gebhart/patrepeval huggingface dataset:
Genetic instability coupled to clonal selection as a mechanism for tumor progression in the Dunning R-3327 rat prostatic adenocarcinoma system. (1982)

The androgen-sensitive Dunning R-3327-H prostatic adenocarcinoma has been maintained by continuous serial passage in intact male rats for many years. While it has been possible to maintain the original characteristics of the well-differentiated H tumor over 16 years, there have evolved spontaneously, however, more aberrant sublines from this tumor at several subpassages in intact male rats. Serial passage of these individual sublines has established five additional R-3327 tumors each with distinct phenotypes and each more aberrant than the parent H tumor. In addition, it has been possible by passage of the H tumor in castrated male rats to obtain a well-differentiated slow-growing adrogen-insensitive tumor termed the Hl-S tumor. The continuous serial passage of this Hl-S tumor has likewise resulted in the emergence of three new types of Dunning tumors. The results from the biochemical and chromosomal studies presented demonstrate that there is a consistent association in each of these tumor progressions between the expression of genetic instability, which results in the addition of phenotypically new clones of cells to the tumor population, and the subsequent selection of these newly developed clone. These results suggest that the process of genetic instability coupled to clonal selection is one mechanism for the change in tumor phenotype characteristically associated with tumor progression within this system of prostatic tumors.
Zirconocene-catalyzed stereoselective cyclocopolymerization of 2-methyl-1,5-hexadiene with propylene (2014)

The copolymerization of 2-methyl-1,5-hexadiene (MHD) with propylene has been studied with different single-site group 4 metal catalysts. Systems based on ansa-zirconocene precursors such as rac-{Me2Si(2-Me-4-Ph-Ind}ZrCl2 (1) and C1- or CS-symmetric ansa-{CpCR2Flu}ZrCl2 (2 and 3, respectively), once activated by MAO, are highly active (20–600 kgpol gcat−1 h−1 at 60–70 °C) and yield copolymers in which MHD is cyclopolymerized as methylene-(1-methyl)-1,3-cyclopentane (MMCP) units. 13C NMR studies revealed, depending on the symmetry of the precatalyst used, either highly isotactic (1, 2) or syndiotactic (3) polypropylene (PP) backbones, with isolated MMCP units. Fully trans-diastereoselective cyclopolymerization of MHD was observed with 1/MAO, while a mixture of trans and cis MMCP rings was observed with 2 and 3/MAO. The amount of MMCP units in PP (0.2–1.6 mol%) can be controlled by the amount of MHD in the feed. In contrast, the constrained geometry catalyst system based on {C5Me4SiMe2NtBu}TiCl2 (4) and MAO showed a much lower productivity (ca. 3 kgpol gcat−1 h−1 at 60 °C) and yielded a regioirregular, atactic copolymer in which MHD is simply vinyl-inserted in quite moderate amounts (0.2 mol%).
Discovery of Soliton Self-Mode Conversion in Multimode Optical Fibers (2018)

Nonlinear optical wave propagation manifests in a multitude of frequencies generated from quantum-noise, and selecting desired nonlinear products usually requires seeding the medium with extraneous waves, employing spatial or spectral filters, or operation in resonant cavities. This is especially true for multimode systems because of their high density of states. Here we report the discovery of a self-action effect, originating from quantum noise, leading to complete nonlinear optical conversion of an ultrashort soliton pulse between two distinct, spatially coherent eigenmodes that are frequency-separated by one Raman Stokes shift. That systematic nonlinear spatial reconfiguration occurs in fibers with mode counts exceeding 10,000, which are often deemed to be chaotic, points to the fundamental role of intermodal group velocity dispersion in the selection rules for multimode nonlinear optics. We demonstrate wideband spectral translations of ~70% of the carrier frequency, and the generation of record, Megawatt peak-power pulses in the biologically crucial 1300-nm spectral window, directly out of a flexible optical fiber. More generally, this novel nonlinear coupling mechanism may be applied to fibers or on-chip waveguides, and facilitate, power-scalable spatially coherent, ultrashort pulse generation from the visible to the mid-IR.
Mini direct drive robot arm for biomedical application (1991)

