gebhart/patrepeval huggingface dataset:
Pesticide Transformation Products in the Environment (1991)

Pesticides applied in the environment are transformed by biological or nonbiological processes into one or more transformation products. For most pesticides, transformation results in detoxification to innocuous products. Major degradation products of some currently used pesticides, however, play an important role in pest control and environmental contamination. Some pesticide degradation products are of significance in crop protection by being effective against the target pests. Some can be responsible for inadequate pest control by inducing rapid degradation of their parent compounds. Degradation products as potential contaminants of environmental and food resources has been reported recently. Although most of the currently used pesticides are biodegradable, their major degradation products should also be considered in evaluating the overall bioactivity and environmental contamination potential of the parent compound.
Breaking immune tolerance by targeting Foxp3+ regulatory T cells mitigates Alzheimer’s disease pathology (2015)

Alzheimer's disease (AD) is a neurodegenerative disorder in which chronic neuroinflammation contributes to disease escalation. Nevertheless, while immunosuppressive drugs have repeatedly failed in treating this disease, recruitment of myeloid cells to the CNS was shown to play a reparative role in animal models. Here we show, using the 5XFAD AD mouse model, that transient depletion of Foxp3(+) regulatory T cells (Tregs), or pharmacological inhibition of their activity, is followed by amyloid-β plaque clearance, mitigation of the neuroinflammatory response and reversal of cognitive decline. We further show that transient Treg depletion affects the brain's choroid plexus, a selective gateway for immune cell trafficking to the CNS, and is associated with subsequent recruitment of immunoregulatory cells, including monocyte-derived macrophages and Tregs, to cerebral sites of plaque pathology. Our findings suggest targeting Treg-mediated systemic immunosuppression for treating AD.
Formation of indigo and related compounds from indolecarboxylic acids by aromatic acid-degrading bacteria: chromogenic reactions for cloning genes encoding dioxygenases that act on aromatic acids (1995)

The p-cumate-degrading strain Pseudomonas putida F1 and the m- and p-toluate-degrading strain P. putida mt-2 transform indole-2-carboxylate and indole-3-carboxylate to colored products identified here as indigo, indirubin, and isatin. A mechanism by which these products could be formed spontaneously following dioxygenase-catalyzed dihydroxylation of the indolecarboxylates is proposed. Indolecarboxylates were employed as chromogenic substrates for identifying recombinant bacteria carrying genes encoding p-cumate dioxygenase and toluate dioxygenase. Dioxygenase gene-carrying bacteria could be readily distinguished as dark green-blue colonies among other colorless recombinant Escherichia coli colonies on selective agar plates containing either indole-2-carboxylate or indole-3-carboxylate.
Searching for historical word-forms in a database of 17th-century English text using spelling-correction methods (1992)

This paper discusses the application of algorithmic spelling-correction techniques to the identification of those words in a database of 17th century English text that are most similar to a query word in modern English. The experiments have used n-gram matching, non-phonetic coding and dynamic programming methods for spelling correction, and have demonstrated that high-recall searches can be carried out, although some of the searches are very demanding of computational resources. The methods are, in principle, applicable to historical texts in many languages and from many diffeent periods.
MIGHTI: The Spatial Heterodyne Instrument for Thermospheric Wind Measurements on Board the ICON Mission (2015)

We describe the Michelson Interferometer for Global High-resolution Thermospheric Imaging (MIGHTI), an instrument currently being built to measure thermospheric wind and temperature as part of the NASA Ionospheric Connection (ICON) Explorer mission.
Network-based analysis of calcium-binding protein genes identifies Grp94 as a target in human oral carcinogenesis (2007)

To characterise Ca(2+) -binding protein gene expression changes in oral squamous cell carcinomas (OSCCs), we compared the gene expression profiles in OSCC-derived cell lines with normal oral tissues. One hundred Ca(2+) -binding protein genes differentially expressed in OSCCs were identified, and genetic pathways associated with expression changes were generated. Among genes mapped to the network with the highest significance, glucose-regulated protein 94 kDa (Grp94) was evaluated further for mRNA and protein expression in the OSCC cell lines, primary OSCCs, and oral premalignant lesions (OPLs). A significant (P<0.001) overexpression of Grp94 protein was observed in all cell lines compared to normal oral epithelium. Immunohistochemical analysis showed highly expressed Grp94 in primary OSCCs and OPLs, whereas most of the corresponding normal tissues had no protein immunoreaction. Real-time quantitative reverse transcriptase-PCR data agreed with the protein expression status. Moreover, overexpression of Grp94 in primary tumours was significantly (P<0.001) correlated with poor disease-free survival. The results suggested that Grp94 may have potential clinical application as a novel diagnosis and prognostic biomarker for human OSCCs.
A framework for authentication in NBD tactical Ad Hoc networks (2011)

