gebhart/patrepeval huggingface dataset:
High-throughput analysis of Yersinia pseudotuberculosis gene essentiality in optimised in vitro conditions, and implications for the speciation of Yersinia pestis (2018)

The discovery of uniquely essential genes between the closely related Yersinia spp. represent some of the fundamental, species-defining points of divergence that arose during the evolution of Y. pestis from its ancestor. Furthermore, the shared essential genes represent ideal candidates for the development of novel antimicrobials against both species.
Safety, Immunogenicity, and Surrogate Markers of Clinical Efficacy for Modified Vaccinia Ankara as a Smallpox Vaccine in HIV-Infected Subjects (2012)

MVA is a promising candidate as a safer smallpox vaccine, even for immunocompromised individuals, a group for whom current smallpox vaccines have an unacceptable safety profile.
Development of a Carbon Nanotube Paste for the High-Performance Field Emitters by Using the Simple Ball-Milling Method (2014)

The carbon nanotube (CNT) paste was fabricated by a very simple method where the paste composition could be controlled precisely. We have fabricated several types of field emitters from the CNT paste mixture consisting of the thin multi-walled CNT, the nanosized inorganic fillers, the ethyl cellulose binder and the terpineol solvent. The field emission current density was found to be more than 100 mA/cm 2 at a field of 2.5 V/μm for the planar-type CNT emitter and ~5 A/cm 2 for the tip-type emitter, respectively. We also optimized the filler material in the paste to make the emitter reliable under the high-temperature conditions. The developed CNT paste had good reproducibility and the field emitters made of the paste showed excellent characteristics as the electron sources for the various applications.
Supplementary Table 3 from A Cross-Species Analysis in Pancreatic Neuroendocrine Tumors Reveals Molecular Subtypes with Distinctive Clinical, Metastatic, Developmental, and Metabolic Characteristics (2023)

&lt;p&gt;Supplementary Table 3 includes two worksheets - a) evaluation of insulin and Enpp2 IHC staining of human PanNET TMA and b) protein expression levels determined by global proteomic analysis of mouse PanNET samples.&lt;/p&gt;
Adaptive frequency sampling using linear Bayesian vector fitting (2018)

The authors present a novel Bayesian approach to adaptively select frequency samples to obtain a rational macromodel of device responses over a broad frequency range while performing as few electromagnetic simulations as possible. The method leverages a Bayesian approach to vector fitting to construct a data‐driven uncertainty measure. The presented technique is demonstrated by application to a double semi‐circular patch antenna and is shown to accurately and efficiently construct a rational macromodel over the frequency range of interest.
Abstract 68: The WWOX Gene Modulates HDL Metabolism and Lipoprotein Gene Expression (2013)

Low plasma HDL cholesterol (HDL-C) constitutes a major risk factor for coronary artery disease. We previously identified a region-wide association between low HDL-C and the WW domain-containing oxidoreductase ( WWOX ) gene in dyslipidemic families and low HDL-C cases and controls (rs2548861, P=6.9x10 -7 ). Here, through a combination of in vivo functional studies, gene microarray and next generation resequencing, we investigated the role of WWOX in lipoprotein and HDL metabolism. Using total Wwox -/- and Wwox liver-specific ( hep -/- ) mice, we found decreased apoA-I and ABCA1 protein levels in hepatic tissues. Analyses of lipoprotein profiles in Wwox -/- littermates also showed marked reductions in serum HDL-C and apoA-I levels, with no effect in Wwox hep -/- mice. A sex-specific difference was however observed in female Wwox hep -/- mice, showing a significant increase in plasma triglycerides levels. We further obtained evidence of a gender-specific effect by gene microarray analyses in Wwox hep -/- hepatocytes, where it was identified that WWOX disruption alters primarily lipid metabolic pathways in females. We observed a significant reduction (P&lt;0.05,
Immunotargeting of Catalase to the Pulmonary Vascular Endothelium (2003)

