gebhart/patrepeval huggingface dataset:
The structure of the culturable root bacterial endophyte community of Nicotiana attenuata is organized by soil composition and host plant ethylene production and perception (2009)

*A plant's bacterial endophyte community is thought to be recruited from the rhizosphere, but how this recruitment is influenced by the plant's phytohormone signaling is unknown. Ethylene regulates plant-microbe interactions; here, we assess the role of ethylene in the recruitment of culturable endophytic bacteria from native soils. *We grew wild-type Nicotiana attenuata plants and isogenic transformed plants deficient in ethylene biosynthesis (ir-aco1) or perception (35S-etr1) in four native soils and quantified the extent of culturable bacterial endophyte colonization (by plate counting) and diversity (by amplified rDNA restriction analysis and 16S rDNA sequencing). *The endophyte community composition was influenced by soil type and ethylene signaling. Plants grown in organic (vs mineral) soils harbored a more diverse community and plants impaired in ethylene homeostasis harbored a less diverse community than wild-type plants. Wild-type and ethylene signaling-impaired plants fostered distinct bacteria in addition to common ones. In vitro re-colonization by common and genotype-specific isolates demonstrated the specificity of some associations and the susceptibility of 35S-etr1 seedlings to all tested bacterial isolates, suggesting an active process of colonization driven by plant- and microbe-specific genes. *We propose that soil composition and ethylene homeostasis play central roles in structuring the bacterial endophyte community in N. attenuata roots.
Organization of Capsid-Associated Tegument Components in Kaposi's Sarcoma-Associated Herpesvirus (2014)

Several capsid-associated tegument proteins have been identified in the alpha- and betaherpesvirus subfamilies of the Herpesviridae. These tegument proteins play essential roles in viral propagation and are potential drug targets for curbing herpesvirus infections. However, no such tegument proteins have been identified for gammaherpesviruses, the third herpesvirus subfamily, which contains members causing several human cancers. Here, by high-resolution cryo-EM, we show the three-dimensional structure of the capsid-associated tegument proteins in the prototypical member of gammaherpesviruses, KSHV. The cryo-EM structure reveals that the organization of KSHV capsid-associated tegument proteins is highly similar to that in alphaherpesvirus but completely different from that in betaherpesvirus. Structural analyses further localize ORF19 and ORF32 proteins (the alphaherpesvirus UL25 and UL17 homologs in KSHV, respectively) in the KSHV capsid-associated tegument cryo-EM structure. These findings also resolve a long-standing mystery regarding the location and conformation of alphaherpesvirus UL25 protein inside the virion.
Reconciling mobile app privacy and usability on smartphones (2014)

As they compete for developers, mobile app ecosystems have been exposing a growing number of APIs through their software development kits. Many of these APIs involve accessing sensitive functionality and/or user data and require approval by users. Android for instance allows developers to select from over 130 possible permissions. Expecting users to review and possibly adjust settings related to these permissions has proven unrealistic. In this paper, we report on the results of a study analyzing people's privacy preferences when it comes to granting permissions to different mobile apps. Our results suggest that, while people's mobile app privacy preferences are diverse, a relatively small number of profiles can be identified that offer the promise of significantly simplifying the decisions mobile users have to make. Specifically, our results are based on the analysis of settings of 4.8 million smartphone users of a mobile security and privacy platform. The platform relies on a rooted version of Android where users are allowed to choose between "granting", "denying" or "requesting to be dynamically prompted" when it comes to granting 12 different Android permissions to mobile apps they have downloaded.
From organic single crystals to solution processed thin-films: Charge transport and trapping with varying degree of order (2013)