Network-based defense (NBD) and the all-IP network make authentication ever more important. However, a generally accepted and comprehensive authentication suite is lacking. This work is a step toward filling the gap. The article proposes a three-level framework for authentication in NBD tactical ad hoc networks. Hop-by-hop network-level authentication provides basic protection. End-to-end application-level authentication is included only when finer resolution is needed. The third level of authentication relates to physical node access. The framework may serve as a reference for authentication in other networks as well. An additional contribution is the approach used to derive the authentication framework, which has general relevance.
Semantics-preserving sharing actors (2013)

Actors interact by asynchronous message passing. A key semantic property of actors is that they do not share state. This facilitates data-race freedom, fault isolation and location transparency. On the other hand, strict avoidance of sharing can lead to inefficiency. We propose the sharing actor programming model that extends the actor programming model with single-writer multiple-reader sharing of data. We define the sharing actor theory and prove its semantic equivalence to the pure actor theory. We realize the sharing actor theory with an efficient implementation. The implementation benefits from sharing data but keeps it transparent to actors. To increase the confidence that the implementation complies with the semantics, we have built a checking tool based on deterministic replay of actor programs.
Inhibition of Neuronal Nitric Oxide Synthase by 4-Amino Pteridine Derivatives:  Structure−Activity Relationship of Antagonists of (6R)-5,6,7,8-Tetrahydrobiopterin Cofactor (1999)

The family of nitric oxide synthases (NOS) catalyzes the conversion of L-arginine to L-citrulline and nitric oxide (NO), an important cellular messenger molecule which has been implicated in the pathophysiology of septic shock and inflammatory and neurodegenerative disease states. NOS can be maximally activated by the ubiquitous cofactor, (6R)-5,6,7,8-tetrahydrobiopterin (H(4)Bip), and antagonists of H(4)Bip may be of therapeutic importance to inhibit pathologically high NO formation. The 4-amino substituted analogue of H(4)Bip was reported to be a potent NOS inhibitor. Therefore, we developed a series of novel 4-amino pteridine derivatives, anti-pterins, to pharmacologically target the neuronal isoform of nitric oxide synthase (NOS-I). To functionally characterize the pterin/anti-pterin interaction and establish a structure-activity relationship (SAR), we systematically altered the substituents in the 2-, 4-, 5-, 6-, and 7-position of the pteridine nucleus. Varying the substitution pattern in the 2-, 5-, and 7-position resulted in no significant inhibitory effect on enzyme activity. In contrast, bulky substituents in the 6-position, such as phenyl, markedly increased the inhibitory potency of the reduced 4-amino-5,6,7,8-tetrahydropteridines, possibly as a consequence of hydrophobic interactions within NOS-I. However, this was not the case for the aromatic 4-amino pteridines. Interestingly, chemical modification of the 4-amino substituent by dialkyl/diaralkylation together with 6-arylation of the aromatic 2,4-diamino pteridine resulted in potent and efficacious inhibitors of NOS-I, suggesting possible hydrophilic and hydrophobic interactions within NOS-I. This SAR agrees with (a) the recently published crystal structure of the oxygenase domain of the inducible NOS isoform (NOS-II) and (b) the comparative molecular field analysis of selected NOS-I inhibitors, which resulted in a 3D-QSAR model of the pterin binding site interactions. Further optimization should be possible when the full length structure of NOS-I becomes available.
Enlazin, a Natural Fusion of Two Classes of Canonical Cytoskeletal Proteins, Contributes to Cytokinesis Dynamics (2006)

