gebhart/patrepeval huggingface dataset:
Outer Domain of HIV-1 gp120: Antigenic Optimization, Structural Malleability, and Crystal Structure with Antibody VRC-PG04 (2012)

The outer domain of the HIV-1 gp120 envelope glycoprotein contains the epitope for broadly neutralizing antibodies directed to the CD4-binding site, many of which are able to neutralize over 90% of circulating HIV-1 isolates. While the outer domain is conformationally more stable than other portions of the HIV-1 envelope, efforts to express the outer domain as an immunogen for eliciting broadly neutralizing antibodies have not been successful, potentially because natural outer domain variants do not bind strongly to antibodies such as VRC01. In this study, we optimized the antigenic properties of the HIV-1 Env outer domain to generate OD4.2.2, from the KER2018 strain of clade A HIV-1, enabling it to bind antibodies such as VRC01 with nanomolar affinity. The crystal structure of OD4.2.2 in complex with VRC-PG04 was solved at 3.0-Å resolution and compared to known crystal structures including (i) the structure of core gp120 bound by VRC-PG04 and (ii) a circularly permutated version of the outer domain in complex with antibody PGT128. Much of the VRC-PG04 epitope was preserved in the OD4.2.2 structure, though with altered N and C termini conformations. Overall, roughly one-third of the outer domain structure appeared to be fixed in conformation, independent of alterations in termini, clade, or ligand, while other portions of the outer domain displayed substantial structural malleability. The crystal structure of OD4.2.2 with VRC-PG04 provides atomic-level details for an HIV-1 domain recognized by broadly neutralizing antibodies and insights relevant to the rational design of an immunogen that could elicit such antibodies by vaccination.
Francisella tularensis Molecular Typing Using Differential Insertion Sequence Amplification (2011)

Tularemia is a potentially fatal disease that is caused by the highly infectious and zoonotic pathogen Francisella tularensis. Despite the monomorphic nature of sequenced F. tularensis genomes, there is a significant degree of plasticity in the organization of genetic elements. The observed variability in these genomes is due primarily to the transposition of direct repeats and insertion sequence (IS) elements. Since current methods used to genotype F. tularensis are time-consuming and require extensive laboratory resources, IS elements were investigated as a means to subtype this organism. The unique spatial location of specific IS elements provided the basis for the development of a differential IS amplification (DISA) assay to detect and distinguish the more virulent F. tularensis subsp. tularensis (subtypes A.I and A.II) and subsp. holarctica (type B) strains from F. tularensis subsp. novicida and other near neighbors, including Francisella philomiragia and Francisella-like endosymbionts found in ticks. Amplicon sizes and sequences derived from DISA showed heterogeneity within members of the subtype A.I and A.II isolates but not the type B strains. These differences were due to a 312-bp fragment derived from the IS element ISFtu1. Analysis of wild-type F. tularensis isolates by DISA correlated with pulsed-field gel electrophoresis genotyping utilizing two different restriction endonucleases and provided rapid results with minimal sample processing. The applicability of this molecular typing assay for environmental studies was demonstrated by the accurate identification and differentiation of tick-borne F. tularensis. The described approach to IS targeting and amplification provides new capability for epidemiological investigations and characterizations of tularemia source outbreaks.
Distributing CRC Bits to Aid Polar Decoding (2017)

One recent and important advancement in information and coding theory is polar code, which is selected as the coding scheme for 5G eMBB control channels. In this paper, we propose a variant of polar codes that provides significant coding gain in the regime of short blocks and enables early termination of decoding processes. The overall scheme depends on distributing CRC bits in the whole information block, and a single interleaving/deinterleaving pattern can be defined to implement CRC distribution. The design can reduce the decoding latency and energy consumption of hardware, which is crucial for mobile applications like 5G.
Four DEF-Like MADS Box Genes Displayed Distinct Floral Morphogenetic Roles in Phalaenopsis Orchid (2004)

