gebhart/patrepeval huggingface dataset:
In Vivo Postantibiotic Effect in a Thigh Infection in Neutropenic Mice (1988)

The postantibiotic effect (PAE) is the suppression of bacterial growth that persists after limited exposure of organisms to antimicrobial agents. We demonstrated and standardized the in vivo PAE in a thigh infection model in neutropenic mice. Inhibitors of protein and nucleic acid synthesis induced PAEs of 1.4-7.5 h against aerobic gram-negative bacilli, whereas beta-lactam antibiotics did not induce significant PAEs. Against aerobic gram-positive cocci, cell wall-active agents and inhibitors of protein and nucleic acid synthesis induced PAEs of 1.2-7.1 h, except for penicillins, which did not induce PAEs against streptococci. With few exceptions the in vivo PAE correlated well with the PAE reported in prior in vitro studies. Residual drug in thigh tissue did not cause the PAE. Theoretically, the presence of a PAE may allow antimicrobial agents to be given more intermittently without organism regrowth after drug levels fall below the minimal inhibitory concentration.
Fabrication of high quality, deep-submicron Nb/AlO/sub x//Nb Josephson junctions using chemical mechanical polishing (1995)

A reliable process based on Chemical Mechanical Polishing (CMP) has been developed for the fabrication of high quality, deep-submicron Nb/AlO/sub x//Nb Josephson junctions on 2 inch wafers. The Nb counter electrode is defined using low pressure SF/sub 6/ reactive ion etching (RIE) with a mask of SiO, which is thermally evaporated through a bilayer resist stencil patterned by electron beam lithography. After RIE, the entire wafer is coated with SiO, which is then planarized using CMP (which also removes the etch mask) to expose the counter electrode. This technique has produced high quality (V/sub m//spl sime/60 mV for J/sub c/ of 2 kA/cm/sup 2/) junctions with areas as small as 0.003 /spl mu/m/sup 2/ demonstrating that the process does not degrade the junction quality. Junctions with critical currents of 22 /spl mu/A and areas of 0.006 /spl mu/m/sup 2/ have been fabricated from trilayers with J/sub c/>300 kA/cm/sup 2/.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supramolecular Hydrogel Formation Based on Tannic Acid (2017)

The development of facile and versatile strategies with low-cost for hydrogel construction is of tremendous scientific interest. Herein, we demonstrate that naturally derived, cost-effective tannic acid (TA) can be an efficient gelation binder for the hydrogel formation with a series of commercially available water-soluble polymers. With a five-polyphenol-arm structure, TA molecules are able to grasp polymer chains through either hydrogen or ionic bonds and cross-link them together by coordinate bonds in the presence of Fe(III) ions. These two interactions can be elegantly balanced by tuning the weight ratios of polymer/TA and TA/Fe3+, which is the key point for the construction of supramolecular hydrogels. The supramolecular hydrogels exhibit multiple functionalities including mechanical tenability, rapid self-healing, pH-stimuli responsiveness, and free radical scavenging abilities. TA as a dynamic and versatile catechol group modifier provides a simple path to the construction of multifunctional hydrogels, which shows obvious advantages such as easy and green processing, low cost, and large-scale preparation.
Immunological and Antitumor Effects of IL-23 as a Cancer Vaccine Adjuvant (2006)

The promising, but modest, clinical results of many human cancer vaccines indicate a need for vaccine adjuvants that can increase both the quantity and the quality of vaccine-induced, tumor-specific T cells. In this study we tested the immunological and antitumor effects of the proinflammatory cytokine, IL-23, in gp100 peptide vaccine therapy of established murine melanoma. Neither systemic nor local IL-23 alone had any impact on tumor growth or tumor-specific T cell numbers. Upon specific vaccination, however, systemic IL-23 greatly increased the relative and absolute numbers of vaccine-induced CD8(+) T cells and enhanced their effector function at the tumor site. Although IL-23 specifically increased IFN-gamma production by tumor-specific T cells, IFN-gamma itself was not a primary mediator of the vaccine adjuvant effect. The IL-23-induced antitumor effect and accompanying reversible weight loss were both partially mediated by TNF-alpha. In contrast, local expression of IL-23 at the tumor site maintained antitumor activity in the absence of weight loss. Under these conditions, it was also clear that enhanced effector function of vaccine-induced CD8(+) T cells, rather than increased T cell number, is a primary mechanism underlying the antitumor effect of IL-23. Collectively, these results suggest that IL-23 is a potent vaccine adjuvant for the induction of therapeutic, tumor-specific CD8(+) T cell responses.
Interpreting the biological relevance of bioinformatic analyses with T-DNA sequence for protein allergenicity (2012)

