gebhart/patrepeval huggingface dataset:
Droplet-based micro oscillating-flow PCR chip (2005)

Polymerase chain reactions (PCR), thermally activated chemical reactions which are widely used for nucleic acid amplification, have recently received much attention in microelectromechanical systems and micro total analysis systems because a wide variety of DNA/RNA molecules can be enriched by PCR for further analyses. In the present work, a droplet-based micro oscillating-flow PCR chip was designed and fabricated by the silicon microfabrication technique. Three different temperature zones, which were stable at denaturation, extension and annealing temperatures and isolated from each other by a thin-wall linkage, were integrated with a single, simple and straight microchannel to form the chip's basic functional structure. The PCR mixture was injected into the chip as a single droplet and flowed through the three temperature zones in the main microchannel in an oscillating manner to achieve the temperature maintenance and transitions. The chip's thermal performance was theoretically analyzed and numerically simulated. The results indicated that the time needed for the temperature of the droplet to change to the target value is less than 1 s, and the root mean square error of temperature is less than 0.2 °C. A droplet of 1 µl PCR mixture with standard HPV (Human Papilloma Virus)-DNA sample inside was amplified by the present chip and the results were analyzed by slab gel electrophoresis with separation of DNA markers in parallel. The electrophoresis results demonstrated that the micro oscillating-flow PCR chip successfully amplified the HPV-DNA, with a processing time of about 15 min which is significantly reduced compared to that for the conventional PCR instrument.
Dinuclear Zinc Complexes Using Pentadentate Phenolate Ligands (2008)

The synthesis and characterization of 15 dinuclear zinc complexes are reported, including the X-ray crystal structures of 5 complexes. The ligand motif utilizing p-cresol as a bridging unit between the two zinc centers and a set of three related ligands has been synthesized; 2,6-bis(R)-p-cresol (where R is CH(2)NMe(CH(2))(2)NMe(2) = L(1), CH=N(CH(2))(2)NMe(2) = L(2), and CH(2)NH(CH(2))(2)NMe(2) = L(3)). Dizinc trihalide complexes [L(n)Zn(2)(mu-X)X(2)] (where X = Cl, Br, I) have been prepared. The trihalide complexes were treated with potassium ethoxide, resulting in quantitative substitution of the bridging halide group to give [L(n)Zn(2)(mu-OEt)X(2)]. The dizinc ethoxide complexes were tested in situ as initiators for lactide ring opening polymerization. Dizinc triacetate complexes have also been synthesized [L(n)Zn(2)(OAc)(3)], as well as cationic diacetate species containing two bridging acetate groups, [L(n)Zn(2)(mu-OAc)(2)][BPh(4)]. Structural differences between complexes of the three ligands are discussed.
Synthesis, structure, and dynamic properties of the lanthanum(III) complex of 1,4,7,10-tetrakis(2-carbamoylethyl)-1,4,7,10-tetraazacyclododecane (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis, structure, and dynamic properties of the lanthanum(III) complex of 1,4,7,10-tetrakis(2-carbamoylethyl)-1,4,7,10-tetraazacyclododecaneJanet R. Morrow, Shahid Amin, Charles H. Lake, and Melvyn Rowen ChurchillCite this: Inorg. Chem. 1993, 32, 21, 4566–4572Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/ic00073a017https://doi.org/10.1021/ic00073a017research-articleACS PublicationsRequest reuse permissionsArticle Views404Altmetric-Citations60LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Mild Preparation of Haloarenes by Ipso-Substitution of Arylboronic Acids with N-Halosuccinimides (1998)

Aryl and heteroaryl boronic acids react with N-iodosuccinimide and N-bromosuccinimide to give the corresponding iodo- and bromo-arenes in good to excellent yields. The reaction is usually highly regioselective and yields only the ipso-substituted product. Esters of arylboronic acids react similarly, but less readily.
Peroxisomal multifunctional enzyme of β-oxidation metabolizing d-3-hydroxyacyl-CoA esters in rat liver: molecular cloning, expression and characterization (1997)

