gebhart/patrepeval huggingface dataset:
Detection and Quantification of Heteroplasmic Mutant Mitochondrial DNA by Real-Time Amplification Refractory Mutation System Quantitative PCR Analysis: A Single-Step Approach (2004)

The real-time ARMS-qPCR method provides rapid, reliable, one-step quantitative detection of heteroplasmic mutant mtDNA.
Invasive candidiasis and candidemia: from current opinions to future perspectives (2009)

Candida spp. are the fourth most common cause of nosocomial bloodstream infections in the United States, as well as the single most important cause of opportunistic fungal infections worldwide. A delayed diagnosis of invasive candidiasis and/or inadequate treatment choice is associated with high mortality rates and prolonged hospital stays. Even though the antifungal armamentarium has been broadened significantly over the last years, the best options for diagnosing and treating invasive candidiasis still remain a matter of discussion. In this article we present and analyze current evidence on the epidemiology, diagnostic methods and treatment options of invasive candidiasis, with a focus on results from randomized clinical trials. Finally, the reader is provided with a brief overview on promising clinical trial designs and antifungals that might shape the treatment of invasive candidiasis in the years to come.
The synthesis of some mechanistic probes for sialic acid processing enzymes and the labeling of a sialidase from Trypanosoma rangeli (2004)

Sialyl hydrolases, trans-sialidases, and sialyl transferases are biologically important enzymes that are responsible for the incorporation and removal of sialic acid residues, which decorate many cell surface glycocongugates. Two fluorinated sialic acid derivatives have been synthesized as mechanism-based inactivators, to probe the catalytic mechanisms through which sialidases and trans-sialidases operate. Both compounds are known to be covalent inactivators of a trans-sialidase from Trypanosoma cruzi. Here, 3-fluorosialosyl fluoride has been found to covalently label the catalytic nucleophile of a sialidase from T. rangeli, and the residue involved is shown to be Tyr346 within the sequence DENSGYSSVL. This is the first demonstration that sialidases operate through a covalent glycosyl-enzyme intermediate, strongly suggesting a common catalytic mechanism amongst all members of the sialidase superfamily. CMP-3-fluoro sialic acid is a competitive inhibitor of sialyl transferases and was synthesized via a two-step enzymatic process from commercially available N-acetyl mannosamine, 3-fluoropyruvic acid, and cytidine triphosphate in around 84% yield.Key words: sialidase, mechanism, labeling, nucleophile, inhibitor.
The control of dynamically interacting systems (1988)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1988.
Safer Classification by Synthesis (2017)

The discriminative approach to classification using deep neural networks has become the de-facto standard in various fields. Complementing recent reservations about safety against adversarial examples, we show that conventional discriminative methods can easily be fooled to provide incorrect labels with very high confidence to out of distribution examples. We posit that a generative approach is the natural remedy for this problem, and propose a method for classification using generative models. At training time, we learn a generative model for each class, while at test time, given an example to classify, we query each generator for its most similar generation, and select the class corresponding to the most similar one. Our approach is general and can be used with expressive models such as GANs and VAEs. At test time, our method accurately "knows when it does not know," and provides resilience to out of distribution examples while maintaining competitive performance for standard examples.
Realization of high tunability barium strontium titanate thin films by rf magnetron sputtering (1999)

Ferroelectric thin films are currently being used to develop tunable microwave circuits based on the electric-field dependence of the dielectric constant. (Ba0.5Sr0.5)TiO3 (BST) films prepared by sputtering on Pt/TiO2/SiO2/Si substrates are found to exhibit a capacitance change (tunability) of nearly 4:1. Higher tunability has been attributed to the (100) texturing of the BST films and is a result of the biaxial tensile stress imposed by Si on BST making the polar axis oriented in plane. Electrical characterization shows that the dielectric permittivity increases with increase in film thickness (up to ∼200 nm).
Neuronal pentraxin II is highly upregulated in Parkinson’s disease and a novel component of Lewy bodies (2007)

