gebhart/patrepeval huggingface dataset:
A Yeast Model of the Neurogenic Ataxia Retinitis Pigmentosa (NARP) T8993G Mutation in the Mitochondrial ATP Synthase-6 Gene (2007)

NARP (neuropathy, ataxia, and retinitis pigmentosa) and MILS (maternally inherited Leigh syndrome) are mitochondrial disorders associated with point mutations of the mitochondrial DNA (mtDNA) in the gene encoding the Atp6p subunit of the ATP synthase. The most common and studied of these mutations is T8993G converting the highly conserved leucine 156 into arginine. We have introduced this mutation at the corresponding position (183) of yeast Saccharomyces cerevisiae mitochondrially encoded Atp6p. The "yeast NARP mutant" grew very slowly on respiratory substrates, possibly because mitochondrial ATP synthesis was only 10% of the wild type level. The mutated ATP synthase was found to be correctly assembled and present at nearly normal levels (80% of the wild type). Contrary to what has been reported for human NARP cells, the reverse functioning of the ATP synthase, i.e. ATP hydrolysis in the F(1) coupled to F(0)-mediated proton translocation out of the mitochondrial matrix, was significantly compromised in the yeast NARP mutant. Interestingly, the oxygen consumption rate in the yeast NARP mutant was decreased by about 80% compared with the wild type, due to a selective lowering in cytochrome c oxidase (complex IV) content. This finding suggests a possible regulatory mechanism between ATP synthase activity and complex IV expression in yeast mitochondria. The availability of a yeast NARP model could ease the search for rescuing mechanisms against this mitochondrial disease.
Dual-Spun Shape Memory Elastomeric Composites (2015)

Thermally responsive shape memory polymers (SMPs) are typically relatively stiff due to the need to vitrify the polymer chains to fix a temporary shape. A need exists for elastomeric SMPs with mechanical properties that more closely match those of human tissue. In this communication, we present a novel approach to fabricate a fully thermoplastic elastomeric SMP. Two polymers are simultaneously electrospun, or dual-spun, forming a composite fiber mat with a controllable composition. The two polymers were chosen such that one assists in "shape fixing" and the other in "shape recovery". We envision that the versatility and simplicity of this fabrication approach will allow for large scale production of shape memory elastomeric composites (SMECs) for a wide range of applications.
Matching and retrieval based on the vocabulary and grammar of color patterns (2000)

We propose a perceptually based system for pattern retrieval and matching. The central idea is that similarity judgment has to be modeled along perceptual dimensions. Hence, we detect basic visual categories that people use in their judgment of similarity, and design a computational model that accepts patterns as input and, depending on the query, produces a set of choices that follow human behavior in pattern matching. There are two major research aspects to our work. The first one addresses the issue of how humans perceive and measure similarity within the domain of color patterns. To understand and describe this mechanism, we performed a subjective experiment which yielded five perceptual criteria used in comparison between color patterns (vocabulary), as well as a set of rules governing the use of these criteria in similarity judgment (grammar). The second research aspect is the implementation of the perceptual criteria and rules in an image retrieval system. Following the processing typical for human vision, we design a system to: (1) extract perceptual features from the vocabulary and (2) perform the comparison between the patterns according to the grammar rules. The modeling of human perception of color patterns is new--starting with a new color codebook design, compact color representation, and texture description through multi-scale edge distribution along different directions. Moreover, we propose new color and texture distance functions that correlate with human performance. The performance of the system is illustrated with numerous examples from image databases from different application domains.
Ex Uno Plures (“Out of One, Many”): New Paradigms for Expanding the Range of Polyolefins through Reversible Group Transfers (2008)

