gebhart/patrepeval huggingface dataset:
Two Membrane-Associated NiFeS-Carbon Monoxide Dehydrogenases from the Anaerobic Carbon-Monoxide-Utilizing Eubacterium Carboxydothermus hydrogenoformans (2001)

Two monofunctional NiFeS carbon monoxide (CO) dehydrogenases, designated CODH I and CODH II, were purified to homogeneity from the anaerobic CO-utilizing eubacterium Carboxydothermus hydrogenoformans. Both enzymes differ in their subunit molecular masses, N-terminal sequences, peptide maps, and immunological reactivities. Immunogold labeling of ultrathin sections revealed both CODHs in association with the inner aspect of the cytoplasmic membrane. Both enzymes catalyze the reaction CO + H(2)O --> CO(2) + 2 e(-) + 2 H(+). Oxidized viologen dyes are effective electron acceptors. The specific enzyme activities were 15,756 (CODH I) and 13,828 (CODH II) micromol of CO oxidized min(-1) mg(-1) of protein (methyl viologen, pH 8.0, 70 degrees C). The two enzymes oxidize CO very efficiently, as indicated by k(cat)/K(m) values at 70 degrees C of 1.3. 10(9) M(-1) CO s(-1) (CODH I) and 1.7. 10(9) M(-1) CO s(-1) (CODH II). The apparent K(m) values at pH 8.0 and 70 degrees C are 30 and 18 microM CO for CODH I and CODH II, respectively. Acetyl coenzyme A synthase activity is not associated with the enzymes. CODH I (125 kDa, 62.5-kDa subunit) and CODH II (129 kDa, 64.5-kDa subunit) are homodimers containing 1.3 to 1.4 and 1.7 atoms of Ni, 20 to 22 and 20 to 24 atoms of Fe, and 22 and 19 atoms of acid-labile sulfur, respectively. Electron paramagnetic resonance (EPR) spectroscopy revealed signals indicative of [4Fe-4S] clusters. Ni was EPR silent under any conditions tested. It is proposed that CODH I is involved in energy generation and that CODH II serves in anabolic functions.
Experimental Determination of the Extinction Coefficient of CdTe, CdSe, and CdS Nanocrystals (2003)

The extinction coefficient per mole of nanocrystals at the first exitonic absorption peak, ε, for high-quality CdTe, CdSe, and CdS nanocrystals was found to be strongly dependent on the size of the nanocrystals, between a square and a cubic dependence. The measurements were carried out using either nanocrystals purified with monitored purification procedures or nanocrystals prepared through controlled etching methods. The nature of the surface ligands, the refractive index of the solvents, the PL quantum yield of the nanocrystals, the methods used for the synthesis of the nanocrystals, and the temperature for the measurements all did not show detectable influence on the extinction coefficient for a given sized nanocrystal within experimental error.
Decreased plasma and tissue isoleucine levels after simulated gastrointestinal bleeding by blood gavages in chronic portacaval shunted rats. (1997)

Simulated gastrointestinal bleeding by blood gavages in rats with and without impaired liver function leads to hypoisoleucinaemia and decreased tissue Ile pools.
[The breathing pattern and inspiratory drive in chronic obstructive pulmonary disease]. (1992)

Quantitative analysis of breathing pattern in 20 cases of COPD patients and 15 normal persons showed a significant correlation between values of VT/TI and P0.1; VT/TI value may be used clinically as an index of inspiratory drive. The elevation of VT/TI values of COPD patients at the end of high CO2-rebreathing denoted the sensitivity of their respiratory center is still preserved. However, the impairment of respiratory muscle endurance in hypercapnic COPD patients under rebreathing stress showed a prolongation of TI/TT.
Competitive Bidding: A Comprehensive Bibliography (1979)

This bibliography identifies almost 500 titles, which, with a few exceptions, deal with quantitative models related to competitive bidding. The papers vary widely. They include ad hoc advice to bidders, analytical models of single and multiple auctions, evaluations of the use of auctions for allocating resources, and analyses of historical data on bidding. Some deal with competitive bidding in general while others relate to particular markets. Many of the entries are devoted to competitive bidding for construction contracts, oil exploration rights, and securities.
Interaction of Δ5-Androstene-3β,17β-diol with Estradiol and Dihydrotestosterone Receptors in Human Myometrial and Mammary Cancer Tissue1 (1975)

