gebhart/patrepeval huggingface dataset:
Autocorrelation measurement of femtosecond laser pulses based on two-photon absorption in GaP photodiode (2014)

Semiconductor materials which exhibit two-photon absorption characteristic within a spectral region of interest can be useful in building an ultra-compact interferometric autocorrelator. In this paper, we report on the evidence of a nonlinear absorption process in GaP photodiodes which was exploited to measure the temporal profile of femtosecond Ti:sapphire laser pulses with a tunable peak wavelength above 680 nm. The two-photon mediated conductivity measurements were performed at an average laser power of less than a few tenths of milliwatts. Its suitability as a single detector in a broadband autocorrelator setup was assessed by investigating the nonlinear spectral sensitivity bandwidth of a GaP photodiode. The highly favourable nonlinear response was found to cover the entire tuning range of our Ti:sapphire laser and can potentially be extended to wavelengths below 680 nm. We also demonstrated the flexibility of GaP in determining the optimum compensation value of the group delay dispersion required to restore the positively chirped pulses inherent in our experimental optical system to the shortest pulse width possible. With the rise in the popularity of nonlinear microscopy, the broad two-photon response of GaP and the simplicity of this technique can provide an alternative way of measuring the excitation laser pulse duration at the focal point of any microscopy systems.
Cloning and expression of functional fragment C of tetanus toxin (1990)

A segment of Clostridium tetani DNA corresponding to fragment C of tetanus toxin was amplified by using the polymerase chain reaction. This fragment was cloned into expression vector pTTQ8, under the control of the tac promoter. Expression of this plasmid in Escherichia coli resulted in the production of a protein consisting of 8 amino acids of the vector fused to the C-terminal 460 amino acids of tetanus toxin. This protein (rFragment C) was recognized by an antipeptide antibody specific for fragment C in an enzyme-linked immunosorbent assay and on immunoblots. rFragment C could be purified significantly in one step by immunoaffinity chromatography. Immunization of mice with rFragment C resulted in the production of antibodies that were able to protect the mice against a challenge with tetanus toxin. rFragment C bound to ganglioside GT1b and to neuronal cells in a manner indistinguishable from that of fragment C obtained by papain cleavage of tetanus toxin. For many applications, rFragment C appears to be a suitable alternative to tetanus toxin or toxin-derived fragment C.
Culture methods and detection of glucanases in suspension cultures of wheat and barley (1968)

Suspension cultures of Triticum monococcum L., Triticum vulgare Vill. var. Thatcher, Hordeum vulgare L. var. Gateway, and Hordeum vulgare L. var. Gateway mutant yv 2 have been established. The cultures were derived from root sections of seedlings and cultured in a denned medium consisting of mineral salts, sucrose, B vitamins, and 2,4-dichlorophenoxyacetic acid, with nitrate and ammonia as the sources of nitrogen. In the early period of the cultures the cell aggregates readily, differentiated to form roots, but this characteristic diminished after several generations of subculture. The cells and medium contained a number of glucanases. The presence of a laminaranase (endo-β-(1 → 3)-D-glucan glucanohydrolase (EC 3.2.1.99)) that did not attack lichenan was established. The culture media of the wheat contained an oligosaccharide which on acid hydrolysis yielded galactose, arabinose, and xylose. Hydrolysis of a cell-wall fraction yielded the same sugars in addition to glucose and mannose.
Chronic Lymphocytic Leukemia B Cells Can Undergo Somatic Hypermutation and Intraclonal Immunoglobulin VHDJH Gene Diversification (2002)

Chronic lymphocytic leukemia (CLL) arises from the clonal expansion of a CD5(+) B lymphocyte that is thought not to undergo intraclonal diversification. Using V(H)DJ(H) cDNA single strand conformation polymorphism analyses, we detected intraclonal mobility variants in 11 of 18 CLL cases. cDNA sequence analyses indicated that these variants represented unique point-mutations (1-35/patient). In nine cases, these mutations were unique to individual submembers of the CLL clone, although in two cases they occurred in a large percentage of the clonal submembers and genealogical trees could be identified. The diversification process responsible for these changes led to single nucleotide changes that favored transitions over transversions, but did not target A nucleotides and did not have the replacement/silent nucleotide change characteristics of antigen-selected B cells. Intraclonal diversification did not correlate with the original mutational load of an individual CLL case in that diversification was as frequent in CLL cells with little or no somatic mutations as in those with considerable mutations. Finally, CLL B cells that did not exhibit intraclonal diversification in vivo could be induced to mutate their V(H)DJ(H) genes in vitro after stimulation. These data indicate that a somatic mutation mechanism remains functional in CLL cells and could play a role in the evolution of the clone.
CHIR-258, a novel, multitargeted tyrosine kinase inhibitor for the potential treatment of t(4;14) multiple myeloma (2004)