Hydrogen peroxide formed in the lung tissue in ischemia/reperfusion or released from activated leukocytes causes oxidative injury of the vascular endothelial cells (1-3). H(2)O(2)-degrading enzyme, catalase, has been extensively explored in order to protect cells and tissues against H(2)O(2)-mediated injury (4). Catalase, however, has short lifetime in the bloodstream and provides only marginal protective effect after intravascular administration in animals (5). Catalase modification (conjugation with polyethylene glycol (6) or encapsulation in liposomes [7]), prolongs catalase lifetime in the circulation and facilitate its cellular uptake. These modifications, however, do not provide it with an affinity to the endothelial cells. In order to provide catalase with such an affinity, catalase could be chemically conjugated with a carrier antibodies recognizing the surface endothelial antigens (8). A monoclonal antibody (MAb) against such an antigen, angiotensin-converting enzyme (anti-ACE MAb 9B9, produced by Dr. Sergei M. Danilov [9]), accumulates in the pulmonary endothelium after systemic injection (10). Therefore, MAb 9B9 may serve as an affinity carrier for targeting of catalase to the pulmonary endothelial cells, for specific augmentation of their antioxidative defense.
Plasma enhanced chemical vapour deposition carbon nanotubes/nanofibres how uniform do they grow? (2003)

The ability to grow carbon nanotubes/nanofibres (CNs) with a high degree of uniformity is desirable in many applications. In this paper, the structural uniformity of CNs produced by plasma enhanced chemical vapour deposition is evaluated for field emission applications. When single isolated CNs were deposited using this technology, the structures exhibited remarkable uniformity in terms of diameter and height (standard deviations were 4.1 and 6.3% respectively of the average diameter and height). The lithographic conditions to achieve a high yield of single CNs are also discussed. Using the height and diameter uniformity statistics, we show that it is indeed possible to accurately predict the average field enhancement factor and the distribution of enhancement factors of the structures, which was confirmed by electrical emission measurements on individual CNs in an array.
Optimization of Micro-SOFC Performance through the Control of the Architecture Using a Low Cost Process (2011)

International audience
Specialty flat-top beam delivery fibers with controlled beam parameter product (2016)

Beam delivery fibers have been used widely for transporting the optical beams from the laser to the subject of irradiation in a variety of markets including industrial, medical and defense applications. Standard beam delivery fibers range from 50 to 1500 &mu;m core diameter and are used to guide CW or pulsed laser light, generated by solid state, fiber or diode lasers. Here, we introduce a novel fiber technology capable of simultaneously controlling the beam profile and the angular divergence of single-mode (SM) and multi-mode (MM) beams using a single-optical fiber. Results of beam transformation from a SM to a MM beam with flat-top intensity profile are presented in the case of a controlled BPP at 3.8 mm*mrad. The scaling capabilities of this flat-top fiber design to achieve a range of BPP values while ensuring a flat-top beam profile are discussed. In addition, we demonstrate, for the first time to the best of our knowledge, the homogenizer capabilities of this novel technology, able to transform random MM beams into uniform flat-top beam profiles with very limited impact on the beam brightness. This study is concluded with a discussion on the scalability of this fiber technology to fit from 50 up to 1500 &mu;m core fibers and its potential for a broader range of applications.
Fluoroazaindolines by an Uncommon Radical ipso-Substitution of a C-F Bond (2011)

Trifluoroazaindoline derivatives are prepared using the first synthetically useful radical ipso-substitution of a fluorine atom. The initial procedure has been improved to allow the gram scale synthesis of these building blocks, which can be regioselectively substituted by nucleophiles under mild conditions to rapidly access a library of new molecules. Oxidation to the corresponding fluoroazaindole core has also been accomplished.
Electrode Kinetics of Fuel Oxidation at Copper in Molten Carbonate (1984)

Copper appears to be a promising anode material for the molten carbonate fuel cell, as an alternative to nickel. Therefore, polarization data have been obtained for oxidation of fuel gases on a fully immersed copper rod. The electrode‐kinetic parameters have been determined using the potential‐step technique. The reaction mechanism on copper appears to be similar to that on nickel, and the exchange current density only slightly less than that on nickel. The importance of a correct extrapolation technique to obtain the time‐zero current response is emphasized.
Radiation Therapy: Age-Related Macular Degeneration (2013)