We have fabricated single crystal, thermally evaporated, and spin-coated thin-film transistors (TFTs) from the same organic semiconductor N,N′-1H,1H-perfluorobutyl dicyanoperylene carboxydiimide (PDIF-CN2) using various combinations of deposition methods and gate dielectrics to investigate how the charge transport properties vary with the degree of crystalline order. Never before has a semiconductor been studied in such a wide variety of processing methods, allowing cross-comparison of the microscopic factors influencing the charge transport, and in particular the trap density of states (DOS). Excellent transistor performance was achieved for PDIF-CN2 single crystals in combination with Cytop as a dielectric layer resulting in a mobility of up to 6 cm2/Vs, an on/off-ratio exceeding 108, and a subthreshold swing of 0.45 V/dec. Furthermore, gate-bias-stress effects are not present in these transistors and we observed low stress effects in the evaporated TFTs with Cytop as the gate dielectric. These findings are reflected in the trap DOS. The single crystal field-effect transistor with Cytop has a low trap DOS, whereas in evaporated TFTs, the trap DOS is higher by 2–3 orders of magnitude. Surprisingly, the trap DOS of the spin-coated TFT is similar to that in evaporated TFTs, except for additional discrete trap states centered around 0.24 eV below the conduction band.
Aminoglycoside-resistant mutants of Pseudomonas aeruginosa deficient in cytochrome d, nitrite reductase, and aerobic transport (1981)

Two gentamicin-resistant mutants of Pseudomonas aeruginosa PAO 503 were selected after ethyl methane sulfonate mutagenesis. Mutant PAO 2403 had significantly increased resistance to aminoglycoside but not to other antibiotics. Mutant PAO 2402 showed a similar spectrum of resistance but of lower magnitude. Both mutants showed no detectable cytochrome d and had a high frequency of reversion to a fully wild-type phenotype. PAO 2403 had a marked decrease and PAO 2402 had a moderate decrease in nitrite reductase activity. Both mutants had reduced uptake of gentamicin and dihydrostreptomycin. Mutant PAO 2403 showed a general decrease in transport rate of cationic compounds, whereas mutant PAO 2402 had only deficient glucose transport. Both mutants showed enhanced rates of glutamine transport and no change in glutamic acid transport. Other components of electron transport and oxidative phosphorylation were normal. These mutants involve ferrocytochrome C551 oxidoreductase formed only on anaerobic growth but illustrate transport defects in aerobically grown cells.
Single-Amino Acid Substitutions Alter the Specificity and Affinity of PDZ Domains for Their Ligands (2000)

PDZ domains are modular protein-protein interaction domains that bind to specific C-terminal sequences of membrane proteins and/or to other PDZ domains. Certain PDZ domains in PSD-95 and syntrophins interact with C-terminal peptide ligands and heterodimerize with the extended nNOS PDZ domain. The capacity to interact with nNOS correlates with the presence of a Lys residue in the carboxylate- binding loop of these PDZ domains. Here, we report that substitution of an Arg for Lys-165 in PSD-95 PDZ2 disrupted its interaction with nNOS, but not with the C terminus of the Shaker-type K(+) channel Kv1.4. The same mutation affected nNOS binding to alpha1- and beta1-syntrophin PDZ domains to a lesser extent, due in part to the stabilizing effect of tertiary interactions with the canonical nNOS PDZ domain. PDZ domains with an Arg in the carboxylate-binding loop do not bind nNOS; however, substitution with Lys or Ala was able to confer nNOS binding. Our results indicate that the carboxylate-binding loop Lys or Arg is a critical determinant of nNOS binding and that the identity of this residue can profoundly alter one mode of PDZ recognition without affecting another. We also analyzed the effects of mutating Asp-143, a residue in the alphaB helix of alpha1-syntrophin that forms a tertiary contact with the nNOS PDZ domain. This residue is important for both nNOS and C-terminal peptide binding and confers a preference for peptides with a positively charged residue at position -4. On this basis, we have identified the C terminus of the Kir2.1 channel as a possible binding partner for syntrophin PDZ domains. Together, our results demonstrate that single-amino acid substitutions alter the specificity and affinity of PDZ domains for their ligands.
Severe and protracted cholestasis in 44 young men taking bodybuilding supplements: assessment of genetic, clinical and chemical risk factors (2019)