The t(4;14) translocation that occurs uniquely in a subset (15%) of patients with multiple myeloma (MM) results in the ectopic expression of the receptor tyrosine kinase (RTK), fibroblast growth factor receptor 3 (FGFR3). Inhibition of activated FGFR3 in MM cells induces apoptosis, validating FGFR3 as a therapeutic target in t(4;14) MM and encouraging the clinical development of FGFR3 inhibitors for the treatment of these patients, who have a poor prognosis. We describe here the characterization of a novel, small-molecule inhibitor of class III, IV, and V RTKs, CHIR-258, as an inhibitor of FGFR3. CHIR-258 potently inhibits FGFR3 with an inhibitory concentration of 50% (IC50) of 5 nM in in vitro kinase assays and selectively inhibited the growth of B9 cells and human myeloma cell lines expressing wild-type (WT) or activated mutant FGFR3. In responsive cell lines, CHIR-258 induced cytostatic and cytotoxic effects. Importantly, addition of interleukin 6 (IL-6) or insulin growth factor 1 (IGF-1) or coculture on stroma did not confer resistance to CHIR-258. In primary myeloma cells from t(4;14) patients, CHIR-258 inhibited downstream extracellular signal-regulated kinase (ERK) 1/2 phosphorylation with an associated cytotoxic response. Finally, therapeutic efficacy of CHIR-258 was demonstrated in a xenograft mouse model of FGFR3 MM. These studies support the clinical evaluation of CHIR-258 in MM.
Biochemistry and Immunology of Infectious Bursal Disease Virus (1988)

Introduction. The aetiological agent of infectious bursal disease (IBD), IBD virus (IBDV), belongs to a new group of viruses referred to as 'birnaviruses' (Dobos et al., 1979), which has been characterized only recently (Brown, 1986). There are excellent reviews dealing with the clinical, pathological, serological and epidemiological aspects of IBDV infection (Faragher, 1972; Becht, 1980; Okoye, 1984; Cummings et al., 1986). The molecular biology of birnaviruses has also been reviewed (Dobos & Roberts, 1983) but with an emphasis on infectious pancreatic necrosis virus (IPNV), the birnavirus genus prototype. The purpose of the present review is to compile information on structural and immunological aspects of IBDV. These are subjects of much recent interest, and have great relevance to the control of IBD in chickens. IBD is a highly contagious viral disease of young chickens which is characterized by destruction of the lymphoid cells in the bursa of Fabricius; other lymphoid organs are also affected but to a lesser degree (Cheville, 1967).
Escherichia coli DNA polymerase II is stimulated by DNA polymerase III holoenzyme auxiliary subunits (1991)

DNA polymerase III of Escherichia coli requires multiple auxiliary factors to enable it to serve as a replicative complex. We demonstrate that auxiliary components of the DNA polymerase III holoenzyme, the gamma delta complex and beta subunit, markedly stimulate DNA polymerase II on long single-stranded templates. DNA polymerase II activity is enhanced by single-stranded DNA binding protein, but the stimulation by gamma delta and beta can be observed either in the absence or presence of single-stranded DNA binding protein. In contrast with DNA polymerase III, the requirement of DNA polymerase II for gamma delta cannot be bypassed by large excesses of the beta subunit at low ionic strength in the absence of the single-stranded DNA binding protein. The product of the DNA polymerase II-gamma delta-beta reaction on a uniquely primed single-stranded circle is of full template length; the reconstituted enzyme apparently is incapable of strand displacement synthesis. The possible biological implications of these observations are discussed.
2‘-O-[2-(Amino)-2-oxoethyl] Oligonucleotides (2003)