Age-related macular degeneration (AMD) is the leading cause of severe irreversible vision loss in patients over the age of 50 years in the developed world. Neovascular AMD (NVAMD) is responsible for 90% of the cases with severe visual loss. In the last decade, the treatment paradigm for NVAMD has been transformed by the advent of anti-vascular endothelial growth factor therapy. Despite the excellent results of anti-vascular endothelial growth factor therapy, frequent injections remain a necessity for most patients. The burden of these frequent visits as well as the cumulative risks of indefinite intravitreal injections demand continued pursuit of more enduring therapy that provides similar functional results. Radiotherapy has been studied for two decades as a potential therapy for NVAMD. Because of its antiangiogenic properties, radiation therapy remains a promising potential adjunctive resource for the treatment of choroidal neovascularization secondary to NVAMD. This review considers the past, present and future of radiation as a treatment or combination treatment of NVAMD.
<title>A 200 Million Operations Per Second (MOPS) Systolic Processor</title> (1982)

In building a proof of concept model of a systolic processor, several design issues are resolved. Flexibility is achieved through a hierarchy of software which resides on a host computer and through extensive interface and control hardware. Buffer memories with pro-grammable address generators are provided in the interface. The control system is general enough to support command chaining and loops. Each cell of the systolic array is equipped with its own memory which allows a single cell design to perform a number of algorithms. As a result of designing for flexibility, the system can accommodate a wide variety of algorithms, data representations, and problem dimensions. A useful system computation rate of 200 million operations per second (MOPS) is achieved with a peak rate of 350 MOPS.
A linearized Doherty amplifier using complex baseband digital predistortion driven by CDMA signals (2005)

This work proposes a digitally linearized Doherty amplifier for CDMA applications. A fully digital complex baseband predistorter is used to improve the linearity of the amplifier over the whole input power range. This results in an improvement of the linearity of the Doherty amplifier without degrading its power efficiency. Experimental validation was carried on a designed 1-watt power Doherty amplifier operating at 1900 MHz. The performance of the linearized Doherty amplifier (LDA) was evaluated under a cdma2000 SRI signal. A power added efficiency of 50% was obtained with an ACPR level better than 35 dBc.
The brain structural disposition to social interaction (2009)

Social reward dependence (RD) in humans is a stable pattern of attitudes and behaviour hypothesized to represent a favourable disposition towards social relationships and attachment as a personality dimension. It has been theorized that this long-term disposition to openness is linked to the capacity to process primary reward. Using brain structure measures from magnetic resonance imaging, and a measure of RD from Cloninger's temperament and character inventory, a self-reported questionnaire, in 41 male subjects sampled from a general population birth cohort, we investigated the neuro-anatomical basis of social RD. We found that higher social RD in men was significantly associated with increased gray matter density in the orbitofrontal cortex, basal ganglia and temporal lobes, regions that have been previously shown to be involved in processing of primary rewards. These findings provide evidence for a brain structural disposition to social interaction, and that sensitivity to social reward shares a common neural basis with systems for processing primary reward information.
The fixation strength of a novel ACL soft‐tissue graft fixation device compared with conventional interference screws: a biomechanical study in vitro (2010)

