gebhart/patrepeval huggingface dataset:
Identification of a DNA binding domain in simian virus 40 capsid proteins Vp2 and Vp3. (1993)

We have identified both biochemically and genetically a protein domain within the simian virus 40 virion protein Vp3, and within Vp2 since its carboxyl two-thirds are identical to the full-length Vp3, that binds DNA in a sequence nonspecific manner. Both the Vp2 and Vp3 (Vp2/3) components of SV40 and mutant SV40(202T) bound either SV40 or pBR322 DNA equally well. Wild type and mutant Vp2/3 proteins, expressed as fusion proteins with glutathione S-transferase (GST), were tested for their ability to bind DNA. GST-Vp3 bound DNA at physiological salt concentrations with an apparent Kd of 2.5 x 10(-8) M and also bound RNA with 4-fold higher affinity. Over 90% of the nucleic acid binding, and all of the activity, was lost upon removal of the carboxyl-terminal 13 and 35 residues, respectively. The DNA binding domain was shown to be distinct and separable from the Vp2/3 nuclear transport signal since mutations within the nuclear transport signal that reduce or abolish nuclear localization of Vp2/3 had no effect on the DNA binding activity of mutant Vp2/3 fusion proteins. The carboxyl-terminal 40 residues of Vp2/3 in the form of a beta-galactosidase fusion protein, F6, are sufficient for DNA binding and may cause compaction of the DNA. The significance of this DNA binding and possible compaction are discussed in relation to the assembly of virion particles.
Incorporation of Trifluoroisoleucine into Proteins in Vivo (2003)

Two fluorinated derivatives of isoleucine: d,l-2-amino-3-trifluoromethyl pentanoic acid (3TFI, 2) and d,l-2-amino-5,5,5-trifluoro-3-methyl pentanoic acid (5TFI, 3) were prepared. 5TFI was incorporated into a model target protein, murine dihydrofolate reductase (mDHFR), in an isoleucine auxotrophic Escherichia coli host strain suspended in 5TFI-supplemented minimal medium depleted of isoleucine. Incorporation of 5TFI was confirmed by tryptic peptide analysis and matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) of the protein product. Amino acid analysis showed that more than 93% of the encoded isoleucine residues were replaced by 5TFI. Measurement of the rate of activation of 5TFI by the E. coli isoleucyl-tRNA synthetase (IleRS) yielded a specificity constant (k(cat)/K(m)) 134-fold lower than that for isoleucine. 5TFI was successfully introduced into the cytokine murine interleukin-2 (mIL-2) at the encoded isoleucine positions. The concentration of fluorinated protein that elicits 50% of the maximal proliferative response is 3.87 ng/mL, about 30% higher than that of wild-type mIL-2 (EC(50) = 2.70 ng/mL). The maximal responses are equivalent for the fluorinated and wild-type cytokines, indicating that fluorinated proteins can fold into stable and functional structures. 3TFI yielded no evidence for in vivo incorporation into recombinant proteins, and no evidence for activation by IleRS in vitro.
Monoclonal-antibody studies of creatine kinase. The proteinase K-cleavage site (1985)

Proteinase K cleaves a small peptide from native muscle-specific creatine kinase. We present evidence, from the binding of two monoclonal antibodies to formic acid-cleavage fragments and proteinase K-digest fragments of chick muscle creatine kinase, that the proteinase K-cleavage site is in the C-terminal region of the molecule. This specificity of proteinase K, which is not normally a highly specific enzyme, and the continued association of the two peptide fragments after cleavage suggest an unusual conformational feature in the cleavage-site region. By applying predictive methods for hydrophobicity and secondary structure to an amino acid sequence in this region, we suggest possible structural features at the cleavage site that are evidently conserved across avian and mammalian species. The most likely site is next to, or within, a beta-turn on the surface of the molecule.
Nucleosidsynthesen, XVIII. Aminierung von Heterocyclen, II. Einfache neue Synthese von N<sup>6</sup>‐substituierten Adenosinen und Adeninen sowie ihrer 2‐Amino‐ und 2‐Hydroxyderivate (1976)

