gebhart/patrepeval huggingface dataset:
Optical frequency domain reflectometry based on real-time Fourier transformation (2007)

We propose and demonstrate an ultrahigh-speed optical frequency domain reflectometry (OFDR) system based on optical frequency-to-time conversion by pulse time stretching with a linearly chirped fiber Bragg grating (LCFG). This method will be referred to as OFDR based on real-time Fourier transformation (OFDR-RTFT). In this approach, the frequency domain interference pattern, from which the desired axial depth profile is reconstructed, can be captured directly in the time-domain over the duration of a single stretched pulse, which translates into unprecedented axial line acquisition rates (as high as the input pulse repetition rate). We provide here a comprehensive, rigorous mathematical analysis of this new OFDR approach. In particular, we derive the main design equations of an OFDR-RTFT system in terms of its key performance parameters. Our analysis reveals the detrimental influence of nonlinear phase variations in the input optical pulse (including higher-order dispersion terms and group delay ripples introduced by the LCFG stretcher) on the system performance, e.g. achievable resolution. A simple and powerful method based on Hilbert transformation is successfully demonstrated to compensate for these detrimental phase distortions. We show that besides its potential to provide ultrahigh acquisition speeds (in the MHz range), LCFG-based OFDR-RTFT also offers the potential for performance advantages in terms of axial resolution, depth range and sensitivity. All these features make this approach particularly attractive for imaging applications based on optical coherence tomography (OCT). In our experiments, single-reflection depth profiles with nearly transform-limited approximately 92.8 mum (average) axial resolutions over a remarkable 18 mm depth range have been obtained from OFDR-RTFT interferograms, each one measured over a time window of approximately 50 ns at 20 MHz repetition rate. Improved sensitivities up to -61 dB have been achieved without using any balanced detection scheme.
Ketimines From Ketones and Ammonia (1988)

The direct synthesis of ketimines from ammonia and ketones catalyzed by ammonium chloride is described.
Real-world safety data and differentiation of second-line (2L) 5-fluorouracil (5-FU) based regimens among patients with metastatic pancreatic ductal adenocarcinoma (mPDAC). (2021)

390 Background: Chemotherapy related adverse events (AEs) can impact the treatment of patients, reducing quality of life and leading to dose delays and treatment discontinuation. This study examined the proportion of patients (pts) with mPDAC treated with 5-FU-based regimens in the 2L setting who experienced AEs during treatment. Methods: Data were extracted for pts diagnosed with mPDAC who initiated 2L treatment between January 2016 and July 2020 from the Flatiron Health electronic health database. Pts included in the study were treated with FOLFIRINOX (FFX), FOLFOX, FOLFIRI, or a regimen containing liposomal irinotecan. The occurrence of grade 3 (G3) and grade 4 (G4) neutropenia, G3/G4 elevated alanine transaminase (ALT) and anemia where transfusion was indicated were determined using lab results and the grading criteria from the Common Terminology Criteria for Adverse Events v4.03. The occurrence of diarrhea, fatigue, nausea and vomiting (N/V), and neuropathy were identified from structured diagnosis records through ICD-10-CM codes. Duration of therapy (DOT) was assessed for each regimen. Descriptive statistics for AEs and DOT were reported. Results: Of the 804 pts included in the study, 28.4% (n=228) received FFX, 39.8% (n=320) received regimens containing liposomal irinotecan, 24.8% (n=199) received FOLFOX, and 7.1% (n=57) received FOLFIRI. The median DOT (IQR) was 86 days (d) (43 – 206), 79d (41 – 169), 72d (43 – 166), and 84d (46 – 148) for pts who received FFX, liposomal irinotecan, FOLFOX, and FOLFIRI, respectively. G3/G4 neutropenia (<1000/mm3) presented in 28.1% (n=64) of pts treated with FFX, 11.9% (n=38) of pts treated with liposomal irinotecan, 17.1% (n=34) of pts treated with FOLFOX, and 36.8% (n=21) of pts treated with FOLFIRI. NV occurred in 14.9% (n=34), 13.1% (n=42), 12.6% (n=25), and 10.5% (n=6), respectively. The full AE results are summarized in the table. Conclusions: In this assessment of often dose-limiting AEs among pts with mPDAC treated in 2L, pts who received liposomal irinotecan had the lowest proportion of neutropenia. No clear pattern was noted for N/V, neuropathy, fatigue, anemia, and elevated ALT. Further research is necessary to determine the real-world cost implications of AEs in this patient population. [Table: see text]
<i>Salmonella enterica</i> Serovar Typhimurium Vaccine Strains Expressing a Nontoxic Shiga-Like Toxin 2 Derivative Induce Partial Protective Immunity to the Toxin Expressed by Enterohemorrhagic <i>Escherichia coli</i> (2010)

