gebhart/patrepeval huggingface dataset:
Rapid One-step Enzymatic Synthesis and All-aqueous Purification of Trehalose Analogues (2017)

Chemically modified versions of trehalose, or trehalose analogues, have applications in biology, biotechnology, and pharmaceutical science, among other fields. For instance, trehalose analogues bearing detectable tags have been used to detect Mycobacterium tuberculosis and may have applications as tuberculosis diagnostic imaging agents. Hydrolytically stable versions of trehalose are also being pursued due to their potential for use as non-caloric sweeteners and bioprotective agents. Despite the appeal of this class of compounds for various applications, their potential remains unfulfilled due to the lack of a robust route for their production. Here, we report a detailed protocol for the rapid and efficient one-step biocatalytic synthesis of trehalose analogues that bypasses the problems associated with chemical synthesis. By utilizing the thermostable trehalose synthase (TreT) enzyme from Thermoproteus tenax, trehalose analogues can be generated in a single step from glucose analogues and uridine diphosphate glucose in high yield (up to quantitative conversion) in 15-60 min. A simple and rapid non-chromatographic purification protocol, which consists of spin dialysis and ion exchange, can deliver many trehalose analogues of known concentration in aqueous solution in as little as 45 min. In cases where unreacted glucose analogue still remains, chromatographic purification of the trehalose analogue product can be performed. Overall, this method provides a "green" biocatalytic platform for the expedited synthesis and purification of trehalose analogues that is efficient and accessible to non-chemists. To exemplify the applicability of this method, we describe a protocol for the synthesis, all-aqueous purification, and administration of a trehalose-based click chemistry probe to mycobacteria, all of which took less than 1 hour and enabled fluorescence detection of mycobacteria. In the future, we envision that, among other applications, this protocol may be applied to the rapid synthesis of trehalose-based probes for tuberculosis diagnostics. For instance, short-lived radionuclide-modified trehalose analogues (e.g., 18F-modified trehalose) could be used for advanced clinical imaging modalities such as positron emission tomography-computed tomography (PET-CT).
A Mach-Zender digital holographic microscope with sub-micrometer resolution for imaging and tracking of marine micro-organisms (2014)

Digital holographic microscopy is an ideal tool for investigation of microbial motility. However, most designs do not exhibit sufficient spatial resolution for imaging bacteria. In this study we present an off-axis Mach-Zehnder design of a holographic microscope with spatial resolution of better than 800 nm and the ability to resolve bacterial samples at varying densities over a 380 μm × 380 μm × 600 μm three-dimensional field of view. Larger organisms, such as protozoa, can be resolved in detail, including cilia and flagella. The instrument design and performance are presented, including images and tracks of bacterial and protozoal mixed samples and pure cultures of six selected species. Organisms as small as 1 μm (bacterial spores) and as large as 60 μm (Paramecium bursaria) may be resolved and tracked without changes in the instrument configuration. Finally, we present a dilution series investigating the maximum cell density that can be imaged, a type of analysis that has not been presented in previous holographic microscopy studies.
Remote sensing by nuclear quadrupole resonance (2001)

Detection of explosives has the flavor of those mathematical problems that are not invertible. It is easier to hide explosives than to find them. Many approaches have been proposed and executed for the remote detection of explosives, contraband materials, weapons of mass destruction, currency, etc. Most detection technologies suffer from a common problem: the features they look for, such as discontinuities in electrical conductivity, are not unique properties of the target but are contained, to some degree, in the more benign surroundings. Such a degeneracy leads to "clutter" in the response. For example, resolving the false alarms generated by this clutter can determine the rate of advance of a conventional electromagnetic metal detector employed as a landmine detector. One approach that provides a "unique" signature is nuclear quadrupole resonance (NQR) (the technique is also called QR, to avoid confusion with strictly nuclear techniques). This paper outlines the important physical principles behind the use of NQR for remote detection, indicates areas of applicability, and presents results of field trials of a prototype landmine detection system.
Infliximab therapy decreases the levels of TNF-α and IFN-γ mRNA in colonic mucosa of ulcerative colitis (2009)

IFX induced down-regulation of the mucosal TNF-alpha and IFN-gamma mRNA expression in UC patients. The numbers of T lymphocytes and macrophages were significantly decreased in patients with endoscopically healed mucosa after IFX treatment.
4x3 Mueller matrix imager for cervical health diagnosis (2021)

Invasive cervical cancer is a slow progressing disease, taking more than 10 years to fully develop from infection. The anatomic accessibility and possible treatment of precancerous lesions make early screening a suitable and effective management. An imager based on Mueller matrix polarimetry consisting of a polarization state generator of four input polarization states and a polarization state analyzer on board of the detector, a polarized camera, is introduced. A 4x3 reduced form of the Mueller matrix is decomposed to extract polarimetric parameters such as the retardance, depolarization and orientation. The use of this device on biological samples is tested.
Synthesis and Structural—Activity Relationships of 3‐Hydroxyquinazoline‐2,4‐dione Antibacterial Agents. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Metal-bonded Co-ferrite composites for magnetostrictive torque sensor applications (1999)