The "mature" status presently enjoyed by polyolefins prepared with homogeneous (soluble) single-site catalysts through the transition-metal-catalyzed coordination polymerization of ethene and 1-alkenes brings with it a common impression that it is now routinely possible to obtain, with a high degree of confidence, any desired stereochemical microstructure or copolymer composition through iterative optimization employing a set of mutationally related synthetic derivatives generated from an initial molecular design. The dominant reliance on this "one catalyst, one material" strategic approach to discovery is intrinsically self-limiting, however, owing to the limited pool of molecular structures that can be reasonably synthesized and drawn upon. Recently, non-chain-terminating, reversible group-transfer processes have been purposefully introduced to olefin coordination polymerization. These processes, which are highly competitive with propagation, can be controlled externally and now provide the basis for new "one catalyst, many materials" paradigms that have the potential to greatly expand the reach of polyolefin materials for the 21st century.
Thermal, atmospheric and ionospheric anomalies around the time of the Colima M7.8 earthquake of 21 January 2003 (2006)

Abstract. The paper examines the possible relationship of anomalous variations of different atmospheric and ionospheric parameters observed around the time of a strong earthquake (Mw 7.8) which occurred in Mexico (state of Colima) on 21 January 2003. These variations are interpreted within the framework of the developed model of the Lithosphere-Atmosphere-Ionosphere coupling. The main attention is focused on the processes in the near ground layer of the atmosphere involving the ionization of air by radon, the water molecules' attachment to the formed ions, and the corresponding changes in the latent heat. Model considerations are supported by experimental measurements showing the local diminution of air humidity one week prior to the earthquake, accompanied by the anomalous thermal infrared (TIR) signals and surface latent heat flux (SLHF) and anomalous variations of the total electron content (TEC) registered over the epicenter of the impending earthquake three days prior to the main earthquake event. Statistical processing of the data of the GPS receivers network, together with various other atmospheric parameters demonstrate the possibility of an early warning of an impending strong earthquake.
Retrospective Interference Alignment: Degrees of Freedom Scaling With Distributed Transmitters (2017)

In this paper, we consider the K-user singleinput single-output interference channel with delayed channel state information at the transmitters (CSIT). Our main contribution is to show that even with delayed CSIT and distributed transmitters, the achievable degrees of freedom (DoFs) still scale with the number of users. More specifically, we propose a method that achieves K/(2√K -1) ≥ √K/2 DoF. The main idea behind the proposed method is to use interference alignment (IA) at the receiver side in conjunction with repetition coding at the transmitters. Repetition coding repeats the data R times while IA makes the interference generated by a given transmitter identical: 1) at all non-intended receivers and 2) all transmission repetitions. Therefore, one retransmission per transmitter is sufficient to cancel all the interference. This reduces significantly the overhead required for interference removal since the number of interference terms is reduced from RK(K - 1) to K.
A cognitive radio antenna design based on optically pumped reconfigurable antenna system (OPRAS) (2011)

This paper presents a new antenna scheme for cognitive radio communication. The antenna structure consists of two ports. The first antenna port is a UWB structure for channel sensing while the second one is a reconfigurable structure for communication. The reconfigurability is based on integrating laser diodes within the antenna substrate in order to activate the photoconductive switches. A prototype was fabricated and tested. A good agreement between the simulation and the measurement data is noticed. A coupling of less than -20 dB is achieved between the 2 antenna ports.
Molecular Design, Cloning, Expression and Purification of NH(2)-terminal Mutant of Staphylokinase deltaNSak (1999)

The 3-D structure of human microplasminogen was predicted by the method of homology modeling. The binding sites of staphylokinase and microplasminogen were determined by high-resolution genetic docking. This model is consistent with several known experimental properties of staphylokinase. To elucidate the function of NH(2)-terminus of staphylokinase for further rational reconstruction, a NH(2)-terminal-deletion mutant of staphylokinase(deltaNSak) was designed. The soluble deltaNSak was achieved with fibrinolytic activity. deltaNSak was purified by two-step ion exchange chromatography. The purity was over 95% and the specific activity of deltaNSak was 9x10(4) IU/mg. These data suggest that the 15 NH(2)-terminal amino acids of staphylokinase are not required for its plasminogen activating potential and the computer model is reasonable.
Observation of memory effect in germanium nanocrystals embedded in an amorphous silicon oxide matrix of a metal–insulator– semiconductor structure (2002)