Shiga-like toxin 2 (Stx2)-producing enterohemorrhagic Escherichia coli (referred to as EHEC or STEC) strains are the primary etiologic agents of hemolytic-uremic syndrome (HUS), which leads to renal failure and high mortality rates. Expression of Stx2 is the most relevant virulence-associated factor of EHEC strains, and toxin neutralization by antigen-specific serum antibodies represents the main target for both preventive and therapeutic anti-HUS approaches. In the present report, we describe two Salmonella enterica serovar Typhimurium aroA vaccine strains expressing a nontoxic plasmid-encoded derivative of Stx2 (Stx2DeltaAB) containing the complete nontoxic A2 subunit and the receptor binding B subunit. The two S. Typhimurium strains differ in the expression of flagellin, the structural subunit of the flagellar shaft, which exerts strong adjuvant effects. The vaccine strains expressed Stx2DeltaAB, either cell bound or secreted into the extracellular environment, and showed enhanced mouse gut colonization and high plasmid stability under both in vitro and in vivo conditions. Oral immunization of mice with three doses of the S. Typhimurium vaccine strains elicited serum anti-Stx2B (IgG) antibodies that neutralized the toxic effects of the native toxin under in vitro conditions (Vero cells) and conferred partial protection under in vivo conditions. No significant differences with respect to gut colonization or the induction of antigen-specific antibody responses were detected in mice vaccinated with flagellated versus nonflagellated bacterial strains. The present results indicate that expression of Stx2DeltaAB by attenuated S. Typhimurium strains is an alternative vaccine approach for HUS control, but additional improvements in the immunogenicity of Stx2 toxoids are still required.
Office 2010 Bible (2010)

The best of the best from the bestselling authors of Excel, Word, and PowerPoint Bibles! Take your pick of applications from the Office 2010 suite and your choice of leading experts to show you how to use them. This Office 2010 Bible features the best-of-the-best content from the Excel 2010 Bible, by Mr. Spreadsheet John Walkenbach; the Word 2010 Bible by Microsoft MVP Herb Tyson; the PowerPoint 2010 Bible, by PowerPoint expert Faithe Wempen; and coverage of Access 2010 from Microsoft MVP Michael Alexander. If you want to quickly and effectively begin using Office 2010, start in the experts' corner with this must-have book. Gives you the best-of-the-best content on Office 2010 from the leading experts, authors, and contributors to our Excel, Word, PowerPoint, and Access Bibles Includes content from John Walkenbach, aka Mr. Spreadsheet; Word expert and Microsoft MVP Herb Tyson; PowerPoint expert Faithe Wempen; and Excel and Access expert and Microsoft MVP Michael Alexander Takes you beyond creating simple text documents, spreadsheets, and presentations to help you use multiple Office applications at once to conquer critical business tasks Hones in with expert coverage of the topics within each application that you need to know most Covers even more from Outlook and other key Office topics Get the best of four books in one with this power-packed reference!
RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes (2007)

Toxin/antitoxin (TA) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. We present RASTA-Bacteria, an automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they are annotated open reading frames or not. The tool successfully confirmed all reported TA systems, and spotted new putative loci upon screening of sequenced genomes. RASTA-Bacteria is publicly available at http://genoweb.univ-rennes1.fr/duals/RASTA-Bacteria.
Primary Culture of Smooth Muscle Cells from Benigin Prostatic Hyperplasia. (1994)