In the present study we have cloned and characterized a novel rat peroxisomal multifunctional enzyme (MFE) named perMFE-II. The purified 2-enoyl-CoA hydratase 2 with an M(r) of 31500 from rat liver [Malila, Siivari, Mäkelä, Jalonen, Latipää, Kunau and Hiltunen (1993) J. Biol. Chem. 268, 21578-21585] was subjected to tryptic fragmentation and the resulting peptides were isolated and sequenced. Surprisingly, the full-length cDNA, amplified by PCR, had an open reading frame of 2205 bp encoding a polypeptide with a predicted M(r) of 79,331 and contained a potential peroxisomal targeting signal in the C-terminus (Ala-Lys-Leu). The sequenced peptide fragments of hydratase 2 gave a full match in the middle portion of the cDNA-derived amino acid sequence. The predicted amino acid sequence showed a high degree of similarity with pig 17 beta-hydroxysteroid dehydrogenase type IV and MFE of yeast peroxisomal beta-oxidation. Recombinant perMFE-II (produced in Pichia pastoris) had 2-enoyl-CoA hydratase 2 and D-specific 3-hydroxyacyl-CoA dehydrogenase activities and was catalytically active with several straight-chain trans-2-enoyl-CoA, 2-methyltetradecenoyl-CoA and pristenoyl-CoA esters. The results showed that in addition to an earlier described multifunctional isomerase-hydratase-dehydrogenase enzyme from rat liver peroxisomes (perMFE-I), another MFE exists in rat liver peroxisomes. They both catalyse sequential hydratase and dehydrogenase reactions of beta-oxidation but through reciprocal stereochemical courses.
Let in a Little Sunshine: Limiting Confidential Settlements in Missouri (2004)

This Comment will first address the different ways that parties are able to keep secret information obtained during discovery and litigation. Next, it will address how different jurisdictions control public access, focusing specifically on the current laws and rules in Missouri. Finally, the Comment will suggest components of an ideal “sunshine in litigation” statute and how the law in Missouri currently compares to that ideal.
Transcranial magnetic stimulation: a neuropsychiatric tool for the 21st century (1996)

Neuroscientists have constantly sought new methods of evaluating brain function, with progressive improvement in the last century in imaging brain structure and function. However, except for direct surgical stimulation, neuropsychiatrists can only infer causality between the signal obtained on an image and a behavior or disease. Transcranial magnetic stimulation (TMS) is a new, noninvasive technique for directly stimulating cortical neurons. It has been used to map attention, memory, movement, speech, and vision. Preliminary investigations have also used rapid-rate TMS to improve motor speed in Parkinson's disease and mood in depression. TMS is likely to be an important future neuropsychiatric tool.
Insulin-like Growth Factor 1 Inhibits Apoptosis Using the Phosphatidylinositol 3′-Kinase and Mitogen-activated Protein Kinase Pathways (1997)

The role of insulin-like growth factor 1 (IGF-1) in preventing apoptosis was examined in differentiated PC12 cells. Induction of differentiation was achieved using nerve growth factor, and apoptosis was provoked by serum withdrawal. After 4-6 h of serum deprivation, apoptosis was initiated, concomitant with a 30% decrease in cell number and a 75% decrease in MTT activity. IGF-1 was capable of preventing apoptosis at concentrations as low as 10(-9) M and as early as 4 h. The phosphatidylinositol 3' (PI3')-kinase inhibitors wortmannin (at concentrations of 10(-8) M) and LY294002 (10(-6) M) blocked the effect of IGF-1. The pp70 S6 kinase (pp70S6K) inhibitor rapamycin (10(-8) M) was, however, less effective in blocking IGF-1 action. Moreover, stable transfection of a dominant-negative p85 (subunit of PI3'-kinase) construct in PC12 cells enhanced apoptosis provoked by serum deprivation. Interestingly, in the cells overexpressing the dominant-negative p85 protein, IGF-1 was still capable of inhibiting apoptosis, suggesting the existence of a second pathway involved in the IGF-1 effect. Blocking the mitogen-activated protein kinase pathway with the specific mitogen-activated protein kinase/extracellular-response kinase kinase inhibitor PD098059 (10(-5) M) inhibited the IGF-1 effect. When wortmannin and PD098059 were given together, the effect was synergistic. The results presented here suggest that IGF-1 is capable of preventing apoptosis by activation of multiple signal transduction pathways.
Metagenomic analysis of the pinewood nematode microbiome reveals a symbiotic relationship critical for xenobiotics degradation (2013)

