gebhart/patrepeval huggingface dataset:
Alteration in carbon partitioning induced by the movement protein of tobacco mosaic virus originates in the mesophyll and is independent of change in the plasmodesmal size exclusion limit (1995)

ABSTRACT The influence of the 30 kDa movement protein of tobacco mosaic virus (TMV‐MP) on carbon partitioning in trans‐genie tobacco plants ( Nicotiana tabacum cv. Xanthi) expressing the TMV‐MP was investigated. Using reciprocal grafting of transgenic tobacco plants expressing this movement protein and vector control plants, as well as transgenic tobacco plants expressing the TMV‐MP in phloem cells only, we showed that the interactive site involved in carbon allocation to roots is localized to the mesophyll tissue. Biomass partitioning experiments conducted on transgenic plants, in which various deletion mutant forms of the TMV‐MP (two of which included deletions in the domain responsible for increasing the size exclusion limit) were expressed, revealed that the TMV‐MP exerts its influence on carbon allocation via a mechanism that is completely independent of the TMV‐MP‐induced increase in the plasmodesmal size exclusion limit. Furthermore, small N‐ and C‐terminal deletions in the MP revealed the complexity of the interactions likely to be involved between the MP and an endogenous regulatory mechanism. We propose that the TMV‐MP interferes with an endogenous signal transduction pathway that involves macromolecular trafficking through plasmodesmata to regulate biomass partitioning between the source and various sink tissues.
Calibrating free-space measurement systems for microwave moisture sensing in granular materials (2003)

The universal character of a permittivity-based calibration function for moisture determination in granular materials such as cereal grain and seed is tested through measurement at microwave frequencies on materials of different structure and composition using two free-space measurement arrangements. Results obtained from measurements on wheat, corn and soybeans provide moisture calibration equations with temperature compensation that are very similar for both systems leading to a single moisture calibration equation and the potential of transferability of the calibration routine across instruments of different designs.
Biochemical rationale and the cardiac response of patients with muscle disease to therapy with coenzyme Q10. (1985)

Cardiac disease is commonly associated with virtually every form of muscular dystrophy and myopathy. A double-blind and open crossover trial on the oral administration of coenzyme Q10 (CoQ10) to 12 patients with progressive muscular dystrophies and neurogenic atrophies was conducted. These diseases included the Duchenne, Becker, and limb-girdle dystrophies, myotonic dystrophy, Charcot-Marie-Tooth disease, and Welander disease. The impaired cardiac function was noninvasively and extensively monitored by impedance cardiography. Solely by significant change or no change in stroke volume and cardiac output, all 8 patients on blind CoQ10 and all 4 on blind placebo were correctly assigned (P less than 0.003). After the limited 3-month trial, improved physical well-being was observed for 4/8 treated patients and for 0/4 placebo patients; of the latter, 3/4 improved on CoQ10; 2/8 patients resigned before crossover; 5/6 on CoQ10 in crossover maintained improved cardiac function; 1/6 crossed over from CoQ10 to placebo relapsed. The rationale of this trial was based on known mitochondrial myopathies, which involve respiratory enzymes, the known presence of CoQ10 in respiration, and prior clinical data on CoQ10 and dystrophy. These results indicate that the impaired myocardial function of such patients with muscular disease may have some association with impaired function of skeletal muscle, both of which may be improved by CoQ10 therapy. The cardiac improvement was definitely positive. The improvement in well-being was subjective, but probably real. Likely, CoQ10 does not alter genetic defects but can benefit the sequelae of mitochondrial impairment from such defects. CoQ10 is the only known substance that offers a safe and improved quality of life for such patients having muscle disease, and it is based on intrinsic bioenergetics.
Images from an adaptive current tomograph (1988)

The authors have designed, built, and tested an electric current tomograph suitable for applying the adaptive current algorithm described by D. Isaacson et al. (1988). Usable images can be obtained by a relatively primitive reconstruction algorithm. Demonstrable improvement in these images is obtained when optimal current patterns are used.< <ETX>></ETX>
A current-measurement front-end with 160dB dynamic range and 7ppm INL (2018)