Neuronal pentraxin II (NPTX2) is the most highly upregulated gene in the Parkinsonian substantia nigra based on our whole genome expression profiling results. We show here that it is a novel component of Lewy bodies and Lewy neurites in sporadic Parkinson's disease (PD). NPTX2 is also known as the neuronal activity-regulated protein (Narp), which is secreted and involved in long-term neuronal plasticity. Narp further regulates AMPA receptors which have been found to mediate highly selective non-apoptotic cell death of dopaminergic neurons. NPTX2/Narp is found in close association with alpha-synuclein aggregates in both substantia nigra and cerebral cortex in PD but unlike alpha-synuclein gene expression, which is down-regulated in the Parkinsonian nigra, NPTX2 could represent a driver of the disease process. In view of its profound (>800%) upregulation and its established role in synaptic plasticity as well as dopaminergic nerve cell death, NPTX2 is a very interesting novel player which is likely to be involved in the pathway dysregulation which underlies PD.
Cerebral autoregulation dynamics in humans. (1989)

We studied the response of cerebral blood flow to acute step decreases in arterial blood pressure noninvasively and nonpharmacologically in 10 normal volunteers during normocapnia, hypocapnia, and hypercapnia. The step (approximately 20 mm Hg) was induced by rapidly deflating thigh blood pressure cuffs following a 2-minute inflation above systolic blood pressure. Instantaneous arterial blood pressure was measured by a new servo-cuff method, and cerebral blood flow changes were assessed by transcranial Doppler recording of middle cerebral artery blood flow velocity. In hypocapnia, full restoration of blood flow to the pretest level was seen as early as 4.1 seconds after the step decrease in blood pressure, while the response was slower in normocapnia and hypercapnia. The time course of cerebrovascular resistance was calculated from blood pressure and blood flow recordings, and rate of regulation was determined as the normalized change in cerebrovascular resistance per second during 2.5 seconds just after the step decrease in blood pressure. The reference for normalization was the calculated change in cerebrovascular resistance that would have nullified the effects of the step decrease in arterial blood pressure on cerebral blood flow. The rate of regulation was 0.38, 0.20, and 0.11/sec in hypocapnia, normocapnia, and hypercapnia, respectively. There was a highly significant inverse relation between rate of regulation and PaCO2 (p less than 0.001), indicating that the response rate of cerebral autoregulation in awake normal humans is profoundly dependent on vascular tone.
Security Mechanisms in High-Level Network Protocols (1983)

article Security Mechanisms in High-Level Network Protocols Share on Authors: Victor L. Voydock Bolt, Beranek and Newman, Inc., Cambridge, Massachusetts Bolt, Beranek and Newman, Inc., Cambridge, MassachusettsView Profile , Stephen T. Kent Bolt, Beranek and Newman, Inc., Cambridge, Massachusetts Bolt, Beranek and Newman, Inc., Cambridge, MassachusettsView Profile Authors Info & Claims ACM Computing SurveysVolume 15Issue 2June 1983 pp 135–171https://doi.org/10.1145/356909.356913Online:01 June 1983Publication History 198citation4,374DownloadsMetricsTotal Citations198Total Downloads4,374Last 12 Months47Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Low-temperature silicon epitaxy by ultrahigh vacuum/chemical vapor deposition (1986)

We have successfully demonstrated the use of a novel chemical vapor deposition technique, ultrahigh vacuum/chemical vapor deposition, to deposit homoepitaxial silicon layers of high crystalline perfection at low temperatures (T≥750 °C). Rutherford backscattering and transmission electron microscopy showed the transition to epitaxial silicon growth took place in the range 700–750 °C, and secondary ion mass spectrometry showed typical oxygen and carbon levels to be near the detection limits of the technique 1016–1017 cm−3. In addition, abrupt dopant transitions have been demonstrated, with B levels dropping four orders of magnitude, 1019–1015 B/cm3, in the first 1000 angstroms of an intrinsic epilayer.
Complications and Predictive Factors for the Successful Treatment of Flatback Deformity (Fixed Sagittal Imbalance) (1999)