Abstract Reaktion von Inosin, Guanosin, Xanthosin sowie ihrer 5′‐Phosphate mit Hexamethyldisilazan und Ammoniak, primaren oder sekundaren Aminen in Gegenwart von Lewissäuren wie (NH 4 ) 2 SO 4 , (CH 3 ) 3 Si0SO 2 CF 3 , p ‐Toluolsulfonsäurehydrat und Hg(I1)‐salzen ergibt in hohen Ausbeuten die entsprechenden N 6 ‐substituierten Adenosine bzw. 2‐Amino‐ oder 2‐Hydroxyadenosine. Analog lassen sich Hypoxanthin und Guanosin in die entsprechenden N6‐substituierten Adenine bzw. 2‐Aminoadenine umwandeln.
Selective in vitro and in vivo activities of 5-(2-haloalkyl)pyrimidine nucleoside analogs, particularly 5-(2-chloroethyl)-2'-deoxyuridine, against herpes simplex virus (1985)

5-(2-Chloroethyl)-2'-deoxyuridine (CEDU), 5-(3-chloropropyl)-2'-deoxyuridine (CPDU), and 5-(2-chloroethyl)-2'-deoxycytidine (CEDC) were evaluated for activity against herpes simplex virus type 1 (HSV-1) and HSV-2 in vitro. Their MICs for HSV-1 in primary rabbit kidney cell cultures were 0.15, 0.20, and 0.60 micrograms/ml, respectively; their MICs for HSV-2 were about 10-fold higher. When tested in parallel, the reference compounds 5-ethyl-2'-deoxyuridine, 5-iodo-2'-deoxyuridine, acyclovir, and (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU) gave MICs of 0.20, 0.18, 0.04, and 0.015 micrograms/ml, respectively. The antiviral indexes of CEDU, CPDU, and CEDC, as determined by the ratio of the minimum toxic dose for the normal host cell to the minimum inhibitory dose for HSV-1, were about 2,000, 100, and greater than or equal to 400, respectively. The three 5-(2-haloalkyl)pyrimidine derivatives were further evaluated for their antiviral effects in vivo. In hairless mice, CEDU suppressed the development of cutaneous HSV-1 lesions, and associated mortality, when applied topically at a concentration as low as 0.1%. For the treatment of systemic HSV-1 infection in Naval Medical Research Institute mice, a single oral dose per day of 5 mg of CEDU per kg achieved a significant reduction in the mortality rate. Against HSV-1 encephalitis, CEDU exerted a significant protective effect at a dosage of 50 mg/kg per day when administered intraperitoneally. CEDU was effective against systemic HSV-1 infection and HSV-1 encephalitis in mice at a 5- to 15-fold-lower dose than either BVDU or acyclovir. When given orally, CPDU and CEDC were considerably less active than CEDU against systemic HSV-1 infection.
Estimates of Historical Tree Densities in the North Lachlan River Catchment, New South Wales, Australia (2005)

Abstract Vegetation structure and composition during the pre‐ and early‐European period in Australia is often proposed as a benchmark against which to measure the effects of modern landscape management practices. However, little quantifiable information exists for that historical period. One potential source of information is the land survey record, used in this study to provide estimates of tree densities that existed during the period 1870 to 1900 in part of central New South Wales. Estimates were obtained for 23 parishes in the north Lachlan River valley, between the towns of Condobolin and Tottenham. Densities were calculated from portion corner to nearest tree data obtained from historical survey plans, using the plotless, closest individual method. Densities ranged from 6.0 to 31.4 trees per hectare for parishes with enough data points for reliable calculation. These figures would account for trees of a diameter large enough to be blazed with a survey mark. Any smaller trees would be additional and, although no quantitative data existed for this, qualitative evidence suggested that the figures obtained were more likely to be underestimates due to the presence of such small trees. The study area was predominantly covered by woodlands which varied in density across the landscape, in comparison to the modern landscape where much of the native vegetation has been cleared for agriculture. Although the tree density figures should be considered to be indicative rather than precise, they provide quantifiable historical figures for past conditions in an area where the historical record is otherwise sparse. Such information is valuable for interpreting ecological changes brought about by modern land management.
The Church-Turing Thesis (2007)

There are various equivalent formulations of the Church-Turing thesis. A common one is that every effective computation can be carried out by a Turing machine. The Church-Turing thesis is often misunderstood, particularly in recent writing in the philosophy of mind.
Self-curing acrylic formulations with applications in intervertebral disk restoration: drug release and biological behaviour (2007)