Specific receptor binding of estradiol (E-2) and dihydrotestosterone (DHT) was studied in human myometrial tissue and in human mammary cancer tissue. The inhibition of binding for E-2 and DHT by E-2, testosterone (T), DHT, dehydroepiandosterone (DHEA), dehydroepiandrosterone-sulfate (DHEA-S), androstendione (A) and 5-androstene-3beta, 17beta-diol (Adiol) was tested with the use of dextran-coated charcoal separation of bound and free E-2, respectively, and DHT. The percentage of binding inhibition was calculated with reference to the inhibition obtained with nafoxidine in a molar concentration ratio of 1,000 for E-2 binding, respectively, with cyproterone acetate in a molar concentration ratio of 10,000 for DHT binding. In 15 samples of myometrium tested, receptors were found for both E-2 and DHT. From 19 samples of mammary carcinoma tissue one showed no binding activity, three samples did bind E-2 only, five samples DHT only, and ten samples showed binding of both steroids. A 50% inhibition of E-2 binding, in myometrial as well as in tumor tissue, required a molar concentration ratio of 40 for Adiol, of more than 2,000 for DHEA. No significant inhibiting activity could be found for A up to a molar concentration ratio of 10,000 and for DHEA-S up to 40,000. With regard to DHT binding, Adiol is more active than E-2 and less active than T. Of the substances tested Adiol is therefore the only one which exerts a significant inhibiting influence at a molar ratio not far beyond the physiological range. This signifies that Adiol might interfere at the receptor level in the estrogenic stimulation of mammary cancer cells.
A Metal−Organic Framework with Covalently Bound Organometallic Complexes (2010)

A procedure for making covalently linked organometallic complexes within the pores of metal-organic frameworks (MOFs) has been described. An N-heterocyclic carbene precursor containing link L0 was prepared and then constructed into a MOF-5-type structure (IRMOF-76). Attempts to produce covalently bound organometallic complexes in IRMOF-76 were unsuccessful. An alternative way of linking the first metalated link, L1, into the desired metalated MOF structure, IRMOF-77, was successful. IRMOF-76 and -77 were characterized by single-crystal X-ray studies. Demonstration of permanent porosity and successful substitution of the pyridine coligand in IRMOF-77 are also described.
Botulinum toxin: a new ally of an old adversary. (1989)

<b>Objective:</b> Musician’s focal dystonia is usually considered to be task specific but secondary motor disturbances have been reported as well. We carried out a detailed evaluation of the incidence of these secondary motor problems in 101 patients. <b>Method:</b> Symptoms were assessed using clinical histories, neurological examinations and observation of instrumental manoeuvres. Results: 53.5% of patients reported secondary motor disturbances in activities other than playing their main instrument, with the onset delayed, in some cases, by up to 12 years from the awareness of dystonic symptoms. 46.5% suffered from simple, 19.8% from complex, and 33.7% from progressive, cramps. Plucked string players (guitarists) mainly suffered from simple cramps while keyboardists more frequently displayed the progressive form. In all patients symptoms were focal, and the type of cramp was unrelated to the severity of the perceived symptoms. Those patients playing a second instrument similar to their main instrument showed symptoms which worsened to a higher degree than those playing either only one instrument, or whose second instrument was different. <b>Conclusions:</b> Longer follow-up assessments may reveal secondary motor symptoms that are not visible over shorter examination periods. Therefore, a throughout evaluation of everyday life motor activities should be considered in any clinical and treatment protocol. We speculate that the avoidance of movements that are similar to the main affected task may be of help in limiting symptoms. Consequently, focal dystonia may be considered more movement than task-specific.
Synergistic growth stimulation of mouse fibroblasts by tumor-derived adhesion factor with insulin-like growth factors and insulin. (1996)

Tumor-derived adhesion factor (TAF) has been purified as a major secretory protein with cell-adhesion activity from culture medium conditioned by human bladder carcinoma cells (K. Akaogi et al., Biochem. Biophys. Res. Commun., 198: 1046-1053, 1994). TAF is closely related or identical to a putative protein encoded by the mac25 gene (M. Murphy et al., Cell Growth & Differ., 4: 715-722, 1993) and prostacyclin-stimulating factor (T. Yamauchi et al., Biochem. J., 303: 591-598, 1994). TAF has a characteristic cysteine cluster in its NH2-terminal sequence, which is conserved in the NH2 termini of insulin-like growth factor-binding proteins. In the present study, we examined the interaction of TAF with insulin-like growth factors (IGFs) and insulin. Although in a ligand blotting assay TAF bound neither IGFs nor insulin, immunoprecipitation assay showed weak interaction of TAF with IGF-I, IGF-II, and insulin. TAF by itself stimulated the growth of BALB/c3T3 cells on the usual plastic substrates and significantly enhanced IGF- or insulin-mediated cell growth. Moreover, marked potentiation of the mitogenic activities of IGFs and insulin by TAF was found in the culture on type IV collagen substrates. The synergistic growth stimulation was completely blocked by heparin. These results suggest that TAF may regulate the growth of fibroblastic cells in collaboration with IGFs and insulin.
Precision timing in the NEPTUNE Canada network (2009)

