gebhart/patrepeval huggingface dataset:
Rapid genome walking: a simplified oligo-cassette mediated polymerase chain reaction using a single genome-specific primer (2000)

In the present report we show that unknown DNA fragments are easily amplified in a single PCR reaction from an oligo-cassette library with a single genome-specific primer in combination with a cassette-specific primer. The novelty of the system, in comparison to the vectorette PCR method, lies in the use of unphosphorylated in contrast with phosphorylated oligo-cassettes in the ligation to the chromosomal DNA fragments. After denaturation of the DNA library, all chromosomal fragments carry a single-stranded linker attached to the 5'-end only. Therefore, the presence of the vectorette mismatched region is not required when unphosphorylated cassettes are used. As an example we report the amplification of the era gene from Lactococcus lactis.
Severe Radiation Dermatitis is Related to Staphylococcus Aureus (2004)

Acute radiation dermatitis commonly occurs following local radiation therapy for various cancers and, when severe, may necessitate disruption of treatment. Intense inflammatory reaction may result in a breakdown of the skin's barrier function and accompanying bacterial colonization. Bacterial superantigens may exacerbate inflammation through activation of T-cells and subsequent cytokine release. We report six cases of severe radiation dermatitis in cancer patients. Four of the six grew pathogenic bacteria, and three had psoriasiform or eczematous reactions at distant sites. Both the radiation dermatitis and the distant cutaneous reactions resolved rapidly on a combination of topical steroids and oral plus topical antibiotic therapy. We suggest that staphylococcal superinfection of acute radiodermatitis intensifies the inflammatory process and hinders repair of the epidermal barrier. Patients with acute radiation dermatitis should be investigated for secondary infection. We emphasize the importance of including topical and oral antibiotic therapy in conjunction with topical corticosteroids to eradicate infection as well as hasten repair of the skin's barrier function. These cases are presented to call attention to the role of Staphylococcus aureus in the pathogenesis of severe radiation dermatitis and the need to include appropriate antibiotic therapy based on culture in the management of acute radiation dermatitis.
Analysis of Gene-Specific DNA Methylation Patterns by Pyrosequencing<sup>®</sup> Technology (2007)

As the sequence of the human genome is now nearly finished, genome research turns to elucidate gene function and regulation. DNA methylation is of particular importance for gene regulation and is strongly implicated in the pathogenesis of various diseases. The real-time luminometric detection of pyrophosphate release upon nucleotide incorporation in the Pyrosequencing technology is ideally suited for the simultaneous analysis and quantification of the methylation degree of several CpG positions in close proximity. We developed and improved this analysis to obtain reproducible results for as many as 10 successive CpGs in a single sequencing reaction spanning up to 80 nt. Advantages of the Pyrosequencing technology are the ease of its implementation, the high quality and the quantitative nature of the results, and its ability to identify differentially methylated positions in close proximity, which may be used as DNA methylation markers.
Flow cytometric analysis of tracheary element differentiation in <i>Zinnia elegans</i> cells (2005)

We have used flow cytometry to characterize the morphological and physiological changes that occur during TE differentiation, and our findings indicate that this process is a form of autophagic PCD in which microtubule rearrangement appears to play a role.
Differences in experimental tumor localization of dual-labeled monoclonal antibody. (1986)

To determine the importance of the label in the radioimmunoimaging of lesions, we studied the distribution of a monoclonal antibody (103D2) that had been labeled with both 125I and 111In. Antibody 103D2 is specific for a tumor-associated, 126-kd phosphoglycoprotein. We used the dual-labeled antibody to localize BT-20 human mammary tumors hosted in nude mice (n = 20). The means of the ratios of 111In to 125I activity in the blood, heart, lungs, liver, spleen, kidneys, thyroid, and tumors were compared at 1, 2, 3, 5, and 6 days after the i.v. administration of antibody. The mean (+/- s.d.) of the ratios of 111In to 125I activity in the tumor was 2.3 +/- 0.8 at Day 1, which increased to 9.6 +/- 1.7 by Day 5 and 12.7 +/- 5.5 by Day 6, whereas the mean of the ratios in the blood was 1.1 +/- 0.3 at Day 1, 0.9 +/- 0.2 at Day 5 and 2.0 +/- 1.0 by Day 6. These results suggest that the circulating dual-labeled antibody remains intact, but that dehalogenation occurs at the tumor site.
Aromatic Trap Analysis of Free Radicals Production in Experimental Collagen-induced Arthritis in the Rat: Protective Effect of Glycosaminoglycans Treatment (2003)