Patients with bodybuilding supplements liver injury uniformly presented with cholestatic injury, which slowly resolved. The ingested products often contained anabolic steroids not identified on the label, and no enrichment in genetic variants was found, indicating a need for additional studies.
Efficient Synthesis of an Aldehyde Functionalized Hyaluronic Acid and Its Application in the Preparation of Hyaluronan−Lipid Conjugates (2006)

An efficient method to synthesize hyaluronan oligosaccharide lipid conjugates is described. This strategy is based on the introduction of a double bond in the glucuronic acid of the hyaluronic acid (HA), by the biodegradation of HA with hyaluronate lyase, followed by the generation of a free aldehyde group at the nonreducing end of hyaluronic acid via ozonolysis and the subsequent reduction of the generated ozonide. The resulting aldehyde-functionalized HA is then coupled to dipalmitoyl phosphatidylethanolamine (DPPE) using reductive amination chemistry. This methodology can be extended to link molecules such as biotin, polymers, or proteins to HA for numerous applications in drug delivery and in the creation of biocompatible materials for tissue repair and engineering.
Interleukin-6 Protects against Fas-mediated Death by Establishing a Critical Level of Anti-apoptotic Hepatic Proteins FLIP, Bcl-2, and Bcl-xL (2001)

Previous studies showed that following acute carbon tetrachloride (CCl(4)) treatment, interleukin-6 null (IL-6-/-) mice develop increased hepatocellular injury, defective regeneration, delayed wound healing, and increased hepatocyte apoptosis. Pretreatment with IL-6 prior to CCl(4) reduces injury, hepatocyte apoptosis, and accelerates regeneration in both IL-6-/- and +/+ livers. To demonstrate whether IL-6 can prevent liver injury that involves direct stimulation of hepatocyte apoptosis, IL-6-/- and +/+ mice were treated with the Fas agonist, Jo-2 mAb. At low Fas agonist doses, IL-6+/+ mice developed mild hepatic injury and survived, whereas IL-6-/- mice developed severe apoptotic hepatitis within 12 h and died. Pretreatment with IL-6 improved survival in IL-6-/- mice and reduced injury in both IL-6-/- and +/+ livers. The direct anti-apoptotic effects of IL-6 were demonstrated in vitro as IL-6 decreased Fas-mediated apoptosis in both IL-6-/- and +/+ primary hepatocyte cultures, and suggested that IL-6-/- hepatocytes have a pre-existing defect in anti-apoptotic pathways. After Fas activation, IL-6-/- livers demonstrated evidence of both proximal and distal alterations in the apoptotic pathways including elevated caspase 8 and 3 activation-associated fragments, and loss of cytochrome c staining. IL-6-/- livers had reduced pre-existing protein expression of the anti-apoptotic factors Bcl-2 and Bcl-xL as well as more rapid degradation of FLIP following Fas treatment that appeared to be post-transcriptionally regulated. FLIP is a crucial proximal inhibitor of caspase 8 activation in Fas, tumor necrosis factor, and DR3/DR4-mediated apoptosis, and Bcl-2 and Bcl-xL more downstream anti-apoptotic regulators. IL-6 may function as a critical anti-apoptotic factor in the liver by its ability to establish and maintain an adequate level of FLIP and downstream anti-apoptotic factors.
Explantation of Infected Hemostatic Puncture Closure Devices (1999)

Hemostatic puncture closure devices for the femoral artery are currently marketed as a means of shortening hemostasis, ambulation, and observation times after cardiac catheterization procedures. Some of these devices are deployed external to the artery, but at least one device, Angio-SealA (Sherwood, Davis &amp; Geck), includes a polymer anchor that is deployed inside the artery. Major complications may arise from the use of this device, including thrombosis, embolization of the anchor, and infection. The manufacturer does not claim that the device reduces the incidence of local complications as compared to the traditional technique of manual compression. The author presents a case of infection of the groin involving the Angio-Seal device in which the patient presented with septic shock and renal failure after cardiac catheterization. A large abscess was present, and removal of the device required arterial surgery in an infected field. The author reports on the technique and precautions used to surgically remove the device and to prevent further complications.
Lipid composition of platelets from patients with atherosclerosis: Effect of purified eicosapentaenoic acid ethyl ester administration (1988)