Global regulatory agencies require bioinformatic sequence analysis as part of their safety evaluation for transgenic crops. Analysis typically focuses on encoded proteins and adjacent endogenous flanking sequences. Recently, regulatory expectations have expanded to include all reading frames of the inserted DNA. The intent is to provide biologically relevant results that can be used in the overall assessment of safety. This paper evaluates the relevance of assessing the allergenic potential of all DNA reading frames found in common food genes using methods considered for the analysis of T-DNA sequences used in transgenic crops. FASTA and BLASTX algorithms were used to compare genes from maize, rice, soybean, cucumber, melon, watermelon, and tomato using international regulatory guidance. Results show that BLASTX for maize yielded 7254 alignments that exceeded allergen similarity thresholds and 210,772 alignments that matched eight or more consecutive amino acids with an allergen; other crops produced similar results. This analysis suggests that each nontransgenic crop has a much greater potential for allergenic risk than what has been observed clinically. We demonstrate that a meaningful safety assessment is unlikely to be provided by using methods with inherently high frequencies of false positive alignments when broadly applied to all reading frames of DNA sequence.
Preventing and treating medication overuse headache (2017)

Medication overuse headache is a secondary headache-a worsening of a pre-existing headache (usually a primary headache) owing to overuse of one or more attack-aborting or pain-relieving medications.
Exacerbating factors of itch in atopic dermatitis (2016)

Atopic dermatitis (AD) displays different clinical symptoms, progress, and response to treatment during early infancy and after childhood. After the childhood period, itch appears first, followed by formation of well-circumscribed plaque or polymorphous dermatoses at the same site. When accompanied with dermatitis and dry skin, treatment of skin lesions should be prioritized. When itch appears first, disease history, such as causes and time of appearance of itch should be obtained by history taking. In many cases, itch increases in the evening when the sympathetic nerve activity decreased. Treatment is provided considering that hypersensitivity to various external stimulations can cause itch. Heat and sweating are thought to especially exacerbate itch. Factors causing itch, such as cytokines and chemical messengers, also induce itch mainly by stimulating the nerve. Scratching further aggravates dermatitis. Skin hypersensibility, where other non-itch senses, such as pain and heat, are felt as itch, sometimes occurs in AD. Abnormal elongation of the sensory nerve into the epidermis, as well as sensitizing of the peripheral/central nerve, are possible causes of hypersensitivity, leading to itch. To control itch induced by environmental factors such as heat, treatment for dermatitis is given priority. In the background of itch exacerbated by sweating, attention should be given to the negative impact of sweat on skin homeostasis due to 1) leaving excess sweat on the skin, and 2) heat retention due to insufficient sweating. Excess sweat on the skin should be properly wiped off, and dermatitis should be controlled so that appropriate amount of sweat can be produced. Not only stimulation from the skin surface, but also visual and auditory stimulation can induce new itch. This "contagious itch" can be notably observed in patients with AD. This article reviews and introduces causes of aggravation of itch and information regarding how to cope with such causes.
The role of SAP in murine CD150 (SLAM)-mediated T-cell proliferation and interferon γ production (2002)