Many findings demonstrated that Glycosaminoglycans (GAGs) and Proteoglycans (PGs) possess antioxidant activity. Collagen-induced arthritis (CIA) is an experimental animal model similar to human rheumatoid arthritis (RA) in which free radicals are involved. Sodium salicylate can be used as a chemical trap for hydroxyl radicals (OH*), the most damaging reactive oxygen species (ROS), yielding 2,5-dihydroxybenzoic acid), (2,5-DHBA) and 2,3-dihydroxybenzoic acid (2,3-DHBA). The measurement of these two acids in the plasma allows to indirectly assess the production of OH* radicals. The aim of the study was to investigate the effect of hyaluronic acid (HYA) (30 mg/kg i.p.) or chondroitin-4-sulphate (C4S) (30 mg/kg i.p.), on free radical production in Lewis rats subjected to CIA. After the immunization with bovine collagen type II in complete Freund's adjuvant, rats developed an erosive hind paw arthritis, that produced high plasma OH* levels assayed as 2,3-DHBA and 2,5-DHBA, primed lipid peroxidation, evaluated by analyzing conjugated dienes (CD) in the articular cartilage; decreased the concentration of endogenous vitamin E (VE) and catalase (CA) in the joint cartilage; enhanced macrophage inflammatory protein-2 (MIP-2) serum levels and increased elastase (ELA) evaluated as an index of activated leukocyte polymophonuclear (PMNs) accumulation in the articular joints. The administration of HYA and C4S starting at the onset of arthritis (day 11) for 20 days, limited inflammation and the clinical signs in the knee and paw, reduced OH* production, decreased CD levels, partially restored the endogenous antioxidants VE and CA, reduced MIP-2 serum levels and limited PMNs infiltration. The results indicate that the GAGs HYA and C4S significantly reduce free radical production in CIA and could be used as a tool to investigate the role of antioxidants in RA.
State, event, time and diagram in system modeling (2001)

The design of complex systems requires powerful mechanisms for modeling state, concurrent events, and real-time behavior; as well as for visualising and structuring systems in order to control complexity. Methods integration has become a recent research trend in software specification and design. In the graphical area, many object-oriented methods have merged into one, the Unified Modeling Language (UML) which combines various diagrammatic modeling techniques to model static and dynamic aspects of software systems. Although traditional formal methods have not scale-up well, new integrated formal methods show great promise. This tutorial will present the state of the art in formal modeling techniques (state-based Object-Z and event-based Timed CSP), their integration (TCOZ), and transformation techniques from the integrated formalism to UML diagrams. An XML web environment for projecting integrated formal models to UML diagrams will also be demonstrated.
A system for insertional mutagenesis and chromosomal rearrangement using the Ds transposon and Cre—<i>lox</i> (1995)

A system for insertional mutagenesis and chromosomal rearrangement in Arabidopsis has been developed. The T-DNA vectors are based on the maize transposon Ds, lox sites from the Cre-lox site-specific recombination system, and transcriptional fusions expressing Ac transposase or Cre recombinase. The engineered transposon is termed Dslox. Transposed Dslox insertions were created by crossing plants bearing Dslox with plants expressing Ac transposase, then simultaneously selecting for excision and reinsertion in F2 seedlings using the herbicides chlorsulfuron and phosphonothricin, respectively. F2 plants bearing stable Dslox insertions were identified by scoring for the absence of the Ac transposase T-DNA, using a novel, visual marker in that T-DNA. Two independent Dslox insertions were characterized and placed 5.6 and 16.5 cM from their T-DNAlox, which mapped close to m506 on chromosome 4. Plants bearing either of the two different transposed Dsloxs and T-DNAlox were crossed to plants expressing Cre recombinase, which catalyzed recombination between the lox site in transposed Dslox and the lox site in T-DNAlox. Lox-lox recombinants were identified selectively amongst progeny of these crosses. Molecular and genetic analysis of the lox-lox rearrangements indicated that both were inversions. The smaller inversion was germinally transmitted from generation to generation as a simple trait, whereas the larger inversion was not transmitted to progeny of plants bearing the rearrangement.
Ultrafast locking optical clock for IP packet switching applications (2002)