Delivery of accurate timing to subsea instruments is one of the essential functions of the NEPTUNE Canada ocean observatory. In the context of an ocean observing system, ldquotimingrdquo is understood to mean the ability to timestamp data using a clock which is traceable to Universal Time Coordinates (UTC) within some desired level of precision. Transmission or delivery of timing means transporting the necessary timing signals and data to subsea instruments or data collection processors. Timing signals are conventionally delivered in the form of a logic state transition on a dedicated communications line followed by a data string indicating the time at which the transition occurred. NEPTUNE Canada employs Ethernet communications channels to deliver timing. This avoids the need to provision additional communications channels and ensure that timing signals are available at all points within the network. The disadvantage of this approach is that timing signals must share the communications channels on which data is transmitted and may suffer delays or packet loss. Three timing protocols are employed: Network Time Protocol (NTP) described in IETF RFC 1305, simple network time protocol (SNTP) as described in RFC 2030 and IEEE 1588 precision time protocol (PTP) per IEEE 1588. NTP/SNTP are generally accepted to be accurate to within a few milliseconds and are suitable for a wide variety of applications. PTP provides significantly better accuracy which is required for applications such as seismology and acoustic thermography. Master clocks located in the shore station acquire time from the Global Positioning System for transmission to subsea instruments. Alcatel-Lucent Submarine Networks and NEPTUNE Canada have successfully demonstrated PTP operation on a test bed which is representative of the NEPTUNE Canada network under simulated data traffic conditions, achieving a precision of plusmn10 microseconds or better. Ongoing development of IEEE 1588 will allow precision to within 100s of nanoseconds in future observatories. Science instruments which can take advantage of PTP timing delivery are currently under development.
The Tomato Terpene Synthase Gene Family (2011)

Compounds of the terpenoid class play numerous roles in the interactions of plants with their environment, such as attracting pollinators and defending the plant against pests. We show here that the genome of cultivated tomato (Solanum lycopersicum) contains 44 terpene synthase (TPS) genes, including 29 that are functional or potentially functional. Of these 29 TPS genes, 26 were expressed in at least some organs or tissues of the plant. The enzymatic functions of eight of the TPS proteins were previously reported, and here we report the specific in vitro catalytic activity of 10 additional tomato terpene synthases. Many of the tomato TPS genes are found in clusters, notably on chromosomes 1, 2, 6, 8, and 10. All TPS family clades previously identified in angiosperms are also present in tomato. The largest clade of functional TPS genes found in tomato, with 12 members, is the TPS-a clade, and it appears to encode only sesquiterpene synthases, one of which is localized to the mitochondria, while the rest are likely cytosolic. A few additional sesquiterpene synthases are encoded by TPS-b clade genes. Some of the tomato sesquiterpene synthases use z,z-farnesyl diphosphate in vitro as well, or more efficiently than, the e,e-farnesyl diphosphate substrate. Genes encoding monoterpene synthases are also prevalent, and they fall into three clades: TPS-b, TPS-g, and TPS-e/f. With the exception of two enzymes involved in the synthesis of ent-kaurene, the precursor of gibberellins, no other tomato TPS genes could be demonstrated to encode diterpene synthases so far.
Design-Flow and Synthesis for ASICs: A Case Study (1995)

The growing complexity of devices to be designed and manufactured, and the need to reduce the time-to-market, stress the importance of sound design methodologies. In this framework formal synthesis has the advantage of increasing the quality both of the design process and of the realized devices. The problem of relating the different abstraction levels involved in the extended design process is solved through the use of logic synthesis tools. The evaluation of the design constraints, characterizing optimal implementations such as area and timing, provide the most pragmatic approach to identify efficient guidelines applicable in the abstract phases of the design flow. The resulting design methodology combining both formal and more traditional design tools has been tested on a complex device in the area of telecommunications.
Vaccination against Shigellosis with Attenuated Shigella flexneri 2a Strain SC602 (1999)