A new class of magnetomechanical sensor materials, Co-ferrite (CoO/spl middot/Fe/sub 2/O/sub 3/) and metal-bonded (Ag, Ni, Co) Co-ferrite composites, has been investigated. These materials exhibited magnetostriction in excess of 200 ppm and high d/sub 33/ (/spl part//spl lambda///spl part/H)/sub /spl sigma// coefficient, 1.3/spl times/10/sup -9/ A/sup -1/ m, at low applied field (<100 kA/m). Selected compositions were formed into test samples in the form of rings brazed to stainless steel through-shafts. Changes of surface axial magnetic field in response to applied torque as high as 64 AN/sup -1/ m/sup -2/ were observed for a demonstration sample of dimensions 25 mm OD, 12.5 mm ID, and 8 mm high. A hysteresis of /spl plusmn/0.5 N/spl middot/m was observed. These materials appear to be promising candidates for torque sensors, and other magnetostrictive sensor and actuator applications.
Avian infectious laryngotracheitis: Virus‐host interactions in relation to prospects for eradication (1995)

This review examines the virology, immunology and molecular biology of infectious laryngotracheitis virus (ILTV) and its interactions with the chicken, in the context of assessing the feasibility of eradication. Establishment of the latent phase during infection of the host, its central role in biological survival of ILTV and the host-viral events that are associated with reactivation of infection, are considered. In counterpoint there are several features of the biology of ILTV in its natural mode of infection which can be exploited in eradicating this pathogen from intensive poultry production sites. These include the high degree of host-specificity of ILTV, dependence on contact for spread, the short-lived infectivity outside the chicken and the stability of the genome and lack of significant antigenic variation. Further, ILTV cannot replicate productively in its main target organ, the trachea, in the face of local specific cell-mediated immunity. Genetically-engineered vaccines that are capable of generating immunity, but without the ILTV latent infections induced by conventional modified-live ILT vaccine strains, are now well into development. This paper postulates that, used in conjunction with specific site quarantine and hygiene measures, such vaccines can provide the technological tools required to eradicate ILTV from production sites, and then regionally, in developed poultry industries from around the year 2000.
Third harmonic generation in ultrathin epsilon-near-zero media (2015)

We demonstrate efficient third harmonic generation from a 21.6nm-thick indium tin oxide film on glass substrate for a pump fundamental wavelength of 1350nm using the field enhancement properties of optical modes supported by epsilon-near-zero media.
Scalable modulator for frequency shift keying in free space optical communications (2013)

Frequency shift keyed (FSK) modulation formats are well-suited to deep space links and other high loss links. FSK's advantage comes from its use of bandwidth expansion. I.e., FSK counteracts power losses in the link by using an optical bandwidth that is greater than the data rate, just as pulse position modulation (PPM) does. Unlike PPM, increasing FSK's bandwidth expansion does not require increased bandwidth in electronic components. We present an FSK modulator whose component count rises logarithmically with the bandwidth expansion. We tested it with four-fold bandwidth expansion at 5 and 20 Gbit/s. When paired with a pre-amplified receiver, the required received power was about 4 and 5 dB from the theoretical best for such receivers. We also tested the FSK transmitter with a photon counting receiver.
Flatbed-type autostereoscopic display system and its image format for encoding (2006)

We have developed a flatbed-type autostereoscopic display system showing continuous motion parallax as an extended form of a one-dimensional integral imaging (1D-II) display system. The 1D-II display architecture is suitable for both flatbed and upright configurations. We have also designed an image format specification for encoding 1D-II data. In this parallax image array format, two (or more) viewpoint images whose viewpoint numbers are separated by a constant number are paired, and all of the paired images are combined to obtain an image the same size as the elemental image array. By using the format, 3-D image quality is hardly degraded by lossy codec. The conversion from this format to the elemental image array is simple and does not depend on changes in the viewing distance and associated changes in camera number. Decoding and converting speeds are sufficiently high due to utilization of middleware based on DirectX.
Mobile Testbed for Video-Rate Multistatic Microwave Imaging Array (2018)

A mobile testbed capable of real-time (10 Hz) standoff microwave imaging for concealed threat detection is presented. The system samples a scene with a 1m x 1m multistatic switched antenna array operating at 24–29 GHz. It constructs images on a cost-effective processor at video rate, through the use of Fast Fourier Transform (FFT) imaging. Design and operation of the testbed are discussed, and representative experimental images are presented.
Shape-Aware Organ Segmentation by Predicting Signed Distance Maps (2020)