The locking time of an all-optical clock is investigated. Self-pulsating, DFB lasers with detuned gratings are applied the clock locks within 10 "one" bits (1 ns) to injected data packets and keeps synchronized for some hundred "zero" bits.
The performance of depressed-cladding single-mode fibers with different b/a ratios (1991)

Depressed-cladding single-mode fibers with a first cladding-to-core ratio (b/a) ranging from seven to one and relative refractive-index differences of the core from 0.25 to 0.35% and of the cladding from 0 to -0.2% are investigated experimentally with respect to the LP/sub 11/ mode cutoff properties, the mode-field diameter, the dispersion, and the bending attenuation. Numerical calculations based on actual profile parameters of the bend loss and the mode-field diameter agree well with experiment. It is demonstrated that low attenuation and bend losses independent of b/a can be obtained if the cutoff wavelength is kept constant by adjusting the core radius, the core index or the index of the first cladding.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The relationship of “high risk” mammographic patterns to histological risk factors for development of cancer in the human breast (1990)

In the UK Trial for the Early Detection of Breast Cancer in Nottingham, 119 women were identified as having fibrocystic change with epithelial hyperplasia or in situ carcinoma. Their mammograms were classified according to Wolfe's criteria and the corresponding histology for each patient was classified for degrees of epithelial hyperplasia, atypia and in situ neoplasia using Page's criteria. A control population of patients presenting for breast screening was used to represent the general population. No correlation was found between the four mammographic Wolfe patterns, N1, P1, P2 and DY and histological evidence of epithelial hyperplasia, atypia or in situ carcinoma. A further study was carried out to determine histological features of Wolfe pattern, using radiological examination of resected breast tissue. The variation in Wolfe pattern was related to the distribution of fibrous and adipose tissue in the breast interlobular stroma and appeared to have no relationship to epithelial parenchymal content. This information does not support the hypothesis that radiographic densities of P2 and DY patterns correspond to high risk epithelial proliferation.
An R Package for Analysis of Whole-Genome Association Studies (2007)

At the current state of development the package only supports population-based studies, although we would hope to provide support for family-based studies soon. Both quantitative and qualitative phenotypes may be analysed. Flexible association testing functions are provided which can carry out single SNP tests which control for potential confounding by quantitative and qualitative covariates. Tests involving several SNPs taken together as 'tags' are also supported. Efficient calculation of pair-wise linkage disequilibrium measures is implemented and data input functions include a function which can download data directly from the international HapMap project website.
Evaluation of the Relative Importance of Parameters Influencing Perforation Cleanup (2004)

Abstract Completion of cased and cemented wells by shaped-charge perforation results in damage to the formation, which can significantly reduce well productivity. Typically, underbalanced conditions are imposed during perforation in an effort to remove damaged rock and shaped-charge debris from the perforation tunnel. Immediately after the shaped-charge jet penetrates the formation, there is a transient surge of fluid from the formation through the perforation and into the well bore. Experimental evidence suggests that it is this transient pressure surge that leads to the removal of damaged rock and charge debris leaving an open perforation tunnel. We have developed a two-stage computational model to simulate the perforation process and subsequent pressure surge and debris removal. The first stage of the model couples a hydrocode with a model of stress-induced permeability evolution to calculate damage to the formation and the resulting permeability field. The second stage simulates the non-Darcy, transient fluid flow from the formation and removes damaged rock and charge debris from the perforation tunnel. We compare the model to a series of API RP19B section 4 flow tests and explore the influence of fluid viscosity and rock strength on the final perforation geometry and permeability.
SUN-460 Anticipating Hypokalemia in Patients With ACTH-Dependent Cushing Syndrome Treated With Mifepristone: Utilization of Cortisol and ACTH Levels to Identify At-Risk Patients (2019)