Although eicosapentaenoic acid (EPA) has been shown to have beneficial effects in the prevention of atherosclerosis, the mechanism by which these effects occur is not entirely clear. We investigated the lipid composition of platelets in paired subjects with and without atherosclerotic disease, either hypercholesterolemic (low density lipoprotein [LDL] cholesterol [Chol] greater than or equal to 170 mg/dl) or normocholesterolemic (LDL-Chol less than 170 mg/dl). Platelets from patients with atherosclerotic disease had a lower phosphatidylcholine (PC)/Chol ratio, when compared with those from patients without atherosclerotic disease, irrespective of LDL-Chol levels. Eleven patients with atherosclerotic disease were treated with purified EPA ethyl ester (1.8 g/day), and changes in lipid composition of platelets were investigated. Plasma levels of total Chol and LDL-Chol decreased significantly after EPA administration. The phospholipid (PL)/Chol ratio and the PC/Chol ratio in platelets from patients with atherosclerotic disease increased significantly after 4-10 wk EPA treatment. The EPA content in platelets increased, while the arachidonic acid (AA) content decreased. EPA-induced changes in the PL/Chol and the PC/Chol ratios of platelets, as well as fatty acyl chain shifts, may be related to the beneficial effects in preventing atherosclerosis, possibly by increase in the membrane fluidity.
Levels of Interleukin-2, Interferon-γ, and Interleukin-4 in Bronchoalveolar Lavage Fluid From Patients WithMycoplasmaPneumonia: Implication of Tendency Toward Increased Immunoglobulin E Production (2001)

IL-4 levels and IL-4/IFN-gamma ratios in BAL fluid are significantly higher in patients with Mycoplasma pneumonia than in patients with pneumococcal pneumonia or control participants. The BAL cytokine data suggest a predominant TH2-like cytokine response in Mycoplasma pneumonia, thus representing a favorable condition for IgE production.
Síntesis y actividad biológica de análogos espirostánicos de brasinoesteroides a partir de la 9(11)-deshidrohecogenina (2004)

Se reporta la síntesis, caracterización espectroscópica y evaluación preliminar de la actividad biológica in vitro de tres análogos espirostánicos de brasinoesteroides [(25R)-3b-acetoxi-9a,11a-epoxi-5a-espirostan-12-ona (3), (25R)- 3b-hidroxi-9a,11a-epoxi-5a-espirostan-12-ona (5) y (25R)-3b-acetoxi-9a,11a-epoxi- C-homo-11a-oxa-5a-espirostan12-ona (4)] a partir de la 9(11)-deshidrohecogenina (1). El sustrato de partida, la cetona a,b-insaturada (1), fue acetilado en la posición 3 y a continuación, este derivado acetilado (2) se oxidó con ácido mcloroperbenzoico. Se obtuvo como producto principal de la reacción la epoxicetona (3) y como producto colateral la epoxilactona (4). La hidrólisis del compuesto 3 en medio básico dio lugar al compuesto 5. La actividad biológica de los compuestos sintetizados se evaluó en los bioensayos del crecimiento de hipocótilos y expansión de cotiledones del rábano. Todos los compuestos sintetizados mostraron algún tipo de efecto sobre el crecimiento de hipocótilos del rábano.
Volatile Terpenes from Actinomycetes: A Biosynthetic Study Correlating Chemical Analyses to Genome Data (2013)

The volatile terpenes of 24 actinomycetes whose genomes have been sequenced (or are currently being sequenced) were collected by use of a closed-loop stripping apparatus and identified by GC/MS. The analytical data were compared against a phylogenetic analysis of all 192 currently available sequences of bacterial terpene cyclases (excluding geosmin and 2-methylisoborneol synthases). In addition to the several groups of terpenes with known biosynthetic origin, selinadienes were identified as a large group of biosynthetically related sesquiterpenes that are produced by several streptomycetes. The detection of a large number of previously unrecognised side products of known terpene cyclases proved to be particularly important for an in depth understanding of biosynthetic pathways to known terpenes in actinomycetes. Interpretation of the chemical analytical data in the context of the phylogenetic tree of bacterial terpene cyclases pointed to the function of three new enzymes: (E)-β-caryophyllene synthase, selina-3,7(11)-diene synthase and aristolochene synthase.
Glycoproteins as differentiation markers in human malignant melanoma and melanocytes. (1983)