Accurate current measurement is crucial in many biosensing applications, such as the detection of neurotransmitters [1] and the monitoring of intercellular molecular dynamics. This need has become even more critical recently with single-molecule biosensors where sub-pA signal currents are superimposed on a slowly varying nA-to-μA background current, as is the case with nanopores [2]. As such, the readout circuitry requires wide dynamic range (>120dB) and high linearity (>14b) albeit often with low bandwidth (a few Hz to kHz). This paper presents a current measurement front-end using a modified asynchronous ΔΣ modulator architecture that achieves 7ppm INL and 160dB dynamic range (100fA to 10μA) for a state-of-the-art 197dB FoM due to: 1) a continuous-time, oscillator-based Hourglass ADC that asynchronously folds the input signal within the supply, 2) noise shaping to suppress the quantization noise, and 3) a digital linearity correction technique that relaxes the amplifier bandwidth requirement thus reducing power.
Linking Sequence to Function in Soil Bacteria: Sequence-Directed Isolation of Novel Bacteria Contributing to Soilborne Plant Disease Suppression (2008)

Microbial community profiling of samples differing in a specific ecological function, i.e., soilborne plant disease suppression, can be used to mark, recover, and ultimately identify the bacteria responsible for that specific function. Previously, several terminal restriction fragments (TRF) of 16S rRNA genes were statistically associated with damping-off disease suppression. This work presents the development of sequence-based TRF length polymorphism (T-RFLP)-derived molecular markers to direct the identification and isolation of novel bacteria involved in damping-off pathogen suppression. Multiple sequences matching TRF M139 and M141 were cloned and displayed identity to multiple database entries in the genera incertae sedis of the Burkholderiales. Sequences matching TRF M148, in contrast, displayed greater sequence diversity. A sequence-directed culturing strategy was developed using M139- and M141-derived markers and media reported to be selective for the genera identified within this group. Using this approach, we isolated and identified novel Mitsuaria and Burkholderia species with high levels of sequence similarity to the targeted M139 and M141 TRF, respectively. As predicted, these Mitsuaria and Burkholderia isolates displayed the targeted function by reducing fungal and oomycete plant pathogen growth in vitro and reducing disease severity in infected tomato and soybean seedlings. This work represents the first successful example of the use of T-RFLP-derived markers to direct the isolation of microbes with pathogen-suppressing activities, and it establishes the power of low-cost molecular screening to identify and direct the recovery of functionally important microbes, such as these novel biocontrol strains.
New processable polyaromatic esters curable by intramolecular cyclization. XVIII (1981)

Abstract New processable polyaromatic esters were prepared from 2,2′‐diiododiphenyl‐4,4′‐dicarbonyl dichloride (I), isophthaloyl chloride (II), and/or terephthaloyl chloride (III) with 4,4′‐isopropylidene diphenol (IV), 4,4′‐sulfonyldiphenol (V), or resorcinol by interfacial condensation. In these polymers phenylacetylenyl groups were introduced by replacing the iodine. This process led to soluble and curable polymers. Polymer films can be prepared. After curing the polymers were insoluble and showed excellent thermal and chemical resistance. The curing process increased the polymers' softening temperature about 20°C.
Low power consumption electrically pumped photonic crystal membrane devices (2011)

A fabrication procedure for electrically pumping photonic crystal membrane devices using a lateral p-i-n junction has been developed and is described in this work. The lateral junction is optimized to efficiently inject current into a photonic crystal nanocavity. We have demonstrated electrically pumped lasing by using the lateral junction to pump a quantum dot photonic crystal nanocavity laser. Continuous wave lasing is observed at temperatures up to 150K, and a threshold of 181nA at 50K is demonstrated - the lowest threshold ever demonstrated in an electrically pumped laser. We have demonstrated electrical pumping of photonic crystal nanobeam light emitting diodes, and observe linewidth narrowing at room temperature.
Tracking the Evolutionary Origin of the Methicillin Resistance Gene: Cloning and Sequencing of a Homologue of <i>mecA</i> from a Methicillin Susceptible Strain of <i>Staphylococcus sciuri</i> (1996)

