gebhart/patrepeval huggingface dataset:
Galileo evolution: Enhanced error correction strategies and integrity assessments (2007)

Galileo corrections will be generated and broadcasted to the users in the navigation message using the same principle as GPS. For that reason the Galileo ground segment determines the ephemeris and satellite clock parameters for all satellites using observations from monitoring stations and estimates the extrapolation parameters to be uplinked to the satellites.&#13;\nBy using measured GPS data, from IGS stations (International GPS Service) and post processing data, it is possible to compute the instantaneous pseudo range errors for a given period of time. Thanks to a fast Fourier transformation of these time series, an error spectrum is generated and among other characteristics, the periodicities of errors are extracted.&#13;\nFrom these GPS measurements, an error model is build taking into account these periodicities of errors and their magnitudes. Thanks to the foreseen UERE (User Equivalent Range Error) budget for Galileo, a corresponding error model for Galileo is generated.&#13;\nFrom these models, simulations using different correction rates are made and the impact of these simulations at error spectrum level will allow to draw conclusions on the relationship between error correction rates and periodicities of effects. This analysis acts as basis for identifying the best extrapolation strategy to be used in order to minimize the residual pseudo range error.&#13;\nThe above defined work is made at pseudo range level and constitutes the first part of our study.&#13;\nA second part of the work deals with the impact of these corrections strategies at position level. The above defined techniques will have impact on both the accuracy and the integrity of the overall system.&#13;\nThese performances are assessed, their applicability to Galileo is studied and recommendations for Galileo evolutions are given.
Human interleukin‐1 receptor antagonist is expressed in liver (1992)

Using PCR and Northern blot analysis, an IL-1 receptor antagonist specific transcript was amplified from HepG2- and liver mRNA. cDNA clones coding for IL-1 receptor antagonist were isolated from a liver cDNA library and sequence comparison revealed complete identity with the secreted, monocytic form of IL-1 receptor antagonist.
Shareable Technology Mash-Up for Situation Awareness in Catastrophic Events (2012)

This paper offers a descriptive account of the use of a shareable mash-up of technologies designed to create situation awareness during catastrophic events. In particular, we focus on the exploratory use of technologies for information aggregation and sharing between public and private sector entities during a national emergency simulation--National Level Exercise 2011. The goal of this research is to seek a proper way to integrate ubiquitous technologies such as Twitter, Google Earth Map, and Person Finder to share situation updates as well as monitor resource allocation during response to a catastrophic event. We implement an emergent use of micro syntaxes on feeds from Twitter to facilitate coordination of efforts among responding agencies. This paper concludes with a discussion of several implications for design based on our findings that may be beneficial to crisis management as well as other domains.
Middle Ear Administration of a Particulate Chitosan Gel in an in vivo Model of Cisplatin Ototoxicity (2019)

Particulate chitosan is a promising drug carrier for IT administration. Future studies should assess whether the physical properties of this technique allow for a smaller injection volume that would reduce conductive hearing loss.
Multiple Myeloma Sequencing Reveals Subclonality and Timing of Genetic Alterations (2011)

Abstract Abstract 2897 Multiple myeloma is considered to be a homogenous disease within a given patient, and current classification systems and treatment algorithms are based on this assumption. We have asked if there is genetic heterogeneity of multiple myeloma within a patient and if this heterogeneity can be quantified. To address this question, we have used massively parallel whole exome and whole genome sequencing of tumors and matched normal controls of 64 patients with multiple myeloma. We present an analytic strategy to distinguish potential driver mutations based on their clonality. We demonstrate that in some patients there are many somatic mutations that are only present in a subclonal fraction of the malignant plasma cells, and the subclonal fraction comprises up to 50%. These mutations are therefore less likely to confer a selective clonal advantage and are less attractive therapeutic targets because they only affect a small fraction of the myeloma cells. As an example, we found KRAS to be one of the most prevalent mutated genes in multiple myeloma, and KRAS mutations are significantly more likely clonal than subclonal, while other mutations in other genes are predominantly subclonal. We also used this approach to investigate how copy number variations are related to somatic mutations, i.e. to define the temporal sequence of these events. This question is particularly relevant for hyperdiploidy in multiple myeloma, since this is associated with trisomies of odd numbered chromosomes. However, these trisomies do not occur with the same frequency in all odd numbered chromosomes and some hyperdiploid samples are also associated with trisomies of various even numbered chromosomes. It is unclear if these trisomies occur as a single catastrophic event, or rather in a sequential fashion. By assuming a constant rate of somatic mutations and utilizing this rate as a “timer” for chromosomal duplications we demonstrate that trisomies of odd-numbered chromosomes appear to occur early in a distinct order, whereas trisomies of even-numbered chromosomes and chromosome 1q occur late. Our analyses allow us to determine which somatic mutations occurred before chromosomal duplication and may therefore give insight in the time course of pathogenic genetic alterations in multiple myeloma. Our work may also play an important role in prioritizing somatic mutations for therapeutic targeting in multiple myeloma. Disclosures: No relevant conflicts of interest to declare.
Lactulose Breath Testing Predicts the Response to Rifaximin (2017)