The potential of electromagnetic actuation in a very small machine has been investigated. It has been compared to the newer technology of electrostatic micro-machines. Considerations on energy density, scaling capability, heat dissipation and actual geometry of a design have lead the authors to the conclusion that electromagnetic actuators are also competitive in the submillimeter range. The authors give a description of their 4 degree of freedom direct drive force feedback mini robot. It uses winchester disk drive technology, which is compact, powerful, clean and getting smaller, year after year. This robot could be the prototype of a family of mini-robots adapted to micro-surgery, biology and clean-room environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Surface domain inversion in LiNbO 3 by direct UV writing (2007)

Ferroelectric domain inversion has been achieved on the +z and the -z faces of congruent undoped lithium niobate (LiNbO3) single crystals by direct UV writing using a continuous wave (c.w.) frequency doubled argon ion laser (lambda = 244 nm). The width and the depth of the domains were observed to depend on the intensity and the spot size of the laser beam as well as the writing speed. The inverted domain structures were investigated by scanning electron microscopy (SEM), after HF acid differential etching, and piezoresponse force microscopy (PFM) [1]. UV laser inverted domains directly written on a multi domain crystal (PPLN) show that the PFM contrast of the UV written domains is lower as compared to the bulk domains (Fig. 1b). This indicates that the UV written domains are shallower than 1 micron because any domain depth exceeding ~ 1 micron in LiNbO3 would appear as bulk in PFM imaging. This is consistent with the extremely small absorption depth of Although shallow these UV laser written domains can be also remarkably narrow and also they can be fabricated onto any surface independent of the crystal orientation. Driving these surface domains deeper in the crystal by optical or electric field post processing is currently under investigation.
Directed evolution of Diels-Alderase ribozymes using in vitro compartmentalisation. (2006)

Darwinian evolution in nature has produced many remarkable biocatalysts. By emulating the same processes in the laboratory there is great potential to produce catalysts that rival natural enzymes for efficiency, and are tailor made to the needs of science and industry. In addition, it may be possible to gain a deeper understanding of the evolutionary process itself. In vitro compartmentalization (IVC) has previously been used to evolve protein enzymes. In this thesis, I demonstrate how IVC can be applied to select RNA enzymes (ribozymes) for a property that has until now been unselectable: true intermolecular catalysis. Libraries containing up to 10<sup>11</sup> ribozyme genes are compartmentalized in the aqueous droplets of a water-in-oil emulsion, such that most droplets contain no more than one gene, and transcribed in situ. By co-encapsulating the gene, RNA, and the substrates/products of the catalysed reaction, ribozymes can be selected for all enzymatic properties: substrate recognition, product formation, rate acceleration and turnover. Starting from a large random library of RNAs, a previous study using SELEX, which is based on selection for single-turnover, intramolecular reactions, yielded Diels-Alderase ribozymes which all contained the same catalytic motif. Selecting exactly the same library using IVC, in addition to ribozymes with the motif found in the SELEX study, it was possible to select Diels-Alderase ribozymes with a completely novel catalytic motif. All the selected ribozymes were capable of catalysing the reaction between dienes and dienophiles in solution in a truly bimolecular fashion and with multiple turnover. Interestingly, the catalytic properties of all the selected ribozymes were quite similar. The ribozymes are strongly product inhibited consistent with the Diels-Alder transition state closely resembling the product. More efficient Diels-AIderases may also need to catalyse a second reaction that transforms the product and prevents product inhibition.
On robustness of turbo coded OFDM systems over frequency selective channels (2003)

The robustness of fixed Turbo coded communication systems over frequency selective channels are investigated. The simulated amplitude functions are based on an idealised two level function and a decaying function. The results indicate that the system can cope with severe disturbances without to much loss.
Novel Genomic Aberrations in Testicular Germ Cell Tumors by Array‐CGH, and Associated Gene Expression Changes (2006)

This first genome-wide integrated array-CGH and gene expression profiling of TGCT provides novel insights into the genome biology underlying testicular tumorigenesis.
Simple model for patterned bidirectional anchoring of nematic liquid crystal and its bistability (2002)