The memory effect of a trilayer structure (rapid thermal oxide/Ge nanocrystals in SiO2/sputtered SiO2) was investigated via capacitance versus voltage (C–V) measurements. The Ge nanocrystals were synthesized by rapid thermal annealing of the cosputtered Ge+SiO2 films. The memory effect was manifested by the hysteresis in the C–V curve. Transmission electron microscope and C–V results indicated that the hysteresis was due to Ge nanocrystals in the middle layer of the trilayer structure.
In-Duct and Farfield Experimental Measurements from the ANCF for the Purpose of Improved Broadband Liner Optimization (2014)

A process for the design and evaluation of novel broadband acoustic liner concepts with limited fan source information is being evaluated. A pair of advanced broad-bandwidth liners were designed and manufactured for the NASA Glenn Research Center's Advanced Noise Control Fan (ANCF): (i) a constant impedance liner and (ii) a variable impedance liner. The insertion loss of both liners was measured in-duct utilizing the ANCF's Configurable Fan Artificial Noise System in a clean configuration with no-flow. Additionally, the acoustic characteristics of the Variable Impedance Liner were measured in the standard ANCF configuration with and without flow. The experimental setup, in-duct mode power levels, and far-field directivity are presented herein.
Discovery of Inhibitors for Proliferating Cell Nuclear Antigen Using a Computational-Based Linked-Multiple-Fragment Screen (2019)

Proliferating cell nuclear antigen (PCNA) is a central factor in DNA replication and repair pathways that plays an essential role in genome stability. The functional roles of PCNA are mediated through an extensive list of protein-protein interactions, each of which transmits specific information in protein assemblies. The flexibility at the PCNA-protein interaction interfaces offers opportunities for the discovery of functionally selective inhibitors of DNA repair pathways. Current fragment-based drug design methodologies can be limited by the flexibility of protein interfaces. These factors motivated an approach to defining compounds that could leverage previously identified subpockets on PCNA that are suitable for fragment-binding sites. Methodologies for screening multiple connected fragment-binding events in distinct subpockets are deployed to improve the selection of fragment combinations. A flexible backbone based on <i>N</i>-alkyl-glycine amides offers a scaffold to combinatorically link multiple fragments for in silico screening libraries that explore the diversity of subpockets at protein interfaces. This approach was applied to discover new potential inhibitors of DNA replication and repair that target PCNA in a multiprotein recognition site. The screens of the libraries were designed to computationally filter ligands based upon the fragments and positions to <1%, which were synthesized and tested for direct binding to PCNA. Molecular dynamics simulations also revealed distinct features of these novel molecules that block key PCNA-protein interactions. Furthermore, a Bayesian classifier predicted 15 of the 16 new inhibitors to be modulators of protein-protein interactions, demonstrating the method's utility as an effective screening filter. The cellular activities of example ligands with similar affinity for PCNA demonstrate unique properties for novel selective synergy with therapeutic DNA-damaging agents in drug-resistant contexts.
Porous Hybrid Organic‐Inorganic Particles in Reversed‐Phase Liquid Chromatography (2006)

Abstract Reversed‐phase chromatographic media have recently become available that are based on porous hybrid organic‐inorganic particles. The present paper reviews hybrid particles that are made from organosilanes (organic moiety) and tetraalkoxysilanes (inorganic moiety). The hybrid particles are defined and classified within the context of a broader definition of hybrid materials. First syntheses and chromatographic evaluations are discussed for this class of hybrid packing materials. Publications are then described, which characterize two distinguishing chemical properties of hybrid particles vs. silica gel: 1) less acidic silanols, and 2) markedly longer lifetimes in alkaline mobile phases. These properties are achieved without sacrificing mechanical strength, as is found for fully organic particles, i.e., polymers, with the same chemical features. Literature reports are then reviewed that employ hybrid based reversed‐phase column packings for HPLC. Topics covered include fundamental retention mechanism studies, methods development studies, and applications made possible with the hybrid based products. Further review is presented on the use of theses hybrid particles for UPLC. The hybrid particles afford good mechanical strength without sacrificing retention and loading capacity, as is found for non‐porous particles. Applications employing hybrid based particles in the UPLC mode are then reported.
High resolution low-temperature superconductivity superconducting quantum interference device microscope for imaging magnetic fields of samples at room temperatures (2002)

We have developed a microscope to image weak magnetic fields using submillimeter pickup coils made from conventional low-temperature superconducting niobium wire coupled to the input circuit of a superconducting quantum interference device (SQUID). The pickup coil and the SQUID sensor are mounted in the vacuum space of the cryostat and are thermally anchored to the liquid helium reservoir. A 25 μm thick sapphire window separates the room temperature (RT) sample and the vacuum space. The spacing between the pickup coil and RT sample was typically less than 130 μm. The spatial resolution is limited by the diameter of the pickup coil. The pickup coils are easily interchangeable, allowing us to adapt the SQUID microscope to a variety of different measurements. We have achieved a spatial resolution of 250 μm with a magnetic field sensitivity of 850 fT/Hz1/2 or a spatial resolution of 500 μm with a magnetic field sensitivity of 330 fT/Hz1/2. We have used this instrument to measure various biomagnetic and paleomagnetic fields.
Slow-Frequency Pulsed Transcranial Electrical Stimulation for Modulation of Cortical Plasticity Based on Reciprocity Targeting with Precision Electrical Head Modeling (2016)

In pain management as well as other clinical applications of neuromodulation, it is important to consider the timing parameters influencing activity-dependent plasticity, including pulsed versus sustained currents, as well as the spatial action of electrical currents as they polarize the complex convolutions of the cortical mantle. These factors are of course related; studying temporal factors is not possible when the spatial resolution of current delivery to the cortex is so uncertain to make it unclear whether excitability is increased or decreased with anodal vs. cathodal current flow. In the present study we attempted to improve the targeting of specific cortical locations by applying current through flexible source-sink configurations of 256 electrodes in a geodesic array. We constructed a precision electric head model for 12 healthy individuals. Extraction of the individual's cortical surface allowed computation of the component of the induced current that is normal to the target cortical surface. In an effort to replicate the long-term depression (LTD) induced with pulsed protocols in invasive animal research and transcranial magnetic stimulation studies, we applied 100 ms pulses at 1.9 s intervals either in cortical-surface-anodal or cortical-surface-cathodal directions, with a placebo (sham) control. The results showed significant LTD of the motor evoked potential as a result of the cortical-surface-cathodal pulses in contrast to the placebo control, with a smaller but similar LTD effect for anodal pulses. The cathodal LTD after-effect was sustained over 90 min following current injection. These results support the feasibility of pulsed protocols with low total charge in non-invasive neuromodulation when the precision of targeting is improved with a dense electrode array and accurate head modeling.
A family of receptor-like kinases are regulated by BES1 and involved in plant growth in<i>Arabidopsis thaliana</i> (2009)

Plant growth is dictated by both developmental and environmental cues, many of which are perceived by receptor-like kinases (RLKs). In Arabidopsis, there are more than 600 RLKs; but the functions of most of them are unknown. We recently found that several members of CrRLK1L family RLKs are regulated by plant steroid hormone Brassinosteroids (BRs). Two of the RLKs, FERONIA (FER) and THESEUS1 (THE1) have been previously found to inhibit cell elongation during pollen tube/synergid cell recognition and in sensing cell wall integrity after damage, respectively. However, we found that HERCULES1 (HERK1), another member in the family, as well as THE1 and FER, are regulated by BRs and required for cell elongation during vegetative growth. Here we provide additional evidence for the regulation of the family members by BR effector protein BES1. We also show that another member in the family, designated as HERCULES2 (HERK2), functions redundantly with HERK1 and THE1 to promote stem elongation. Our results, together with those from others, provide compelling evidence that the CrRLK1L family members play important role in plant growth.
ELECTRICAL CAPACITANCE VOLUME TOMOGRAPHY: A COMPARISON BETWEEN 12- AND 24-CHANNELS SENSOR SYSTEMS (2015)

Spatial resolution represents akey performance aspect in electrical capacitance volume tomography (ECVT). Factors affecting the resolution include the ``soft-field'' nature of ECVT, the number of capacitance channels used, the ill-conditioned nature of the imaging reconstruction problem, and the signal-to-noise ratio of the measurement apparatus. In this study, the effect of choosing different numbers of capacitance plates on the performance of ECVT is investigated. Specifically, two ECVT sensors with 12 and 24 capacitance channels but covering equal volumes of a cylinder are used to examine the resulting impact on the image resolution.
Reproduction, Cytology, and Fertility of Pearl Millet × Pennisetum squamulatum BC4 Plants (1993)

Asexual reproduction by means of apomixis that allows production of true-breeding hybrids has tremendous potential for improving world food and feed production. Genes that control obligate apomixis are usually found in the noncultivated wild species. In the study reported here, progenies were established from seven apomictic backcross (BC)-4 plants in a program designed to transfer genes controlling apomixis from Pennisetum squamulatum Frens (2n=6x = 54) to cultivated pearl millet [P. glaucum (L.) R. Br. (2n = 4x = 28)]. The most highly apomictic plants had 2n = 27 or 29 chromosomes. A highly apomictic derivative from a 29-chromosome plant had 28 chromosomes plus a telocentric fragment. BC4 plants and their apomictic progeny more closely resembled cultivated pearl millet in morphology than did an apomictic BC3 plant. On the average, chromosomes of the BC4 plants had one more bivalent and two less univalents than those of the BC3 plants, indicating that the alien chromosomes are being lost. Seed set for BC4 plants ranged from 3% to 16% compared to about 5% for BC3 plants. High rates of ovule abortion were observed after day 11 or 12 in both BC3 and BC4 plants. No BC4 plants were obligately apomictic, but one (A22) produced 89% maternal progenies. Six of the seven BC4 plants produced some progeny that formed only aposporous embryo sacs. This study indicates that it should be possible to produce apomictic pearl millet.
EXPERIMENTAL INVESTIGATION OF HIGH EFFICIENCY SINGLE-STAGE MEMBRANE DISTILLATION CONFIGURATIONS (2015)

A novel single-stage membrane distillation (MD) configuration, known as conductive gap membrane distillation (CGMD), has been suggested by numerical modeling results to achieve up to two times higher energy efficiencies than conventional air gap MD systems. CGMD consists of an MD module with a high thermal conductivity material in the gap region between the membrane and condensing plate, increasing the effective thermal conductivity of the gap. Such systems, if realized practically, could make MD competitive as a large scale thermal desalination technology that is not restricted only to specialized waste heat applications and could also make a stronger case for MD’s use in waste-heat applications. In this study, an experimental comparison of different MD configurations is carried out on a bench scale system keeping membrane area constant, and results are compared to model predictions. The role of energy recovery within the module on improving CGMD efficiency is illustrated. A system with a simple copper woven mesh introduced in the gap in the place of plastic spacers is found to have 40% to 60% higher GOR than AGMD. The potential for further improvements in GOR and issues associated with studying MD efficiency at a laboratory bench scale are also discussed.
Full-wave simulations of electromagnetic cloaking structures (2006)

Pendry et al. have reported electromagnetically anisotropic and inhomogeneous shells that, in theory, completely shield an interior structure of arbitrary size from electromagnetic fields without perturbing the external fields. Neither the coordinate transformation-based analytical formulation nor the supporting ray-tracing simulation indicate how material perturbations and full-wave effects might affect the solution. We report fully electromagnetic simulations of the cylindrical version of this cloaking structure using ideal and nonideal (but physically realizable) electromagnetic parameters that show that the low-reflection and power-flow bending properties of the electromagnetic cloaking structure are not especially sensitive to modest permittivity and permeability variations. The cloaking performance degrades smoothly with increasing loss, and effective low-reflection shielding can be achieved with a cylindrical shell composed of an eight- (homogeneous) layer approximation of the ideal continuous medium. An imperfect but simpler version of the cloaking material is derived and is shown to reproduce the ray bending of the ideal material in a manner that may be easier to experimentally realize.