In this work, we propose to resolve the issue existing in current deep learning based organ segmentation systems that they often produce results that do not capture the overall shape of the target organ and often lack smoothness. Since there is a rigorous mapping between the Signed Distance Map (SDM) calculated from object boundary contours and the binary segmentation map, we exploit the feasibility of learning the SDM directly from medical scans. By converting the segmentation task into predicting an SDM, we show that our proposed method retains superior segmentation performance and has better smoothness and continuity in shape. To leverage the complementary information in traditional segmentation training, we introduce an approximated Heaviside function to train the model by predicting SDMs and segmentation maps simultaneously. We validate our proposed models by conducting extensive experiments on a hippocampus segmentation dataset and the public MICCAI 2015 Head and Neck Auto Segmentation Challenge dataset with multiple organs. While our carefully designed backbone 3D segmentation network improves the Dice coefficient by more than 5% compared to current state-of-the-arts, the proposed model with SDM learning produces smoother segmentation results with smaller Hausdorff distance and average surface distance, thus proving the effectiveness of our method.
Development of a Novel High Efficiency, Low Cost Hybrid SOFC/Internal Combustion Engine Power Generator (2019)

The unique and beneficial characteristics of solid oxide fuel cell (SOFC) technology hold much promise for their eventual widespread adoption in numerous residential and commercial building applications. Nevertheless, cost and durability challenges remain that currently limit SOFC technology penetration in stationary energy applications. Under the U.S. DOE ARPA-E INTEGRATE program, the Colorado School of Mines and it partners are developing a novel hybrid stationary power system comprised of an intermediate temperature (600°C), solid oxide fuel cell stack integrated with a high efficiency stationary engine and novel balance-of-plant (BOP) equipment. In collaboration with Colorado State University, Kohler Power Systems, and Air-Squared, Inc., the project aims to demonstrate a system that can generate power (125 kW) from natural gas at high electric efficiency (>70%-LHV), and low cost (<900 $/kW). Project activities on the hybrid SOFC/IC engine system development and system requirements are discussed.
Field emission from H- and O-terminated heavily P-doped homoepitaxial diamond (2006)

Field emission properties of phosphorus (P)-doped homoepitaxial diamonds are measured after hydrogen plasma treatment and wet chemical oxidization. We also measure field emission properties of H-terminated B-doped diamond for comparison. P-doped diamonds are grown on type Ib single crystalline diamond by microwave plasma chemical vapor deposition. The resistivity of the films is in the range of (5–8)×102Ωcm. Phosphorus concentration measured by secondary ion mass spectroscopy is in the range of (5–7)×1019cm−3. The threshold voltage for field emission of O-terminated P-doped diamond with positive electron affinity is lower than that of H-terminated P-doped diamond with negative electron affinity. Upward band bending due to ionized phosphorus donors exists at the H-terminated surface. This upward bend bending prevents electrons from reaching to the emitting surface. An effective emission barrier height of O-terminated P-doped diamond surface is estimated to be 1.3eV using slopes of Fowler-Nordheim plots. This value is in good agreement with the reported electron affinities in literature.
Sum-Rate Analysis of Downlink Channels with 1-Bit Feedback (2007)

The sum-rate capacity of a single-input single-output (SISO) downlink with Rayleigh flat fading channels and K users, grows as log log K when optimal scheduling is employed. However, the optimal scheduling requires that the full channel state information (CSI) for all users be available to the transmitter. In this work it is shown that the same rate growth holds even if the feedback rate from the users to the transmitter is reduced to 1-bit per fading block. A simple analysis for this setup is presented, resulting in a closed form expression for the achievable ergodic sum-rate. The mechanism of setting a sub-optimal threshold is elucidated by simple lower and upper bounds to the sum-rate. Among the insights afforded by the sum-rate expression and the bounds, is that application of the sub-optimal threshold demonstrates the same scaling law as the optimal full CSI scheme, asymptotically with the number of users K
Single Antenna GPS Spoof Detection that is Simple, Static, Instantaneous and Backwards Compatible for Aerial Applications (2014)

