gebhart/patrepeval huggingface dataset:
Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover (2014)

The inability of the yeast Saccharomyces cerevisiae to ferment xylose effectively under anaerobic conditions is a major barrier to economical production of lignocellulosic biofuels. Although genetic approaches have enabled engineering of S. cerevisiae to convert xylose efficiently into ethanol in defined lab medium, few strains are able to ferment xylose from lignocellulosic hydrolysates in the absence of oxygen. This limited xylose conversion is believed to result from small molecules generated during biomass pretreatment and hydrolysis, which induce cellular stress and impair metabolism. Here, we describe the development of a xylose-fermenting S. cerevisiae strain with tolerance to a range of pretreated and hydrolyzed lignocellulose, including Ammonia Fiber Expansion (AFEX)-pretreated corn stover hydrolysate (ACSH). We genetically engineered a hydrolysate-resistant yeast strain with bacterial xylose isomerase and then applied two separate stages of aerobic and anaerobic directed evolution. The emergent S. cerevisiae strain rapidly converted xylose from lab medium and ACSH to ethanol under strict anaerobic conditions. Metabolomic, genetic and biochemical analyses suggested that a missense mutation in GRE3, which was acquired during the anaerobic evolution, contributed toward improved xylose conversion by reducing intracellular production of xylitol, an inhibitor of xylose isomerase. These results validate our combinatorial approach, which utilized phenotypic strain selection, rational engineering and directed evolution for the generation of a robust S. cerevisiae strain with the ability to ferment xylose anaerobically from ACSH.
Imide/Arylene Ether Copolymers-Part II (1991)

A series of novel imide/arylene ether copolymers were prepared from the reaction of an amorphous arylene ether oligomer and a semi-crystalline imide oligomer. These copolymers were thermally characterized and mechanical properties were measured. One block copolymer was end-capped and the molecular weight was controlled to provide a material that displayed good compression moldability and attractive adhesive and composite properties.
Simulation of writing head in perpendicular magnetic recording system (2002)

For perpendicular magnetic recording system, we suggest the modeling scheme combining finite element method and the fine field analysis. We did not use the Karlqvist head field but simulated a head field by the finite element method with precise simulation. For this purpose, we developed a Laplace program to calculate the head field at micromagnetic domains. We simulated the write process for a conventional head with a single layer perpendicular media and compared magnetic force microscopy images of simulated written bit patterns and tested patterns.
The θ-Defensin, Retrocyclin, Inhibits HIV-1 Entry (2003)

Retrocyclin is a circular antimicrobial 18-residue peptide encoded in the human genome by a θ-defensin pseudogene. In the human genome, the gene for retrocyclin is inactivated by an in-frame stop codon in its signal sequence but its mature coding sequence is intact. The peptide corresponding to the processed human retrocyclin, generated by solid phase peptide synthesis, inhibited replication of R5 and X4 strains of HIV-1 in human cells. Luciferase reporter virus and Vpr-BLaM entry assays were used to demonstrate that retrocyclin specifically blocked R5 and X4 HIV-1 replication at entry. Surface plasmon resonance demonstrated that retrocyclin bound to soluble CD4 and gp120, but gp120 cell-binding assays revealed that retrocyclin did not fully inhibit the binding of soluble CD4 to gp120. A fluorescent retrocyclin congener localized in cell-surface patches either alone or colocalized with CD4, CXCR4, and CCR5. In the aggregate, these results suggest that retrocyclin blocks an entry step in HIV-1 replication. Retrocyclin represents a new class of small molecule HIV-1 entry inhibitors.
Microencapsulated Antidegradants for Extending Rubber Lifetime (1992)