CD150 (signaling lymphocyte activation molecule [SLAM]) is a self-ligand cell surface glycoprotein expressed on T cells, B cells, macrophages, and dendritic cells. To further explore the role of CD150 signaling in costimulation and T(H)1 priming we have generated a panel of rat antimouse CD150 monoclonal antibodies. CD150 cell surface expression is up-regulated with rapid kinetics in activated T cells and lipopolysaccharide/interferon gamma (IFN-gamma)-activated macrophages. Anti-CD150 triggering induces strong costimulation of T cells triggered through CD3. DNA synthesis of murine T cells induced by anti-CD150 is not dependent on SLAM-associated protein (SAP, SH2D1A), because anti-CD150 induces similar levels of DNA synthesis in SAP(-/-) T cells. Antibodies to CD150 also enhance IFN-gamma production both in wild-type and SAP(-/-) T cells during primary stimulation. The level of IFN-gamma production is higher in SAP(-/-) T cells than in wild-type T cells. Anti-CD150 antibodies also synergize with interleukin 12 (IL-12) treatment in up-regulation of IL-12 receptor beta(2) mRNA during T(H)1 priming, and inhibit primary T(H)2 polarization in an IFN-gamma-dependent fashion. Cross-linking CD150 on CD4 T cells induces rapid serine phosphorylation of Akt/PKB. We speculate that this is an important pathway contributing to CD150-mediated T-cell proliferation.
Physical and Chemical Analytical Analysis: A key component of Bioforensics (2005)

The anthrax letters event of 2001 has raised our awareness of the potential importance of non-biological measurements on samples of biological agents used in a terrorism incident. Such measurements include a variety of mass spectral, spectroscopic, and other instrumental techniques that are part of the current armamentarium of the modern materials analysis or analytical chemistry laboratory. They can provide morphological, trace element, isotopic, and other molecular ''fingerprints'' of the agent that may be key pieces of evidence, supplementing that obtained from genetic analysis or other biological properties. The generation and interpretation of such data represents a new domain of forensic science, closely aligned with other areas of ''microbial forensics''. This paper describes some major elements of the R&amp;D agenda that will define this sub-field in the immediate future and provide the foundations for a coherent national capability. Data from chemical and physical analysis of BW materials can be useful to an investigation of a bio-terror event in two ways. First, it can be used to compare evidence samples collected at different locations where such incidents have occurred (e.g. between the powders in the New York and Washington letters in the Amerithrax investigation) or between the attack samples and those seized during the investigation of sites where it is suspected the material was manufactured (if such samples exist). Matching of sample properties can help establish the relatedness of disparate incidents, and mis-matches might exclude certain scenarios, or signify a more complex etiology of the events under investigation. Chemical and morphological analysis for sample matching has a long history in forensics, and is likely to be acceptable in principle in court, assuming that match criteria are well defined and derived from known limits of precision of the measurement techniques in question. Thus, apart from certain operational issues (such as how to prioritize such measurements in the face of limited sample availability, or how to render samples safe for handling in the analytical laboratory,) instrumental analysis of biological agents for purposes of sample matching alone is unlikely to present fundamental problems that require extensive research and development investments. The second way that the data generated by instrumental analysis can be useful to an investigation is through inferences that can be drawn regarding the processes used to grow and ''weaponize'' the agent. In contrast to the case of sample matching, there are significant R&amp;D challenges associated with developing a robust capability that will reliably permit such inferential uses of instrumental data. Elaborating these challenges occupies the major portion of this paper.
miTarget: microRNA target gene prediction using a support vector machine (2006)

miTarget is a reliable miRNA target gene prediction tool and is a successful application of an SVM classifier. Compared with previous tools, its predictions are meaningful by GO analysis and its performance can be improved given more training examples.
Light-Directed, Spatially Addressable Parallel Chemical Synthesis (1991)

Solid-phase chemistry, photolabile protecting groups, and photolithography have been combined to achieve light-directed, spatially addressable parallel chemical synthesis to yield a highly diverse set of chemical products. Binary masking, one of many possible combinatorial synthesis strategies, yields 2n compounds in n chemical steps. An array of 1024 peptides was synthesized in ten steps, and its interaction with a monoclonal antibody was assayed by epifluorescence microscopy. High-density arrays formed by light-directed synthesis are potentially rich sources of chemical diversity for discovering new ligands that bind to biological receptors and for elucidating principles governing molecular interactions. The generality of this approach is illustrated by the light-directed synthesis of a dinucleotide. Spatially directed synthesis of complex compounds could also be used for microfabrication of devices.
Differentiation of Sinus Rhythms from Supraventricular Tachydysrhythmias by Activation Sequence and Timing (1990)