An effective anchoring model for the patterned surface with bidirectional rubbing by atomic force microscope was proposed. The model was a simple additive function of two bidirectional anchoring contributions of the patterned surface, with consideration of higher-order terms of the anchoring function. The bistable switching behavior of the nematic liquid crystal cells with the patterned surface was investigated analytically and numerically using this anchoring model.
Highly accelerated cardiovascular magnetic resonance imaging: concepts and clinical applications (2006)

Cardiovascular MR imaging (CVMR) has become a valuable diagnostic imaging modality for the non-invasive detection cardiovascular diseases. In this review, first key concepts and practical considerations of parallel CVMR are outlined. Next, highly accelerated CVMR applications are reviewed, ranging from cardiac anatomical and functional assessment to myocardial perfusion and viability to MR angiography of the coronary arteries and the large vessels. Finally, current trends, including the broad move towards high field imaging, and future directions in highly parallel CVMR are considered.
A single-cable PVDF transducer readout IC for intravascular photoacoustic imaging (2015)

This paper presents a custom-designed single-cable readout IC for the reception of the broadband photoacoustic (PA) signal in intravascular photoacoustic (IVPA) imaging. The readout IC is intended for direct integration behind a broadband polyvinylidene fluoride (PVDF) transducer in an IVPA catheter tip to match the impedance between the small PVDF element and the connecting cable. The capability of the readout IC to work with a single cable that combines the output signal and the power supply ensures the mechanical flexibility of the IVPA catheter. Electrical measurements show that the readout IC provides a flat frequency response from 1 MHz to 20 MHz with a 6 mA external current supply. The acoustical measurements involving the readout IC and the PVDF transducer demonstrate a 60 dB dynamic range, a sensitivity of 3.8 μV/Pa at 2.25 MHz, and a broad receiving bandwidth from 2 MHz to 15 MHz.
The complex Impact of Five Years of Stress Related to Life-Threatening Events on Pregnancy Outcomes: A Preliminary Retrospective Study (2014)

Exposure to chronic life-threatening stress resulted in more pregnancy complications and in particular more premature membrane ruptures. The impact was most significant during the middle period of the 5-year-exposure to the stressor. Hence it seems that factors of duration and habituation may play a role in the impact of chronic, life-threatening stressors on pregnancy.
Advanced MRI Protocols to Discriminate Glioma From Treatment Effects: State of the Art and Future Directions (2022)

In the follow-up treatment of high-grade gliomas (HGGs), differentiating true tumor progression from treatment-related effects, such as pseudoprogression and radiation necrosis, presents an ongoing clinical challenge. Conventional MRI with and without intravenous contrast serves as the clinical benchmark for the posttreatment surveillance imaging of HGG. However, many advanced imaging techniques have shown promise in helping better delineate the findings in indeterminate scenarios, as posttreatment effects can often mimic true tumor progression on conventional imaging. These challenges are further confounded by the histologic admixture that can commonly occur between tumor growth and treatment-related effects within the posttreatment bed. This review discusses the current practices in the surveillance imaging of HGG and the role of advanced imaging techniques, including perfusion MRI and metabolic MRI.
Automatic Gear Shifting in Sport Motorcycles (2013)

Performing safe and effective gear shifts on two-wheeled vehicles in an automatic way is a challenging task, mainly due to the complexity of the system dynamics and the safety-critical aspects of the application. This work offers one of the first contributions in this area, analyzing all the aspects related to this control problem. Specifically, this work provides two main results: an objective quality assessment of the gear-shifting performance and a new gear shift control strategy that optimizes the tradeoff between duration and comfort. The results obtained on an instrumented vehicle confirm the suitability of the proposed approach.
Exchangeable Miniaturized Mass Spectrometer Chip Based on Silicon Structures (2018)

This paper reports a design of an exchangeable miniaturized mass spectrometry chip using spring-loaded pins and O-rings for electrical and fluidic connections. This planar microelectromechanical system (MEMS)-chip works with 300 µm high silicon structures between two borosilicate glasses and has a size of 13 mm × 7 mm. Because of its small size a small vacuum pump is sufficient, and it is suitable for mobile measurements and portable applications. Because of exchangeability of MEMS-chips with fluidic and electrical high voltage connections a direct comparison between chips is possible.
Reply to TA Schiffer et al. (2019)