Oligonucleotides with novel modifications, 2‘-O-[2-(amino)-2-oxoethyl] (2‘-O-NAc), 2‘-O-[2-(methylamino)-2-oxoethyl] (2‘-O-NMAc), 2‘-O-[2-(dimethylamino)-2-oxoethyl] (2‘-O-DMAc), and 2‘-O-[2-[[2-(dimethylamino)ethyl]amino]-2-oxoethyl] (2‘-O-DMAEAc), have been synthesized. These modified oligonucleotides exhibit high binding affinity to complementary RNA (and not to DNA) and considerably enhance the nuclease stability of oligonucleotides with t1/2 > 24 h.
Coding for tag collision recovery (2015)

It has been recently observed that some information can be extracted from the received signal by the reader when the tag collision happens. Using the radio cross section (RCS) technique one can determine how many tags are backscattering simultaneously. Motivated by this technique we introduce the new notion of singulation code. In a singulation code, any two collection of codewords, of size up to some number s, have distinct vector-sums. We propose a new protocol for tag singulation problem using the singulation codes. Upper and lower bounds on the size of singulation codes are provided. It is shown that there exists families of singulation codes that guarantee any positive throughput, asymptotically, using the singulation coding protocol. Two explicit constructions of singulation codes, with low complexity encoding and decoding algorithms, are proposed. It is shown that these constructions are feasible to be implemented in RFID tags. The singulation protocol with these explicit constructions is compared with the randomized ALOHA based algorithm. It is shown that the time required for the tag identification with the proposed protocol is reduced by a factor of log s comparing to the randomized ALOHA based algorithm, where s is the number of tags to be identified. Other advantages of the proposed protocol are also discussed.
In vitro cell proliferation evaluation of porous nano-zirconia scaffolds with different porosity for bone tissue engineering (2015)

The selection of scaffold materials and the optimization of scaffold morphological and mechanical properties are critical for successful bone tissue engineering. We fabricated porous scaffolds of nano-sized zirconia using a replication technique. The study aimed to explore the relationship between porosity, pore size, mechanical strength, cell adhesion, and cell proliferation in the zirconia scaffolds. Macro- and micro-structures and compressive strength were comparatively tested. Beagle bone marrow stromal cells were seeded onto the scaffolds to evaluate cell seeding efficiency and cell proliferation profile over 14 d of incubation. The zirconia scaffolds presented a complex porous structure with good interconnectivity of pores. By increasing the sinter cycles, the porosity and pore size of the scaffolds decreased, with mean values ranging from 92.7-68.0% and 830-577 μm, respectively, accompanied by increased compressive strengths of 0.6-4.4 MPa. Cell seeding efficiency and cell proliferation over the first 7 d of incubation increased when the porosity decreased, with cell viability highest in the scaffold with a porosity of 75.2%. After 7 d of incubation, the cell proliferation increased when the porosity increased, highest in the scaffolds with a porosity of 92.7%. These results showed that the zirconia scaffold with a porosity of 75.2% possesses favorable mechanical and biological properties for future applications in bone tissue engineering.
Superior Lithium Electroactive Mesoporous Si@Carbon Core−Shell Nanowires for Lithium Battery Anode Material (2008)

Mesoporous Si@carbon core-shell nanowires with a diameter of approximately 6.5 nm were prepared for a lithium battery anode material using a SBA-15 template. As-synthesized nanowires demonstrated excellent first charge capacity of 3163 mA h/g with a Coulombic efficiency of 86% at a rate of 0.2 C (600 mA/g) between 1.5 and 0 V in coin-type half-cells. Moreover, the capacity retention after 80 cycles was 87% and the rate capability at 2 C (6000 mA/g) was 78% the capacity at 0.2 C.
Hypomethylation of DNA: a possible epigenetic mechanism involved in tumor promotion. (1995)

