomic emission spectrometry, were found to be stoichiometric and nearly independent of the number of cycles and the Cd deposition potential. In addition, the deposition rate was shown to be one monolayer per cycle (half monolayer of Cd and half monolayer of Te per ECALE cycle).
Interferon Alfa-2b Alone or in Combination with Ribavirin for the Treatment of Relapse of Chronic Hepatitis C (1998)

In patients with chronic hepatitis C who relapse after treatment with interferon, therapy with interferon and oral ribavirin results in higher rates of sustained virologic, biochemical, and histologic response than treatment with interferon alone.
Exploiting light chains for the scalable generation and platform purification of native human bispecific IgG (2015)

Bispecific antibodies enable unique therapeutic approaches but it remains a challenge to produce them at the industrial scale, and the modifications introduced to achieve bispecificity often have an impact on stability and risk of immunogenicity. Here we describe a fully human bispecific IgG devoid of any modification, which can be produced at the industrial scale, using a platform process. This format, referred to as a κλ-body, is assembled by co-expressing one heavy chain and two different light chains, one κ and one λ. Using ten different targets, we demonstrate that light chains can play a dominant role in mediating specificity and high affinity. The κλ-bodies support multiple modes of action, and their stability and pharmacokinetic properties are indistinguishable from therapeutic antibodies. Thus, the κλ-body represents a unique, fully human format that exploits light-chain variable domains for antigen binding and light-chain constant domains for robust downstream processing, to realize the potential of bispecific antibodies.
Interruption of vascular thrombus formation and vascular lesion formation by dietary n-3 fatty acids in fish oil in nonhuman primates. (1993)

In nonhuman primates, dietary n-3FAs in high doses eliminate both vascular thrombus formation and vascular lesion formation after mechanical vascular injury while largely sparing hemostatic function and modestly reducing blood thrombotic responses. These effects are attributed to selective n-3FA-dependent alterations in cellular membrane functions.
Lamellar Gratings as Polarization Components for Specularly Reflected Beams (1993)

Abstract High spatial frequency lamellar gratings are shown to function as phase compensators, quarter-wave and half-wave retarders, and polarization rotators that operate on specularly reflected (zeroth-order) beams. These gratings are designed using rigorous coupled-wave and modal grating diffraction theories. Controlling the geometrical parameters of these gratings allows for engineering the phase retardation and polarization conversion introduced to a reflected beam. Fabrication and operational tolerances for these elements are discussed. Wavelength and polar angle of incidence variation affect the performance of these elements more strongly than variations in other geometrical and operational parameters.
Self-referenced measurement of the complete electric field of ultrashort pulses (2004)

A self-referenced technique based on digital holography and frequency-resolved optical gating is proposed in order to characterize the complete complex electric field E (x, y, z, t) of a train of ultrashort laser pulses. We apply this technique to pulses generated by a mode-locked Ti:Sapphire oscillator and demonstrate that our device reveals and measures common linear spatio-temporal couplings such as spatial chirp and pulse-front tilt.
Chickenpox monoarthritis: demonstration of varicella-zoster virus in joint fluid by polymerase chain reaction (1998)

A case of chickenpox monoarthritis is described. The presence of varicella zoster virus (VZV) within the joint was demonstrated by the detection of viral DNA in synovial fluid at a time when peripheral blood cells were negative. This strongly suggests a direct role of VZV in causing monoarthritis complicating chickenpox. The use of the polymerase chain reaction allows more rapid (2 days) confirmation of the diagnosis. Early enough diagnosis would raise the question of using acyclovir to shorten the duration of arthritis.
STAT3 and suppressor of cytokine signaling 3: potential targets in lung inflammatory responses (2007)

The expanding knowledge involving the cytokine transcription factor network has provided new insights into the acute lung inflammatory response. There are numerous lung inflammatory diseases that at present lack effective treatment (adult respiratory distress syndrome, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, asthma and so on). Although cytokines themselves and their receptors comprise a communication system that is crucial to detect the presence of pathogens and the injured lung, the cytokine signals and the milieu that surrounds these signals can clearly determine the nature of the lung responses that are elicited. Functioning as a transcription factor, STAT3 participates in the signaling pathways for many cytokines in various cells and organs that are regulated by the suppressor of cytokine signaling (SOCS) family, including SOCS3. Recently, data on the activation and function of STAT3 and SOCS3 in the lung during the acute inflammatory response are emerging, suggesting that these molecules can be potential targets for regulating pulmonary inflammatory responses. The authors review the progress in understanding how STAT3 and SOCS3 regulate the lung inflammatory response.
Quantum dot cascade laser (2014)