Primary cultures of smooth muscle cells (SMCs) were derived from the human prostate obtained from four patients with symptomatic benign prostatic hyperplasia (BPH) undergoing open prostatectomy, using collagenase digestion and preferential adhesion techniques. SMCs attached to the plastic substrate by 6 to 10 h, proliferated by 2 to 3 days, and reached confluency by 10 to 14 days with a "hill-and-vallery" pattern. Immunocytochemical staining of cultured SMCs using anti human muscle-specific actin monoclonal antibody (HHF35), confirmed that more than 90% primary cultured cells were positive for HHF-35. Transmission electron microscopy of SMCs revealed dense myofibrils (6-8 nm width) showing focal density, and was compatible to smooth muscle cells. This primary culture will be utilized to provide a useful model to investigate the character of smooth muscle cells and their role in the development of BPH.
Acute Pancreatitis (2012)

Acute pancreatitis is an inflammatory response to pancreatic injury., The response can be mild and local, or extend to peripancreatic and systemic inflammation. The systemic inflammatory response can also lead to vascular leak, pulmonary edema, hypovolemia hypotension and shock, and ischemic injury to the pancreas, kidney and intestines. The most common etiologies of acute pancreatitis are gallstones, alcoholism, and idiopathic. Treatment is initially aimed at fluid resuscitation, support of organ dysfunction, and in severe cases enteral feeding. Therapeutic endoscopy may be needed to dislodge an impacted gallstone to treat bacterial cholangitis. Treatment is supportive, and a plan to prevent recurrence should be implemented before discharge.
OMNI-a heterogeneous distributed advice giver (2002)

The author presents an architecture for heterogeneous, distributed problem solving and describes work in progress on an application called OMNI, aimed at giving advice to users of enterprise level computing systems. Since OMNI's domain is too large to be manageable by any single intelligent program, the author employs a distributed problem-solving approach in which a heterogeneous collection of existing specialists is used to solve a user's problem. Participation among these various systems is accomplished through a blackboard and a set of contracts. The author uses a general practitioner with a high-level model of the domain to encourage coordination among specialists. Model based reasoning is intrinsic in OMNI; it allows interaction based on an understanding of the domain which is not possible in any purely syntactic scheme.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
New zwitterionic detergents improve the analysis of membrane proteins by two‐dimensional electrophoresis (1998)

Severe quantitative loss of protein is often observed in high-resolution two-dimensional electrophoresis of membrane proteins, while the resolution is usually not affected. To improve the solubility of proteins in this technique, we tested denaturing cocktails containing various detergents and chaotropes. Best results were obtained with a denaturing solution containing urea, thiourea, and zwitterionic detergents, synthesized for this purpose. Among the dozen detergents synthesized and tested, amidosulfobetaines with an alkyl tail containing 14-16 carbons proved most efficient, solubilizing previously undetected membrane proteins.
Analysis of the Protein S Gene in Protein S Deficiency (2003)

Protein S (PS) is a 71-kDa vitamin K-dependent glycoprotein first identified in human plasma by DiScipio and colleagues in 1977 (1), a year after the discovery of the anticoagulant protein C (PC) (2,3). A few years later, Walker demonstrated that PS acts as a cofactor for activated protein C (APC) in the proteolytic inactivation of the procoagulant factors Va and VIIIa (4,5) and in 1984, the first families with hereditary PS deficiency and venous thrombotic disease were identified (6,7). This demonstrated the physiological importance of PS as an antithrombotic protein, which has been further confirmed by the identification of many other families in which the heterozygotes for PS deficiency have an increased risk of developing venous thrombosis in early adulthood (8-10). PS deficient homozygotes with severe thrombotic events and purpura fulminans in the neonatal period have also been described (11,12). Although the molecular mechanism by which PS enhances APC activity has not yet been completely elucidated (2,3), it has been proposed that PS increases the affinity of APC for the phospholipid membranes where the inactivation complex will form and the inactivation reactions take place (13). PS might also have APC independent anticoagulant properties through direct inhibition of prothrombin and factor X activation (14-16).
Lemon juice as a natural biocide for disinfecting drinking water. (1994)