Introduction: There has been an ongoing debate on the relevance of breath testing (BT) in identifying small intestinal bacterial overgrowth (SIBO), especially in subjects with irritable bowel syndrome (IBS). Although the nonsystemic antibiotic rifaximin is approved for the treatment of IBS with diarrhea (IBS-D) in adults, determinants of response remain unclear. In this analysis, we examined the potential utility of BT in predicting response to rifaximin treatment. Methods: As part of the previously published TARGET 3 trial,1 home kits were used to conduct lactulose breath testing in a subset of patients with IBS-D. Subjects had a breath test at baseline, after completion of a 2-week course of open-label rifaximin 550 mg twice daily, after relapse (retreatment baseline), and after subsequent retreatment with rifaximin. Breath test results were categorized as positive or negative based on the 2017 North American Consensus publication.2 These results were then compared, based on patient response to rifaximin (FDA-defined composite endpoint). Response was defined as meeting weekly response for abdominal pain (≥30% decrease from baseline in mean weekly pain score) and stool consistency (≥50% decrease from baseline in number of days/week with Bristol Stool Scale type 6 or 7 stool) during ≥2 of the first 4 weeks after treatment. Results: Of 98 subjects enrolled in the substudy, 93 had interpretable breath tests without missing values. SIBO was detected in 66.7% of subjects prior to treatment with rifaximin. There was no significant difference in demographics or symptom profile of patients with or without SIBO (Table). Baseline demographics and symptoms did not predict response to open-label rifaximin; however, 59.7% of patients with IBS-D and a positive baseline BT responded to rifaximin vs 25.8% of patients with a negative BT (P=0.002; odds ratio 4.3, 95% CI, 1.5-12.7). BT after rifaximin therapy did not predict response (P=0.2); however, response rate in patients whose breath test results normalized after rifaximin treatment was 76.5%. Pre-/post-rifaximin BT did not predict the time to recurrence in patients (P=0.5).Table: Table. Baseline Demographics and Symptom CharacteristicsConclusion: A positive lactulose breath test predicted a higher likelihood of response to rifaximin in patients with IBS-D. These results point to a gut microbiome-related mechanism of action for rifaximin and the utility of breath testing in IBS.
Stiffness Estimation and Experiments for the Exechon Parallel Self-Reconfiguring Fixture Mechanism (2012)

The Exechon X150, a new smaller member of a successful series of parallel kinematic machines, has been recently developed as a component of a mobile self-reconfigurable fixture system within an inter-European project. This paper is the first to address the stiffness analysis of the parallel mechanism on which the design is based. The stiffness modeling method uses reciprocal screw theory as well as the virtual work principle, resulting in a simpler formulation and more convenient than ones obtained with traditional stiffness-modeling methods. Based on this model, the stiffness map within the workspace is obtained. The stiffness of the mechanism at a typical configuration is carried out. The complete finite element analysis and simulation used to verify the effectiveness of the stiffness model. Using geometric spatial decomposition, numerical examples of the mechanism at three typical configurations are presented.
The prevalence of Helicobacter pylori in peptic ulcer disease. (1995)

