gebhart/patrepeval huggingface dataset:
<i>Phytophthora infestans</i> Isolates Lacking Class I <i>ipiO</i> Variants Are Virulent on <i>Rpi-blb1</i> Potato (2009)

A strategy to control the devastating late blight disease is providing potato cultivars with genes that are effective in resistance to a broad spectrum of Phytophthora infestans isolates. Thus far, most late blight resistance (R) genes that were introgressed in potato were quickly defeated. In contrast, the Rpi-blb1 gene originating from Solanum bulbocastanum has performed as an exclusive broad-spectrum R gene for many years. Recently, the RXLR effector family ipiO was identified to contain Avr-blb1. Monitoring the genetic diversity of the ipiO family in a large set of isolates of P. infestans and related species resulted in 16 ipiO variants in three distinct classes. Class I and class II but not class III ipiO variants induce cell death when coinfiltrated with Rpi-blb1 in Nicotiana benthamiana. Class I is highly diverse and is represented in all analyzed P. infestans isolates except two Mexican P. infestans isolates, and these were found virulent on Rpi-blb1 plants. In its C-terminal domain, IPI-O contains a W motif that is essential for triggering Rpi-blb1-mediated cell death and is under positive selection. This study shows that profiling the variation of Avr-blb1 within a P. infestans population is instrumental for predicting the effectiveness of Rpi-blb1-mediated resistance in potato.
Comparative Infectivities of Gypsy Moth (Lepidoptera: Lymantriidae) Nucleopolyhedrosis Virus Isolates from North America, Europe, and Asia (1984)

Biological activities of 19 geographical isolates of Lymantria dispar (L.) nucleopolyhedrosis virus (NPV) were determined in the laboratory. LC50 values varied from 1.7 × 103 polyhedral inclusion bodies (PIB)/ml to greater than 5 × 106 PIB/ml. Twelve statistically different activity levels were observed. The North American isolates were generally most active, whereas the least active isolate originated from Asia (Japan). The North American isolates varied in activity by 16-fold, whereas the European isolates varied by only 6-fold. Five isolates were more active than the Connecticut standard. NPV isolates from Romania, Spain, Yugoslavia,the Soviet Union, Japan, and the United States were passed serially through L. dispar larvae. Although the activity of the American isolate did not change, activities of all other isolate increased significantly by the fourth passage. In general, activities became stabilized from the second to the fourth passage and were comparable to that of the American standard.
Mass Spectrometric Determination of Disulfide Linkages in Recombinant Therapeutic Proteins Using Online LC−MS with Electron-Transfer Dissociation (2008)

In the biotechnology industry, the generation of incorrectly folded recombinant proteins, either from an E.coli expression system or from an overexpressed CHO cell line (disulfide scrambling), is often a great concern as such incorrectly folded forms may not be completely removed in the final product. Thus, significant efforts have been devoted to map disulfide bonds to ensure drug quality. Similar to ECD, disulfide bond cleavages are preferred over peptide backbone fragmentation in ETD. Thus, an online LC-MS strategy combining collision-induced dissociation (CID-MS(2)), electron-transfer dissociation (ETD-MS(2)), and CID of an isolated product ion derived from ETD (MS(3)) has been used to characterize disulfide-linked peptides. Disulfide-linked peptide ions were identified by CID and ETD fragmentation, and the disulfide-dissociated (or partially dissociated) peptide ions were characterized in the subsequent MS(3) step. The online LC-MS approach is successfully demonstrated in the characterization of disulfide linkages of recombinant human growth hormone (Nutropin), a therapeutic monoclonal antibody, and tissue plasminogen activator (Activase). The characterization of disulfide-dissociated or partially dissociated peptide ions in the MS(3) step is important to assign the disulfide linkages, particularly, for intertwined disulfide bridges and the unexpected disulfide scrambling of tissue plasminogen activator. The disulfide-dissociated peptide ions are shown to be obtained either directly from the ETD fragmentation of the precursors (disulfide-linked peptide ions) or indirectly from the charge-reduced species in the ETD fragmentation of the precursors. The simultaneous observation of disulfide-linked and disulfide-dissociated peptide ions with high abundance not only provided facile interpretation with high confidence but also simplified the conventional approach for determination of disulfide linkages, which often requires two separate experiments (with and without chemical reduction). The online LC-MS with ETD methodology represents a powerful approach to aid in the characterization of the correct folding of therapeutic proteins.
Activation of the Phenylpropanoid Pathway in Nicotiana tabacum Improves the Performance of the Whitefly Bemisia tabaci via Reduced Jasmonate Signaling (2013)