Our recent research revealed that pinewood nematode (PWN) possesses few genes encoding enzymes for degrading α-pinene, which is the main compound in pine resin. In this study, we examined the role of PWN microbiome in xenobiotics detoxification by metagenomic and bacteria culture analyses. Functional annotation of metagenomes illustrated that benzoate degradation and its related metabolisms may provide the main metabolic pathways for xenobiotics detoxification in the microbiome, which is obviously different from that in PWN that uses cytochrome P450 metabolism as the main pathway for detoxification. The metabolic pathway of degrading α-pinene is complete in microbiome, but incomplete in PWN genome. Experimental analysis demonstrated that most of tested cultivable bacteria can not only survive the stress of 0.4% α-pinene, but also utilize α-pinene as carbon source for their growth. Our results indicate that PWN and its microbiome have established a potentially mutualistic symbiotic relationship with complementary pathways in detoxification metabolism.
Analysis of volatile organic compounds in exhaled breath to diagnose ventilator-associated pneumonia (2015)

Ventilator-associated pneumonia (VAP) is a nosocomial infection occurring in the intensive care unit (ICU). The diagnostic standard is based on clinical criteria and bronchoalveolar lavage (BAL). Exhaled breath analysis is a promising non-invasive method for rapid diagnosis of diseases and contains volatile organic compounds (VOCs) that can differentiate diseased from healthy individuals. The aim of this study was to determine whether analysis of VOCs in exhaled breath can be used as a non-invasive monitoring tool for VAP. One hundred critically ill patients with clinical suspicion of VAP underwent BAL. Before BAL, exhaled air samples were collected and analysed by gas chromatography time-of-flight mass spectrometry (GC-tof-MS). The clinical suspicion of VAP was confirmed by BAL diagnostic criteria in 32 patients [VAP(+)] and rejected in 68 patients [VAP(-)]. Multivariate statistical comparison of VOC profiles between VAP(+) and VAP(-) revealed a subset of 12 VOCs that correctly discriminated between those two patient groups with a sensitivity and specificity of 75.8% ± 13.5% and 73.0% ± 11.8%, respectively. These results suggest that detection of VAP in ICU patients is possible by examining exhaled breath, enabling a simple, safe and non-invasive approach that could diminish diagnostic burden of VAP.
Mechanisms of O-Antigen Structural Variation of Bacterial Lipopolysaccharide (LPS) (2012)

One of the most complex topics within bacterial anatomy and physiology is that of exopolysaccharides. These molecules have various structures and functions and also provide different types of advantages to their producing microorganisms, including surface variability, resistance to innate and acquired immunity mechanisms, the ability to adhere to different surface and cell types and resistance to antibiotic activity.
Aberrations of the tumor suppressor p53 and retinoblastoma genes in human hepatocellular carcinomas. (1991)

Aberrations of the p53 gene in 43 primary hepatocellular carcinomas (HCCs) were examined by single-strand conformation polymorphism analysis of polymerase chain reaction products. Of these hepatocellular carcinomas, 22 were advanced HCCs, and 21 were early HCCs. Structural abnormalities of the p53 gene were observed in eight of the 22 advanced HCCs, but in none of the early HCCs. Of the eight tumors with an abnormal p53 gene, seven had lost one of the two p53 alleles and, in the seven tumors with identifiable mutations, point mutations were found in four tumors and deletions of several nucleotides were observed in two tumors. The remaining one retained both alleles and carried two point mutations. In addition to the aberrations of the p53 gene, loss of the retinoblastoma gene or loss of heterozygosity at chromosome 13q was observed in six of seven informative cases of eight tumors carrying a mutated p53 gene. These results suggest the involvement of at least two tumor suppressor genes in a late stage of hepatocarcinogenesis.
The effects of the microstructure of ZnO films on the electrical performance of their thin film transistors (2008)