Anterior cruciate ligament reconstruction using autologous hamstring tendons is an established surgical procedure but some grafts fail due to poor fixation. This study compared the fixation of a new ACL graft fixation device (the EZ KneeSpan) to conventional soft-tissue threaded titanium interference screws (IS). The EZ device was designed to provide secure fixation while avoiding soft-tissue graft damage associated with use of an IS. Eight paired fresh-frozen cadaveric human knees and bovine digital extensor tendons were used. Two tunnels were placed in each tibia and femur, and grafts were fixed using the EZ device and the IS in each bone. Cyclic tensile loading and pull-out testing measured graft slippage (mm) and ultimate strength (N) of the fixation. The results were compared using the non-parametric Wilcoxon signed-rank test. Graft slippage after cyclic loading was significantly lower in the EZ group at 2.4 ± 0.1 mm versus 9.5 ± 6.2 mm for the IS group in the femur and 3.3 ± 1.4 mm versus 17.7 ± 13.6 mm in the tibia. The mean ultimate load for the femoral EZ group was significantly higher than the IS group (769 ± 223 N versus 468 ± 60 N), but they did not differ significantly in the tibia (518 ± 48 N versus 546 ± 139 N). Our results indicate that with the EZ device the initial fixation of cyclically loaded hamstring grafts could be superior to that with an IS. The EZ KneeSpan device also had similar tibial and higher femoral ultimate fixation strength than an IS.
The quality assurance of EUV mask pattern based on 3D-SEM and lithography simulation (2012)

Extreme Ultra Violet (EUV) lithography is a leading candidate technology to succeed ArF lithography for high-volume manufacturing (HVM) in the next generation. A serious obstacle to the realization of EUV lithography is that the evaluation tool for EUV masks is insufficient. In particular, although the evaluation of mask pattern quality by means of an aerial image is essential for the supply of defect-free masks, timely establishment of EUV AIMS operation is difficult. We are developing a system that evaluates the printability to wafer of a mask pattern by a combination of mask pattern measurement using three-dimensional (3D) SEM and wafer image prediction using lithography simulation. The measurement of the mask pattern is a key technique of the system. It is performed by 3D-SEM, which enables the highly accurate measurement of the mask pattern sidewall angle using a tilted SEM image. Because EUV lithography is off-axis illumination on a mask pattern, the sidewall angle management of a mask pattern is important. Besides, 3D-SEM acquires a mask pattern image with high resolution and wide area. The wafer image can be predicted with high accuracy on the basis of the 3D mask pattern data, which are highly accurate and cover a wide area. In this paper, we describe the method of 3D mask pattern data measurement. Additionally, we report the experimental results concerning the 3D mask pattern measurements and the wafer image predictions.
Detection of scattered ambient noise by fish. (1992)

It has been hypothesized that one role of the fish’s auditory system may be to detect and localize nearby fish by ‘‘imaging’’ ambient noise scattered by their swimbladders. This is analogous to the role of the visual system of most animals, where the relevant signal is ambient light scattered by objects rather than light emitted by luminous objects. A classical conditioning experiment has been performed which indicates that the fish auditory system is capable of functioning in this manner. The ambient noise was provided by a J-9 transducer driven by Gaussian noise. Scattering of ambient noise by the resonant swimbladder was simulated by applying a filtered version of the same Gaussian noise to a small spherical projector. The target strength and bandwidth of the scattered noise were controlled by the attenuation and passband of the filter. The fish was conditioned to respond to the presence of the signal from the spherical projector. Thresholds of simulated scattered noise as a function of range to the subject were measured for the species Carassiusauratus (common goldfish). The fish’s ability to discriminate this signal is taken to be a measure of its ability to detect scattered ambient noise. [Work supported by ONR.]
Multilingual Language Processing From Bytes (2015)

We describe an LSTM-based model which we call Byte-to-Span (BTS) that reads text as bytes and outputs span annotations of the form [start, length, label] where start positions, lengths, and labels are separate entries in our vocabulary. Because we operate directly on unicode bytes rather than language-specific words or characters, we can analyze text in many languages with a single model. Due to the small vocabulary size, these multilingual models are very compact, but produce results similar to or better than the state-of- the-art in Part-of-Speech tagging and Named Entity Recognition that use only the provided training datasets (no external data sources). Our models are learning "from scratch" in that they do not rely on any elements of the standard pipeline in Natural Language Processing (including tokenization), and thus can run in standalone fashion on raw text.
Figure S3 from Delivering Type I Interferon to Dendritic Cells Empowers Tumor Eradication and Immune Combination Treatments (2023)