Despite the antenna’s privileged position as the first line of defense against interferes, jammers and spoofers, most detection and mitigation techniques are realized in the receiver’s backed signal processing blocks. Nonetheless, these solutions often require considerable additional hard-ware added to the receiver’s fronted and antenna design. For example, multi-antenna arrays replace a single antenna design for the purpose of detection/mitigation of interference, jamming [1] and spoofing [2] [3]. Among the single antenna detection/mitigation designs, some form of antenna movement over time is required. For example, the use of a synthetic aperture [4] and the generation of high frequency antenna motion [5] has been proposed for spoof detection/mitigation. All of the aforementioned innovations utilize additional signal processing blocks in the back-end, in conjunction with the supplemented frontend hardware, to achieve their intended goals.
A primary technique for achieving this type of adaptability in sub-wavelength single antenna systems is the use of discrete circuit components on or near the antenna element [6]. Circuit components manipulating signals in the RF domain can achieve analog “signal processing” directly on the antenna, essentially eliminating additional computational complexity. However, signal processing in the digital domain often affords far more flexibility and applicability. The primary limitation of this design is that the spoof-detection technique is most effective when spoofed signals are originating from a source below the antenna, thus limiting its applicability to predominantly aerial implementations. Nonetheless, we feel this solution is well suited to the form-factor and payload constraints that aerial applications such as commercial aviation and UAVs demand. Additionally, we introduce some techniques for extending the applicability of this design.
In our design we simply add an electronic switch inside the radome of the antenna that permits high speed switching from the default radiation pattern that is predominantly right-hand circularly polarized (RHCP) to one that is predominantly left-hand circularly polarized (LHCP), in the upper hemisphere of the antenna. However, at very low angles of elevation and generally below the antenna, the radiation pattern is neither predominantly RHCP or LHCP [7], so the switching has little effect on the radiation pattern at all. We can exploit this expected telltale drop in the received SNR or C=N0 to identify if the signal is originating from above the antenna or from below it, and thus, if the signal is genuine or spoofed.
Biomarkers of Attenuation in the Leishmania donovani Centrin Gene Deleted Cell Line-Requirements for Safety in a Live Vaccine Candidate (2009)

Biomarkers of the attenuated phenotype are needed to develop live attenuated parasites into safe Leishmania vaccines. The centrin-1 gene deleted strain of Leishmania donovani (LdCEN1 -/-) shows promise as a vaccine candidate. To identify genes whose expression patterns are indicators of attenuation, the LdCEN1 -/-line was compared to wild type by gene expression microarray. Two genes, one coding for a 27kDa protein (p27) and another coding for putative Argininosuccinate Synthase (AS) have such expression patterns. Both genes express a higher RNA level in the amastigote stage than in the promastigote stage of wild type cells; however they are down-regulated in the LdCEN1 -/-amastigote cells. Western blots indicated that the AS protein level is also reduced in the LdCEN1 -/-amastigotes, while the p27 protein level is not reduced even when its mRNA level has diminished. Northern and Western blot analysis with these two biomarkers showed that LdCEN1 -/-parasites recovered after five weeks of infection in mice had the same expression pattern as they had prior to infection and episomal expression of centrin in the LdCEN1 -/-cells restored normal expression of both genes. Measurement of the expression of these two genes in infected macrophages by RT-PCR indicated the same pattern as in cultured cells. Therefore, both the mRNA and/or the protein levels of these two genes could be used as biomarkers of attenuation to monitor the safety of the LdCEN1 -/-cell line as it is developed as a potential vaccine.
Quick eviction of virtual machines through proactive live snapshots (2016)

Cloud computing platforms routinely use virtualization to improve service availability, resiliency, and flexibility. Live migration of Virtual Machines (VM) is a key technique to quickly migrate workloads in response to events such as impending failure or load changes. Despite extensive research, state-of-the-art live migration approaches take a long time to migrate a VM (in the order of tens of seconds for moderately sized VMs) which in turn negatively impacts the application performance during migration. We present Quick Eviction, a new approach to significantly speed up the eviction of a VM from the source host with low impact on VM's performance during migration. Our approach can also improve the effectiveness of VM resilience tools that back up a VM's state in anticipation of system failures. The insight behind Quick Eviction is that the majority of time to evict a VM during migration is due to the transfer of memory contents over the network, sometimes repeatedly. Before migration, Quick Eviction regularly snapshots the VM's memory to a destination or a failover node. During the actual migration, Quick Eviction has to transfer only a small amount of dirtied memory resulting in a very short time to completely evict the VM out of the source. The key challenge is to dynamically adapt the snapshot intervals so as to have minimal impact on application performance during migration. We show that our implementation of Quick Eviction in the KVM/QEMU platform reduces the eviction time of a VM by significant factors for both idle and write-intensive VMs compared to traditional pre-copy algorithm, while maintaining low overheads on application performance and network.
Magnesium Alloy Development using Phase Equilibria Computation and Microstructure Validation (2012)

This paper summarizes the development of new cast and wrought magnesium alloys using computational thermodynamics and experimental methods. The work illustrates the role of calculated phase diagrams, solidification paths and phases in predicting and interpreting the final microstructure of Mg-Al-Ca and Mg-Al-Sn cast alloy systems and Mg-Al-Mn and Mg-Zn-Ce wrought alloy systems.