The natural biocidal activity of lemon juice was studied in order to explore its possible use as a disinfectant and inhibitor of Vibrio cholerae in drinking water for areas lacking water treatment plants. From January through July 1993, water samples of varying alkalinity and hardness were prepared artificially, and underground and surface water samples were obtained from a number of different rural and urban areas in Argentina's Buenos Aires Province. After measuring the latter samples' hardness and alkalinity, a range of concentrations of lemon juice and other acidifiers were added to each sample, and the resulting pH as well as the samples' ability to destroy V. cholerae were determined. The results show that lemon juice can actively prevent survival of V. cholerae but that such activity is reduced in markedly alkaline water. For example, treatment of underground drinking water, which is characterized as having the greatest degree of alkalinity in our area, will typically destroy V. cholerae if the alkalinity of the water is the equivalent of that produced by 200 mg CaCO3 per liter, if enough lemon juice is added to bring the lemon juice concentration to 2%, and if the lemon juice is allowed to act for 30 minutes. All this points up the need to determine the alkalinity of water from any local source to be treated in the process of assessing the minimum concentration of lemon juice required.
Phase object power mapping and cosmetic defects enhancement by Fourier-based deflectometry (2009)

Optical deflectometry, likewise many other optical methods, permits to reconstruct the wavefront deformations induced by a refractive or a phase object. In this paper, a Fourier based deflectometry method is presented. A telecentric imaging system acquires pictures of a grating being the superposition of two crossed Ronchi rulings of the same spatial frequency. The object under test is inserted in the optical path between the grating and the telecentric imaging system. The presented Fourier based image analysis permits to extract the wavefront derivatives, and therefore permits to reconstruct the wavefront or the local power of the object. In this paper, the method is illustrated on several free form thermoplasic elements, the sensitivity is determined experimentally, the precision is analyzed and the ability to characterize cosmetic defects is evaluated.
The Role of the Infectious Bursal Agent and Several Avian Adenoviruses in the Hemorrhagic-Aplastic-Anemia Syndrome and Gangrenous Dermatitis (1975)

The effect that breeder-flock immune status regarding the infectious bursal agent (IBA) and two avian adenoviruses (DPI-1 and DPI-2) has on the susceptibility of their commercially reared Delmarva broiler progeny to the hemorrhagic-aplastic-anemia syndrome and concurrent gangrenous dermatitis was determined. Lack of immunity to the IBA in breeder flocks was related to an increased susceptibility of progeny to anemia and dermatitis. Breeder-flock immunity to the two adenoviruses tested could not be related to the resistance or susceptibility of their progeny to the hemorrhagic-aplastic-anemia syndrome and gangrenous dermatitis.
Functional topography of band 3: specific structural alteration linked to functional aberrations in human erythrocytes. (1988)

Band 3 is the major anion transport polypeptide of erythrocytes. It appears to be the binding site of several glycolytic enzymes. Structurally, band 3 is the major protein spanning the erythrocyte membrane and connects the plasma membrane to band 2.1, which binds to the cytoskeleton. In the present study, we report an alteration of band 3 molecule that is associated with the following changes: erythrocyte shape change from discoid to "thorny cells" (acanthocytes), restriction of rotational diffusion of band 3 in the membrane, increase in anion transport, and decrease in the number of high-affinity ankyrin-binding sites. Changes in erythrocyte IgG binding, glyceraldehyde-3-phosphate dehydrogenase, fluorescence polarization (indicative of membrane fluidity), and other membrane proteins as determined by polyacrylamide gel electrophoresis were not detected. Cells containing the altered band 3 polypeptide were obtained from individuals with abnormal erythrocyte morphology. Two-dimensional peptide maps revealed differences in the Mr 17,000 anion transport segment of band 3 consistent with additions of tyrosines or tyrosine-containing peptides. The data suggest that (i) this alteration of band 3 does not result in accelerated aging as does cleavage and (ii) structural changes in the anion transport region result in alterations in anion transport.
Guidelines for topical PUVA: a report of a workshop of the British Photodermatology Group (2000)

Psoralen photochemotherapy [psoralen ultraviolet A (PUVA)] plays an important part in dermatological therapeutics, being an effective and generally safe treatment for psoriasis and other dermatoses. In order to maintain optimal efficacy and safety, guidelines concerning best practice should be available to operators and supervisors. The British Photodermatology Group (BPG) have previously published recommendations on PUVA, including UVA dosimetry and calibration, patient pretreatment assessment, indications and contraindications, and the management of adverse reactions.1 While most current knowledge relates to oral PUVA, the use of topical PUVA regimens is also popular and presents a number of questions peculiar to this modality, including the choice of psoralen, formulation, method of application, optimal timing of treatment, UVA regimens and relative benefits or risks as compared with oral PUVA. Bath PUVA, i.e. generalized immersion, is the most frequently used modality of topical treatment, practised by about 100 centres in the U.K., while other topical preparations tend to be used for localized diseases such as those affecting the hands and feet. This paper is the product of a recent workshop of the BPG and includes guidelines for bath, local immersion and other topical PUVA. These recommendations are based, where possible, on the results of controlled studies, or otherwise on the consensus view on current practice.
The Estrogen Antagonist EM‐652 and Dehydroepiandrosterone Prevent Diet‐ and Ovariectomy‐Induced Obesity (2003)