Both duodenal and gastric ulcer disease are closely associated with Helicobacter pylori infection. An infected individual has an estimated lifetime risk of 10-20% for the development of peptic ulcer disease, which is at least 3-4 fold higher than in non-infected subjects. H. pylori infection can be diagnosed in 90-100% of duodenal ulcer patients and in 60-100% of gastric ulcer patients. Subjects infected with a cytotoxin-producing bacterial strain, or a strain possessing cagA, are at a higher risk of duodenal ulcer. Other factors that may influence the peptic ulcer risk in infected subjects are the amount of gastric acid production (which is increased in duodenal ulcer disease and decreased in gastric ulcer disease), the presence of gastric metaplasia in the duodenal bulb, smoking, and genetic factors (e.g. blood group O and lack of the secretor gene). After eradication of the infection, the risk of recurrence of ulcer disease is reduced to below 10% for gastric ulcer disease and to approximately 0% for duodenal ulcer disease.
Bacteriolytic Activity of Enzymes Derived from Streptomyces Species (1972)

Journal Article Bacteriolytic Activity of Enzymes Derived from Streptomyces Species Get access Kanae Yokogawa, Kanae Yokogawa Research and Development Division, Dainippon Pharmaceutical Co., Ltd. Search for other works by this author on: Oxford Academic Google Scholar Shigeo Kawata, Shigeo Kawata Research and Development Division, Dainippon Pharmaceutical Co., Ltd. Search for other works by this author on: Oxford Academic Google Scholar Yoshio Yoshimura Yoshio Yoshimura Research and Development Division, Dainippon Pharmaceutical Co., Ltd. Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 36, Issue 12, 1 December 1972, Pages 2055–2065, https://doi.org/10.1080/00021369.1972.10860539 Published: 01 December 1972 Article history Received: 07 March 1972 Published: 01 December 1972
STANDARDIZATION OF SPECIFIC RADIOIMMUNOASSAYS FOR PLASMA PROGESTERONE, ESTRADIOL, ESTRONE AND ANDROSTENEDIONE (1974)

Journal Article STANDARDIZATION OF SPECIFIC RADIOIMMUNOASSAYS FOR PLASMA PROGESTERONE, ESTRADIOL, ESTRONE AND ANDROSTENEDIONE Supported in part by Deutsche Forschungsgemeinschaft. Get access E Friedrich, E Friedrich Universitäts-Frauenklinik Tübingen Search for other works by this author on: Oxford Academic Google Scholar E R Jaeger-Whitegiver, E R Jaeger-Whitegiver Universitäts-Frauenklinik Tübingen Search for other works by this author on: Oxford Academic Google Scholar M Bieder, M Bieder Universitäts-Frauenklinik Tübingen Search for other works by this author on: Oxford Academic Google Scholar H Halverscheidt, H Halverscheidt Universitäts-Frauenklinik Tübingen Hewlett Packard, Böblingen Search for other works by this author on: Oxford Academic Google Scholar B Penke, B Penke Universitäts-Frauenklinik Tübingen Institute of Organic Chemistry, Szeged, Hungary Search for other works by this author on: Oxford Academic Google Scholar P Pallai, P Pallai Universitäts-Frauenklinik Tübingen Institute of Organic Chemistry, Szeged, Hungary Search for other works by this author on: Oxford Academic Google Scholar E Keller, E Keller Universitäts-Frauenklinik Tübingen Search for other works by this author on: Oxford Academic Google Scholar A E Schindler A E Schindler Universitäts-Frauenklinik Tübingen Search for other works by this author on: Oxford Academic Google Scholar Acta Endocrinologica (Norway), Volume 77, Issue 1_Supplement, Apr 1974, Page S89, https://doi.org/10.1530/acta.0.077S089 Published: 01 April 1974
Eradication of drug-resistant Acinetobacter baumannii by cell-penetrating peptide fused endolysin (2022)