We appreciate the interest that Schiffer et al. have shown in our recent work
Chemical conjugation of ΔF508-CFTR corrector deoxyspergualin to transporter human serum albumin enhances its ability to rescue Cl−channel functions (2008)

The most common mutation of the cystic fibrosis (CF) gene, the deletion of Phe508, encodes a protein (DeltaF508-CFTR) that fails to fold properly, thus mutated DeltaF508-cystic fibrosis transmembrane conductance regulator (CFTR) is recognized and degraded via the ubiquitin-proteasome endoplasmic reticulum-associated degradation pathway. Chemical and pharmacological chaperones and ligand-induced transport open options for designing specific drugs to control protein (mis)folding or transport. A class of compounds that has been proposed as having potential utility in DeltaF508-CFTR is that which targets the molecular chaperone and proteasome systems. In this study, we have selected deoxyspergualin (DSG) as a reference molecule for this class of compounds and for ease of cross-linking to human serum albumin (HSA) as a protein transporter. Chemical cross-linking of DSG to HSA via a disulfide-based cross-linker and its administration to cells carrying DeltaF508-CFTR resulted in a greater enhancement of DeltaF508-CFTR function than when free DSG was used. Function of the selenium-dependent oxidoreductase system was required to allow intracellular activation of HSA-DSG conjugates. The principle that carrier proteins can deliver pharmacological chaperones to cells leading to correction of defective CFTR functions is therefore proven and warrants further investigations.
Clades of huge phage from across Earth’s ecosystems (2019)

Phage typically have small genomes and depend on their bacterial hosts for replication. DNA sequenced from many diverse ecosystems revealed hundreds of huge phage genomes, between 200 kbp and 716 kbp in length. Thirty-four genomes were manually curated to completion, including the largest phage genomes yet reported. Expanded genetic repertoires include diverse and new CRISPR-Cas systems, tRNAs, tRNA synthetases, tRNA modification enzymes, translation initiation and elongation factors, and ribosomal proteins. Phage CRISPR-Cas systems have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phage may repurpose bacterial CRISPR-Cas systems to eliminate competing phage. We phylogenetically define major clades of huge phage from human and other animal microbiomes, oceans, lakes, sediments, soils and the built environment. We conclude that their large gene inventories reflect a conserved biological strategy, observed over a broad bacterial host range and across Earth’s ecosystems.
Trichoderma And Gliocladium, Volume 2 (1998)

Fungi belonging to the genera Trichoderma and Gliocladium are soil- bourne saprophytes which have been used for industrial and agricultural applications for decades. Some strains produce enzymes and antibiotics while others are useful as biological agents for the protection of plants against pathogens.This second volume of two describes the com
Low-dose self-amplifying mRNA COVID-19 vaccine drives strong protective immunity in non-human primates against SARS-CoV-2 infection (2022)

The coronavirus disease 2019 (COVID-19) pandemic continues to spread globally, highlighting the urgent need for safe and effective vaccines that could be rapidly mobilized to immunize large populations. We report the preclinical development of a self-amplifying mRNA (SAM) vaccine encoding a prefusion stabilized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein and demonstrate strong cellular and humoral immune responses at low doses in mice and rhesus macaques. The homologous prime-boost vaccination regimen of SAM at 3, 10 and 30 μg induced potent neutralizing antibody (nAb) titers in rhesus macaques following two SAM vaccinations at all dose levels, with the 10 μg dose generating geometric mean titers (GMT) 48-fold greater than the GMT of a panel of SARS-CoV-2 convalescent human sera. Spike-specific T cell responses were observed with all tested vaccine regimens. SAM vaccination provided protective efficacy against SARS-CoV-2 challenge as both a homologous prime-boost and as a single boost following ChAd prime, demonstrating reduction of viral replication in both the upper and lower airways. The SAM vaccine is currently being evaluated in clinical trials as both a homologous prime-boost regimen at low doses and as a boost following heterologous prime.
Infrared free-electron laser as a probe of vibrational dynamics on surfaces (1989)