Background: Hypokalemia (K+ level <3.5 mEq/L) is common in patients with hypercortisolism. Treatment with mifepristone, a glucocorticoid receptor antagonist, can exacerbate hypokalemia due to the mineralocorticoid effects produced by the rapid and significant increase in cortisol levels that result from the loss of negative feedback of the HPA axis. Correction of hypokalemia is required prior to initiating mifepristone and K+ levels must be closely monitored during treatment. However, there is little guidance to help clinicians identify patients who may be at a greater risk for developing hypokalemia during mifepristone therapy and who may benefit from prophylactic treatment (eg, mineralocorticoid antagonists, potassium replacement). Method: Using data from the 24-week, open-label, phase 3 SEISMIC study, this report investigated associations between cortisol and adrenocorticotropic hormone (ACTH) levels and the development of hypokalemia in patients with ACTH-dependent Cushing syndrome treated with mifepristone. Data from 47 patients were retrospectively analyzed using logistic regressions and receiver operating characteristic (ROC) curves. Analyses were performed to identify factors associated with early-onset hypokalemia (occurring within the first 2 weeks of mifepristone treatment during doses of 300 mg/day) and late-onset hypokalemia (occurring after 2 weeks of mifepristone treatment during dose escalation). Results: Nineteen patients (40.4%) developed hypokalemia at least once during mifepristone treatment. Of these 19 patients, 10 (52.6%) developed hypokalemia by day 14. Early-onset hypokalemia was significantly related to baseline serum cortisol levels (P=.0155). Baseline serum cortisol levels >27 µg/dL (>750 nmol/L) were associated with a 6.8-fold increase in the occurrence of early-onset hypokalemia vs patients with cortisol ≤27 µg/dL (≤750 nmol/L) (58.3% vs 8.6%, P<.0011). Late-onset hypokalemia was significantly related to the 2-week ACTH levels (P=.0032). At 2 weeks, ACTH levels >112 pg/mL (>25 pmol/L) were associated with a 5.64-fold higher risk of late-onset hypokalemia vs patients with ACTH ≤112 pg/mL (≤25 pmol/L) (75% vs 13.3%; P<.0001). ACTH levels >112 pg/mL (>25 pmol/L) at 2 weeks were also associated with a greater risk of severe (K+ ≤2.5 mEq/L) or recurrent hypokalemia. Conclusions: Serum cortisol and ACTH levels may be useful in identifying patients at risk for developing hypokalemia while being treated with mifepristone. Patients with serum cortisol levels >27 µg/dL (>750 nmol/L) assessed before mifepristone initiation had a 6.8-fold increase in occurrence of early-onset hypokalemia. Patients with ACTH levels >112 pg/mL (>25 pmol/L) at 2 weeks after initiation of mifepristone (prior to dose escalation) had a 5.64-fold higher risk of late-onset hypokalemia.
Wearable Obstacle Avoidance Electronic Travel Aids for Blind: A Survey (2009)

The last decades a variety of portable or wearable navigation systems have been developed to assist visually impaired people during navigation in known or unknown, indoor or outdoor environments. There are three main categories of these systems: electronic travel aids (ETAs), electronic orientation aids (EOAs), and position locator devices (PLDs). This paper presents a comparative survey among portable/wearable obstacle detection/avoidance systems (a subcategory of ETAs) in an effort to inform the research community and users about the capabilities of these systems and about the progress in assistive technology for visually impaired people. The survey is based on various features and performance parameters of the systems that classify them in categories, giving qualitative-quantitative measures. Finally, it offers a ranking, which will serve only as a reference point and not as a critique on these systems.
Synthesis of Discrete Micrometer-Sized Spherical Particles of MCM-48 (2005)