The overall objective of our research is to discern mechanisms that can facilitate the aberrant expression of oncogenes involved in carcinogenesis. We are testing the hypothesis that hypomethylation of DNA is a nongenotoxic mechanism underlying the aberrant expression of oncogenes involved in carcinogenesis. Hypomethylation may be a mechanism underlying the role of cell proliferation in carcinogenesis, and hypomethylation could possibly result from an enzymatic replacement of 5-methylcytosine (5MeC) with cytosine that is not linked to DNA replication. The testing of this hypothesis can serve as a focal point for a mechanism of action-oriented approach for considering key aspects of carcinogenesis: aberrant gene expression, heritable epigenetic events, species-to-species extrapolation/unique species sensitivity, tumor promotion, and thresholds. DNA methylation plays a role in the regulation of gene activity. There is a persuasive body of evidence indicating that differential methylation of DNA (i.e., 5-methylcytosine v. cytosine) is a determinant of chromatin structure and that the methyl group provides a chemical signal which is recognized by trans-acting factors that regulate transcription. Hypomethylation of a gene is necessary but not sufficient for its expression and, therefore, a hypomethylated gene can be considered to possess an increased potential for expression as compared to a hypermethylated gene. Changes in the methylation status of a gene provide a mechanism by which its potential for expression can be altered in an epigenetic heritable manner, and it is expected that modifications in DNA methylation would result from threshold-exhibiting events. Our experimental model is liver tumorigenesis, we focus upon oncogenes (e.g., Ha-ras and raf) relevant to mouse liver tumorigenesis, employ the liver tumor prone B6C3F1 (C57BL/6 x C3H/He) mouse, and make relevant comparisons with the sensitive C3H/He paternal strain and the resistant C57BL/6 maternal strain. A unique aspect of this research is that it offers the potential to provide insight regarding molecular mechanisms that underlie promotion of carcinogenesis while at the same time the results can provide the type of information that is required in order to take a more rational approach towards carcinogen risk assessment. Specifically, the practical significance of our research is that it addresses the areas of dose-response relationships, e.g., the existence of threshold-exhibiting mechanisms, and species-to-species extrapolation issues. This is discussed within the context of the requirement for a rational approach to risk assessment.
Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy (2011)

The bacterial RsgA, a circularly permutated GTPase, whose GTPase activity is dependent on the 30S ribosomal subunit, is a late-stage ribosome biogenesis factor involved in the 30S subunit maturation. The role of RsgA is to release another 30S biogenesis factor, RbfA, from the mature 30S subunit in a GTP-dependent manner. Using cryoelectron microscopy, we have determined the structure of the 30S subunit bound with RsgA in the presence of GMPPNP at subnanometer resolution. In the structure, RsgA binds to the central part of the 30S subunit, close to the decoding center, in a position that is incompatible with multiple biogenesis factors, all three translation initiation factors, as well as A-, P-site tRNAs and the 50S subunit. Further structural analysis not only provides a structural model for the RsgA-dependent release of RbfA from the nascent 30S subunit, but also indicates RsgA's role in the ribosomal protein assembly, to promote some tertiary binding protein incorporation. Moreover, together with available biochemical and genetic data, our results suggest that RsgA might be a general checkpoint protein in the late stage of the 30S subunit biogenesis, whose function is not only to release biogenesis factors (e.g., RbfA) from the nascent 30S subunit, but also to block the association of initiation factors to the premature 30S subunit.
Total lung irradiation and chemotherapy in pulmonary metastases from carcinoma of the uterine cervix and endometrium. (1979)

Despite the radiocurability of stage I and II squamous cell carcinoma (SCC) of the cervix, palliation of patients with pulmonary metastases has been disappointing. Four patients with pulmonary metastases (three from cervical and one from endometrial carcinoma) were treated with total lung irradiation, followed two to three weeks after termination of radiotherapy with combination chemotherapy consisting of vincristine 1.4 mg/m(2) IV+ adriamycin 50 mg/m(2) IV + cyclophosphamide 500 mg/m(2) IV repeated at four-week intervals. Radiotherapy was delivered through a Co(60) teletherapy unit in a daily dosage of 100 rads in anterior and posterior opposing fields. After completion of irradiation in one lung, the other lung was similarly treated if involved with gross disease. Two out of four patients (both with cervix SCC) obtained complete tumor regression, whereas the other two patients had stabilization of their pulmonary lesions. The survival of the two responders was 216+ and 621 days from the start of irradiation. The two nonresponders survived 56 and 109 days. Except for one patient who died of pulmonary metastases, the remaining three patients died of metastases elsewhere. While only one patient developed radiation pneumonitis, all four had alopecia and leukopenia <4000/mm(3) from chemotherapy. Total lung irradiation and combination chemotherapy appear to have activity in the treatment of pulmonary metastases from SCC of the cervix and warrant further exploration.
Effects of chicken anaemia virus and infectious bursal disease virus-induced immunodeficiency on infectious bronchitis virus replication and genotypic drift (2012)