42.55.Px; 78.55.Cr; 78.67.Hc.
Role of donor–acceptor macrocycles in sequence specific peptide recognition and their optoelectronic properties: a detailed computational insight (2016)

In this study, we have considered an experimentally synthesized organic donor-acceptor (D-A) macrocycle (CPP-TCAQ) and have modified it by incorporating different acceptor groups. We have performed density functional theory and classical molecular dynamics studies on these D-A macrocycles. We have clearly shown that cyclo[10]paraphenylene-2,6-tetracyanoanthraquinodimethanylene (CPP-TCAQ) isomers interact specifically with one particular peptide sequence tyr-leu-ala, over its structural isomer, tyr-ala-leu. However, other functionalized macrocycles bind to the tyr-ala-leu peptide sequence over tyr-leu-ala. Our calculations show that the presence of hydrogen bonds as well as π-π interactions responsible for this specific selection. Interestingly, it is the additional charge transfer induced dipolar interactions that favour binding of the tripeptide with the bulky C-terminal leucine amino acid, tyr-ala-leu. We confirmed that these host-guest complexes are stable in water medium as well as at room temperature. Thus, these hosts can bind effectively to any protein fragment bearing a particular tripeptide. Interestingly, the macrocycle, which recognizes the peptide sequence with a bulky C-terminal amino acid, also shows photophysical properties. The reasons for this happen to be the same (dipolar interactions introduce dipole allowed states for optical absorption as well as attracting the oppositely oriented dipolar groups). Recognition of the peptide sequence with a bulky C-terminal group is carried out for the first time with this functionalised macrocycle, which in addition shows photophysical properties.
Improved vaccine protection against retrovirus infection after co-administration of adenoviral vectors encoding viral antigens and type I interferon subtypes (2011)

Our results indicate that certain IFNα subtypes have the potential to improve the protective effect of adenovirus-based vaccines against retroviruses. This correlated with augmented virus-specific CD4(+) T cell and antibody responses. Thus, co-expression of select type I IFNs may be a valuable tool for the development of anti-retroviral vaccines.
Therapeutic Potential of in vitro Expansion of Foxp3+ Tregs Utilizing GM-CSF-treated Bone Marrow Dentritic Cell Precusors in Experimental Myathenia Gravis (143.6) (2010)

Abstract We have previously shown that regulatory T cells (Tregs) generated in vivo by the selective activation of particular subsets of dendritic cells (DCs) in response to low-dose granulocyte-macrophage colony-stimulating factor (GM-CSF) have the capacity to prevent and reverse experiemental autoimmune myasthenia gravis (EAMG). To further understand the underlying mechanisms of GM-CSF-induced Treg mobilization, we studied the effects of GM-CSF on T cell/DC co-cultures using matured splenic DCs as well bone marrow (BM) - derived DC precursors in vitro. Compared to splenic DCs, bone marrow-derived DC precursors, when cultured in the presence of GM-CSF, gave rise to a population of CD11c+CD11bhighCD8α- DCs (BMDCs) which were able to expand Foxp3+ regulatory T cells (Tregs) in the absence of TCR stimulation. Additionally, the BMDCs secreted high levels of TGF-β which was required for adaptive differentiation of naive T cells to Foxp3+ Tregs upon TCR stimulation. Adoptive transfer of expanded Tregs effectively suppressed ongoing EAMG. These results strongly indicate that BMDCs differentiated in the presence of GM-CSF can expand natural Tregs and induce adaptive Tregs through different mechanisms. Expansion of polyclonal and antigen-specific Tregs in vitro using this strategy may represent an effective treatment for restoring immune tolerance and ameliorating EAMG.
Smart Growth, State Policy and Public Process in Maine: The Dunstan Crossing Experience (2004)

Sprawling development in Maine’s growth areas continues in spite of the state’s emphasis on comprehensive planning over the past 20 years. In this article, the authors present some lessons to be learned from Scarborough’s Dunstan Crossing project, a planned development which would have incorporated many of the goals of the national “smart growth” movement. The project was approved by the elected town council (one of whom is co-author Sylvia Most), and it was in compliance with Scarborough’s town comprehensive plan. Nonetheless, the project for now has effectively been blocked after a lengthy period, described here, that saw a citizen referendum, lawsuits, mediation, and many kinds of public participation. Based on the Dunstan Crossing experience, the authors make recommendations regarding the state’s Growth Management Act, about more effective regional planning, and more generally about how to structure public participation in potentially contentious projects.
Chemoenzymatic Synthesis of a Library of Human Milk Oligosaccharides (2016)