The direct synthesis of a mesostructured silica with a tridimensional mesopore network with micrometer-sized and -shaped particles control is reported for the first time. Micrometer-sized beads of the cubic silica mesostructure MCM-48 have been obtained through a MCM-41 pseudomorphic synthesis procedure using preformed porous silica particles as silica source combined with a MCM-41/-48 phase transition. The low degree of polymerization of the MCM-41 formed in high alkaline conditions allows the further MCM-41/-48 phase transition. The kinetics of MCM-48 formation depends on the surface area of the parent silica, indicating that the dissolution of the silica in a confined environment is the rate-determining step of the process. The reaction time required to produce MCM-48 decreases from 7 to 2 h when the surface area of the parent silica increases from 160 to 740 m2/g. The MCM-48 mesostructure is metastable toward a lamellar mesostructure at longer synthesis times (>20 h). The domain of existence of the different mesostructures as a function of synthesis time and surface area of the parent silica sources has been established. The aggregation state of the MCM-48 particles can be controlled by adjusting the dilution and the alkalinity of the synthesis medium.
Surgical Endocardial Resection for the Treatment of Malignant Ventricular Tachycardia (1979)

VENTRICULAR TACHYCARDIA is a frequent post-infarction and perioperative arrhythmia. Recurrent ventricular tachycardia is less common, but is both physiologically and psychologically incapacitating when it occurs. Despite early reports of success with coronary artery bypass grafting as a treatment for these arrhythmias, recent series report disappointing results of revascularization with or without concurrent left ventricular aneurysmectomy.2,12,14 The purpose of this manuscript is to describe a new surgical technique—endocardial excision —as a treatment for recurrent ventricular tachycardia in 12 patients.
Improvement of fatigue properties of poly(methyl methacrylate) bone cement by means of plasma surface treatment of fillers (1999)

The fatigue properties of poly(methyl methacrylate) (PMMA) bone cement were significantly improved through 13.56-MHz radio frequency plasma treatments on the X-ray opaque powder and on the reinforcing fibers. For the plasma treatments of particle surfaces, a specially designed plasma reactor was used to modify the surfaces of the ZrO2 powder (X-ray opaque filler) and milled carbon fibers (reinforcing filler). The reactor chamber was designed to be rotated continuously to mix the particles during the plasma treatments to obtain uniformly treated particle surfaces. The surface peroxides resulting from the plasma treatments seemed to have a significant effect on the improvement of fatigue properties. The peroxides on the particles may yield free radicals by the reaction with the reducing agent (N,N-dimethyl-p-toluidine) in the bone cement mixture, which can initiate methyl methacrylate (MMA) polymerization. Through this graft polymerization process, the interfacial bond strength between the filler particles and the MMA matrix may be enhanced, resulting in efficient stress transfer from the matrix to the fillers.The best results of the fatigue tests were seen in the reinforced bone cement, which contained surface modified fillers, with hexamethyldisiloxane plasma, and with O2 plasma posttreatment. © 1999 John Wiley & Sons, Inc. J Biomed Mater Res (Appl Biomater) 48: 135–142, 1999
A Sequential Matching Framework for Multi-Turn Response Selection in Retrieval-Based Chatbots (2018)

We study the problem of response selection for multi-turn conversation in retrieval-based chatbots. The task involves matching a response candidate with a conversation context, the challenges for which include how to recognize important parts of the context, and how to model the relationships among utterances in the context. Existing matching methods may lose important information in contexts as we can interpret them with a unified framework in which contexts are transformed to fixed-length vectors without any interaction with responses before matching. This motivates us to propose a new matching framework that can sufficiently carry important information in contexts to matching and model relationships among utterances at the same time. The new framework, which we call a sequential matching framework (SMF), lets each utterance in a context interact with a response candidate at the first step and transforms the pair to a matching vector. The matching vectors are then accumulated following the order of the utterances in the context with a recurrent neural network (RNN) that models relationships among utterances. Context-response matching is then calculated with the hidden states of the RNN. Under SMF, we propose a sequential convolutional network and sequential attention network and conduct experiments on two public data sets to test their performance. Experiment results show that both models can significantly outperform state-of-the-art matching methods. We also show that the models are interpretable with visualizations that provide us insights on how they capture and leverage important information in contexts for matching.