Implantable device detection of tachydysrhythmias remains unreliable and inexact. False responses may occur because of misinterpretation of sinus tachycardia (ST) as a supraventricular tachydysrhythmia (SVTD). Timing of atrioventricular (AV) activation and ventricular dispersion identified and discriminated between ST and SVTDs in 11 dogs. Three bipolar epicardial electrodes recorded left atrial and left and right ventricular depolarizations simultaneously during normal sinus rhythm (NSR) (mean of 5 beats in 11/11 dogs), ST produced by phlebotomy (50 beats in 10 episodes in 6/11) or isoproterenol infusion (105 beats in 21 episodes in 10/11), sinus bradycardia (SB) produced by vagal stimulation (140 beats in 29 episodes in 10/11), and during atrial flutter (AFL) (15 beats in 3 episodes in 3/11) and atrial fibrillation (AF) (152 beats in 31 episodes in 9/11) induced by programmed electrical stimulation. During lidocaine infusion, NSR (55 beats in 11 episodes in 10/11 dogs), SB (84 beats in 17 episodes in 7/11), AFL (10 beats in 2 episodes in 1/11), and AF (103 beats in 21 episodes in 7/11) were recorded. During isoproterenol infusion, SB (45 beats in 9 episodes in 5/11), AFL (15 beats in 3 episodes in 2/11), and AF (64 beats in 13 episodes in 5/11) were recorded in addition to ST. The interval between the left atrial and left ventricular intrinsic deflections (A-V1) and between the left and right ventricular intrinsic deflections (V1-V2) of each beat was measured. The mean value (msec) of A-V1 and V1-V2 in each episode was compared to NSR in the same dogs. A difference of greater than or equal to 16 ms was used for differentiation. In all cases except SB with first-degree AV block, V1-V2 in each episode was insignificant (0-14 msec), categorizing the rhythms as supraventricular. During NSR, ST and SB without AV block, delta A-V1 was small (0-15 msec). In contrast delta A-V1 was greater than or equal to 16 ms in 6/8 episodes of AFL. The remaining two episodes could be differentiated by the greater number of atrial versus ventricular beats. AF could be detected by the variability of A-V1.(ABSTRACT TRUNCATED AT 250 WORDS)
Cloning of the macrolide antibiotic biosynthesis gene acyA, which encodes 3-O-acyltransferase, from Streptomyces thermotolerans and its use for direct fermentative production of a hybrid macrolide antibiotic (1994)

A gene encoding the macrolide modification enzyme 3-O-acyltransferase (acyA) was cloned by chromosome walking onto the carbomycin biosynthetic region in Streptomyces thermotolerans TH475, with the 3' region of the gene encoding the macrolide modification enzyme 4"-O-acyltransferase (acyB1) as a probe. A shortened fragment (1.8 kb) containing acyA was subcloned with pIJ350. A high-level tylosin producer, Streptomyces fradiae MBBF, transformed with the plasmid could produce a hybrid macrolide, 3-O-acetyltylosin, most efficiently.
Electroabsorption modulated laser for long transmission spans (2002)

Strain-compensated AlGaInAs quantum-well electroabsorption modulated lasers (EMLs) transmit at 10 Gbits/s on uncompensated transmission spans of >75 km of standard fiber and >225 km of MetroCor fiber. Details of the design, fabrication, and testing are presented. A complex-coupled distributed feedback (DFB) grating is used to enable high output power. The epitaxy and chip structure are described. The paper studies what is needed to accomplish long-span transmission in terms of minimum physical requirements for laser mode control, facet reflection, index grating strength, laser-modulator matching, laser-modulator electrical isolation, modulator extinction ratio, modulator capacitance, linewidth enhancement factor, etc. The interaction of the modulator with the laser is analyzed and a requirement for this structure is computed for the electrical isolation resistance between modulator and laser contacts. Stability of the laser source is discussed and a method is derived for determining the grating's gain-coupling coefficient at operating power. Chirp due to the modulator is analyzed. Nonzero chirp of the modulator is shown to have beneficial impact on the quality of the signal after transmission. The effect of a bias-dependent alpha parameter is analyzed. Because bit-error rate is a strong function of mean alpha parameter and not a strong function of the range of alpha during nonreturn-to-zero modulation, we determine that tuning the chirp of the EML modulator to suit different fiber types (MetroCor, SMF-28, etc.) is practical. Specific tradeoffs are also required. Experimental results verify the analysis.
Critical Influence of the Fluorinated Chain Length in the Self-Assembly of Terminally Perfluorinated Alkanethiol Monolayers on Gold Surfaces. An Electrochemical Study (2001)