Cytokinesis requires a complex network of equatorial and global proteins to regulate cell shape changes. Here, using interaction genetics, we report the first characterization of a novel protein, enlazin. Enlazin is a natural fusion of two canonical classes of actin-associated proteins, the ezrin-radixin-moesin family and fimbrin, and it is localized to actin-rich structures. A fragment of enlazin, enl-tr, was isolated as a genetic suppressor of the cytokinesis defect of cortexillin-I mutants. Expression of enl-tr disrupts expression of endogenous enlazin, indicating that enl-tr functions as a dominant-negative lesion. Enlazin is distributed globally during cytokinesis and is required for cortical tension and cell adhesion. Consistent with a role in cell mechanics, inhibition of enlazin in a cortexillin-I background restores cytokinesis furrowing dynamics and suppresses the growth-in-suspension defect. However, as expected for a role in cell adhesion, inhibiting enlazin in a myosin-II background induces a synthetic cytokinesis phenotype, frequently arresting furrow ingression at the dumbbell shape and/or causing recession of the furrow. Thus, enlazin has roles in cell mechanics and adhesion, and these roles seem to be differentially significant for cytokinesis, depending on the genetic background.
Receptor radionuclide therapy of tumors: a road from basic research to clinical applications. (2006)

Publication in this issue of The Journal of Nuclear Medicine of the article by Cescato et al. ( [1][1] ) prompts some considerations on receptor-guided tumor targeting with radionuclides. The term receptor-guided tumor targeting includes several techniques implying the direct and selective
Role of self-formed InGaN quantum dots for exciton localization in the purple laser diode emitting at 420 nm (1997)

Structural analysis was performed on a purple laser diode composed of In0.20Ga0.80N (3 nm)/ In0.05Ga0.95N (6 nm) multiple quantum wells, by employing transmission electron microscopy and energy-dispersive x-ray microanalysis, both of which are assessed from the cross-sectional direction. It was found that the contrast of light and shade in the well layers corresponds to the difference in In composition. The main radiative recombination was attributed to excitons localized at deep traps which probably originate from the In-rich region in the wells acting as quantum dots. Photopumped lasing was observed at the high energy side of the main spontaneous emission bands.
Laboratory/Field Study of Oil-Soluble Resin-Diverting Agents in Prudhoe Bay, Alaska, Acidizing Operations (1990)

Abstract Treatment of long intervals of varying permeabilities and thief zones requires fluid diversion control to assure well distributed fluid placement. Oil Soluble Resins (OSR) , when properIy appl i ed, ar e effective, readily removable diverting agents. Application of laboratory studies of 15 OSR products from 5 service companies combined with additional OSR field experiments at Prudhoe Bay ( PB) , br ought about the use of higher concentrations and larger size OSR particles and resulted in improved diversion during acid stimulation and scale inhibitor squeeze treatments. Successful OSR field applications depend both on selecting proper OSR particle size distributi ons and sufficient OSR concentrations for rapid bridging on pores and/or fractures being contacted. Tests of sand/gravel packs, confirmed that effective sealing was achieved when the median OSR size was equal to or greater than 1/3 of the calculated mean sand pore diameter. With fractured cor es, however, effective seal i ng by OSR concentrations up to 10 wt% required that 1020% of the OSR particles be as large or slightly larger than the fracture width. Smaller volumes of higher OSR concentrations were more effective in diversion than larger volumes of lower concentrations. Generally, a broad particle size distribution was desirable for sealing fractures whereas fine particle sizes were better for 350 md to 3500 md sandstone cores.
A New Model for the K+-Induced Macromolecular Structure of Guanosine 5‘-Monophosphate in Solution (1999)

The (31)P NMR spectra of (TMA)(2)(5'-GMP), where TMA is [(CH(3))(4)N](+) and 5'-GMP is guanosine 5'-monophosphate, and K(2)(5'-GMP), containing various amounts of KCl or TMACl, have been obtained at 2 degrees C. Variable-temperature spectra have also been obtained for K(2)(5'-GMP). The TMA(+) ion serves to neutralize the charge on the dianionic 5'-GMP and permits the added K(+) to bond preferentially in structure-forming sites. (1)H NMR spectra (one- and two-dimensional) have been obtained for K(2)(5'-GMP) and used to assign the proton resonances in the self-associated structures and determine that all residues have the anti glycosidic conformation. The (31)P and (1)H NMR spectra are very complex and indicate the presence of a large number of molecular environments and a structural variation dependent upon the mole ratio of 5'-GMP to K(+). A new model for the solution structure is proposed in which the 5'-GMP forms a pseudo-four-stranded helix with guanine-guanine hydrogen bonding forming a continuous helical strand, rather than the usual planar G-tetrad structure. The guanine-guanine hydrogen bonding sites are the same as that found in a G-tetrad. The K(+) ions would be located in the center of the helix and bonding to the carbonyl oxygens. They are interacting with the phosphates as well. Integration data from the largest sized species give an estimate of 14.3 +/- 1.1 residues in a helical structure.
Novel Engineered Programmable Systems for ADAR-Mediated RNA Editing (2020)

One of the most prevalent forms of post-transcriptional RNA modification is the conversion of adenosine-to-inosine (A-to-I), mediated by adenosine deaminase acting on RNA (ADAR) enzymes. The advent of the CRISPR/Cas systems inspires researchers to work actively in the engineering of programmable RNA-guided machines for basic research and biomedical applications. In this regard, CIRTS (CRISPR-Cas-Inspired RNA Targeting System), RESCUE (RNA Editing for Specific C to U Exchange), RESTORE (Recruiting Endogenous ADAR to Specific Transcripts for Oligonucleotide-mediated RNA Editing), and LEAPER (Leveraging Endogenous ADAR for Programmable Editing of RNA) are innovative RNA base-editing platforms that have recently been engineered to perform programmable base conversions on target RNAs mediated by ADAR enzymes in mammalian cells. Thus, these four currently characterized RNA-editing systems constitute novel molecular tools with compelling programmability, specificity, and efficiency that show us some creative ways to take advantage of the engineered deaminases for precise base editing. Moreover, the advanced engineering of these systems permits editing of full-length transcripts containing disease-causing point mutations without the loss of genomic information, providing an attractive alternative for in vivo research and in the therapeutic setting if the challenges encountered in off-target edits and delivery are appropriately addressed. Here, I present an analytical approach of the current status and rapid progress of the novel ADAR-mediated RNA-editing systems when highlighting the qualities of each new RNA-editing platform and how these RNA-targeting strategies could be used to recruit human ADARs on endogenous transcripts, not only for our understanding of RNA-modification-mediated regulation of gene expression but also for editing clinically relevant mutations in a programmable and straightforward manner.
Calcium-Calmodulin Modulation of the Olfactory Cyclic Nucleotide-Gated Cation Channel (1994)

Although several ion channels have been reported to be directly modulated by calcium-calmodulin, they have not been conclusively shown to bind calmodulin, nor are the modulatory mechanisms understood. Study of the olfactory cyclic nucleotide-activated cation channel, which is modulated by calcium-calmodulin, indicates that calcium-calmodulin directly binds to a specific domain on the amino terminus of the channel. This binding reduces the effective affinity of the channel for cyclic nucleotides, apparently by acting on channel gating, which is tightly coupled to ligand binding. The data reveal a control mechanism that resembles those underlying the regulation of enzymes by calmodulin. The results also point to the amino-terminal part of the olfactory channel as an element for gating, which may have general significance in the operation of ion channels with similar overall structures.
Immunochemical analysis of the glucocorticoid receptor: identification of a third domain separate from the steroid-binding and DNA-binding domains. (1982)

The glucocorticoid-receptor complex can be subdivided into three separate domains by limited proteolysis with trypsin or alpha-chymotrypsin. The following characteristics can be separated: steroid-binding activity (domain A), DNA-binding activity (domain B), and immunoactivity (domain C). We have previously reported the separation of the steroid-binding domain from the DNA-binding domain by limited proteolysis of the receptor with trypsin. In this paper, we report the detection by immunochemical analysis of a third domain of the glucocorticoid receptor, which does not bind hormone. Immunoactivity was detected by using specific antiglucocorticoid receptor antibodies raised in rabbits against purified rat liver glucocorticoid receptor and the assay used was an enzyme-linked immunosorbent assay. After digestion with alpha-chymotrypsin, the immunoactive region of the receptor (domain C) was separated from the other two domains (A and B). The immunoactive fragment was found to have a Stokes radius of 2.6 nm. Further digestion with alpha-chymotrypsin resulted in separation of the immunoactive fragment to give a fragment having a Stokes radius of 1.4 nm. The immunoactive domain could be separated from the half of the glucocorticoid receptor containing the steroid-binding and the DNA-binding domains (Stokes radius, 3.3 nm), by limited proteolysis of the receptor by alpha-chymotrypsin followed by gel filtration or chromatography on DNA-cellulose.
Abbruch und Neubau einer Bruecke ueber die Iller in Kempten (2003)