EM-652 is an effective agent to prevent diet- and OVX-induced obesity and its associated cardiovascular risk factors such as insulin resistance. The addition of DHEA prevents hepatic lipid accumulation and further ameliorates insulin sensitivity. The beneficial metabolic effects of such combined steroid therapy may, therefore, eventually prove to be clinically relevant.
Introduction (2016)

In August of 1715 Alexander Pope Pope, Alexander placed the following advertisement in London’s Daily Courant:
CloudMap: A Cloud-Based Pipeline for Analysis of Mutant Genome Sequences (2012)

Abstract Whole genome sequencing (WGS) allows researchers to pinpoint genetic differences between individuals and significantly shortcuts the costly and time-consuming part of forward genetic analysis in model organism systems. Currently, the most effort-intensive part of WGS is the bioinformatic analysis of the relatively short reads generated by second generation sequencing platforms. We describe here a novel, easily accessible and cloud-based pipeline, called CloudMap, which greatly simplifies the analysis of mutant genome sequences. Available on the Galaxy web platform, CloudMap requires no software installation when run on the cloud, but it can also be run locally or via Amazon's Elastic Compute Cloud (EC2) service. CloudMap uses a series of predefined workflows to pinpoint sequence variations in animal genomes, such as those of premutagenized and mutagenized Caenorhabditis elegans strains. In combination with a variant-based mapping procedure, CloudMap allows users to sharply define genetic map intervals graphically and to retrieve very short lists of candidate variants with a few simple clicks. Automated workflows and extensive video user guides are available to detail the individual analysis steps performed (http://usegalaxy.org/cloudmap). We demonstrate the utility of CloudMap for WGS analysis of C. elegans and Arabidopsis genomes and describe how other organisms (e.g., Zebrafish and Drosophila) can easily be accommodated by this software platform. To accommodate rapid analysis of many mutants from large-scale genetic screens, CloudMap contains an in silico complementation testing tool that allows users to rapidly identify instances where multiple alleles of the same gene are present in the mutant collection. Lastly, we describe the application of a novel mapping/WGS method (“Variant Discovery Mapping”) that does not rely on a defined polymorphic mapping strain, and we integrate the application of this method into CloudMap. CloudMap tools and documentation are continually updated at http://usegalaxy.org/cloudmap.
On Evaluating Video-based Generative Adversarial Networks (GANs) (2018)

We study the problem of evaluating video-based Generative Adversarial Networks (GANs) by applying existing image quality assessment methods to the explicit evaluation of videos generated by state-of-the-art frameworks [1]-[3]. Specifically, we provide results and discussion on using quantitative methods such as the Fréchet Inception Distance [4], the Multi-scale Structural Similarity Measure (MS-SSIM) [5], as well as the Birthday Paradox inspired test [6] and compare these to the prevalent performance evaluation methods in the literature. We summarize that current testing methodologies are not sufficient for quality assurance in video-based GAN frameworks, and that methods based on the image-based GAN literature can be useful to consider. The results of our experiments and a discussion on evaluating video-based GANs provide key insight that may be useful in generating new measures of quality assurance in future work.
Apoptosis and cell proliferation in the metaplasia-dysplasia-carcinoma-sequence of Barrett's esophagus. (2001)

The higher levels of both apoptosis and proliferation indicate an increased cell turnover in Barrett's epithelium. Apoptosis seems to maintain tissue homeostasis, which is regulated by p53, and gradually lost in the metaplasia-dysplasia-carcinoma-sequence of Barrett's esophagus.
Acetyl‐ <scp>l</scp> ‐carnitine vs tamoxifen in the oral therapy of Peyronie's disease: a preliminary report (2001)

These results suggest that acetyl-L-carnitine is significantly more effective and safe than tamoxifen in the therapy of acute and early chronic Peyronie's disease.