The Shigella flexneri 2a SC602 vaccine candidate carries deletions of the plasmid-borne virulence gene icsA (mediating intra- and intercellular spread) and the chromosomal locus iuc (encoding aerobactin) (S. Barzu, A. Fontaine, P. J. Sansonetti, and A. Phalipon, Infect. Immun. 64:1190-1196, 1996). Dose selection studies showed that SC602 causes shigellosis in a majority of volunteers when 3 x 10(8) or 2 x 10(6) CFU are ingested. In contrast, a dose of 10(4) CFU was associated with transient fever or mild diarrhea in 2 of 15 volunteers. All volunteers receiving single doses of >/=10(4) CFU excreted S. flexneri 2a, and this colonization induced significant antibody-secreting cell and enzyme-linked immunosorbent assay responses against S. flexneri 2a lipopolysaccharide in two-thirds of the vaccinees. Seven volunteers who had been vaccinated 8 weeks earlier with a single dose of 10(4) CFU and 7 control subjects were challenged with 2 x 10(3) CFU of virulent S. flexneri 2a organisms. Six of the control volunteers developed shigellosis with fever and severe diarrhea or dysentery, while none of the vaccinees had fever, dysentery, or severe symptoms (P = 0. 005). Three vaccinees experienced mild diarrhea, and these subjects had lower antibody titers than did the fully protected volunteers. Although the apparent window of safety is narrow, SC602 is the first example of an attenuated S. flexneri 2a candidate vaccine that provides protection against shigellosis in a stringent, human challenge model.
Humanization of the murine anti-human CD3 monoclonal antibody OKT3 (1994)

OKT3 is a murine monoclonal antibody which recognizes an epitope on the epsilon-subunit within the human CD3 complex. OKT3 possesses potent immunosuppressive properties in vivo and has been proven effective in the treatment of renal, heart and liver allograft rejection. Despite its efficacy, significant problems remain associated with OKT3 therapy, i.e. T-cell activation and the anti-murine antibody response. To address the problem of the anti-murine antibody response we have constructed humanized versions of OKT3. One of the humanized derivatives, gOKT3-7 incorporating the OKT3 complementarity determining regions plus a small number of alterations to the human framework, has an affinity of 1.4 x 10(9) M-1 compared with 1.2 x 10(9) M-1 for the murine OKT3. A humanized antibody (gOKT3-1) incorporating only the CDRs from OKT3 was found to be functionally inactive, confirming the requirement for nonCDR substitutions. gOKT3-7 retains the ability of mOKT3 to induce T cell proliferation in vitro and appears to be a good candidate for further development for in vivo therapy.
Localization and analysis of bovine papillomavirus type 1 transforming functions (1984)

Bovine papillomavirus type 1 (BPV-1) or cloned BPV-1 DNA can transform susceptible rodent cells, and the viral DNA remains as a stable extrachromosomal plasmid in the transformed cells. The transforming region of the BPV-1 genome has previously been localized to a specific fragment comprising 69% of the genome, which also contains the elements sufficient for extrachromosomal plasmid maintenance. To define more precisely the viral DNA sequences which are involved in cellular transformation, we have tested the ability of defined deletion mutants of BPV-1 DNA to morphologically transform mouse C127 cells. Cells containing the mutated DNAs have been examined for anchorage independence and tumorigenicity in nude mice. Several distinct regions of the BPV-1 genome were found to influence expression of the viral transformation functions. A transcriptional regulatory region located in the noncoding region 5' to the early open reading frames is essential for transcriptional activity and transformation. A transcriptional enhancer element, located 3' to the polyadenylation site for the viral RNAs expressed in transformed cells, has previously been shown to be essential for transformation (Lusky et al., Mol. Cell. Biol., 3:1108-1122, 1983). Deletion mutants affecting the E2 open reading frame, particularly the NH2 half, are significantly impaired in their ability to transform, suggesting that the E2 gene product is an important transforming protein of BPV-1. Mutants lacking the E6 and E7 open reading frames are still able to induce transformation but at a lowered efficiency, and the transformants have altered characteristics. Mutations localized within the E1 open reading frame do not significantly affect the transforming functions but result in the integration of the viral genome in the transformed cells, implicating the E1 gene product in stable plasmid replication and maintenance.
Immobilization of Peroxidase on SiO2 Surfaces with the Help of a Dendronized Polymer and the Avidin‐Biotin System (2011)