The gene mecA, a central genetic determinant of methicillin resistance in Staphylococcus aureus and coagulase-negative staphylococci of human origin, has an unknown extra species origin in these human pathogens. After screening isolates representing over 15 different species within the genus Staphylococcus we could identify only one--S. sciuri--in which each of over 150 independent isolates showed positive hybridization with a mecA-specific DNA probe isolated from a methicillin-resistant strain of S. aureus, (MRSA). Yet, the majority of these isolates showed no resistance to penicillin or methicillin. The mecA gene homologue was cloned and sequenced from a S. sciuri strain and the sequence of mecA was compared to that of the mecA of prototype strains of methicillin resistant S. aureus and S. epidermidis. Similarly to mecA of MRSA, the mecA homologue of S. sciuri was composed of a putative transglycosylase and a transpeptidase domain the latter showing all the conserved motifs typical of the active sites of the penicillin binding domain of transpeptidases. Overall similarity between the deduced amino acid sequences of mecA of MRSA and the mecA homologue of S. sciuri was 88%. On the other hand, comparison of the transpeptidase domain of the S. sciuri mecA to the corresponding domain alone of the MRSA mecA showed a similarity of 96% and an identity of 91%, while comparison of the putative transglycosylase domains of the two bacteria showed only a 80% similarity and 68% identity of amino acid sequences. Our data suggests that mecA of methicillin-resistant strains of staphylococci pathogenic to Man originated within the genus of Staphylococcus from an evolutionary relative of the mecA homologue that we have identified in S. sciuri and which may perform a normal physiological function in this bacterium unrelated to beta-lactam resistance.
Immunopurification and protease inhibitory properties of protease nexin-2/amyloid beta-protein precursor. (1990)

Protease nexin-2 (PN-2) is a protease inhibitor that is synthesized and secreted by a variety of extravascular cells including human fibroblasts. It forms sodium dodecyl sulfate-stable complexes with trypsin, the epidermal growth factor binding protein and the gamma-subunit of nerve growth factor. Recently we reported that PN-2 is the secreted form of the amyloid beta-protein precursor (APP) and is a potent inhibitor of chymotrypsin. Here we describe a two-step procedure to purify PN-2/APP using a monoclonal antibody immunoaffinity column. We also quantitated the protease inhibitory properties of purified PN-2/APP on a number of serine proteases. PN-2/APP was a potent inhibitor of coagulation factor XIa with a Ki = 2.9 x 10(-10). The inhibition of factor XIa by PN-2/APP was augmented by heparin and resulted in a Ki = 5.5 x 10(-11) M. Trypsin and chymotrypsin were also effectively inhibited with a Ki = 4.2 x 10(-10) and 1.6 x 10(-9), respectively. PN-2/APP also inhibited the epidermal growth factor binding protein, the gamma-subunit of nerve growth factor, and chymase and plasmin to a lesser extent. In view of recent findings that PN-2/APP is contained in alpha-granules of platelets and is secreted upon platelet activation, the potent inhibition of factor XIa suggests that PN-2/APP may play a regulatory role in the coagulation pathway at vascular wound sites. In addition, these studies define biochemical activities of PN-2/APP which may be involved in regulating proteases that lead to the generation and deposition of the beta-protein in neurodegenerative lesions associated with Alzheimer's disease and Down's syndrome.
Identification of peptides inhibiting enzyme I of the bacterial phosphotransferase system using combinatorial cellulose‐bound peptide libraries (1998)