Satisfaction with the results of treatment may be reduced in patients with four or more major co-existent medical problems, insufficient sagittal correction, and resultant pseudarthrosis.
Absolute Quantification of the G Protein-Coupled Receptor Rhodopsin by LC/MS/MS Using Proteolysis Product Peptides and Synthetic Peptide Standards (2003)

Methods for the absolute quantification of a membrane protein are described using isotopically labeled or unlabeled synthetic peptides as standards. Synthetic peptides are designed to mimic peptides that are cleaved from target analyte proteins by proteolytic or chemical digestion, and the peptides selected serve as standards for quantification by LC/MS/MS on a triple quadrupole mass spectrometer. The technique is complementary to relative quantification techniques in widespread use by providing absolute quantitation of selected targets with greater sensitivity, dynamic range, and precision. Proteins that are found to be of interest by global proteome searches can be selected as targets for quantitation by the present method. This method has a much shorter analytical cycle time (minutes versus hours for the global proteome experiments), making it well suited for high-throughput environments. The present approach using synthetic peptides as standards, in conjunction with proteolytic or chemical cleavage of target proteins, allows mass spectrometry to be used as a highly selective detector for providing absolute quantification of proteins for which no standards are available. We demonstrate that quantification is simple and reliable for the integral membrane protein rhodopsin with reasonable recoveries for replicate experiments using low-micromolar solutions of rhodopsin from rod outer segments.
Targeting heat-shock protein 90 improves efficacy of rapamycin in a model of hepatocellular carcinoma in mice # (2008)

Blocking Hsp90 disrupts rapamycin-induced activation of alternative signaling pathways in HCCs and substantially improves the growth-inhibitory effects of mTOR inhibition in vivo. Hence, the concept of targeting tumor cells, ECs, and VSMCs by blocking Hsp90/mTOR could prove valuable for treatment of HCC.
Abrupt changes in fibrillatory wave characteristics at the termination of paroxysmal atrial fibrillation in humans (2007)

Low frequency fibrillation was found to be much more likely to terminate. Frequency changes preceding spontaneous termination were abrupt, in contrast to the gradual frequency drop reported with drug-induced termination. The analysis of fibrillatory wave characteristics and their change over time might be used to target specific moments for pacing therapy in patients with AF.
Electrophoresis of duplex deoxyribonucleic acid in multiple-concentration agarose gels: fractionation of molecules with molecular weights between 2 .times. 106 and 110 .times. 106 (1980)

By use of multiple-concentration agarose gels, the distance migrated by linear, duplex DNA during agarose gel electrophoresis has been measured as a function of agarose concentration (A) and molecular weight of the DNA (Mr) for molecules with an Mr between 1.88 X 10(6) and 110 X 10(6). Conditions for obtaining a linear plot of log Mr as a function of distance migrated (D) have been found for DNA molecules with an Mr between 5.47 X 10(6) and 110 X 10(6); improved conditions for fractionating such molecules are described. The ratio of the D of a DNA with an Mr of 26.5 X 10(6) to the D of a DNA with an Mr of 77 X 10(6) was plotted as a function of A and electrical field (E). By use of A values between 0.075 and 0.70% and a constant E, this plot had a single maximum. The maximal value of the above ratio was a decreasing function of E, and the A at this maximal value was also a decreasing function of E.
Printed Loop Antenna With a Perpendicular Feed for Penta-Band Mobile Phone Application (2008)

A promising printed loop antenna is described that can be mounted in perpendicular to the top edge of the system circuit board of the mobile phone for penta-band operation. The antenna comprises a loop pattern printed on a thin FR4 substrate of small size 10 X 60 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and a perpendicular feeding portion printed on the narrow top ungrounded region of the system circuit board. Since the top ungrounded region is 4 mm in length only, the antenna is very low profile to the top edge of the ground plane on the system circuit board; that is, the antenna occupies a small volume inside the mobile phone housing and is suitable to operate as an internal antenna. In addition, the antenna generates two wide operating bands centered at about 900 and 1900 MHz to cover GSM850/900 and DCS/PCS/UMTS operations, respectively.
Gyde-Petersen, A Skagen Artist in America (2006)