Self-assembled monolayers of semifluorinated n-alkanethiols having the general formula F(CF2)n(CH2)mSH (n = 4, 6, 8, 10 and m = 2, 11) have been formed from ethanolic solutions, with an incubation time of 96 h, on unannealed polycrystalline Au films vapor deposited on glass supports. Determination of the adlayer capacitances through cyclic voltammetry has been validated from its independence of the potential scan rate and its constancy when using two electrolytes, NaF and KCl, whose anions have different hydrated radii. The thickness of the monolayers has been estimated on the basis of capacitance values, and an indicative average tilt angle deduced. The monolayer's organization appears to largely depend on the n and m values. Short fluorinated chains (n = 4) are unable to self-organize in a position near the surface normal. This fact is independent of the length of the hydrogenated spacer (m = 2, 11), so it appears as an inherent characteristic for these short fluorinated chains. Fluorinated chains containing eight or ten carbon atoms are able to self-organize in a packing near the surface normal (average tilt angle 26°), independently of the length of the hydrogenated spacer length (m = 2, 11). Compounds with n = 6 and m = 2, 11 are in an intermediate situation.
α-Synuclein occurs in lipid-rich high molecular weight complexes, binds fatty acids, and shows homology to the fatty acid-binding proteins (2001)

alpha-Synuclein (alphaS) is a 140-residue neuronal protein that forms insoluble cytoplasmic aggregates in Parkinson's disease (PD) and several other neurodegenerative disorders. Two missense mutations (A53T and A30P) are linked to rare forms of familial PD. The normal function of alphaS is unknown, and cultured cell systems that model its modification from soluble monomers to aggregated forms have not been reported. Through a systematic centrifugal fractionation of mesencephalic neuronal cell lines and transgenic mouse brains expressing wild-type or A53T human alphaS, we observed unusual, previously unrecognized species of alphaS that migrate well above the 17-kDa monomeric form in denaturing gels. Incubation at 65 degrees C of high-speed cytosols from cells or brains revealed a modified alphaS species migrating at approximately 36 kDa and an extensive higher molecular mass alphaS-reactive smear. Extraction of the cytosols with chloroform/methanol or with a resin (Lipidex 1000) that binds fatty acids resulted in a similar pattern of higher molecular mass alphaS forms. On the basis of this effect of delipidation, we reexamined the primary structure of alphaS and detected a motif at the N and C termini that is homologous to a fatty acid-binding protein signature. In accord, we found that purified human alphaS binds oleic acid, with an apparent K(d) of 12.5 microM. We also observed an enhanced association of A53T alphaS with microsomal membranes in both mesencephalic cells and transgenic mouse brains. We conclude that alphaS has biochemical properties and a structural motif that suggest it is a novel member of the fatty acid-binding protein family and may thus transport fatty acids between the aqueous and membrane phospholipid compartments of the neuronal cytoplasm.
Rhodium(III)-Catalyzed Isoquinolone Synthesis: The N−O Bond as a Handle for C−N Bond Formation and Catalyst Turnover (2010)

An external-oxidant-free process to access the isoquinolone motif via cross-coupling/cyclization of benzhydroxamic acid with alkynes is described. The reaction features a regioselective cleavage of a C-H bond on the benzhydroxamic acid coupling partner as well as a regioselective alkyne insertion. Mechanistic studies point out the important involvement of a N-O bond as a tool for C-N bond formation and catalyst turnover.