Horseradish peroxidase (HRP) is immobilized in three easy steps on SiO(2) surfaces with the help of a polycationic second generation dendronized polymer (denpol) and the biotin-avidin system. This stepwise immobilization process is monitored and quantitatively analyzed with the transmission interferometric adsorption sensor. Partially biotinylated denpol is first adsorbed onto SiO(2) , followed by addition of avidin and then of biotinylated HRP. Denpols in their molecular structure combine properties of polymers as well as dendrimers which are found to be of clear advantage for this type of non-covalent enzyme immobilization. With respect to the reproducibility of the adsorption process and with respect to the stability of the adsorbed polymer layer, the denpol is superior to α-poly-D-lysine which is used as a reference polymer. Furthermore, HRP immobilized with the denpol on commercial glass slides remains considerably more active upon storage as compared to HRP immobilized with the help of α-poly-D-lysine with a similar number of repeating units. The ease of the denpol-mediated HRP immobilization and the high stability of the immobilized enzyme are promising for bioanalytical applications.
Activated monocytes in peritumoral stroma of hepatocellular carcinoma foster immune privilege and disease progression through PD-L1 (2009)

Macrophages (Mphi) are prominent components of solid tumors and exhibit distinct phenotypes in different microenvironments. We have recently found that tumors can alter the normal developmental process of Mphi to trigger transient activation of monocytes in peritumoral stroma. We showed that a fraction of monocytes/Mphi in peritumoral stroma, but not in cancer nests, expresses surface PD-L1 (also termed B7-H1) molecules in tumors from patients with hepatocellular carcinoma (HCC). Monocytes activated by tumors strongly express PD-L1 proteins with kinetics similar to their activation status, and significant correlations were found between the levels of PD-L1(+) and HLA-DR(high) on tumor-infiltrating monocytes. Autocrine tumor necrosis factor alpha and interleukin 10 released from activated monocytes stimulated monocyte expression of PD-L1. The PD-L1(+) monocytes effectively suppressed tumor-specific T cell immunity and contributed to the growth of human tumors in vivo; the effect could be reversed by blocking PD-L1 on those monocytes. Moreover, we found that PD-L1 expression on tumor-infiltrating monocytes increased with disease progression, and the intensity of the protein was associated with high mortality and reduced survival in the HCC patients. Thus, expression of PD-L1 on activated monocytes/Mphi may represent a novel mechanism that links the proinflammatory response to immune tolerance in the tumor milieu.
Inversion of neurovascular coupling by subarachnoid blood depends on large-conductance Ca 2+ -activated K + (BK) channels (2012)

The cellular events that cause ischemic neurological damage following aneurysmal subarachnoid hemorrhage (SAH) have remained elusive. We report that subarachnoid blood profoundly impacts communication within the neurovascular unit-neurons, astrocytes, and arterioles-causing inversion of neurovascular coupling. Elevation of astrocytic endfoot Ca(2+) to ∼400 nM by neuronal stimulation or to ∼300 nM by Ca(2+) uncaging dilated parenchymal arterioles in control brain slices but caused vasoconstriction in post-SAH brain slices. Inhibition of K(+) efflux via astrocytic endfoot large-conductance Ca(2+)-activated K(+) (BK) channels prevented both neurally evoked vasodilation (control) and vasoconstriction (SAH). Consistent with the dual vasodilator/vasoconstrictor action of extracellular K(+) ([K(+)](o)), [K(+)](o) <10 mM dilated and [K(+)](o) >20 mM constricted isolated brain cortex parenchymal arterioles with or without SAH. Notably, elevation of external K(+) to 10 mM caused vasodilation in brain slices from control animals but caused a modest constriction in brain slices from SAH model rats; this latter effect was reversed by BK channel inhibition, which restored K(+)-induced dilations. Importantly, the amplitude of spontaneous astrocytic Ca(2+) oscillations was increased after SAH, with peak Ca(2+) reaching ∼490 nM. Our data support a model in which SAH increases the amplitude of spontaneous astrocytic Ca(2+) oscillations sufficiently to activate endfoot BK channels and elevate [K(+)](o) in the restricted perivascular space. Abnormally elevated basal [K(+)](o) combined with further K(+) efflux stimulated by neuronal activity elevates [K(+)](o) above the dilation/constriction threshold, switching the polarity of arteriolar responses to vasoconstriction. Inversion of neurovascular coupling may contribute to the decreased cerebral blood flow and development of neurological deficits that commonly follow SAH.