Das Bauwerk wurde im Jahr 1885 als Betriebsbruecke im Auftrag einer Textilfirma zum Transport von Rohstoffen und fuer die Energieversorgung des Werkes erbaut. Es handelte sich um zwei hintereinander liegende einfeldrige Fachwerktraeger aus Stahl mit Spannweiten von 21,5 und 45,0 Metern, die innerhalb des Flusses auf einem gemeinsamen Pfeiler auflagen. Als Belastung kamen zunaechst Fuhrwerke in Betracht. Fuer den spaeteren Betrieb mit Lastkraftwagen mussten die Druckstaebe verstaerkt werden. In den 1970er Jahren wurde wegen des sich zunehmend verschlechternden baulichen Zustandes jeglicher Fahrzeugverkehr untersagt. Schliesslich sollte die Bruecke wegen zunehmendem Fussgaenger-Verkehrsbedarf im Jahr 2000 als Fussgaenger - und Radwegbruecke instandgesetzt werden. Ein katastrophales Hochwasser zu Pfingsten 1999, bei dem die Bruecke den Wassermassen gerade noch standhielt, zwang zu einer Ueberarbeitung der Planung und fuehrte zu der Entscheidung die Hoehe der Gradiente einem neuen zu erwartenden Hochwasser anzupassen und den Ueberbau zu erneuern. Zur Ausfuehrung kam wieder ein Fachwerktraeger aus Stahl. Diesmal aber als Durchlauftraeger ueber zwei Felder. Die Fachwerkstaebe bestehen aus Rohren und sind zum Schutz gegen Korrosion feuerverzinkt. Die Konstruktion und der Bau der Bruecke einschliesslich der Montage mittels Schwerlastkraenen wird eingehend beschrieben.
Increased gene expression for VEGF and the VEGF receptors KDR/Flk and Flt in lungs exposed to acute or to chronic hypoxia. Modulation of gene expression by nitric oxide. (1995)

Endothelial cells constitute an essential integrator of factors that effect blood vessel remodeling induced by chronic hypoxia. We hypothesized that vascular endothelial growth factor (VEGF) may participate in the lung response to acute and to chronic hypoxia. We found that ex vivo perfusion of isolated lungs under hypoxic conditions (when compared with normoxia) caused an increase in lung tissue mRNA of VEGF and of the VEGF receptors KDR/Flk and Flt. Chronic hypobaric hypoxia also increased lung tissue mRNA levels of VEGF, KDR/Flk, and Flt and the amount of VEGF protein. In situ hybridization studies demonstrated increased VEGF and KDR/flk hybridization signals in lungs from chronically hypoxic rats. Since endotoxin treatment of rats decreased lung VEGF mRNA, we postulated that nitric oxide (NO) or an NO-related metabolite might be involved in lung VEGF gene expression. Indeed, sodium nitroprusside, a NO donor, decreased and L-NAME (N-nitro-L-arginine methyl ester), an inhibitor of NO-synthesis, increased both VEGF and VEGF receptor transcripts. We conclude that VEGF in the isolated perfused lung acts as an early gene in response to hypoxia and that lung VEGF and VEGF receptor mRNA levels are influenced by hypoxia and NO-dependent mechanisms.
CO2 Injection for Enhanced Gas Production and Carbon Sequestration (2002)

Abstract Analyses suggest that carbon dioxide (CO2) can be injected into depleted gas reservoirs to enhance methane (CH4) recovery for periods on the order of 10 years, while simultaneously sequestering large amounts of CO2. Simulations applicable to the Rio Vista Gas Field in California show that mixing between CO2 and CH4 is slow relative to repressurization, and that vertical density stratification favors enhanced gas recovery.
Genetics and Biogenesis of Bacterial Flagella (1992)

Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
T Cell Death and Memory (2001)

In typical immune responses, contact with antigen causes naı̈ve T cells to proliferate and differentiate into effector cells. After the pathogen is destroyed, most effector T cells are eliminated—thereby preserving the primary T cell repertoire—but some cells survive and form long-lived memory cells. During each stage of this process, the life or death fate of T cells is strictly regulated.
MHC Class II alleles in ulcerative colitis-associated colorectal cancer (2009)

We report a significant association between specific HLA alleles and either the risk for (DR17) or protection from (DR7, DQ5) UC-CRC. This suggests a possible genetic predisposition for increased UC-CRC risk. In addition, DQ2 and DR17 were associated with CIITA methylation.