gebhart/patrepeval huggingface dataset:
Characterization of a Novel Murine Model of Staphylococcus saprophyticus Urinary Tract Infection Reveals Roles for Ssp and SdrI in Virulence (2010)

Staphylococcus saprophyticus, an obligate human pathogen, is the most common Gram-positive causative agent of urinary tract infection (UTI) in young, healthy women. Despite the clinical importance of S. saprophyticus, little is known about how it causes disease in the urinary tract or how the host responds to the infection. Here we established an in vivo model to study both host and bacterial factors contributing to S. saprophyticus UTI. Using this model, we show that S. saprophyticus preferentially infects C3H/HeN murine kidneys instead of the bladder, a trait observed for multiple clinical isolates. Bacterial persistence in the kidneys was observed in C3H/HeN mice but not in C57BL/6 mice, indicating that host factors strongly contribute to the ability of S. saprophyticus to cause UTI. Using C3H/HeN mice as a model, histologic and immunofluorescence analyses of infected tissues revealed that S. saprophyticus induced epithelial cell shedding in the bladder and an inflammatory response characterized by macrophage and neutrophil infiltration in the bladder and kidneys. The inflammatory response correlated with increased production of proinflammatory cytokines and chemokines in both the bladder and the kidneys. Finally, we observed that the putative S. saprophyticus virulence factors Ssp and SdrI were important for persistence, but not for initial colonization, in the murine urinary tract. Thus, we characterized both host and bacterial factors involved in progression of S. saprophyticus UTI, and we describe a useful model system for studying factors involved in the pathogenesis of this Gram-positive uropathogen.
Morphology and rheological properties of polyethylene/polystyrene blends (2007)

International audience
The cytotoxic Staphylococcus aureus PSMα3 reveals a cross-α amyloid-like fibril (2017)

Amyloids are ordered protein aggregates, found in all kingdoms of life, and are involved in aggregation diseases as well as in physiological activities. In microbes, functional amyloids are often key virulence determinants, yet the structural basis for their activity remains elusive. We determined the fibril structure and function of the highly toxic, 22-residue phenol-soluble modulin α3 (PSMα3) peptide secreted by <i>Staphylococcus aureus</i> PSMα3 formed elongated fibrils that shared the morphological and tinctorial characteristics of canonical cross-β eukaryotic amyloids. However, the crystal structure of full-length PSMα3, solved de novo at 1.45 angstrom resolution, revealed a distinctive "cross-α" amyloid-like architecture, in which amphipathic α helices stacked perpendicular to the fibril axis into tight self-associating sheets. The cross-α fibrillation of PSMα3 facilitated cytotoxicity, suggesting that this assembly mode underlies function in <i>S. aureus</i>.
Chemoenzymatic Synthesis of Enantiopure 1-Azafagomine (1999)

A new chemoenzymatic synthesis of both enantiomeric forms of the glycosidase inhibitor 1-azafagomine (1) is reported. The synthesis starts from the achiral starting materials pentadienol and methylurazol with the key steps being a hetero-Diels−Alder reaction followed by a lipase R/Novozym 435-catalyzed enantioselective esterification of the Diels−Alder adduct.
Programmable performance - One aspect of smart sensing systems (1980)

Programmable performance is the ability to flexibly alter basic spatial, spectral, and radiometric system response as a function of time. In this paper programmable performance is defined as a functional element of smart sensor systems for the 1990's. The uses and benefits of these classes of sensor systems are discussed with reference to multispectral scanners of the earth's surface. An overall technology trend is identified which couples a high degree of sensor performance flexibility to a need for advanced device technology developments.
Cyclases of the 3'-terminal phosphate in RNA: a new family of RNA processing enzymes conserved in eucarya, bacteria and archaea. (1998)

The 2',3'-cyclic phosphate termini are produced, as either intermediates or final products, during RNA cleavage by many different endoribonucleases. Likewise, ribozymes such as hammerheads, hairpins, or the hepatitis delta ribozyme, generate 2',3'-cyclic phosphate ends. Discovery of the RNA 3'-terminal phosphate cyclase has indicated that cyclic phosphate termini in RNA can also be produced by an entirely different mechanism. The RNA 3'-phosphate cyclase converts the 3'-terminal phosphate in RNA into the 2',3'-cyclic phosphodiester in the ATP-dependent reaction which involves formation of the covalent cyclase-AMP and the RNA-N3' pp5' A intermediates. The findings that several eukaryotic and prokaryotic RNA ligases require the 2',3'-cyclic phosphate for the ligation of RNA molecules raised a possibility that the RNA 3'-phosphate cyclase may have an anabolic function in RNA metabolism by generating terminal cyclic groups required for ligation. Recent cloning of a cDNA encoding the human cyclase indicated that genes encoding cyclase-like proteins are conserved among Eucarya, Bacteria, and Archaea. The protein encoded by the Escherichia coli gene was overexpressed and shown to have the RNA 3'-phosphate cyclase activity. This article reviews properties of the human and bacterial cyclases, their mechanism of action and substrate specificity. Possible biological functions of the enzymes are also discussed.
Focus: Putting the Reins on Light (2005)

The speed of light moving through a series of metal strips depends on their dimensions rather than on their composition.
A QA phantom for dynamic stereotactic radiosurgery: Quantitative measurements (1995)

A spherical acrylic phantom was designed for quality assurance measurements of dynamic radiosurgery. The phantom consists of two mating hemispheres mounted on a base plate. The interhemispheric plane may be oriented at any angle to the base, the angle being identified by visible marks on the base plate of the phantom. The phantom has a set of replaceable, radiologically identifiable markers, suitable for Computed Tomography (CT), Magnetic Resonance (MR), and Digital Subtraction Angiography (DSA) imaging. The frame coordinates of each marker are calculated from its known positions with respect to the center of the sphere. The measured errors of these positions using CT and MR images, were within the voxel size of the displayed image, while for DSA images the error was greater than 2.5 mm at the periphery of the image. The calculated depths from the planning software, for various beam intersection points to the isocenter, agreed within 0.6 mm with the known depths. A variation of 3.6 +/- 2.6 mm in the calculated depths was observed between using MR and CT image data. This difference results in a 1% variation in Tissue Maximum ratio (TMR) calculations. Comparisons of measured and known volumes resulted in differences of 8%-10%.
p-type semiconducting Cu2O–CoO thin films prepared by magnetron sputtering (2003)

The preparation by magnetron sputtering of p-type semiconducting thin films consisting of a multicomponent oxide composed of Cu oxide and Co oxide is described. The electrical, optical, and crystallographical properties of films deposited by rf magnetron sputtering using (Cu2O)1−x–(CoO)x powder targets were strongly dependent on not only the deposition condition but also the calcination condition as well as the CoO content of the targets. These properties drastically changed in films prepared with a CoO content around 90 mol %. All prepared films, i.e., CoO content in the range from 0 to 100 mol %, were found to be p type, or positive hole conductors, as evidenced from the Seebeck effect: Resistivities in the range from 103 to 10−3 Ω cm. A hole concentration on the order of 1016 cm−3 and a mobility on the order of 10−1 cm2/V s were obtained in an amorphous multicomponent oxide film prepared with a CoO content of 50 mol %. Fabricated thin-film pin heterojunction diodes consisting of a p-type high-resistance multicomponent oxide combined with undoped ZnO and n-type Al-doped ZnO exhibited a rectifying current–voltage characteristic.
Long-Term Treatment of Overweight and Obesity with Polyglucosamine (PG L112): Randomized Study Compared with Placebo in Subjects after Caloric Restriction (2017)

<b>Background:</b> Short-term treatment of overweight and obesity with polyglucosamine (PG) was found to be more effective than placebo and orlistat in double-blind clinical studies. <b>Objective:</b> The aim of the study was to compare the efficacy of long-term (12-mo) treatment of weight loss with PG and placebo (PL). <b>Methods:</b> This was a double-blind randomized study in 100 participants of both sexes with a body mass index (in kg/m<sup>2</sup>) >30 to <35. One group of 50 participants was treated for 1 y with PG at 1.6 g/d and a similar group received PL. PG is a combination of low-molecular-weight chitosan with organic acids. Participants were instructed to reduce their caloric intake by 10% and increase the physical activity level by 9 metabolic equivalent task hours/wk. Dietary compliance was checked every 3 mo by using a weekly questionnaire [food intake assessment (FIA)] based on 25 different food servings. Body weight (BW), waist circumference (WC), blood pressure (BP), glucose, lipids, and high-sensitivity C-reactive protein (hs-CRP) were also monitored. <b>Results:</b> Ninety-seven participants completed the study (49 in the PG group, 48 in the PL group). The decrease in calories was similar in both groups, as was the change in number of food servings (<i>P</i> > 0.05, ANOVA). Decreases in BW and WC were 8.0 kg and 10.2 cm, respectively, in the PL group, whereas they were 12.1 kg and 13.3 cm in the PG group (<i>P</i> < 0.001, ANOVA). The decrease in BP, plasma lipids, glucose, and hs-CRP was more evident in the group treated with PG (<i>P</i> < 0.05, ANOVA). The intake of lipids was found to correlate directly with hs-CRP, with the exception of extra-virgin olive oil. <b>Conclusions:</b> PG was found to be more effective than PL in reducing BW, WC, glucose, BP, plasma lipids, and hs-CRP in moderately obese individuals undergoing a 10% caloric reduction and a slight increase in physical activity. Dietary monitoring with the use of an FIA was an effective tool in supporting dietary compliance. This trial was registered at clinicaltrials.gov as U111111292405 (WHO).
Implantation of hiPSC-derived Cardiac-muscle Patches after Myocardial Injury in a Guinea Pig Model (2019)

Due to the limited regeneration capacity of the heart in adult mammals, myocardial infarction results in an irreversible loss of cardiomyocytes. This loss of relevant amounts of heart muscle mass can lead to the heart failure. Besides heart transplantation, there is no curative treatment option for the end-stage heart failure. In times of organ donor shortage, organ independent treatment modalities are needed. Left-ventricular assist devices are a promising therapy option, however, especially as destination therapy, limited by its side-effects like stroke, infections and bleedings. In recent years, several cardiac repair strategies including stem cell injection, cardiac progenitors or myocardial tissue engineering have been investigated. Recent improvements in cell biology allow for the differentiation of large amounts of cardiomyocytes derived from human induced pluripotent stem cells (iPSC). One of the cardiac repair strategies currently under evaluation is to transplant artificial heart tissue. Engineered heart tissue (EHT) is a three-dimensional in vitro created cardiomyocyte network, with functional properties of native heart tissue. We have created EHT-patches from hiPSC derived cardiomyocytes. Here we present a protocol for the induction of left ventricular myocardial cryoinjury in a guinea pig, followed by implantation of hiPSC derived EHT on the left ventricular wall.
Comparing Smartphone Speech Recognition and Touchscreen Typing for Composition and Transcription (2020)

Ruan et al. found transcribing short phrases with speech recognition nearly 200% faster than typing on a smartphone. We extend this comparison to a novel composition task, using a protocol that enables a controlled comparison with transcription. Results show that both composing and transcribing with speech is faster than typing. But, the magnitude of this difference is lower with composition, and speech has a lower error rate than keyboard during composition, but not during transcription. When transcribing, speech outperformed typing in most NASA-TLX measures, but when composing, there were no significant differences between typing and speech for any measure except physical demand.
Field trials of a formulation containing moxidectin and 6 in 1 vaccines for sheep (1996)

Administration of a formulation containing moxidectin, five clostridial antigens and caseous lymphadenitis antigen proved safe and efficacious under field conditions.
AuBr3‐Catalyzed [4 + 2] Benzannulation Between an Enynal Unit and Enol. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Patient-specific Modeling and Quantification of the Heart Valves from Multimodal Cardiac Images (2010)

As decisions in cardiology increasingly rely on non-invasive methods, fast and precise image analysis tools have become a crucial component of the clinical workflow. Especially when dealing with complex cardiovascular disorders, such as valvular heart disease, advanced imaging techniques have the potential to significantly improve treatment outcome as well as to reduce procedure risks and correlated costs. 

This thesis concentrates on three aspects: physiological heart valve modeling, algorithms for patient-specific parameter estimation from multimodal images and advanced applications for clinical management of heart valve disease. In particular, a novel physiological model of the complete valvular apparatus is introduced, which captures a large spectrum of morphologic, dynamic and pathologic variations. A robust learning-based framework is proposed to estimate the patient-specific model parameters from cardiac medical scans, mainly transesophageal echocardiography, cardiac computed tomography and cardiac magnetic resonance imaging. 

This original model-driven approach enables a multitude of advanced clinical applications including quantitative valvular analysis, shape-based diagnosis and patient selection as well as computational decision support for valve replacement and repair procedures. In comparison to the gold standard methods, which manually process 2D images, the automatic 4D model-based concept provides fast, precise, reproducible and comprehensive valve quantification. Moreover, in case of emerging percutaneous and minimal invasive valve interventions, cardiac surgeons and interventional cardiologists can substantially benefit from the automated patient selection and virtual valve implantation approaches presented in this thesis. The algorithms proposed in this thesis are validated through extensive quantitative and clinical experiments involving over 476 patients treated in leading medical centers around the world.
High spectral resolution LIDAR source at 1 kHz amplifying spectrally single mode ns-pulses with active ASE suppression (2023)

In our work, we developed a LIDAR (LIght Detection And Ranging) source with high output energy of over 12 mJ and narrow spectral bandwidths &lt; 30 MHz at a repetition rate of 1 kHz. Our approach contains the amplification of pulses with E &le; 50 nJ out of a low energy seed source at the central wavelength 1064.475 nm and spectral width &lt; 20 MHz. The seed pulses were amplified in four sequential Nd:YVO<sub>4</sub> amplification stages. The amplification of parasitic ASE (Amplified Spontaneous Emission) from stage to stage due to the high emission cross section of the material had to be suppressed to guarantee maximal population inversion for the seed pulse amplification. By temporal separation of ASE and seed pulses with an AOM between the first and the second amplification stage, ASE could be suppressed sufficiently.
Speedup OS-EM image reconstruction by PC graphics card technologies for quantitative SPECT with varying focal-length fan-beam collimation (2005)

In the paper, we present a new hardware acceleration method to speedup the ordered-subsets expectation-maximization (OS-EM) algorithm for quantitative SPECT (single photon emission computed tomography) image reconstruction with varying focal-length fan-beam (VFF) collimation. By utilizing the geometrical symmetry of VFF point-spread function (PSF), compensation for object-specific attenuation and system-specific PSF are accelerated using currently available PC video/graphics card technologies. A ten-fold acceleration of quantitative SPECT reconstruction is achieved.
Grieving and Surviving PPS (2001)

Senior Patient Business Rep Editor’s Note:Look for our special focus issue in June, “Occupational Risks: Bloodborne Pathogens and Latex Allergies” with a specific emphasis on the implications of the new Needlestick Legislation for home health and hospice practitioners. A special CE offering will be included. Home Healthcare Nurse welcomes commentary from its readers. If you would like to comment on a recent article or column, please address your correspondence to: The Editor, Home Healthcare Nurse , 3904 Therina Way, Louisville, KY 40241; email: [email protected]
Cell death and DNA fragmentation induced by liposomal platinum(II) complex, L-NDDP in A2780 and A2780/PDD cells. (1994)

The effect of cisplatin and its non-cross resistant analogue, liposomal cis-bis-neodecanoato-trans-R,R-1,2-diamiconocyclohexaneplatinum (II) (L-NDDP) on inducing internucleosomal DNA fragmentation and cell death was examined in A2780 and A2780/PDD cells. In A2780 cells, both drugs were markedly effective in inducing DNA fragmentation, whereas in A2780/PDD cells, only L-NDDP produced significant DNA fragmentation, in good correlation with the observed cytotoxicity. The endonuclease inhibitor (ATA) prevented the DNA fragmentation caused by high (30-60 microM) or low (3-10 microM) concentrations of each drug in A2780 cells. In contrast, the protein synthesis inhibitor (CHX) displayed only a significant inhibitory effect on the DNA fragmentation caused by low concentrations at 48 h post-treatment. These results indicate that there are at least two different pathways leading to both drugs induced-cell death depending on drug concentrations in this cell line.
Phase I/II Study of Fractionated Radioimmunotherapy (RIT) in Relapsed Low Grade Non-Hodgkin’s Lymphoma (NHL). (2004)

Abstract RIT produces high rates of durable complete responses in “low grade” NHL. Clinical studies have thus far been limited to a single infusion of a radiolabeled anti-CD20 mAb (131I tositumomab or 90Y ibritumomab tiuxetan) in patients with &amp;lt; 25% bone marrow involvement. In this study we have tested the safety and efficacy of 4 weekly infusions of Rituximab followed by 2 fractions of 131I labelled rituximab given 8 weeks apart in relapsed "low grade" NHL and have included patients with higher levels than 25% bone marrow infiltration with lymphoma. Whole body dose (WBD) calculations have been used to allow the total dose given in 2 fractions to be increased in cohorts of 30cGy, 60cGy, 90cGy and 120cGy. A unique anti-rituximab idiotype mAb has been generated enabling serial analysis of serum rituximab concentrations (Cragg et al Blood 2004 Jun 22 Epub). This tool has allowed us to accurately quantify the serum levels of rituximab during the entire treatment schedule. We have also analysed the impact made by induction rituximab, the pre-dose of cold antibody and effects of fractionated RIT on the clearance and biodistribution of the 131I labeled rituximab. Sequential pharmacokinetic analyses have identified wide variation in the effective half-life of 131I-rituximab not only between patients but also within the same patient over the course of the treatment protocol. We found that the mean effective half-life of 131I rituximab increased from 43 hours prior to induction rituximab to approximately 106 hours prior to the second fraction of 131I-rituximab. A strong inverse correlation was found between the patients’ disease burden and the clearance of rituximab, both in the same patient as the tumor burden decreased and between different patients. We have demonstrated that higher cumulative WBD doses can be safely delivered by RIT dose fractionation than can be given with a single dose of anti-CD20, with no grade 3–4 myelotoxicity at the 90 cGy dose level. All 12 patients in the first 3 dose cohorts experienced responses and response durations equal to, or in the majority of cases, superior to that seen with their previous chemotherapy regimen. Data on all 16 patients including 120 cGy dose level will be available at the time of presentation. In conclusion, this fractionated RIT protocol is feasible, efficacious and enables larger WBD doses to be safely delivered than has previously been achieved with non-myeloablative RIT.
A game theoretic approach to controller design for hybrid systems (2000)

We present a method to design controllers for safety specifications in hybrid systems. The hybrid system combines discrete event dynamics with nonlinear continuous dynamics: the discrete event dynamics model linguistic and qualitative information and naturally accommodate mode switching logic, and the continuous dynamics model the physical processes themselves, such as the continuous response of an aircraft to the forces of aileron and throttle. Input variables model both continuous and discrete control and disturbance parameters. We translate safety specifications into restrictions on the system's reachable sets of states. Then, using analysis based on optimal control and game theory for automata and continuous dynamical systems, we derive Hamilton-Jacobi equations whose solutions describe the boundaries of reachable sets. These equations are the heart of our general controller synthesis technique for hybrid systems, in which we calculate feedback control laws for the continuous and discrete variables, which guarantee that the hybrid system remains in the "safe subset" of the reachable set. We discuss issues related to computing solutions to Hamilton-Jacobi equations. Throughout, we demonstrate out techniques on examples of hybrid automata modeling aircraft conflict resolution, autopilot flight mode switching, and vehicle collision avoidance.