This study examined a fundamental aspect of ZnO-based thin film transistors (TFTs): the connection between the deposition conditions and the microstructure of ZnO films, and the electrical performance of the TFTs. We characterized the microstructure of ZnO films deposited under various rf powers by using high resolution transmission electron microscopy and x-ray diffraction. In further investigating the effects of the microstructure on the device performance, we experimentally demonstrated that the electrical mobility of the devices was coupled to the grain size of the ZnO films in an exponential function.
Antisense Drug Discovery and Development (2011)

Numerous chemically modified oligonucleotides have been developed so far and show their own unique chemical properties and pharmacodynamic/pharmacokinetic characteristics. Among all non-natural nucleotides, to the best of our knowledge, only five chemistries are currently being tested in clinical trials: phosphorothioate, 2´-O-methyl RNA, 2´-O-methoxyethyl RNA, 2´,4´-bridged nucleic acid/locked nucleic acid and the phosphorodiamidate morpholino oligomer. Since phosphorothioate modification can improve the pharmacokinetics of oligonucleotides, this modification is currently used in combination with all other modifications except phosphorodiamidate morpholino oligomer. For the treatment of metabolic, cardiovascular, cancer and other systemic diseases, the phosphorothioate class of drugs is obviously helpful, while superior efficacies can be observed in phosphorodiamidate morpholino oligomer compared to other classes of oligonucleotides for the treatment of Duchenne muscular dystrophy. Which properties of antisense molecules are actually essential for clinical applications? In this article, we provide an overview of the medicinal chemistry of existing non-natural antisense molecules, as well as their clinical applications, to discuss which properties of antisense oligonuculeotides affect therapeutic potency.
Characterization of plasma-polymerized allyl alcohol polymers and copolymers with styrene (2007)

Pulsed plasma was used to initiate chemical copolymerization of allyl alcohol and styrene. In this way the concentration of OH groups at the surface of the copolymer layer could be adjusted from 0 (styrene homopolymerization) to 31 OH groups/100 C atoms (allyl alcohol homopolymerization). The copolymerization kinetics correspond to those of a pure chemical (radical) copolymerization. Thus, the variation of OH group density is only possible in a small range of comonomers ratio, otherwise styrene homopolymerization dominates.
Functional mapping of the human visual cortex at 4 and 1.5 tesla using deoxygenation contrast EPI (1993)

The effects of photic stimulation on the visual cortex of human brain were studied by means of gradient-echo echo-planar imaging (EPI). Whole-body 4 and 1.5 T MRI systems, equipped with a small z axis head gradient coil, were used. Variations of image intensity of up to 28% at 4 T, and up to 7% at 1.5 T, were observed in primary visual cortex, corresponding to an increase of blood oxygenation in regions of increased neural activity. The larger effects at 4 T are due to the increased importance of the susceptibility difference between deoxygenated and oxygenated blood at high fields.
An Automatic Beat Detection Algorithm for Pressure Signals (2005)

Beat detection algorithms have many clinical applications including pulse oximetry, cardiac arrhythmia detection, and cardiac output monitoring. Most of these algorithms have been developed by medical device companies and are proprietary. Thus, researchers who wish to investigate pulse contour analysis must rely on manual annotations or develop their own algorithms. We designed an automatic detection algorithm for pressure signals that locates the first peak following each heart beat. This is called the percussion peak in intracranial pressure (ICP) signals and the systolic peak in arterial blood pressure (ABP) and pulse oximetry (SpO2) signals. The algorithm incorporates a filter bank with variable cutoff frequencies, spectral estimates of the heart rate, rank-order nonlinear filters, and decision logic. We prospectively measured the performance of the algorithm compared to expert annotations of ICP, ABP, and SpO2 signals acquired from pediatric intensive care unit patients. The algorithm achieved a sensitivity of 99.36% and positive predictivity of 98.43% on a dataset consisting of 42,539 beats.
Variegation of CD4 + T cell phenotypes is regulated by IL‐12 and IFNα (2008)