&lt;p&gt;Clec9A-targeting does not induce hematological deficits.&lt;/p&gt;
In Vivo PET Imaging of Cardiac Presynaptic Sympathoneuronal Mechanisms in the Rat (2008)

Kinetic profiles of HED in the rat myocardium were similar to those of HED in humans, suggesting comparable neuronal transport density. Unlike in humans, however, significant washout of EPI and faster washout of PHEN were encountered, consistent with high intraneuronal metabolic activity, high catecholamine turnover, and reduced vesicular storage. This evidence of increased neuronal activity in rodents has implications for translational studies of cardiac neuronal biology in humans.
Identification of an Inhibitor of the EWS-FLI1 Oncogenic Transcription Factor by High-Throughput Screening (2011)

Mithramycin inhibits EWS-FLI1 activity and demonstrates ESFT antitumor activity both in vitro and in vivo.
Concerted integration of linear retroviral DNA by the avian sarcoma virus integrase in vitro: dependence on both long terminal repeat termini (1996)

We have reconstituted integration reactions in vitro with specially designed donor DNAs, a supercoiled plasmid acceptor, purified bacterium-derived Rous sarcoma virus integrase (IN), and a host cell DNA-bending protein, HMG1. The duplex donor DNAs are approximately 300 deoxynucleotides in length and contain only 15 bp of the RSV U3 and U5 termini at the respective ends. The donor has blunt U3 and U5 termini which end with the sequence 5'CATT. Joining of the donor DNA to the acceptor DNA is detected by using a simple biochemical assay. Integration was found to be dependent on both U3 and U5 termini; mutations in either result in a significant decrease in the level of integration in vitro. Restriction digestion of the products is consistent with most integrants representing a concerted integration in which both long terminal repeat termini come from the same donor molecule. The U5 and U3 sequences in the substrate flank a supF tRNA gene, permitting biological selection of integrants. Many integrants have been sequenced, and have all of the hallmarks of authentic viral integration, including the removal of a terminal TT dinucleotide from each donor DNA end, and duplication of acceptor sequences at the integration site without introducing deletions into the acceptor. Target site selection in the acceptor plasmid was random except that the orientation of integrants selected was apparently influenced by supF transcription. Mutations which substituted the conserved CA dinucleotide with a GA pair led to a decreased rate of integration. In 2 of 14 mutant integrants sequenced, deoxynucleotides were deleted from either the U5 or U3 terminus. In one instance, an internal CA dinucleotide was used, which resulted in a 10-bp U5 donor deletion. In the other, an internal GA dinucleotide was used, which produced a 5-bp U3 donor deletion. Both of these integrants provide further evidence that concerted integration in this reconstituted system requires interactions between IN and the U3 and U5 termini from the same donor molecule.
Through Glass VIAS using an Industry Compatible Glass Handling Solution (2020)

Thin glass (≤ 200 μm) has ideal properties for electronic packaging and RF applications. In electronic packaging, a smooth, dimensionally stable surface allows high resolution line/space patterning, while through glass via (TGV) technology permits integration in many relevant packaging structures. These capabilities combine with a low loss tangent at microwave frequencies and robustness to temperature and humidity to yield high performance for RF applications. In this paper we discuss a thin glass handling solution coupled with recent innovations that give glass an entry point into these applications at large scale using existing fabrication infrastructure. Our new polymer-free bonding process allows glass to be temporarily bonded to a handle such as silicon or other glass substrates. The Viaffirm™ bonding material is non-outgassing and capable of handling temperatures in excess of 400°C while remaining temporary. When silicon is used as the handle, the opacity and form factor of the silicon substrate means that the resulting bonded stack is compatible with existing silicon processing equipment. We discuss the properties of our bonding system including temperature performance, tunability of the bond energy for different applications, and approaches to debonding. We also describe the formation and metallization of TGVs utilizing our proprietary process. When using a silicon wafer as the handle substrate, vias in the glass terminate on the silicon and are thus comparable to blind vias in silicon. We discuss the ability to make tapered TGVs while tuning their size and via profile, as well as results in metallization to produce fully filled, void free vias using a range of seed and plating approaches.