Taken together, these results emphasize the important role JA/ET-induced defenses play in protecting plants from successful infestation by B. tabaci and likely other phloem-feeding insects. It also indicates the necessity of phloem feeders to suppress these defenses for efficient utilization of plant hosts. Our data also indicate that the defensive chemistry produced by the phenylpropanoids pathway has only a minor effect on the insect fitness.
Correlation of herpes simplex virus antibody titers and specific lymphocyte stimulation in adult blood donors (1981)

Antibody titers to herpes simplex virus type 1 in sera from healthy adult donors were assayed by complement fixation, microneutralization, and an enzyme immunoassay (ELISA). This last test proved to be the most sensitive method for antibody detection. It was estimated that ELISA antibody titers were up to 40-fold higher than neutralizing antibody titers and up to 100-fold higher than complement fixation antibody titers. Due to the higher sensitivity of ELISA, only 3 of 36 blood donors tested in this assay were shown to be seronegative, whereas 6 additional persons of the same group were termed seronegative by the microneutralization assay. Furthermore, four of the latter also did not respond in the complement fixation test. In vitro stimulation of peripheral lymphocytes by using a partially purified herpes simplex virus type 1 particle antigen was achieved for all seropositive blood donors. Only those three donors who were ELISA negative reacted negatively in this stimulation assay. From these results it may be concluded that ELISA is an appropriate method not only for rapid and sensitive antibody determination but also for selecting herpes simplex virus-negative patients.
Comparison of the Antioxidative Activity of Some Acid-phenols: Structure-Activity Relationship (1992)

Journal Article Comparison of the Antioxidative Activity of Some Acid-phenols: Structure-Activity Relationship Get access Marie-Elisabeth Cuvelier, Marie-Elisabeth Cuvelier Ecole Nationale Supérieure des Industries Agricoles et Alimentaires, Departement Science de l'Aliment, 1, avenue des Olympiades, 91300 Massy, France Search for other works by this author on: Oxford Academic Google Scholar Hubert Richard, Hubert Richard Ecole Nationale Supérieure des Industries Agricoles et Alimentaires, Departement Science de l'Aliment, 1, avenue des Olympiades, 91300 Massy, France Search for other works by this author on: Oxford Academic Google Scholar Claudette Berset Claudette Berset Ecole Nationale Supérieure des Industries Agricoles et Alimentaires, Departement Science de l'Aliment, 1, avenue des Olympiades, 91300 Massy, France Search for other works by this author on: Oxford Academic Google Scholar Bioscience, Biotechnology, and Biochemistry, Volume 56, Issue 2, 1 January 1992, Pages 324–325, https://doi.org/10.1271/bbb.56.324 Published: 01 January 1992 Article history Received: 22 February 1991 Published: 01 January 1992
Compact folded line rat-race hybrid couplers (2000)

A new, compact folded line configuration for rat-race hybrid couplers is proposed. Simple design equations are presented for the single and double C-section folded line structures. The new configuration exhibits a four- to fivefold reduction in footprint as compared to the conventional rat-race configuration. The design is validated both by using the full-wave electromagnetic simulator and with measurement.
A normally closed in-channel micro check valve (2002)

We present here the first surface-micromachined, normally closed, in-channel, Parylene check valve. This device is fabricated monolithically on a silicon substrate using a five-layer Parylene process. The operating structure of the check valve is a circular sealing plate on top of a ring-shaped valve seat. The sealing plate is center-anchored on top of a chamber diaphragm that is vacuum-collapsed to the bottom of the chamber in order to achieve a normally closed position. A thin gold layer on the roughened valve seat surface is used to reduce stiction between the sealing plate and the valve seat. We have achieved an in-channel check valve with a cracking (opening) pressure of 20/spl sim/40 kPa under forward bias and no measurable leakage under reverse bias up to 270 kPa. Using this design, this valve performs well in two-phase microfluidic systems (i.e. microchannel flows containing gas, liquid, or gas/liquid mixture).
Atg9 Trafficking in Yeast<i>Saccharomyces cerevisiae</i> (2007)