Abstract Microcapsules containing rubber antidegradants were formed in a spray-drying process. Studies were carried out to select the proper wall material based on the processing properties, migration rate of the antidegradant through the capsule wall, thickness of the capsule wall, and overall capsule diameter. The resulting capsules were incorporated into a rubber article, providing a reservoir of antidegradant during the exposure lifetime. Testing of the rubber compounds with microcapsules having diameters less than 50 µm containing A N -(l,3-dimethylbutyl)- N ′-phenyl- p -phenylenediamine in a matrix of cellulose acetate showed a significant increase in the crack-free lifetime of the rubber when flexed in exposure to ozone.
Pit Depth and Width Modulation Multilevel Run-Length Limited Read-Only Optical Storage (2006)

When the techniques of integrating the variation of the pit depth and width simultaneously are adopted to conventional DVD, the high-density multilevel run-length limited read-only optical storage method is achieved. The dynamic range of readout signal is greatly enlarged in comparison with keeping one parameter varied, and the recording levels number can be obviously increased. The discs can be manufactured using standard photoresist mastering and replication techniques with great compatibility to conventional binary read-only discs. Experimental results show that eight-level read-only optical disc can be realized and the capacity can be increased to 20 GB.
Moldable Perfluoropolyether–Polyethylene Glycol Networks with Tunable Wettability and Solvent Resistance for Rapid Prototyping of Droplet Microfluidics (2018)

Soft lithography-based droplet microfluidics has enabled production of highly uniform and complex emulsions. Although there is a significant potential to use these emulsions as templates for functional materials syntheses, conventional elastomers that are used for microfluidic device preparation are significantly deformed and swollen by various organic solvents, limiting the types of materials that can be processed using conventional soft lithography-based droplet microfluidics. In this report, we demonstrate that both water-in-oil and oil-in-water emulsion with organic solvents can be produced by using microfluidic devices that are prepared using cross-linked networks of perfluoropolyether (PFPE) and poly(ethylene glycol) diacrylate (PEGDA). We show that these PFPE–PEG networks are transparent and maintain excellent compatibility with various organic solvents. Importantly, the wettability of these devices can be systematically controlled by changing the ratio of the two macromonomers. By taking advantage of rapid prototyping and controlled surface wettability afforded by the PFPE–PEG network, we prepare three-dimensional monolithic elastomer devices for the parallel generation of oil-in-water and water-in-oil droplets. We also show that, using these devices, solid microparticles with high uniformity can be produced by using an organic solvent-based emulsion as a template. We believe the PFPE–PEG network will have broad impacts in the application of soft lithography-based elastomer microfluidic devices to a wide range of applications, including drug screening and solvent-based separation processes.
The Application of Ultrasonic Inspection to Crimped Electrical Connections (2010)

The development of a new ultrasonic measurement technique to quantitatively assess wire crimp terminations is discussed. The development of a prototype instrument, based on a modified, commercially available, crimp tool, is demonstrated for applying this technique when wire crimps are installed. The crimp tool has three separate crimping locations that accommodate the three different ferrule diameters. The crimp tool in this study is capable of crimping wire diameters ranging from 12 to 26 American Wire Gauge (AWG). A transducer design is presented that allows for interrogation of each of the three crimp locations on the crimp tool without reconfiguring the device. An analysis methodology, based on transmitted ultrasonic energy and timing of the first received pulse is shown to correlate to both crimp location in the tool and the AWG of the crimp/ferrule combination. The detectability of a number of the crimp failure pathologies, such as missing strands, partially inserted wires and incomplete crimp compression, is discussed. A wave propagation model, solved by finite element analysis, describes the compressional ultrasonic wave propagation through the junction during the crimping process.
Adaptive gesture recognition combining HMM models and geometrical features (2011)

Hand gesture recognition is receiving more and more attentions due to its potential use in many applications. In this paper, we propose a novel gesture spotting and recognition method, which combines the information of hand motion parameter, the matching result of HMM models and the recognition result based on geometrical features of hand trajectory to spot and recognize the gesture. Besides, we also study the method of adjusting classifiers to make the gesture recognition system adapt to specific users. Experimental results have proved the effectiveness of the proposed method.
Tracking and recognizing rigid and non-rigid facial motions using local parametric models of image motion (2002)