Human malignant melanoma cell lines have been divided into three broad groups on the basis of morphology, pigmentation, tyrosinase levels, the 2-dimensional electrophoretic patterns of their [3H]glucosamine-labeled glycoproteins and the presence or absence of an extracellular matrix of fibronectin. The most pigmented cell lines were characterized by the synthesis of a novel glycoprotein with a molecular weight of 75,000 and the absence of a fibronectin matrix. As cultured skin melanocytes also had these characteristics, this group of melanomas appears to be the most differentiated. Melanoma cell lines in the amelanotic group were characterized by the synthesis of high levels of HLA-DR antigen and by the production of an extracellular fibronectin matrix.
Data streaming: very low overhead communication for fine-grained multicomputing (2002)

Recent developments have greatly reduced network latencies in multiprocessor networks. Thus, software overhead is becoming the primary cost of multiprocessor communication. This paper proposes data streaming-a technique which places explicit send and receive instructions in the user code-as a means to cut software overhead to a minimum. Data streaming has the added benefit that it can tighten the coupling between processors by reducing the message size to that of a single data item. This paper presents experimental results that indicate data streaming can cut software overhead to less than one instruction per byte of data transmitted.
Structured Language Modeling for Speech Recognition (2000)

A new language model for speech recognition is presented. The model develops hidden hierarchical syntactic-like structure incrementally and uses it to extract meaningful information from the word history, thus complementing the locality of currently used trigram models. The structured language model (SLM) and its performance in a two-pass speech recognizer --- lattice decoding --- are presented. Experiments on the WSJ corpus show an improvement in both perplexity (PPL) and word error rate (WER) over conventional trigram models.
Interallelic class switch recombination can reverse allelic exclusion and allow trans‐complementation of an IgH locus switching defect (2006)

The predominant path of immunoglobulin class switch recombination follows the paradigm of intra-chromosomal deletion enabling expression of another heavy chain instead of micro and delta. This was, however, challenged by observations of inter-allelic class switch recombination in rabbit or mouse IgG3- or IgA-producing B cells. Assuming that the conditions of inter-chromosomal exchange are likely present at any target S regions in stimulated B cells, we explored trans-association of VH and C genes in a model allowing all C genes to be checked simultaneously. Heterozygous mutant mice are thus studied, which carry one non-functional IgH allele inactivated by a non-translatable mutation of VDJ-CH transcripts, while the functional allele is deficient for class switching due to a truncated 3'regulatory region. A fair level of switching to all Ig classes is restored in heterozygous mice despite the fact that cis-recombination is either non productive on one allele or deficient on the other. Molecular evidence at the DNA level of trans-CSR to IgG3 was demonstrated by cloning and sequencing Smu-Sgamma3 hybrid junctions. These data demonstrate that inter-allelic recombination may broadly rescue the production of various class-switched isotypes and allow complementation between mutations located at both ends of the IgH constant gene cluster.
Knowledge-based Approaches to the Maintenance of a Large Controlled Medical Terminology (1994)

The MED is a hybrid of terminology and knowledge. It provides domain coverage, synonymy, consistency of views, explicit relationships, and multiple classification while preventing redundancy, ambiguity (homonymy) and misclassification.
Solubility parameters (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolubility parametersAllan F. M. BartonCite this: Chem. Rev. 1975, 75, 6, 731–753Publication Date (Print):December 1, 1975Publication History Published online1 May 2002Published inissue 1 December 1975https://pubs.acs.org/doi/10.1021/cr60298a003https://doi.org/10.1021/cr60298a003research-articleACS PublicationsRequest reuse permissionsArticle Views11497Altmetric-Citations921LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts