gebhart/patrepeval huggingface dataset:
Mass spectroscopic analysis of a novel enzymatic reaction. Oxidative decarboxylation of the lantibiotic precursor peptide EpiA catalyzed by the flavoprotein EpiD. (1994)

The epidermin biosynthetic reaction between the flavoprotein EpiD and the precursor peptide EpiA was investigated by reversed-phase chromatography and ion spray mass spectrometry. Several products with molecular masses 46 and 104 Da less than that of EpiA were observed; these results were confirmed by using an MBP-EpiD fusion protein as enzyme and the mutant peptides EpiAR-1Q and K-EpiA as substrates. The reaction was inhibited by Zn2+ ions. Modifications were localized in the C-terminal fragment of EpiA as shown by factor Xa cleavage of the products followed by mass spectrometry analysis. In addition, EpiD reacted with the precursor peptides and with proepidermin, indicating that the leader peptide is not necessary for the recognition of EpiA by EpiD. Sequence analysis of modified proepidermin revealed that at least the amino acids Ile(+1)-Tyr+20 are unmodified. The observed decrease in mass of 46 Da and the modification at the C terminus of EpiA is in agreement with the proposed enzymatic function of EpiD, the oxidative decarboxylation of the precursor peptide. In addition, the increased absorbance at 260 nm of the modified peptides indicates the presence of a thioenol group in the C-terminal proepidermin.
Natural fractures in the Barnett Shale and their importance for hydraulic fracture treatments (2007)

Gas production from the Barnett Shale relies on hydraulic fracture stimulation. Natural opening-mode fractures reactivate during stimulation and enhance efficiency by widening the treatment zone. Knowledge of both the present-day maximum horizontal stress, which controls the direction of hydraulic fracture propagation, and the geometry of the natural fracture system, which we discuss here, is therefore necessary for effective hydraulic fracture treatment design. We characterized natural fractures in four Barnett Shale cores in terms of orientation, size, and sealing properties. We measured a mechanical rock property, the subcritical crack index, which governs fracture pattern development. Natural fractures are common, narrow (0.05 mm; 0.002 in.), sealed with calcite, and present in en echelon arrays. Individual fractures have high length/width aspect ratios (1000:1). They are steep (75), and the dominant trend is west-northwest. Other sets trend north-south. The narrow fractures are sealed and cannot contribute to reservoir storage or enhance permeability, but the population may follow a power-law size distribution where the largest fractures are open. The subcritical crack index for the Barnett Shale is high, indicating fracture clustering, and we suggest that large open fractures exist in clusters spaced several hundred feet apart. These fracture clusters may enhance permeability locally, but they may be problematic for hydraulic fracture treatments. The smaller sealed fractures act as planes of weakness and reactivate during hydraulic fracture treatments. Because the maximum horizontal stress trends northeast-southwest and is nearly normal to the dominant natural fractures, reactivation widens the treatment zone along multiple strands.
A hybrid network intrusion detection technique using random forests (2006)

Intrusion detection is important in network security. Most current network intrusion detection systems (NIDSs) employ either misuse detection or anomaly detection. However, misuse detection cannot detect unknown intrusions, and anomaly detection usually has high false positive rate. To overcome the limitations of both techniques, we incorporate both anomaly and misuse detection into the NIDS. In this paper, we present our framework of the hybrid system. The system combines the misuse detection and anomaly detection components in which the random forests algorithm is applied. We discuss the advantages of the framework and also report our experimental results over the KDD'99 dataset. The results show that the proposed approach can improve the detection performance of the NIDSs, where only anomaly or misuse detection technique is used.
异步转移方式(ATM)技术应用到指挥、控制和通信(C~3)系统的框架(续) (1997)

四、ATM实现问题 虽然ATM技术并不是完全新的(80年代末出现的),但它的标准和实现尚未成熟。但已有的标准足以为卖主营销ATM产品和提供基本的ATM业务。关键在于卖主对于那些缺乏标准化的领域采取专门的解决办法。即使有了专营的ATM设备,也还有一些方面需要在完全满足军用要求以前给以重视,按作者的观点,此处所提出的课题代表了当
PAX3-FOXO1 Induces Cannabinoid Receptor 1 to Enhance Cell Invasion and Metastasis (2011)

Alveolar rhabdomyosarcoma (ARMS) is a muscle-derived childhood tumor characterized by production of oncogenic PAX3/7-FOXO1 chimeric transcription factors. While downstream targets of the PAX3-FOXO1 oncoprotein in ARMS have been defined, the functional relevance of these targets is unclear. Here, we show that upregulation of the cannabinoid receptor 1 (Cnr1/Cb1) by PAX3-FOXO1 in mouse primary myoblasts and ARMS cell lines, contributes to PAX3-FOXO1 phenotypes, both in vivo and in vitro. In primary myoblasts, Cnr1 was dispensable for PAX3-FOXO1 to mediate cell proliferation, differentiation, or transformation; however, Cnr1 function was essential to increase the invasive capacity conferred by PAX3-FOXO1 overexpression in these cells. Genetic or pharmacologic abrogation of Cnr1 inhibited the enhanced basement membrane invasion induced by PAX3-FOXO1. Cnr1 loss by either route also dramatically reduced lung metastasis formation. Taken together, our findings strongly implicate Cnr1 as a novel tractable target to inhibit ARMS invasion and metastasis.
Suzuki–Miyaura Cross-Coupling of Potassium Alkoxyethyltrifluoroborates: Access to Aryl/Heteroarylethyloxy Motifs (2012)

The introduction of an alkoxyethyl moiety onto aromatic substructures has remained a long-standing challenge for synthetic organic chemists. The main reasons are the inherent instability of alkoxyethylmetallic species and the lack of general procedures to access them. A new method utilizing a cross-coupling strategy based on the exceptional properties of organotrifluoroborates has been developed, and the method allows an easy and efficient installation of this unit on a broad range of aryl and heteroaryl bromides.
Tissue transglutaminase and apoptosis: sense and antisense transfection studies with human neuroblastoma cells. (1994)

In this report, we show that the overexpression of tissue transglutaminase (tTG) in the human neuroblastoma cell line SK-N-BE(2) renders these neural crest-derived cells highly susceptible to death by apoptosis. Cells transfected with a full-length tTG cDNA, under the control of a constitutive promoter, show a drastic reduction in proliferative capacity paralleled by a large increase in cell death rate. The dying tTG-transfected cells exhibit both cytoplasmic and nuclear changes characteristic of cells undergoing apoptosis. The tTG-transfected cells express high Bcl-2 protein levels as well as phenotypic neural cell adhesion molecule markers (NCAM and neurofilaments) of cells differentiating along the neuronal pathway. In keeping with these findings, transfection of neuroblastoma cells with an expression vector containing segments of the human tTG cDNA in antisense orientation resulted in a pronounced decrease of both spontaneous and retinoic acid (RA)-induced apoptosis. We also present evidence that (i) the apoptotic program of these neuroectodermal cells is strictly regulated by RA and (ii) cell death by apoptosis in the human neuroblastoma SK-N-BE(2) cells preferentially occurs in the substrate-adherent phenotype. For the first time, we report here a direct effect of tTG in the phenotypic maturation toward apoptosis. These results indicate that the tTG-dependent irreversible cross-linking of intracellular protein represents an important biochemical event in the induction of the structural changes featuring cells dying by apoptosis.
A rapid and sensitive assay for quantification of siRNA efficiency and specificity (2005)

RNA Interference has rapidly emerged as an efficient procedure for knocking down gene expression in model systems. However, cross-reactivity, whereby multiple genes may be simultaneously targeted by a single short interfering RNA (siRNA), can potentially jeopardize correct interpretation of gene function. As such, it is essential to test the specificity of a siRNA prior to a full phenotypic analysis. To this end, we have adapted a reporter-based assay harnessing the sensitivity of luciferase activity to provide a quantitative readout of relative RNAi efficacy and specificity. We have tested different siRNAs directed against Thymosin beta4 (Tbeta4); determined their effectiveness at silencing Tbeta4 and have both excluded off-target silencing of the Tbeta4 homologue Thymosin beta10 (Tbeta10) and demonstrated partial knockdown of Tbeta10 despite significant (12/23; 52%) sequence mismatch. This assay system is applicable to any RNAi study where there is a risk of targeting homologous genes and to the monitoring of off-target effects at the genome level following microarray expression profiling.
Synthesis of Puraquinonic Acid Ethyl Ester and Deliquinone via a Common Intermediate (2002)

Both compounds were prepared via a common intermediate. The key features included the direct synthesis of the indan skeleton and the radical addition to a quinone.
Increased Plasma Endothelin-1 in Pulmonary Hypertension: Marker or Mediator of Disease? (1991)

Patient with pulmonary hypertension have substantial alterations in plasma immunoreactive endothelin-1, which may reflect changes in net release or clearance of endothelin-1 by the lung. In patients with primary pulmonary hypertension, the high levels in arterial compared with venous plasma suggest pulmonary production of endothelin-1, which may contribute to elevated pulmonary vascular resistance.
Patterned Self-Assembled Monolayers and Meso-Scale Phenomena (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPatterned Self-Assembled Monolayers and Meso-Scale PhenomenaAmit Kumar, Nicholas L. Abbott, Hans A. Biebuyck, Enoch Kim, and George M. WhitesidesCite this: Acc. Chem. Res. 1995, 28, 5, 219–226Publication Date (Print):May 1, 1995Publication History Published online1 May 2002Published inissue 1 May 1995https://pubs.acs.org/doi/10.1021/ar00053a003https://doi.org/10.1021/ar00053a003research-articleACS PublicationsRequest reuse permissionsArticle Views2095Altmetric-Citations349LEARN 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
Phenotypic and Genotypic Characterization of Nosocomial Staphylococcus aureus Isolates from Trauma Patients (1998)

Staphylococcus aureus is a major cause of nosocomial infections. During the period from March 1992 to March 1994, the patients admitted to the intensive care unit of the University of Maryland Shock Trauma Center were monitored for the development of S. aureus infections. Among the 776 patients eligible for the study, 60 (7.7%) patients developed 65 incidents of nosocomial S. aureus infections. Of the clinical isolates, 43.1% possessed a polysaccharide type 5 capsule, 44.6% possessed a type 8 capsule, and the remaining 12.3% had capsules that were not typed by the type 5 or type 8 antibodies. Six antibiogram types were noted among the infection-related isolates, with the majority of the types being resistant only to penicillin and ampicillin. It was noted that the majority of cases of pneumonia were caused by relatively susceptible strains, while resistant strains were isolated from patients with bacteremia and other infections. Only 16 (6.3%) of the isolates were found to be methicillin-resistant S. aureus (MRSA). DNA fingerprinting by pulsed-field gel electrophoresis showed 36 different patterns, with characteristic patterns being found for MRSA strains and the strains with different capsular types. Clonal relationships were established, and the origins of the infection-related isolates in each patient were determined. We conclude that (i) nosocomial infection-related isolates from the shock trauma patients did not belong to a single clone, although the predominance of a methicillin-resistant genotype was noted, (ii) most infection-related S. aureus isolates were relatively susceptible to antibiotics, but a MRSA strain was endemic, and (iii) for practical purposes, the combination of the results of capsular and antibiogram typing can be used as a useful epidemiological marker.
Plasmid Inhalation: Delivery to the Airways (2005)

This chapter contains sections titled: Introduction Delivery Methods Lung Delivery by Instillation Delivery by Aerosol Aerosol Deposition Aerosolization Devices Metered Dose Inhalers Dry Powder Inhalers Nebulizers Aerosolization of Plasmid DNA Plasmid DNA/Lipid Complexes Optimization of Aerosol Formulation Aerosol Delivery of Lipid/pDNA to Human Lung Plasmid Delivery with Cationic Polymers Future Directions Conclusions References
An Efficient Synthesis of 14-Halogenomethyl-substituted C-Normorphinans (1987)

Bucleophilic ring-opening reaction of 7,14-cyclo-dihydrocodeinone 1 resulted in a watersoluble quaternary ammonium salt 2. However, similar reaction of under acetalization conditions led t o the ring cleavaged 14-halogenomethylacetals 5, 7_ and 8 (e) in high yields.When the acetals were hydrolyzed, the fornation of cyclic ammDnium compounds (3_) was unavoidable.Following our interest in the chemistry of C-normorphinans, we investigated the reactivity of the cyclopropane moiety in 7,14-cyclodihydrocodeinonel i t o w a r d s nucleophiles.-2 -P 2 CH37,J 1 Under the conditions of "ele~tro~hi'le-assisted nucleophilic ring-~~e n i n g " ~-~, complete reaction occurred but no product was available from the organic layer after workup.There was every reason t o believe that the ring-opening product 2_ was readily transformed to the watersoluble quaternary ammonium salt 3_.In addition, the nmr-analysis of the aqueous layer confirmed this presumption.It was unexpected that a ring-opening product could be obtained in excellent yields when thionyl chloride as reagent and dichloromathane and methanol a s solvents were used.The nmr-spectrum of this compound 4 2 showed a dd-signal of one proton at 4.95 ppm (H-8a) which was in correlation with an electron-withdrawing substituent at C-8.The geminal proton H-8b gave a doublet at 3.78 ppm.The second coupling of H-8a was caused by a long-range coupling with H-7-which was additionally splitted by geminal coupling with H-7P.Furthermore, the doublet of the H-78 at 2.16 ppm and the two singlets of the acetal-methyls were detectable.The structure 4 2 was further affirmed by the 13c-nmr and the mass spectrum.Intramolecular alkylation of the nitrogen occurred only when 4 2 was reacted with alcoholic alkali solutions.It was possible to isolate 5 a s perchlorate (a) but the Hofmann-degradation proceedcd quickly to give 5 under these conditions.Acidic hydrolysis of the product 4 3 aff,orded a water-soluble quaternary ammonium salt (3) via intramolecular cyclization.
Monoclonal antibody 9.3 and anti‐CD11 antibodies define reciprocal subsets of lymphocytes (1985)

We have previously described antibody 9.3 which recognizes a 44-kDa polypeptide designated Tp44 expressed on 70-80% of peripheral blood T cells, including nearly all CD4+ cells and some CD8+ cells. Whereas the 9.3+ population contains helper cells, cytotoxic T cell precursors and cytotoxic T cell effectors, the 9.3- population has been reported in several models to contain precursors for suppressor cells. In this report, we demonstrate that 9.3- lymphocytes express CD11, an antigen which is also present on monocytes and granulocytes. Among lymphoid cells, Tp44 and CD11 represent markers that identify reciprocal, nonoverlapping subsets, each of which contains both CD8+ cells and CD4+ cells. With Tp44 and CD11, and CD4 and CD8, the development and function of T cells can thus be examined within the framework of two distinct systems of reciprocally expressed antigens.
Macrophage deactivating factor and transforming growth factors- beta 1 - beta 2 and - beta 3 inhibit induction of macrophage nitrogen oxide synthesis by IFN-gamma. (1990)

Macrophage deactivating factor (MDF) and three members of the transforming growth factor-beta family (TGF-beta 1, -beta 2, and -beta 3) blocked the ability of IFN-gamma to induce release of reactive nitrogen intermediates from mouse peritoneal macrophages. Raising the concentration of IFN-gamma did not diminish the potency of the inhibitors (50% inhibition by approximately 7 nM MDF, 2 pM TGF-beta 1, 4 pM TGF-beta 2, and 8 pM TGF-beta 3). These inhibitors partially blocked induction of nitrite release in macrophages activated with the combination of IFN-gamma plus TNF-alpha, but were incapable of inhibiting when macrophages were activated by the combination of IFN-gamma plus LPS. MDF and TGF-beta 1, -beta 2, and -beta 3 inhibited IFN-gamma-induced nitrite release only if present during the induction phase; once IFN-gamma-nitrite release had commenced, addition of the same cytokines was no longer inhibitory. Maximum inhibition of synthesis over a 48-h period required that the inhibitors be present during the first 3 h of induction. Thus, cytokines can suppress as well as induce macrophage synthesis of reactive nitrogen intermediates, products with cytotoxic, antimicrobial, and vasodilatory properties.
Hairy Skin: Psychophysical Channels and Their Physiological Substrates (1994)

Experiments were conducted in which threshold-frequency characteristics were measured on the hairy skin of the forearm of human observers. Thresholds were measured with two stimulus probe areas (2.9 and 0.008 cm2) at three skin-surface temperatures (15 degrees, 30 degrees, and 40 degrees C). The results suggest that whereas glabrous skin uses four distinct channels of information, only three channels may be involved in mediating the sense of touch for hairy skin. The three channels are defined as Ph, (Pacinian, hairy skin), NPh low (non-Pacinian, hairy skin, low frequencies) and NPh mid (non-Pacinian, hairy skin, middle frequencies). In addition, it is proposed that the neural substrates for the three psychophysically characterized channels are, respectively, the Pacinian corpuscle (PC) nerve fibers, the slowly adapting type II (SAII) fibers, and the rapidly adapting (RA) fibers.
Film property comparison of Ti/TiN deposited by collimated and uncollimated physical vapor deposition techniques (1996)

The film properties of single layers of Ti and TiN and bilayer Ti/TiN film stacks sputtered with and without a collimator on SiO2 substrates were studied and compared by Rutherford backscattering spectrometry, Auger electron spectroscopy, x-ray diffractometry with both glancing angle and θ–2θ coupled diffraction techniques, scanning electron microscopy, transmission electron microscopy of both cross section and plan view, and atomic force microscopy. The properties investigated include color, stoichiometry, density, electrical resistivity, grain and grain boundary structure, preferred orientation (texture), stress, surface morphology (roughness), reflectance, and impurity level. It was found that the density was higher, the surface morphology was less rough, and the electrical resistivity was lower for the collimated films than for the uncollimated films. The lower density and rougher surface of the uncollimated films are caused by shadowing effects.
BMP signaling during bone pattern determination in the developing limb (1996)

To examine the role of BMP signaling during limb pattern formation, we isolated chicken cDNAs encoding type I (BRK-1 and BRK-2) and type II (BRK-3) receptors for bone morphogenetic proteins. BRK-2 and BRK-3, which constitute dual-affinity signaling receptor complexes for BMPs, are co-expressed in condensing precartilaginous cells, while BRK-1 is weakly expressed in the limb mesenchyme. BRK-3 is also expressed in the apical ectodermal ridge and interdigital limb mesenchyme. BRK-2 is intensely expressed in the posterior-distal region of the limb bud. During digit duplication by implanting Sonic hedgehog-producing cells, BRK-2 expression is induced anteriorly in the new digit forming region as observed for BMP-2 and BMP-7 expression in the limb bud. Dominant-negative effects on BMP signaling were obtained by over-expressing kinase domain-deficient forms of the receptors. Chondrogenesis of limb mesenchymal cells is markedly inhibited by dominant-negative BRK-2 and BRK-3, but not by BRK-1. Although the bone pattern was not disturbed by expressing individual dominant-negative BRK independently, preferential distal and posterior limb truncations resulted from co-expressing the dominant-negative forms of BRK-2 and BRK-3 in the whole limb bud, thus providing evidence that BMPs are essential morphogenetic signals for limb bone patterning.
HDAC5 Controls MEF2C-Driven Sclerostin Expression in Osteocytes (2014)

Osteocytes secrete paracrine factors that regulate the balance between bone formation and destruction. Among these molecules, sclerostin (encoded by the gene SOST) inhibits osteoblastic bone formation and is an osteoporosis drug target. The molecular mechanisms underlying SOST expression remain largely unexplored. Here, we report that histone deacetylase 5 (HDAC5) negatively regulates sclerostin levels in osteocytes in vitro and in vivo. HDAC5 shRNA increases, whereas HDAC5 overexpression decreases SOST expression in the novel murine Ocy454 osteocytic cell line. HDAC5 knockout mice show increased levels of SOST mRNA, more sclerostin-positive osteocytes, decreased Wnt activity, low trabecular bone density, and reduced bone formation by osteoblasts. In osteocytes, HDAC5 binds and inhibits the function of MEF2C, a crucial transcription factor for SOST expression. Using chromatin immunoprecipitation, we have mapped endogenous MEF2C binding in the SOST gene to a distal intergenic enhancer 45 kB downstream from the transcription start site. HDAC5 deficiency increases SOST enhancer MEF2C chromatin association and H3K27 acetylation and decreases recruitment of corepressors NCoR and HDAC3. HDAC5 associates with and regulates the transcriptional activity of this enhancer, suggesting direct regulation of SOST gene expression by HDAC5 in osteocytes. Finally, increased sclerostin production achieved by HDAC5 shRNA is abrogated by simultaneous knockdown of MEF2C, indicating that MEF2C is a major target of HDAC5 in osteocytes.