This paper explores the use of local parametrized models of image motion for recovering and recognizing the non-rigid and articulated motion of human faces. Parametric flow models (for example affine) are popular for estimating motion in rigid scenes. We observe that within local regions in space and time, such models not only accurately model non-rigid facial motions but also provide a concise description of the motion in terms of a small number of parameters. These parameters are intuitively related to the motion of facial features during facial expressions and we show how expressions such as anger, happiness, surprise, fear, disgust and sadness can be recognized from the local parametric motions in the presence of significant head motion. The motion tracking and expression recognition approach performs with high accuracy in extensive laboratory experiments involving 40 subjects as well as in television and movie sequences.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Implementation techniques of broadband radio channel simulators (2002)

This paper discusses the advantages and disadvantages of different implementation techniques of radio channel simulators and analyses in more depth the challenges of increasing bandwidth and dynamic range. One selected technology has been implemented and tested. A block diagram of the simulator and test results are shown.
Frequent Simian Foamy Virus Infection in Persons Occupationally Exposed to Nonhuman Primates (2004)

The recognition that AIDS originated as a zoonosis heightens public health concerns associated with human infection by simian retroviruses endemic in nonhuman primates (NHPs). These retroviruses include simian immunodeficiency virus (SIV), simian T-cell lymphotropic virus (STLV), simian type D retrovirus (SRV), and simian foamy virus (SFV). Although occasional infection with SIV, SRV, or SFV in persons occupationally exposed to NHPs has been reported, the characteristics and significance of these zoonotic infections are not fully defined. Surveillance for simian retroviruses at three research centers and two zoos identified no SIV, SRV, or STLV infection in 187 participants. However, 10 of 187 persons (5.3%) tested positive for SFV antibodies by Western blot (WB) analysis. Eight of the 10 were males, and 3 of the 10 worked at zoos. SFV integrase gene (int) and gag sequences were PCR amplified from the peripheral blood lymphocytes available from 9 of the 10 persons. Phylogenetic analysis showed SFV infection originating from chimpanzees (n = 8) and baboons (n = 1). SFV seropositivity for periods of 8 to 26 years (median, 22 years) was documented for six workers for whom archived serum samples were available, demonstrating long-standing SFV infection. All 10 persons reported general good health, and secondary transmission of SFV was not observed in three wives available for WB and PCR testing. Additional phylogenetic analysis of int and gag sequences provided the first direct evidence identifying the source chimpanzees of the SFV infection in two workers. This study documents more frequent infection with SFV than with other simian retroviruses in persons working with NHPs and provides important information on the natural history and species origin of these infections. Our data highlight the importance of studies to better define the public health implications of zoonotic SFV infections.
Electrostatic self-calibration of vibratory gyroscopes (2012)

This paper introduces a new approach to self-calibration of Coriolis-based vibratory gyroscopes that does not require the use of any additional moving parts or a calibration stage. Instead, the effect of the Coriolis force on the device is mimicked by the application of a rotating excitation to the device drive and sense modes. This calibration method is based on the theoretical analysis of an equivalent 2-DOF mass-spring model, which can be used to describe the behavior of a variety of MEMS gyroscopes. The method is validated both by the results of finite-element simulations and by experimental measurement.
Imaging the attenuation coefficients of magnetically constrained positron beams in matter (2016)

This paper describes a method for tomographically imaging the linear attenuation coefficients (LACs) of positron beams in heterogeneous materials. A β+ ray emitter such as 68Ga, placed in a uniform 3T static magnetic field, generates a well-defined positron beam that maintains its spatial coherence over an attenuation of more than 10-3 while signaling its intensity via the annihilation radiation it generates. A positron emission tomography (PET) system embedded in the magnetic field measures the positron–electron annihilation distribution within objects illuminated by the beam. It's shown that this image can be decomposed into maps of the positron beam's flux and its material-dependent LACs without need for auxiliary measurements or transmission of the beam completely through the object. The initial implementation employs a hybrid PET/magnetic resonance imaging (MRI) scanner developed for medical applications. Mass thicknesses up to 0.55 g/cm2 at a spatial resolution of a few millimeters have been imaged.
No Evidence for Binding Between Resistance Gene Product Cf-9 of Tomato and Avirulence Gene Product AVR9 of <i>Cladosporium fulvum</i> (2001)