The phosphoenolpyruvate(P-pyruvate)-dependent sugar phosphotransferase system (PTS) is a transport and signal-transduction system which is almost ubiquitous in bacteria but does not occur in eucaryotes. It catalyzes the uptake and phosphorylation of carbohydrates and is involved in signal transduction, e.g. catabolite repression, chemotaxis, and allosteric regulation of metabolic enzymes and transporters. EI (Enzyme I of the PTS) is the first and central component of the divergent PTS (P-pyruvate-dependent sugar phosphotransferase system) phosphorylation cascade. Using immobilized combinatorial peptide libraries and phosphorimaging, heptapeptides and octapeptides were identified which selectively inhibit EI in vitro. The IC50 of the best peptides is 30 microM which is close to the K(M) (6 microM) of EI for its natural substrate HPr (histidine containing phosphoryl carrier protein of the PTS). The affinity-selected peptides are better inhibitors than a peptide with the active-site sequence of HPr. The selected peptides contain several basic residues and one aromatic residue which do not occur in the active site of HPr. The large proportion of basic residues most likely reflects charge complementarity to the strongly acidic active-site pocket of EI. Guanidino groups might facilitate by complexation of the phosphoryl group the slow phosphorylation of the peptide.
Robust elasticity imaging using external tracker (2009)

The potential of ultrasound elasticity imaging (USEI) have been shown in numerous medical applications especially in detection and diagnosis of cancer. However, the widespread use of this imaging technique in clinical setups is limited by its dependency to the user expertise. Insufficient skill in freehand palpation of the tissue easily translates into poor quality of the images. In this paper, the synchronized data from an external tracker is employed to reduce this dependency and to increase the overall quality of the images. Based on the information from the external tracker, pairs of RF frames suitable for USEI are selected from the pool of incoming RF sequences. The selection of RF frames is tuned to match the known properties of the underlying elasticity estimation technique. Experiments on breast phantom are carried to evaluate the performance of the proposed method.
Polarimetric SAR data compensation for terrain azimuth slope variation (2000)

This paper addresses the problem of polarimetric SAR (POLSAR) data correction for changes in radar cross sections, which are caused by azimuth slopes. Most radiometric slope corrections remove slope effects to account for the effective scattering pixel area. However, few studies address the slope effect on the radar cross section as a function of polarization states. The authors propose two approaches to compensate for this azimuth slope effect for POLSAR data. In the first approach, the digital elevation model (DEM), obtained from interferometric SAR or from other means, is used to estimate orientation angles, and in the second approach, orientation angles are derived directly from the POLSAR data. They have developed three new methods to implement this second approach. One is based on the right-right and left-left circular polarizations, and the other two are based on Cloude's and Huynelt's decompositions. The results are compared with the original polarization signature method using the DEM-generated orientation angles as the reference. POLSAR data is then compensated using the derived orientation angles. Significant changes were observed in many elements of the coherency matrix. The compensated POLSAR data should improve the accuracy of geophysical parameter estimation techniques. NASA/JPL AIRSAR data for an area in central California is used for illustration.
Scalable Similarity Learning Using Large Margin Neighborhood Embedding (2015)

Classifying large-scale image data into object categories is an important problem that has received increasing research attention. Given the huge amount of data, non-parametric approaches such as nearest neighbor classifiers have shown promising results, especially when they are underpinned by a learned distance or similarity measurement. Although metric learning has been well studied in the past decades, most existing algorithms are impractical to handle large-scale data sets. In this paper, we present an image similarity learning method that can scale well in both the number of images and the dimensionality of image descriptors. To this end, similarity comparison is restricted to each sample's local neighbors and a discriminative similarity measure is induced from large margin neighborhood embedding. We also exploit the ensemble of projections so that high-dimensional features can be processed in a set of lower-dimensional subspaces in parallel. The efficiency and scalability of our proposed model are validated on several data sets with scales varying from tens of thousands to one million images.
Complete Bovine Leukemia Virus (BLV) Provirus Is Conserved in BLV-Infected Cattle throughout the Course of B-Cell Lymphosarcoma Development (1998)