Mankato, Minnesota, was thrilled. A famous artist had come to town with his palette, easel, and painter's smock, and people noticed. The Mankato Free Press ran a story under a bold headline: Sir Gyde Pedersen, Artist of Denmark The reporter gushed away for two columns on the delight of having in their midst a European artist who had been knighted by a king.1
Systematic review: Histological remission in inflammatory bowel disease. Is ‘complete’ remission the new treatment paradigm? An IOIBD initiative (2014)

Histological remission in IBD represents a target distinct from endoscopic mucosal healing, not yet routinely sought in clinical trials or practice. There remains a need for a standardized and validated histological scoring system and to confirm the prognostic value of histological remission as a treatment target in IBD.
Recent Advances in β-Lactone Chemistry (1993)

After a brief historical survey, the structure, main methods of preparation and reactivity of β-lactones are examined with emphasis on developments since 1980. The structure of β-lactones is examined through theoretical methods and molecular spectroscopy (IR and NMR). The methods of preparation are rationalized around the main reactions leading to β-lactones; [2+2] cycloaddition (between ketenes and carbonyl compounds) and lactonization via oxygen-acyl bond formation (of β-hydroxy carboxylic acids or derivatives) being the two most important ones. Finally, the reactivity of β-lactones, which has developed significantly over the last years with the better understanding of stereochemical problems, is studied. Decarboxylation (leading to olefins), Lewis acid promoted rearrangement (leading to γ-lactones), nucleophilic attack (inducing oxygen-acyl or oxygen-alkyl cleavage of the β-lactone depending on the reagents and the conditions) and reaction of β-lactone enolates towards electrophiles are more particularly studied. Information on the mechanism (when available) and the implementation in synthesis of all these methods (preparation and reactivity) are given. Thus, several natural β-lactone syntheses and many examples of the use of β-lactones as intermediates are quoted from the literature. 1. Introduction 2. History 3. Structure 3.1. Theoretical Methods 3.2. Molecular Spectroscopy 4. Preparation 4.1. Lactonization via Oxygen-Alkyl Bond Formation 4.1.1. From β-Halocarboxylic Acid Salts 4.1.2. From β,γ-Unsaturated Carboxylic Acids 4.1.3. From β-Hydroxy Carboxylic Acids 4.1.4. From Other Substrates 4.2. Lactonization via Oxygen-Acyl Bond Formation 4.2.1. From β-Hydroxy Carboxylic Acids 4.2.2. From β-Hydroxy Acid Derivatives Including Transition-Metal Complexes 4.2.3. From β-Hydroxy Lithiated Ketenes 4.3. [2+2] Cycloaddition 4.4. Miscellaneous 4.4.1. Transition-Metal Promoted Reactions 4.4.2. Deoxygenation of β-Peroxylactone 4.4.3. Others 5. Reactivity 5.1. Decarboxylation 5.2. Lewis Acid Promoted Rearrangement 5.3. Reactions with Nucleophiles 5.3.1. Grignard, Organolithium and Organocuprate Reagents 5.3.2. Group IV Organometallic Compounds 5.3.3. Group V and Group VI Nucleophiles 5.3.4. Ylides 5.4. Enolate Formation and Reaction Towards Electrophiles 5.5. Miscellaneous 5.6. The Reactivity of α-Methylene-β-lactones and β-Methylene-β-lactones 5.6.1. α-Methylene-β-lactones 5.6.2. β-Methylene-β-lactones 6. Conclusion
Synthesis, Corticotropin-Releasing Factor Receptor Binding Affinity, and Pharmacokinetic Properties of Triazolo-, Imidazo-, and Pyrrolopyrimidines and -pyridines (1999)