Human milk oligosaccharides (HMOs) are a family of diverse unconjugated glycans that exist in human milk as one of the major components. Characterization, quantification, and biofunctional studies of HMOs remain a great challenge due to their diversity and complexity. The accessibility of a homogeneous HMO library is essential to solve these issues which have beset academia for several decades. In this study, an efficient chemoenzymatic strategy, namely core synthesis/enzymatic extension (CSEE), for rapid production of diverse HMOs was reported. On the basis of 3 versatile building blocks, 3 core structures were chemically synthesized via consistent use of oligosaccharyl thioether and oligosaccharyl bromide as glycosylation donors in a convergent fragment coupling strategy. Each of these core structures was then extended to up to 11 HMOs by 4 robust glycosyltransferases. A library of 31 HMOs were chemoenzymatically synthesized and characterized by MS and NMR. CSEE indeed provides a practical approach to harvest structurally defined HMOs for various applications.
Methylation of histone H3 Lys 4 in coding regions of active genes (2002)

Posttranslational modifications of histone tails regulate chromatin structure and transcription. Here we present global analyses of histone acetylation and histone H3 Lys 4 methylation patterns in yeast. We observe a significant correlation between acetylation of histones H3 and H4 in promoter regions and transcriptional activity. In contrast, we find that dimethylation of histone H3 Lys 4 in coding regions correlates with transcriptional activity. The histone methyltransferase Set1 is required to maintain expression of these active, promoter-acetylated, and coding region-methylated genes. Global comparisons reveal that genomic regions deacetylated by the yeast enzymes Rpd3 and Hda1 overlap extensively with Lys 4 hypo- but not hypermethylated regions. In the context of recent studies showing that Lys 4 methylation precludes histone deacetylase recruitment, we conclude that Set1 facilitates transcription, in part, by protecting active coding regions from deacetylation.
Einleitung (1998)

Im Leasingvertrag verpflichtet sich der Leasinggeber, dem Leasingnehmer Leasingobjekte während einer bestimmten Vertragsdauer gegen Zahlung des vereinbarten Entgelts zur Nutzung zu überlassen.
Bioconversion of Sugarcane Biomass into Ethanol: An Overview about Composition, Pretreatment Methods, Detoxification of Hydrolysates, Enzymatic Saccharification, and Ethanol Fermentation (2012)

Depleted supplies of fossil fuel, regular price hikes of gasoline, and environmental damage have necessitated the search for economic and eco-benign alternative of gasoline. Ethanol is produced from food/feed-based substrates (grains, sugars, and molasses), and its application as an energy source does not seem fit for long term due to the increasing fuel, food, feed, and other needs. These concerns have enforced to explore the alternative means of cost competitive and sustainable supply of biofuel. Sugarcane residues, sugarcane bagasse (SB), and straw (SS) could be the ideal feedstock for the second-generation (2G) ethanol production. These raw materials are rich in carbohydrates and renewable and do not compete with food/feed demands. However, the efficient bioconversion of SB/SS (efficient pretreatment technology, depolymerization of cellulose, and fermentation of released sugars) remains challenging to commercialize the cellulosic ethanol. Among the technological challenges, robust pretreatment and development of efficient bioconversion process (implicating suitable ethanol producing strains converting pentose and hexose sugars) have a key role to play. This paper aims to review the compositional profile of SB and SS, pretreatment methods of cane biomass, detoxification methods for the purification of hydrolysates, enzymatic hydrolysis, and the fermentation of released sugars for ethanol production.
An unavailability analysis of firewall sandwich configurations (2002)

Firewalls form the first line of defense in securing internal networks from the Internet. A Firewall only provides security if all traffic into and out of an internal network passes through the firewall. However, a single firewall through which all network traffic must flow represents a single point of failure. If the firewall is down, all access is lost. A common solution to this problem is to use firewall sandwiches, comprising multiple firewall processors running in parallel. A firewall sandwich system needs load-balancing processes executing on separate processors to manage the flow of packets through the firewall processors. The number of redundant load balancing processors and their redundancy management policies have a major impact on system unavailability. We present a model to analyze the steady-state unavailability of firewall sandwiches and compare the unavailability of various load-balancing configurations. The results show that, using representative non-proprietary values for system parameters, redundancy management policies are at least as important as the number of redundant processing nodes.