The complex flower organization of orchids offers an opportunity to discover new variant genes and different levels of complexity in the morphogenesis of flowers. In this study, four B-class Phalaenopsis DEF-like MADS-box genes were identified and characterized, including PeMADS2, PeMADS3, PeMADS4 and PeMADS5. Differential expression profiles of these genes were detected in the floral organs of P. equestris, suggesting distinctive roles in the floral morphogenesis of orchids. Furthermore, expressions of these genes were varied to different extents in the peloric mutants with lip-like petals. Expression of PeMADS4 was in lips and columns of wild type, and it extended to the lip-like petals in the peloric mutant. Expression of PeMADS5 was mainly in petals and to a lesser extent in columns in the wild type, whereas it was completely eliminated in the peloric mutant. Disruption of the PeMADS5 promoter region of the peloric mutant was detected at nucleotide +312 relative to the upstream of translational start codon, suggesting that a DNA rearrangement has occurred in the peloric mutant. Genomic structure analysis of the PeMADS5 showed that the exon length was conserved in exons 1-6, similar to DEF-like genes of other plants. Collectively, this is the first report that four DEF-like MADS genes were identified in a single monocotyledonous species and that they may play distinctive morphogenetic roles in the floral development of an orchid.
Application of Soft Porous Materials to a High-Speed Train Track (2009)

This paper explores the performance of an airborne jet-ski train that flies on a soft porous track within centimeters of the earth’s surface at speeds approaching current commercial jet aircraft. The jet train employs a lift mechanism first described for red cells gliding on the endothelial glycocalyx and subsequently used to predict the lift forces generated in skiing and snowboarding by the transiently trapped air beneath their planing surfaces. Using an asymptotic analysis for large values of the permeability parameter H/√Kp, where H is the porous layer thickness and Kp the Darcy permeability we first show that it is possible to support a 70 metric ton jet train carrying 200 passengers on a confined porous material if its Kp is approximately 5 × 10−9 m2. For this Kp one finds that the tilt of the planform is < 0.1 deg and the liftoff velocity is < 5 m/s. This value of Kp can be satisfied by a random fiber matrix with a fiber radius of 5 μm and a void fraction of 0.995. Compression tests on a fiber-fill material with these properties show that the fibers contribute < 0.2% of the total lift at maximum compression, and hence, the friction force of the fiber phase is negligible. Using jet engines of 10,000 lbf thrust, about 1/5 that of a 200 passenger jet aircraft, one is able to obtain a cruising velocity approaching 700 km/hr. This would allow for huge fuel savings and greatly reduce greenhouse emission.
Novel Procedure for Identification of Compounds Inhibitory to Transcription of Genes Involved in Mycotoxin Biosynthesis (2000)

A novel assay is described for the identification and isolation of compounds that inhibit the transcription of genes involved in mycotoxin biosynthesis. The thin-layer chromatography-based assay was used to screen plant extracts for compounds that would inhibit the expression of the beta-glucuronidase reporter gene under the control of an aflatoxin biosynthesis gene promoter in Aspergillus parasiticus. The assay was used to track purification of an inhibitory compound, cp2, from extracts of black pepper (Piper nigrum). Cp2 did not inhibit mycelial growth or the expression of the beta-tubulin gene but did inhibit aflatoxin biosynthesis at the transcriptional level. Applications of cp2 to the control of mycotoxins are discussed.
Two Novel Antigens Associated with Group B Streptococci Identified by a Rapid Two-Stage Radioimmunoassay (1988)

A two-stage radioimmunoassay (RIA) has been developed that identifies type-specific antigens on the surfaces of group B streptococci. In addition to detecting the type-specific carbohydrate antigens Ia, Ib, II, and III, the RIA identified four unique antigens reactive with the Centers for Disease Control's c-protein typing antiserum. Analysis of hot-acid extracts by immunoelectrophoresis confirmed that two of these reactivities corresponded to the reported alpha and beta antigens of the c-protein marker. In addition, the identification of two heretofore unidentified antigens, gamma and delta, by the two-stage RIA is detailed in this report. The assay uses intact bacteria and does not require hot-acid extraction, a procedure thus enabling detection of acid-labile antigens in their native unmodified form. The semiquantitative RIA requires less typing reagent than does precipitin testing and is more objective, reproducible, and rapid. The assay described here could be applied to the detection of any cell surface antigen for which a monospecific antiserum is available.
Automated planning volume definition in soft-tissue sarcoma adjuvant brachytherapy (2002)

In current practice, the planning volume for adjuvant brachytherapy treatment for soft-tissue sarcoma is either not determined a priori (in this case, seed locations are selected based on isodose curves conforming to a visual estimate of the planning volume), or it is derived via a tedious manual process. In either case, the process is subjective and time consuming, and is highly dependent on the human planner. The focus of the work described herein involves the development of an automated contouring algorithm to outline the planning volume. Such an automatic procedure will save time and provide a consistent and objective method for determining planning volumes. In addition, a definitive representation of the planning volume will allow for sophisticated brachytherapy treatment planning approaches to be applied when designing treatment plans, so as to maximize local tumour control and minimize normal tissue complications. An automated tumour volume contouring algorithm is developed utilizing computational geometry and numerical interpolation techniques in conjunction with an artificial intelligence method. The target volume is defined to be the slab of tissue r cm perpendicularly away from the curvilinear plane defined by the mesh of catheters. We assume that if adjacent catheters are over 2r cm apart, the tissue between the two catheters is part of the tumour bed. Input data consist of the digitized coordinates of the catheter positions in each of several cross-sectional slices of the tumour bed, and the estimated distance r from the catheters to the tumour surface. Mathematically, one can view the planning volume as the volume enclosed within a minimal smoothly-connected surface which contains a set of circles, each circle centred at a given catheter position in a given cross-sectional slice. The algorithm performs local interpolation on consecutive triplets of circles. The effectiveness of the algorithm is evaluated based on its performance on a collection of soft-tissue sarcoma tumour beds within various anatomical structures. For each of 15 patient cases considered, the algorithm takes approximately 2 min to generate the planning volume. Although the tumour shapes are rather different, the algorithm consistently generates planning volumes that visually demonstrate smooth curves compactly encapsulating the circles. This general-purpose contouring algorithm works well whether the catheters are all close together, spread far apart in the plane or arranged in a convoluted way. The automatic contouring algorithm significantly reduces labour time and provides a consistent and objective method for determining planning volumes for soft-tissue sarcoma. Further studies are needed to validate the significance of the resulting planning volumes in designing treatment plans and the role that sophisticated brachytherapy treatment planning optimization may have in producing good plans.
Zirconium-Incorporated Mesoporous Silicates Show Remarkable Lignin Depolymerization Activity (2017)

The depolymerization of dealkaline lignin in CH3OH + H2O mixtures was investigated over various solid acid catalysts, including commercial zeolites (H-FER, H-MOR, H-Beta, H-USY, and H-ZSM-5) with predominantly Brønsted acid sites and zirconium-incorporated mesoporous silicates (Zr-KIT-5 and Zr-KIT-6 with different Si/Zr ratios) with predominantly Lewis acid sites. Gel permeation chromatography (GPC) analyses of the product mixture, obtained from half hour batch reactions on the various catalysts at 250 °C and under a nitrogen pressure of 0.7 MPa, revealed a clear decrease in the molecular weight distribution, compared to the parent lignin. The yields of aromatic monomers (7.5 wt % of the initial lignin) and overall soluble aromatic species (∼77%) observed over Zr-KIT-5 is higher, compared to those observed with H-ZSM-5 (4.1% and 67%, respectively) under identical conditions. Furthermore, the yield of catalyst deposits is lower in Zr-KIT-5 (14%), compared to H-ZSM-5 (27%). The predominant Lewis acidity of Zr-KIT-5 appears to reduce aldehyde condensation reactions promoted by the Brønsted acid sites present in zeolites. However, a lack of hydrothermal stability of the mesoporous silicates is a drawback that must be overcome for practical viability.
Ultraviolet emission from Sb-doped p-type ZnO based heterojunction light-emitting diodes (2008)

Heterojunction light emitting diodes (LEDs) were fabricated by making Au∕Ni top Ohmic contacts on Sb-doped p-type ZnO film with low specific contact resistivity and Al∕Ti back Ohmic contacts on n-type Si substrate. Near-band edge and deep-level emissions were observed from the LED devices at both low temperatures and room temperature, which is due to band-to-band and band-to-deep level radiative recombinations in ZnO, respectively. The electroluminescence emissions precisely match those of photoluminescence spectra from Sb-doped p-type ZnO, indicating that the ZnO layer acts as the active region for the radiative recombinations of electrons and holes in the diode operation.
Advanced protective relaying based on Rogowski coil current sensors (2008)

This paper describes advanced relay protection systems that incorporate Rogowski coils and multifunction relays. The schemes are simple, user friendly and require less wiring and space than conventional solutions. Novel protection schemes for low, medium, and high voltage power system applications are presented. A companion paper presents Rogowski coils current sensor performance characteristics for advanced relay protection.
Evaluation of metropolitan traffic flow with agent-based traffic simulator and approximated vehicle behavior model near intersections (2015)

In this paper, we introduce a metropolitan traffic simulation with microscopic vehicle agents with approximated behavior near intersections. We simulate a metropolitan traffic flow for Tokyo and surrounding four prefectures with fine-grained traffic demand obtained from Tokyo Person Trip survey. Though this simulator has an ability to manage signal control, it is difficult to obtain the real signal data of the city. Without signal data, the behavior of vehicles in a city becomes too smooth because they do not stop at intersections. This causes differences in traffic volume distribution. In this paper, we introduce a virtual vehicle that appears virtually in the front of the lead vehicle on each road to achieve natural deceleration with a car following speed model. We evaluate the aggregated effect of the virtual vehicle by comparing simulated traffic volume and trip length with real traffic data including road traffic census and person trip survey data.
In vitro and in vivo characterization of Recifercept, a soluble fibroblast growth factor receptor 3, as treatment for achondroplasia (2020)

Achondroplasia is a rare genetic disorder caused by mutations in the Fibroblast Growth Factor receptor 3 (FGFR3). These mutations lead to aberrant increase of inhibitory signaling in proliferating chondrocytes at the growth plate. Recifercept is a potential treatment for this disease using a decoy approach to sequester FGFR3 ligands subsequently normalizing activation of the mutated FGFR3 receptor. Recifercept binds to FGF isoforms in vitro and in cellular model systems and reduces FGFR3 signaling. In addition, in a transgenic mouse model of achondroplasia, Recifercept restores reduced body weight and long bone growth in these mice. These data suggest that Recifercept treatment could lead to clinical benefits in children treated with this molecule.
Efficient and robust radiance transfer for probeless photorealistic augmented reality (2014)

Photorealistic Augmented Reality (AR) requires knowledge of the scene geometry and environment lighting to compute photometric registration. Recent work has introduced probeless photometric registration, where environment lighting is estimated directly from observations of reflections in the scene rather than through an invasive probe such as a reflective ball. However, computing the dense radiance transfer of a dynamically changing scene is computationally challenging. In this work, we present an improved radiance transfer sampling approach, which combines adaptive sampling in image and visibility space with robust caching of radiance transfer to yield real time framerates for photorealistic AR scenes with dynamically changing scene geometry and environment lighting.
Dielectric properties of Ta2O5–SiO2 polycrystalline ceramics (1996)

The dielectric properties of (Ta2O5)1−x(SiO2)x polycrystalline ceramics for 0.0≤x≤0.20 are reported. Measurements were made at 1 MHz and temperature between −40 and +100 °C. The dielectric properties are not very sensitive to SiO2 content. A moderate enhancement of the dielectric constant is found, from −30 for pure Ta2O5 to ∼45 at x≂0.10. The temperature coefficient of dielectric constant in the vicinity of room temperature decreases from ∼200 ppm/°C for Ta2O5 to ∼75 ppm/°C for x=0.14.
Magnetic field measurements using magneto-optic Kerr effect sensors (1994)

A novel optically based magnetic field sensing technique is developed that uses a thin magnetic film as the sensing element and the longitudinal and transverse magneto-optic Kerr effects in an optical read technique. The linear system response is tested for small magnetic fields using a simple free-space ellipsometry measurement system. Measurements taken at 8 mHz showed a magnetic field sensitivity of 4 x 10<sup>-3</sup> Oe, with a system dynamic range of over 60 dB. The noise spectrum was dominated by 1/<i>f</i> noise. Calculations for a shot-noise-limited measurement system indicate that a magnetic field sensitivity of 10<sup>-6</sup> Oe/Hz<sup>1/2</sup> may be possible through enhancement of the sensing element parameters and 100-mW light sources.
THE "MICROFLUIDIC PALETTE": GENERATION OF STABLE AND PURELY DIFFUSIVE CHEMICAL GRADIENTS INSIDE A MICROFLUIDIC CHAMBER (2008)

We describe a new device called the microfluidic palette, capable of generating multiple spatial chemical gradients simultaneously inside a microfluidic chamber. The unique aspect of this work is that the chemical gradients are generated by diffusion, without convection, and either can be held constant over long periods of time or modified dynamically. This allows for objects (such as cells or complex sensors) to be exposed to complex chemical gradients without experiencing convective flow.
Tendency of nanosecond optical parametric oscillators to produce purely phase-modulated light (1996)

We show that nanosecond optical parametric oscillators pumped well above threshold by single-longitudinalmode pulses produce signal and idler light that is nearly purely phase modulated under a variety of conditions, including both seeded and unseeded operation.
Incompletely-Condensed Fluorinated Silsesquioxane: Synthesis and Crystal Structure (2011)

Abstract : A recently developed sub-class of POSS, fluorinated polyhedral oligomeric silsesquioxane (F-POSS), consists of a Si-O core with a periphery of fluorinated chains ranging from 6-12 carbon atoms in length. These structures possess some of the lowest surface energies for any known crystalline solid. This sub-class has been based on completely-condensed silsesquioxane cages with no means of chemical functionalization. Herein, an incompletely-condensed silsesquioxane, (CF3(CF2)7CH2CH2)8Si8O11(OH)2, has been synthesized via a multi-step synthesis (52% yield). The structure was confirmed with 29Si NMR, elemental analysis, and Xray diffraction. X-ray diffraction revealed an incompletely-condensed structure that contains inter- and intramolecular hydrogen bonding between silanols. This structure is currently being functionalized to produce a wide variety of functional F-POSS based compounds and polymers.
Genomic Evidence for the Evolution of Streptococcus equi: Host Restriction, Increased Virulence, and Genetic Exchange with Human Pathogens (2009)

The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered. Streptococcus equi subspecies equi (S. equi) is a host-restricted pathogen of horses that has evolved from the zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). These pathogens share approximately 80% genome sequence identity with the important human pathogen Streptococcus pyogenes. We sequenced and compared the genomes of S. equi 4047 and S. zooepidemicus H70 and screened S. equi and S. zooepidemicus strains from around the world to uncover evidence of the genetic events that have shaped the evolution of the S. equi genome and led to its emergence as a host-restricted pathogen. Our analysis provides evidence of functional loss due to mutation and deletion, coupled with pathogenic specialization through the acquisition of bacteriophage encoding a phospholipase A(2) toxin, and four superantigens, and an integrative conjugative element carrying a novel iron acquisition system with similarity to the high pathogenicity island of Yersinia pestis. We also highlight that S. equi, S. zooepidemicus, and S. pyogenes share a common phage pool that enhances cross-species pathogen evolution. We conclude that the complex interplay of functional loss, pathogenic specialization, and genetic exchange between S. equi, S. zooepidemicus, and S. pyogenes continues to influence the evolution of these important streptococci.