The synthesis and CRF receptor binding affinities of several new series of N-aryltriazolo- and -imidazopyrimidines and -pyridines are described. These cyclized systems were prepared from appropriately substituted diaminopyrimidines or -pyridines by nitrous acid, orthoester, or acyl halide treatment. Variations of amino (ether) pendants and aromatic substituents have defined the structure-activity relationships of these series and resulted in the identification of a variety of high-affinity agents (Ki's < 10 nM). On the basis of this property and lipophilicity differences, six of these compounds (4d,i,n,x, 8k, 9a) were initially chosen for rat pharmacokinetic (PK) studies. Good oral bioavailability, high plasma levels, and duration of four of these compounds (4d,i,n,x) prompted further PK studies in the dog following both iv and oral routes of administration. Results from this work indicated 4i,x had properties we believe necessary for a potential therapeutic agent, and 4i1 has been selected for further pharmacological studies that will be reported in due course.
Ferrocene-mediated enzyme electrode for amperometric determination of glucose (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFerrocene-mediated enzyme electrode for amperometric determination of glucoseAnthony E. G. Cass, Graham. Davis, Graeme D. Francis, H. Allen O. Hill, William J. Aston, I. John. Higgins, Elliot V. Plotkin, Lesley D. L. Scott, and Anthony P. F. TurnerCite this: Anal. Chem. 1984, 56, 4, 667–671Publication Date (Print):April 1, 1984Publication History Published online1 May 2002Published inissue 1 April 1984https://pubs.acs.org/doi/10.1021/ac00268a018https://doi.org/10.1021/ac00268a018research-articleACS PublicationsRequest reuse permissionsArticle Views8874Altmetric-Citations1386LEARN 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
Isolation and Structural Identification of a New Simmondsin Ferulate from Jojoba Meal (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsolation and Structural Identification of a New Simmondsin Ferulate from Jojoba MealM. Van Boven, S. Toppet, M. M. Cokelaere, and P. DaenensCite this: J. Agric. Food Chem. 1994, 42, 5, 1118–1121Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 May 1994https://pubs.acs.org/doi/10.1021/jf00041a014https://doi.org/10.1021/jf00041a014research-articleACS PublicationsRequest reuse permissionsArticle Views83Altmetric-Citations18LEARN 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
Genetic Modification of Adeno-Associated Viral Vector Type 2 Capsid Enhances Gene Transfer Efficiency in Polarized Human Airway Epithelial Cells (2008)

Cystic fibrosis (CF) is a common genetic disease characterized by defects in the expression of the CF transmembrane conductance regulator (CFTR) gene. Gene therapy offers better hope for the treatment of CF. Adeno-associated viral (AAV) vectors are capable of stable expression with low immunogenicity. Despite their potential in CF gene therapy, gene transfer efficiency by AAV is limited because of pathophysiological barriers in these patients. Although a few AAV serotypes have shown better transduction compared with the AAV2-based vectors, gene transfer efficiency in human airway epithelium has still not reached therapeutic levels. To engineer better AAV vectors for enhanced gene delivery in human airway epithelium, we developed and characterized mutant AAV vectors by genetic capsid modification, modeling the well-characterized AAV2 serotype. We genetically incorporated putative high-affinity peptide ligands to human airway epithelium on the GH loop region of AAV2 capsid protein. Six independent mutant AAV were constructed, containing peptide ligands previously reported to bind with high affinity for known and unknown receptors on human airway epithelial cells. The vectors were tested on nonairway cells and nonpolarized and polarized human airway epithelial cells for enhanced infectivity. One of the mutant vectors, with the peptide sequence THALWHT, not only showed the highest transduction in undifferentiated human airway epithelial cells but also indicated significant transduction in polarized cells. Interestingly, this modified vector was also able to infect cells independently of the heparan sulfate proteoglycan receptor. Incorporation of this ligand on other AAV serotypes, which have shown improved gene transfer efficiency in the human airway epithelium, may enhance the application of AAV vectors in CF gene therapy.