Innate cytokines secreted by antigen presenting cells shape adaptive immune responses to pathogens. For example, viral infections promote robust production of both IL‐12 and IFNα/β, two cytokines which can regulate CD4 + T helper (Th) cell differentiation and effector function. We have demonstrated that IL‐12 is exclusively responsible for directing Th1 development and effector functions in human CD4 + T cells. In contrast to previous reports, IFNα alone was insufficient to promote Th1 development due to inability to maintain stable T‐bet expression. Furthermore, IFNα neither enhanced nor repressed IL‐12‐induced Th1 development. However, IFNα greatly enhanced IL‐12‐induced IL‐2 secretion in human Th cells. Furthermore, while IL‐12 promoted elevated expression of CXCR3, IFNα enhanced expression of CCR7. In cells activated in the presence of both IL‐12 and IFNα, a phenotypic variegation was observed in which IL‐2‐producing cells possessed a CXCR3 lo CCR7 hi phenotype, while IFNγ‐producing cells were CXCR3 hi CCR7 lo . These phenotypic characteristics correlated with function, such that cells sorted for IL‐2 expression possessed greater capacity and phenotypic plasticity than cells sorted for IFNγ xpression. These results suggest a novel role for IFNα/β in the differentiation of Th cells to effector and memory phenotypes. Supported by grants NIH/NIAID AI056222 and NIH/GM GM00820317.
Vasopressin and terlipressin in adult vasodilatory shock (2012)

We have read with interest the study by Serpa Neto and colleagues showing that vasopressin use in vasodilatory shock is associated with reduced mortality [1]. However, we believe there are three aspects that need clarification.

In relation to the paper recently published by our group on the same topic, the authors correctly state that 'we only analyzed adult patients because pediatric shock has a much lower mortality that adult shock and this may contaminate the overall results' [1]. For the main analysis in our article, we computed data from six randomized trials exploring use of vasopressin/terlipressin only in adults [2]. Mortality in children was examined in a separate subgroup analysis.

Second, we intentionally excluded the paper from Argenziano and colleagues because this study examined the use of vasopressin in patients after cardiopulmonary bypass and ventricular assist device placement, a quite unique patient population with regards to the pathophysiology of shock [3]. Argenziano and colleagues' study was also carried out in a time of very different standards of intensive care (1997), compared with all other studies that were performed in the mid to late 2000s.

Moreover, the 'reduction in norepinephrine requirement' presented by the authors is not in conflict with our finding of a significant inverse relation between the vasopressin dose and the norepinephrine dose [2].

On a side note, we believe the authors' choice of using a fixed-effect model to compute a pooled estimate of the relative risk is questionable because it is based on the unlikely assumption that no statistical heterogeneity is present among the included studies.
Reflective Fourier ptychography (2016)

The Fourier ptychography technique in reflection mode has great potential applications in tissue imaging and optical inspection, but the current configuration either has a limitation on cut-off frequency or is not practical. By placing the imaging aperture stop outside the illumination path, the illumination numerical aperture (NA) can be greater than the imaging NA of the objective lens. Thus, the cut-off frequency achieved in the proposed optical system is greater than twice the objective's NA divided by the wavelength (2NAobj/λ ), which is the diffraction limit for the cut-off frequency in an incoherent epi-illumination configuration. We experimentally demonstrated that the synthesized NA is increased by a factor of 4.5 using the proposed optical concept. The key advantage of the proposed system is that it can achieve high-resolution imaging over a large field of view with a simple objective. It will have a great potential for applications in endoscopy, biomedical imaging, surface metrology, and industrial inspection.