The gene-for-gene model postulates that for every gene determining resistance in the host plant, there is a corresponding gene conditioning avirulence in the pathogen. On the basis of this relationship, products of resistance (R) genes and matching avirulence (Avr) genes are predicted to interact. Here, we report on binding studies between the R gene product Cf-9 of tomato and the Avr gene product AVR9 of the pathogenic fungus Cladosporium fulvum. Because a high-affinity binding site (HABS) for AVR9 is present in tomato lines, with or without the Cf-9 resistance gene, as well as in other solanaceous plants, the Cf-9 protein was produced in COS and insect cells in order to perform binding studies in the absence of the HABS. Binding studies with radio-labeled AVR9 were performed with Cf-9-producing COS and insect cells and with membrane preparations of such cells. Furthermore, the Cf-9 gene was introduced in tobacco, which is known to be able to produce a functional Cf-9 protein. Binding of AVR9 to Cf-9 protein produced in tobacco was studied employing surface plasmon resonance and surface-enhanced laser desorption and ionization. Specific binding between Cf-9 and AVR9 was not detected with any of the procedures. The implications of this observation are discussed.
Polyimides containing carbonyl and ether connecting groups. II (1989)

Abstract In a continuation of our effort on polyimides containing carbonyl and ether connecting groups between aromatic rings, several new polyimides were prepared and characterized. A few of these polymers were semi‐crystalline. Glass transition temperatures ranged from 164 to 258°C and crystalline melt temperatures were observed between 350 and 424°C. The semi‐crystalline polyimide from the reaction of 3,3′,4,4′‐benzophenonetetracarboxylic dianhydride and 1,3‐bis(4‐aminophenoxy‐4′‐benzoyl)benzene provided transparent orange films with excellent tensile properties, exceptional resistance to solvents and strong base, and high thermooxidative stability. In addition, this polyimide provided excellent adhesive strength for joining titanium (6A1–4V) to titanium.
Compensation of Emission Light Waveguiding in Fluorescence Molecular Tomography (2008)

We present a method for identification and compensation of image regions that evidence waveguiding of emission light in fluorescence molecular tomography. Two in vivo case studies are conducted and demonstrate significant improvements in reconstructions.
Live/Dead Bacterial Spore Assay Using DPA-Triggered Tb Luminescence (2003)

A method of measuring the fraction of bacterial spores in a sample that remain viable exploits DPA-triggered luminescence of Tb(3+) and is based partly on the same principles as those described earlier. Unlike prior methods for performing such live/dead assays of bacterial spores, this method does not involve counting colonies formed by cultivation (which can take days), or counting of spores under a microscope, and works whether or not bacterial spores are attached to other small particles (i.e., dust), and can be implemented on a time scale of about 20 minutes.
Molecular characterization of the family of choline transporter‐like proteins and their splice variants (2005)

We show here that the choline transporter-like (CTL) family is more extensive than initially described with five genes in humans and complex alternative splicing. In adult rat tissues, CTL2-4 mRNAs are mainly detected in peripheral tissues, while CTL1 is widely expressed throughout the nervous system. During rat post-natal development, CTL1 is expressed in several subpopulations of neurones and in the white matter, where its spatio-temporal distribution profile recalls that of myelin basic protein, an oligodendrocyte marker. We identified two major rat splice variants of CTL1 (CTL1a and CTL1b) differing in their carboxy-terminal tails with both able to increase choline transport after transfection in neuroblastoma cells. In the developing brain, CTL1a is expressed in both neurones and oligodendroglial cells, whereas CTL1b is restricted to oligodendroglial cells. These findings suggest specific roles for CTL1 splice variants in both neuronal and oligodendrocyte physiology.
Dynamic Predication of Indirect Jumps (2007)