The infrared free-electron laser (IRFEL) is a useful light source that can be employed as a probe of vibrational dynamics on surfaces. We explore in detail two possible applications of the IRFEL. One type of experiment utilizes the IRFEL to measure vibrational relaxation on surfaces directly, using infrared saturation and ground-state recovery techniques. The second application uses the IRFEL to desorb adsorbates from surfaces by resonantly exciting their vibrational modes. This application is illustrated by recent investigations of the resonant desorption of butane from Al2O3(11 2¯0), using the Mark III IRFEL. These studies revealed a greater desorption yield for the asymmetric C—H stretches in comparison with the symmetric C—H stretches. This greater desorption efficiency for the asymmetric C—H stretches was attributed to the orientation of the butane molecules in an ordered adlayer on Al2O3(11 2¯0). Future applications of the IRFEL as a probe of vibrational dynamics on surfaces are also discussed.
Drug-Sensitivity Screening and Genomic Characterization of 45 HPV-Negative Head and Neck Carcinoma Cell Lines for Novel Biomarkers of Drug Efficacy (2018)

There is an unmet need for effective targeted therapies for patients with advanced head and neck squamous cell carcinoma (HNSCC). We correlated gene expression, gene copy numbers, and point mutations in 45 human papillomavirus-negative HNSCC cell lines with the sensitivity to 220 anticancer drugs to discover predictive associations to genetic alterations. The drug response profiles revealed diverse efficacy of the tested drugs across the cell lines. Several genomic abnormalities and gene expression differences were associated with response to mTOR, MEK, and EGFR inhibitors. <i>NOTCH1</i> and <i>FAT1</i> were the most commonly mutated genes after <i>TP53</i> and also showed some association with response to MEK and/or EGFR inhibitors. <i>MYC</i> amplification and <i>FAM83H</i> overexpression associated with sensitivity to EGFR inhibitors, and <i>PTPRD</i> deletion with poor sensitivity to MEK inhibitors. The connection between high <i>FAM83H</i> expression and responsiveness to the EGFR inhibitor erlotinib was validated by gene silencing and from the data set at the Cancer Cell Line Encyclopedia. The data provide several novel genomic alterations that associated to the efficacy of targeted drugs in HNSCC. These findings require further validation in experimental models and clinical series. <i>Mol Cancer Ther; 17(9); 2060-71. ©2018 AACR</i>.
Thrombin Differentially Modulates the Acute Inflammatory Response to Escherichia coli and Staphylococcus aureus in Human Whole Blood (2022)

Thrombin plays a central role in thromboinflammatory responses, but its activity is blocked in the common ex vivo human whole blood models, making an ex vivo study of thrombin effects on thromboinflammatory responses unfeasible. In this study, we exploited the anticoagulant peptide Gly-Pro-Arg-Pro (GPRP) that blocks fibrin polymerization to study the effects of thrombin on acute inflammation in response to <i>Escherichia coli</i> and <i>Staphylococcus aureus</i> Human blood was anticoagulated with either GPRP or the thrombin inhibitor lepirudin and incubated with either <i>E. coli</i> or <i>S. aureus</i> for up to 4 h at 37°C. In GPRP-anticoagulated blood, there were spontaneous elevations in thrombin levels and platelet activation, which further increased in the presence of bacteria. Complement activation and the expression of activation markers on monocytes and granulocytes increased to the same extent in both blood models in response to bacteria. Most cytokines were not elevated in response to thrombin alone, but thrombin presence substantially and heterogeneously modulated several cytokines that increased in response to bacterial incubations. Bacterial-induced releases of IL-8, MIP-1α, and MIP-1β were potentiated in the thrombin-active GPRP model, whereas the levels of IP-10, TNF, IL-6, and IL-1β were elevated in the thrombin-inactive lepirudin model. Complement C5-blockade, combined with CD14 inhibition, reduced the overall cytokine release significantly, both in thrombin-active and thrombin-inactive models. Our data support that thrombin itself marginally induces leukocyte-dependent cytokine release in this isolated human whole blood but is a significant modulator of bacteria-induced inflammation by a differential effect on cytokine patterns.