Antimicrobial agents targeting peptidoglycan have shown successful results in eliminating bacteria with high selective toxicity. Bacteriophage encoded endolysin as an alternative antibiotics is a peptidoglycan degrading enzyme with a low rate of resistance. Here, the engineered endolysin was developed to defeat multiple drug-resistant (MDR) Acinetobacter baumannii. First, putative endolysin PA90 was predicted by genome analysis of isolated Pseudomonas phage PBPA. The His-tagged PA90 was purified from BL21(DE3) pLysS and tested for the enzymatic activity using Gram-negative pathogens known for having a high antibiotic resistance rate including A. baumannii. Since the measured activity of PA90 was low, probably due to the outer membrane, cell-penetrating peptide (CPP) DS4.3 was introduced at the N-terminus of PA90 to aid access to its substrate. This engineered endolysin, DS-PA90, completely killed A. baumannii at 0.25 µM, at which concentration PA90 could only eliminate less than one log in CFU/ml. Additionally, DS-PA90 has tolerance to NaCl, where the ∼50% of activity could be maintained in the presence of 150 mM NaCl, and stable activity was also observed with changes in pH or temperature. Even MDR A. baumannii strains were highly susceptible to DS-PA90 treatment: five out of nine strains were entirely killed and four strains were reduced by 3-4 log in CFU/ml. Consequently, DS-PA90 could protect waxworm from A. baumannii-induced death by ∼70% for ATCC 17978 or ∼44% for MDR strain 1656-2 infection. Collectively, our data suggest that CPP-fused endolysin can be an effective antibacterial agent against Gram-negative pathogens regardless of antibiotics resistance mechanisms.
High-Sensitivity Flow Cytometric Analysis for the Evaluation of Systemic Mastocytosis Including the Identification of a New Flow Cytometric Criterion for Bone Marrow Involvement (2012)

We used high-sensitivity flow cytometry to assess 93 bone marrow aspirates for involvement by systemic mastocytosis. Aberrant CD2/CD25 expression by CD117-gated mast cells was seen in 34 samples (37%), with the majority of mast cells expressing both markers (n = 23; 68%). In 24 cases, a discrete population of mast cells within the CD117-bright gate correlated with a positive morphologic finding in the biopsy, even in the absence of an aberrant immunophenotype. A discrete CD117-bright population, when considered a positive criterion, increases analytic sensitivity from 77% to 95%, exceeding the sensitivity of morphologic analysis (69% for aspirate and 85% for biopsy). We conclude that flow cytometry is a sensitive and specific test for the presence of systemic mastocytosis, particularly when the presence of a discrete CD117-positive mast cell population is regarded as a diagnostic criterion.
Co-PACRR: A Context-Aware Neural IR Model for Ad-hoc Retrieval (2017)

Neural IR models, such as DRMM and PACRR, have achieved strong results by successfully capturing relevance matching signals. We argue that the context of these matching signals is also important. Intuitively, when extracting, modeling, and combining matching signals, one would like to consider the surrounding text (local context) as well as other signals from the same document that can contribute to the overall relevance score. In this work, we highlight three potential shortcomings caused by not considering context information and propose three neural ingredients to address them: a disambiguation component, cascade k-max pooling, and a shuffling combination layer. Incorporating these components into the PACRR model yields Co-PACRR, a novel context-aware neural IR model. Extensive comparisons with established models on Trec Web Track data confirm that the proposed model can achieve superior search results. In addition, an ablation analysis is conducted to gain insights into the impact of and interactions between different components. We release our code to enable future comparisons.
Craniotomy versus Transsphenoidal Excision of Large Pituitary Tumors: The Usefulness of Magnetic Resonance Imaging in Guiding the Operative Approach (1986)

Fifteen patients with large pituitary tumors were studied with computed tomography (CT) and magnetic resonance imaging (MRI). CT was performed using General Electric 8800 and 9800 scanners (General Electric Co., Medical Systems Division, Milwaukee, Wisconsin). MRI was performed utilizing a Technicare superconducting scanner (Technicare, Cleveland, Ohio) at 0.5 tesla. Based on the operative findings, the tumors were divided into two groups. Tumors in Group 1 (n = 12) were described by the surgeon as soft or partially necrotic and easily removed by suction and curettage. Tumors in Group 2 (n = 3) were firm and required sharp dissection or the laser for removal. The tumors were divided into four categories based on MRI signal: (a) isointense with surrounding brain on spin echo (SE) 30 and SE 90, (b) increased signal intensity on SE 30 and SE 90, (c) decreased signal intensity on SE 30 and increased signal intensity on SE 90, and (d) isointense signal on SE 30 and increased signal intensity on SE 90. All three of the firm tumors were isointense with brain on MRI appearance. The tumor consistency (firm vs. soft) was not differentiable on CT scan. The transsphenoidal approach is less satisfactory than craniotomy in cases of firm, fibrous pituitary tumors. Based on our preliminary data, if the MRI signal in the tumor is isointense, then the surgeon should be prepared to deal with a fibrous tumor and might elect a transcranial rather than a transsphenoidal approach.
132. Gene Therapy With Self-Complementary Recombinant Adeno-Associated Virus in Models of Autosomal Dominant Retinitis Pigmentosa Cause by RHO Mutations (2015)