Autophagy can be divided into selective and nonselective modes. This process is considered selective when a precise cargo is specifically and exclusively incorporated into autophagosomes, the double-membrane vesicles that are the hallmark of autophagy. In contrast, during nonselective, bulk autophagy, cytoplasmic components are randomly enwrapped into autophagosomes. To date, approximately 30 autophagy-related genes called ATG have been identified. Sixteen of them compose the general basic machinery catalyzing the formation of double-membrane vesicles in all eukaryotic cells. The rest of them are often not conserved between species and cooperate with the basic Atg proteins during either selective or nonselective autophagy. Atg9 is the only integral membrane component of the conserved Atg machinery and appears to be a crucial organizational element. Recent studies in the S. cerevisiae have shown that Atg9 transport is differentially regulated depending on the autophagy mode. In this addendum, we will review and discuss what has recently been unveiled about yeast S. cerevisiae Atg9 trafficking, its modulators and its potential role in double-membrane vesicle biogenesis.
An integrated geospatial information service system for disaster management in China (2014)

The Chinese Government and citizens face enormous challenges of disaster management as widespread devastation, economic damages, and loss of human lives caused by increasing natural disasters. Disaster management requires a complicated iterative process that includes disaster monitoring, early detection, forecasting, loss assessment, and efficient analysis of disaster reduction. Each task typically involves the use of technologists and multiple geospatial information resources, including sensors, data sources, models, geo-tools, software packages, and computing resources. However, most existing disaster management systems operate in a typical passive data-centric mode, where resources cannot be fully utilized. This impediment is partially being addressed by the increasingly complex application requirements and the growing availability of diverse resources. In this paper, we summarize and analyze the practical problems experienced by the National Disaster Reduction Application System of China. To address the issues of data-centric, centralized, isolated solutions, we propose a novel Focusing Service Mechanism, which is capable of scheduling and allocating for optimum utilization of multiple resources, to dynamically generate collaborative and on-demand disaster information services. We also demonstrate the design and implementation of the Integrated Disaster Information Service System (IDISS). Through the service strategies of Virtualizing, Wrapping, and Integrating, disaster-related resources are constructed into services in the IDISS. These services are dynamically aggregated into focusing service chains, for diverse disaster management tasks. Actual applications illustrate that the proposed service system can significantly improve the capability of disaster management in China.
Fe-12Ni-4Co-2Mo-.05Ti alloy for use at 77°K and below (1975)

A variant of the maraging class of steels is proposed for application at 77°K and below where a combination of very high strength and good toughness is required. The alloy has a composition of Fe-12Ni-4Co-2Mo-0.05Ti where low interstitial content. The as quenched and quenched and aged structures were completely martensitic with a prior austenitic grain size of 10 to 12 μm. This structure had a Y.S. of 138.5 ksi and 154 ksi before and after aging respectively. All aging was done at 444°C for 4 hours. The DBTT was shown to lie above 77°K as measured by Cv testing. Based on dilatometric studies of the α $Yields$ γ and γ → α transformation temperatures a cycling treatment consisting of reportedly heating to above the Af temperature followed by a water quench was utilized to further reduce the prior γ grain size to approximately 4 to 6 μm. The structure was completely martensitic and possessed a Y.S. of 151 ksi at 77°K in the unaged condition with a Y.S./KIC ratio of 1.9 while the aged structure showed a Y.S. of 162 ksi with a Y.S./KIC ratio of 1.3. Cv testing showed the DBTT to lie between 77°K and 4.2°K. Further grain refinement was accomplished by a 2 phase decomposition procedure which resulted in a grain size of 1 to 2 μm. The structure which contained decreasing amounts of austenite with temperature (3.0 percent at R.T. to 1.0 percent at 4.2°K) showed the best combination of strength and ductility at 4.2°K. A Y.S. of 205 ksi with a Y.S./KIC ratio of 0.84 was achieved before aging. The aged structure was brittle at 4.2°K with a Y.S. of 218 ksi and a Y.S./KIC ratio of 0.425.
Viscosity and Surface Tension of Al and Effects of Additional Element (2003)

Aluminum foam metal was produced directly from the foaming method. In this foaming process, the surface tension and the viscosity of molten Al that were measured by the ring method and the rotational method, respectively, and are the two most important factors. The surface tension and the viscosity were investigated at the temperature range of 660-950 °C and the effects of the additional Ca were investigated at the same temperature range. The measured surface tension of the molten Al decreased linearly with the increasing temperature of Ar atmosphere and 1 atm. It follows the function of σ(T)=842-0.204(T-T m )[mNm -1 ]. The viscosity of the molten Al ranged from 3.7 to 4.5[mPa.s] in the temperature range. The effect of additional Ca elements is that the tendency is decreased from the surface tension and increased from the viscosity. The surface tension value was σ 2Ca =530[mNm -1 ] and viscosity value was η 2Ca =14[mPa.s] at the temperature of 700°C, respectively, when adding 2wt% of Ca.
Two Currents in the Sociology of Religion (1967)

“It is widely assumed … that scholars of religion, especially historians and sociologists, should by some magic immunity stand aloof from the heady disputes that are splitting ministers into churchmen and non-churchmen and dividing the theologians into theists and dead-theists … But neither sociology nor history has yet developed a device that enables scholars to be at once deeply interested in their subject and perfectly disinterested with respect to the issues involved in it.”
Characterizing quantum-dot blinking using noise power spectra (2004)

Fluctuations in the fluorescence from macroscopic ensembles of colloidal semiconductor quantum dots have the spectral form of 1∕f noise. The measured power spectral density reflects the fluorescence intermittency of individual dots with power-law distributions of “on” and “off” times, and can thus serve as a simple method for characterizing such blinking behavior.
Insufficient DNA methylation affects healthy aging and promotes age-related health problems (2011)

DNA methylation plays an integral role in development and aging through epigenetic regulation of genome function. DNA methyltransferase 1 (Dnmt1) is the most prevalent DNA methyltransferase that maintains genomic methylation stability. To further elucidate the function of Dnmt1 in aging and age-related diseases, we exploited the Dnmt1+/- mouse model to investigate how Dnmt1 haploinsufficiency impacts the aging process by assessing the changes of several major aging phenotypes. We confirmed that Dnmt1 haploinsufficiency indeed decreases DNA methylation as a result of reduced Dnmt1 expression. To assess the effect of Dnmt1 haploinsufficiency on general body composition, we performed dual-energy X-ray absorptiometry analysis and showed that reduced Dnmt1 activity decreased bone mineral density and body weight, but with no significant impact on mortality or body fat content. Using behavioral tests, we demonstrated that Dnmt1 haploinsufficiency impairs learning and memory functions in an age-dependent manner. Taken together, our findings point to the interesting likelihood that reduced genomic methylation activity adversely affects the healthy aging process without altering survival and mortality. Our studies demonstrated that cognitive functions of the central nervous system are modulated by Dnmt1 activity and genomic methylation, highlighting the significance of the original epigenetic hypothesis underlying memory coding and function.
Improved Tumor Destruction with Arsenic Trioxide and Radiofrequency Ablation in Three Animal Models (2006)

As2O3 administration represents a transient noninvasive method of reducing tumor blood flow during RF ablation, enabling larger zones of tumor destruction in multiple tumor models.
De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides (2014)

Self-association is a common phenomenon in biology and one that can have positive and negative impacts, from the construction of the architectural cytoskeleton of cells to the formation of fibrils in amyloid diseases. Understanding the nature and mechanisms of self-association is important for modulating these systems and in creating biologically-inspired materials. Here, we present a two-stage de novo peptide design framework that can generate novel self-associating peptide systems. The first stage uses a simulated multimeric template structure as input into the optimization-based Sequence Selection to generate low potential energy sequences. The second stage is a computational validation procedure that calculates Fold Specificity and/or Approximate Association Affinity (K*association) based on metrics that we have devised for multimeric systems. This framework was applied to the design of self-associating tripeptides using the known self-associating tripeptide, Ac-IVD, as a structural template. Six computationally predicted tripeptides (Ac-LVE, Ac-YYD, Ac-LLE, Ac-YLD, Ac-MYD, Ac-VIE) were chosen for experimental validation in order to illustrate the self-association outcomes predicted by the three metrics. Self-association and electron microscopy studies revealed that Ac-LLE formed bead-like microstructures, Ac-LVE and Ac-YYD formed fibrillar aggregates, Ac-VIE and Ac-MYD formed hydrogels, and Ac-YLD crystallized under ambient conditions. An X-ray crystallographic study was carried out on a single crystal of Ac-YLD, which revealed that each molecule adopts a β-strand conformation that stack together to form parallel β-sheets. As an additional validation of the approach, the hydrogel-forming sequences of Ac-MYD and Ac-VIE were shuffled. The shuffled sequences were computationally predicted to have lower K*association values and were experimentally verified to not form hydrogels. This illustrates the robustness of the framework in predicting self-associating tripeptides. We expect that this enhanced multimeric de novo peptide design framework will find future application in creating novel self-associating peptides based on unnatural amino acids, and inhibitor peptides of detrimental self-aggregating biological proteins.
In vitro antibiotic removal and bacterial recovery from blood with an antibiotic removal device (1981)

The antibiotic removal device manufactured by Marion Laboratories (Kansas City., Mo.) is intended for treatment, before culture, of blood specimens from hospital patients being treated with antibiotics. Measurement of 13 antibiotics showed that the antibiotic removal device removed amikacin, ampicillin, carbenicillin, cefazolin, cephalothin, chloramphenicol, gentamicin, nafcillin, tetracycline, tobramycin, and vancomycin and reduced cefoxitin and ticarcillin to extremely low levels. Three combinations of antibiotics were similarly removed or reduced. Five species of anaerobic bacteria, one yeast species, and six species of facultative or aerobic bacteria were used to challenge the possibility that the antibiotic removal device would trap or inhibit microorganisms. All were recovered from the device in the same numbers as were inoculated.
Intermolecular C–H Bond Activation of Alkanes and Arenes by NCN Pincer Iridium(III) Acetate Complexes Containing Bis(oxazolinyl)phenyl Ligands (2012)

Carbon–hydrogen bond activation of arenes by the pincer Ir(III) acetate complex (phebox)Ir(OAc)2(H2O) (1; phebox = bis(oxazolinyl)phenyl) proceeded at 100 °C to give the corresponding aryl Ir(III) complexes (phebox)Ir(Ar)(OAc) in high yields. Reactions of the monosubstituted arenes anisole, toluene, chlorobenzene, acetophenone, and nitrobenzene resulted in the formation of meta- and para-substituted aryl complexes in high yields. Competitive experiments between two monosubstituted arenes exhibited relative reaction rates in the order C6H5OMe > C6H5NO2 > C6H5COMe > C6H5Cl > C6H5Me. The kinetic isotope effects of C–H bond activation of benzene and nitrobenzene were determined to be 2.9 ± 0.1 and 2.0 ± 0.4, respectively. The Ir complex 1 underwent catalytic borylation of arenes with bis(pinacolato)diboron (B2(pin)2) or pinacolborane (HB(pin)), giving the corresponding borylated products. The Ir complex 1 was also reactive toward alkane C–H bond activation, demonstrated by the reactions with n-heptane and n-octane at 160 °C that cleanly afforded the corresponding alkyl complexes (phebox)Ir(n-CnH2n+1)(OAc) (n = 7, 8, respectively).
Essential role of brain-derived neurotrophic factor in adult hippocampal function (2004)

Brain-derived neurotrophic factor (BDNF) regulates neuronal development and function. However, it has been difficult to discern its role in the adult brain in influencing complex behavior. Here, we use a recently developed inducible knockout system to show that deleting BDNF in broad forebrain regions of adult mice impairs hippocampal-dependent learning and long-term potentiation. We use the inducible nature of this system to show that the loss of BDNF during earlier stages of development causes hyperactivity and more pronounced hippocampal-dependent learning deficits. We also demonstrate that the loss of forebrain BDNF attenuates the actions of desipramine, an antidepressant, in the forced swim test, suggesting the involvement of BDNF in antidepressant efficacy. These results establish roles for BDNF in the adult, and demonstrate the strength of this inducible knockout system in studying gene function in the adult brain.
Intra‐articular morphine for pain relief after knee arthroscopy (1999)

Postoperative analgesic effect of intra-articular morphine was found only in a subgroup of patients with higher pain intensity in the immediate postanaesthetic period. Possible reasons for our overall negative findings include low study sensitivity due to weak pain stimulus, lack of inflammation that may be a prerequisite for peripheral opioid analgesia, and the local anaesthetic, which impedes local inflammatory reaction and expression of peripheral opioid receptors. These factors may also explain the conflicting results in other studies.