We followed changes in a portion of the S1 gene sequence of the dominant populations of an infectious bronchitis virus (IBV) Arkansas (Ark) vaccine strain during serial passage in chickens infected with the immunosuppressive chicken anaemia virus (CAV) and/or infectious bursal disease virus (IBDV) as well as in immunocompetent chickens. The IBV-Ark vaccine was applied ocularly and tears were collected from infected chickens for subsequent ocular inoculation in later passages. The experiment was performed twice. In both experiments the dominant S1 genotype of the vaccine strain was rapidly and negatively selected in all chicken groups (CAV, IBDV, CAV+IBDV and immunocompetent). Based on the S1 genotype, the same IBV subpopulations previously reported in immunocompetent chickens and named component (C) 1 to C5 emerged both in immunocompetent and immunodeficient chickens. During the first passage different subpopulations emerged, followed by the establishment of one or two predominant populations after further passages. Only when the subpopulation designated C2 became established in either CAV-infected or IBDV-infected chickens was IBV maintained for more than four passages. These results indicate that selection does not cease in immunodeficient chickens and that phenotype C2 may show a distinct adaptation to this environment. Subpopulations C1 or C4 initially became established in immunocompetent birds but became extinct after only a few succeeding passages. A similar result was observed in chickens co-infected with CAV+IBDV. These results suggest that the generation of genetic diversity in IBV is constrained. This finding constitutes further evidence for phenotypic drift occurring mainly as a result of selection.
OXYGEN-SORPTIVE PROPERTIES AND DEFECT STRUCTURE OF PEROVSKITE-TYPE OXIDES (1984)

Abstract The nature of two types of oxygen desorption, α and β, from perovskite-type oxides was studied by TPD and TG experiments. The results show that α oxygen is accomodated in the oxygen vacancies formed by the partial substitution of A site cations, while the desorption of β oxygen corresponds to the reduction of B site cations to lower valencies.
Adiponectin protects against myocardial ischaemia-reperfusion injury via AMP-activated protein kinase, Akt, and nitric oxide (2008)

Adiponectin protects from myocardial contractile dysfunction and limits infarct size following ischaemia and reperfusion by a mechanism involving activation of AMPK and production of NO.
Brain‐derived neurotrophic factor enhances glucose utilization in peripheral tissues of diabetic mice (2006)

These data indicate that BDNF ameliorates glucose metabolism by enhancement of glucose utilization in muscle and BAT, with this effect caused by modulation of the central and peripheral nervous systems.
Development of glycine- and GABA-gated currents in rat spinal motoneurons (1995)

1. Developmental changes in glycine- and gamma-aminobutyric acid (GABA)-activated currents were studied in spinal motoneurons of embryonic and neonatal rats with the use of whole cell recording techniques. 2. Pressure ejection of glycine or GABA onto motoneuron somata produced Cl(-)-mediated inward currents and membrane depolarizations. During embryonic development, the average amplitude of GABA-gated currents was threefold larger than that of glycine-gated currents, but as a result of a large eightfold postnatal increase in glycine-activated currents, similar currents were produced by both amino acids after birth. 3. At all ages the decay of glycine- and GABA-gated currents best fit one-exponential curve, and their time constants were similar. The average decay time constant decreased by twofold after birth. 4. The ionic specificity of glycine- and GABA-gated channels was studied to determine whether the large amplitude of GABA-activated currents in embryonic motoneurons resulted from the contribution of an outward HCO-3 movement. Manipulations of Cl- and HCO-3 concentrations produced changes in the reversal potentials of glycine and GABA that were similar to the calculated changes in the equilibrium potentials of Cl-. This suggested that glycine- and GABA-gated currents were Cl- specific, and HCO-3 movement did not contribute more to the current generated by GABA than that produced by glycine. 5. Glycine- and GABA-gated currents were associated with severalfold increases in membrane conductance. The conductance increase generated by GABA in embryonic motoneurons was sevenfold larger than that generated by glycine, but similar conductance changes were produced by both amino acids after birth.(ABSTRACT TRUNCATED AT 250 WORDS)