Retinitis pigmentosa is the leading hereditary cause of blindness with 30-40% of cases attributable to autosomal dominant retinitis pigmentosa (ADRP). ADRP arises from mutations in at least 24 known genes with 30% arising in the rhodopsin gene (RHO). Given the large heterogeneity of mutations in RHO leading to ADRP, we propose knocking down of endogenous RHO and replacing it with a “hardened” copy, or a RHO with nucleotide changes that preserve the amino acid sequence but decrease the efficiency of knock-down. Here we report the use of a scAAV serotype 8 (Y733F) to express a hardened human rhodopsin (hRHO) under the control of the human opsin proximal promoter (HOPS) and an H1 promoter driven shRNA. Four different knock-down methods were tested, ribozyme (Rz) 407 and Rz525, miRNA 301 and shRNA 301 against both the wildtype and hardened RHO target regions. The transfections were done in HEK293 cells (n=6) with (1) the target plasmid psiCheck2 dual luciferase containing RHO target region, (2) plasmid expressing the shRNA, miRNA or ribozyme against the target region and (3) a control miRNA. The reduction in expression of luciferase was measured at 24 and 48 hours post transfection. We are using adeno-associated virus vectors to deliver these RNA knockdown agents to mouse models of ADRP: Rho I307N and human RHO transgenic T17M and P23H. Mice were injected with AAV-HOP-hRHO and knockdown agents at postnatal day 5. I307N Rho mice were created through the use of N-ethyl-N-nitrosourea (Budzynski et al. JBC 2010). The I307N mouse model exhibits very slow degeneration under ambient light but is reduced in visual response to light by 50% in one week post exposure to 10,000 lux. Intravitreal injections with one of the two constructs, hRHO+shRNA301, or hRHO+shRNA750 in one eye and AAV-HOPS-mCherry or sham injection in the other. The mice were followed using electroretinogram and optical coherence tomography. The knock-down results show shRNA301 and ribozyme 525 to cause the largest reduction of RHO mRNA. At one month post injection there was statistically significant difference between T17M RHO eyes injected with AAV-hRHO-shRNA750 and the sham injected eyes. We have generated a series of combination RNA knockdown and replacement AAV vectors that may be useful for the treatment of ADRP. At early time points, our tests of these specific vectors have not been conclusive. The injected mice will be followed for longer intervals and additional mice will be added to the study to determine if the difference in visual function of the experimentally treated eyes versus the control is statistically significant.
Spatio-Temporal Motion Compensated Noise Filtering Of Image Sequences (1989)

In this paper the filtering of noise in image sequences using spatio-temporal motion compensated techniques is considered. Noise in video signals degrades both the image quality and the performance of subsequent image processing algorithms. Although the filtering of noise in single images has been studied extensively, there have been few results in the literature on the filtering of noise in image sequences. A number of filtering techniques are proposed and compared in this work. They are grouped into recursive spatio-temporal and motion compensated filtering techniques. A 3-D point estimator which is an extension of a 2-D estimator due to Kak [5] belongs in the first group, while a motion compensated recursive 3-D estimator and 2-D estimators followed by motion compensated temporal filters belong in the second group. The motion in the sequences is estimated using the pel-recursive Wiener-based algorithm [8] and the block-matching algorithm. The methods proposed are compared experimentally on the basis of the signal-to-noise ratio improvement and the visual quality of the restored image sequences.