Bovine leukemia virus (BLV) and human T-cell leukemia virus types 1 and 2 (HTLV-1 and HTLV-2) belong to the same subfamily of oncoviruses. Defective HTLV-1 proviral genomes have been found in more than half of all patients with adult T-cell leukemia examined. We have characterized the genomic structure of integrated BLV proviruses in peripheral blood lymphocytes and tumor tissue taken from animals with lymphomas at various stages. Genomic Southern hybridization with SacI, which generates two major fragments of BLV proviral DNA, yielded only bands that corresponded to a full-size provirus in all of 23 cattle at the lymphoma stage and in 7 BLV-infected but healthy cattle. Long PCR with primers located in long terminal repeats clearly demonstrated that almost the complete provirus was retained in all of 27 cattle with lymphomas and in 19 infected but healthy cattle. However, in addition to a PCR product that corresponded to a full-size provirus, a fragment shorter than that of the complete virus was produced in only one of the 27 animals with lymphomas. Moreover, when we performed conventional PCR with a variety of primers that spanned the entire BLV genome to detect even small defects, PCR products were produced that specifically covered the entire BLV genome in all of the 40 BLV-infected cattle tested. Therefore, it appears that at least one copy of the full-length BLV proviral genome was maintained in each animal throughout the course of the disease and, in addition, that either large or small deletions of proviral genomes may be very rare events in BLV-infected cattle.
The Nature of the Attenuation of<i>Salmonella typhimurium</i>Strains Expressing Human Papillomavirus Type 16 Virus-Like Particles Determines the Systemic and Mucosal Antibody Responses in Nasally Immunized Mice (1999)

We have recently shown by using a recombinant Salmonella typhimurium PhoPc strain in mice the feasibility of using a Salmonella-based vaccine to prevent infection by the genital human papillomavirus type 16 (HPV16). Here, we compare the HPV16-specific antibody responses elicited by nasal immunization with recombinant S. typhimurium strains harboring attenuations that, in contrast to PhoPc, are suitable for human use. For this purpose, chi4989 (Deltacya Deltacrp) and chi4990 [Deltacya Delta(crp-cdt)] were constructed in the ATCC 14028 genetic background, and comparison was made with the isogenic PhoPc and PhoP- strains. Although the levels of expression of HPV16 virus-like particle (VLP) were similar in all strains, only PhoPc HPV16 induced sustained specific antibody responses after nasal immunization, while all strains induced high antibody responses with a single nasal immunization when an unrelated viral hepatitis B core antigen was expressed. The level of the specific antibody responses induced did not correlate with the number of recombinant bacteria surviving in various organs 2 weeks after immunization. Our data suggest that the immunogenicity of attenuated Salmonella vaccine strains does not correlate with either the number of persisting bacteria after immunization or the levels of in vitro expression of the antigen carried. Rather, the PhoPc phenotype appears to provide the unique ability in Salmonella to induce immune responses against HPV16 VLPs.
Inkjet Printed Organic Thin Film Transistors: Achievements and Challenges (2012)

Inkjet printing of organic thin film transistors is an enabling technology for many applications requiring low cost electronics such as RFID tags, sensors, e-paper, and displays. This review summarizes the achievements and remaining challendges in the field. An all inkjet printed organic thin film transistor is feasible, but manufacturability needs to be improved. Often, a hybrid process in which only some layers are inkjet printed is used. Development of devices requires optimization of (1) ink chemistry, (2) inkjet process, (3) substrate ink interaction, and (4) new device structures. Several conducting, dielectric and semiconducting materials have been used to formulate ink. It appears that metal nanoparticle based conducting ink and PEDOT:PSS are widely used materials to fabricate source, drain and gate electrodes. PVPh is the most popular dielectric material for inkjet printing. To print semiconducting layer, both polymers and oligomers/small molecules are used. Many high performance organic semiconductors are p-type, but few n-type organic semiconductors show excellent performance. In addition to improved materials, challenges inherent in the inkjet process also need solutions. These are registration, alignment of the source,and drain with gate, resolution, reducing off-state current, and roll-to-roll processing.
ChemInform Abstract: Synthesis of (S,S)‐ and (R,R)‐2‐Alkyl‐2,5‐diazabicyclo(2.2.1)heptanes. (1990)

Abstract 4‐Hydroxy‐L‐proline (I) is N‐tosylated and then reduced to give the diol (IV).
Design and performance of an image-rotating, nanosecond optical parametric oscillator (2003)

Our goal is an efficient, high pulse energy, nanosecond optical parametric oscillator with good beam quality. We find that including 90/spl deg/ image rotation in the cavity helps achieve this performance.