Indirect jumps are used to implement increasingly-common programming language constructs such as virtual function calls, switch-case statements, jump tables, and interface calls. Unfortunately, the prediction accuracy of indirect jumps has remained low because many indirect jumps have multiple targets that are difficult to predict even with specialized hardware. This paper proposes a new way of handling hard-to-predict indirect jumps: dynamically predicating them. The compiler identifies indirect jumps that are suitable for predication along with their control-flow merge (CFM) points. The microarchitecture predicates the instructions between different targets of the jump and its CFM point if the jump turns out to be hard-to-predict at run time. We describe the new indirect jump predication architecture, provide code examples showing why it could reduce the performance impact of jumps, derive an analytical cost-benefit model for deciding which jumps and targets to predicate, and present preliminary evaluation results.
High speed serializing/de-serializing design-for-test method for evaluating a 1 GHz microprocessor (2002)

As microprocessor speeds approach 1 GHz and beyond the difficulties of at-speed testing continue to increase. In particular, automated test equipment which operates at these frequencies is very limited. This paper discusses a design-for-test method which serializes parallel circuit inputs and de-serializes circuit outputs to achieve 1 GHz operation on test equipment operating at frequencies below 100 MHz. This method has been used to successfully characterize the operation of a 1 GHz microprocessor chip.
Preclinical Characterization of NVR 3-778, a First-in-Class Capsid Assembly Modulator against Hepatitis B Virus (2018)

NVR 3-778 is the first capsid assembly modulator (CAM) that has demonstrated antiviral activity in hepatitis B virus (HBV)-infected patients. NVR 3-778 inhibited the generation of infectious HBV DNA-containing virus particles with a mean antiviral 50% effective concentration (EC<sub>50</sub>) of 0.40 µM in HepG2.2.15 cells. The antiviral profile of NVR 3-778 indicates pan-genotypic antiviral activity and a lack of cross-resistance with nucleos(t)ide inhibitors of HBV replication. The combination of NVR 3-778 with nucleos(t)ide analogs <i>in vitro</i> resulted in additive or synergistic antiviral activity. Mutations within the hydrophobic pocket at the dimer-dimer interface of the core protein could confer resistance to NVR 3-778, which is consistent with the ability of the compound to bind to core and to induce capsid assembly. By targeting core, NVR 3-778 inhibits pregenomic RNA encapsidation, viral replication, and the production of HBV DNA- and HBV RNA-containing particles. NVR 3-778 also inhibited <i>de novo</i> infection and viral replication in primary human hepatocytes with EC<sub>50</sub> values of 0.81 µM against HBV DNA and between 3.7 and 4.8 µM against the production of HBV antigens and intracellular HBV RNA. NVR 3-778 showed favorable pharmacokinetics and safety in animal species, allowing serum levels in excess of 100 µM to be achieved in mice and, thus, enabling efficacy studies <i>in vivo</i> The overall preclinical profile of NVR 3-778 predicts antiviral activity <i>in vivo</i> and supports its further evaluation for safety, pharmacokinetics, and antiviral activity in HBV-infected patients.
The opto-electronic high-frequency transconductor and circuit applications (1996)

A new hybrid design approach for high gain high frequency opto-electronic transconductors is proposed. The idea exploits the high output resistance of a p-i-n photodiode to realise a high resistance current source. Measured results on a discrete circuit implementation of a bandpass filter using laser diodes, p-i-n receivers and discrete Si JFETs demonstrates that foQ products of more than an order of magnitude higher than device process f/sub T/ can be obtained. Simulated results of a similar filter employing CMOS technology for the front-end FET shows that using realistic device models filter Qs of the order of 800 can be achieved at 100 MHz. Finally a GaAs based cascode op-amp is realised using LEDs and PIN diodes to realise the opto-electronic current sources and simulations show that voltage gains of the order 80 dB with 5 GHz unity gain bandwidth products can be achieved.