New injectable acrylic formulations have been prepared to be applied in restoration processes for intervertebral disks (IVDs). The solid phase of the formulations is composed of poly(methyl methacrylate) (PMMA), incorporating in some cases chondroitin sulphate (CS) as a regenerative bioactive molecule, whereas the liquid phase is constituted by an amphiphilic macromonomer (MT), 2-hydroxyethyl methacrylate (HEMA) and, in some formulations, acrylic acid (AA). The curing parameters and the mechanical properties of the IVD formulations make them excellent candidates for intervertebral application. In vitro and in vivo evaluation of the prepared IVD formulations is described in terms of CS release, surface analysis after immersion in SBF solutions, and biocompatibility studies based on MTT assay and Alamar blue test, as well as in vivo implantation in female Wistar rats, by injection of the IVD formulations followed by histological evaluations to assess tissue response.
Cluster ion assisted thin film formation (1997)

A new thin films formation technique using gas-cluster ion beams is demonstrated. Oxygen cluster ion beams are utilized to grow oxide films. We have found that high quality SiO2 films of up to 11 nm thick can be formed on Si substrate surfaces at room temperature by direct oxidation using O2 and CO2 cluster ion beams at acceleration voltages of less than 10 keV. O2 cluster ions were also used to irradiate Si substrates covered with SiO2 films, during the evaporation of Pb atoms. Increasing the acceleration voltages, the O2 cluster ion bombardment enhanced the oxidation and surface smoothing. At the acceleration voltages above 5 kV, the polycrystalline lead oxide films were oriented with their (111) direction parallel to the surface. A significant smoothing effect was observed, even if the acceleration voltage was as low as 1 kV. An average surface roughness of 0.9 nm was obtained at 7 kV. These results indicate that O2 cluster ions strongly enhanced the oxidation and the smoothness without causing irradiation damage.
Dispersion Compensation Gratings (1997)

Broadband Chirped fibre gratings allow the upgrade of the existing non-dispersion shifted fibre network to high data rate operation within the 1.55μm low-loss window. The design, fabrication, performance and application of these devices is covered.
A New Architecture for fast Arithmetic Coding in H.264 Advanced Video Coder (2005)

In this work, a new architecture for binary arithmetic coding is presented in the context of the new AVC/H.264 standard for video coding. Among the new technologies included in AVC/H.264 a context adaptive binary arithmetic coder (CABAC) is used that outperforms the baseline entropy coder in a significant manner. In this work we justify the need for a new architecture that implements the unique characteristics of CABAC that are not found in other implementations of arithmetic coding. We show that a fast architecture is needed that combines short cycle time and application-aware scheduling in order to accomplish with the high computational demands. A number of optimizations are introduced that allow processing several symbols per cycle and reduce data binarization overhead. Implementation results are shown for a Virtex-II FPGA and the main conclusions are presented.
Color gamuts in dim illumination (2007)

Rods act as color receptors in dim illumination. Several recent studies have measured the range of colors at low-light levels in different illuminants. This paper reviews these results and adds new experiments using long-wave-rich illumination, appropriate for rod and long-wave cone interactions. The experiment illuminates Munsell ColorChecker papers with 546, and then with 455 nm narrowband lights at radiances below cone thresholds. The third illuminant is 625 nm light, above cone threshold. Observers make asymmetric matches of the ColorChecker using a digital computer display. The observers make these matches while viewing the entire ColorChecker. Observers report a wide range of colors from the combination of cone response to 625 nm plus rod response to 546 nm light. The same is true with the combination of cone response to 625 nm plus rod response to 455 nm light. Although the color matches vary with the ColorChecker's reflectances, the range of colors is the same. Since these experiments use illuminants more appropriate for rod-cone interactions, they measure a much greater color gamut than photopic illuminants. They also provide new data that clarifies how the rod information interacts with the cone-cone color channels. Color appearances indicate rods share M- and S-color channels.
Localized edge detection in sensor fields (2003)

A wireless sensor network that studies relatively widespread phenomena (such as a contaminant flow or a seismic disturbance) may be called upon to provide a description of the boundary of the phenomenon (either a contour or some bounding box). In such cases, it may be necessary for each node to locally determine whether it lies at (or near) the edge of the phenomenon. In this paper, we show that such localized edge detection techniques are non-trivial to design in an arbitrarily deployed sensor network. We define the notion of an edge and develop performance metrics for evaluating localized edge detection algorithms. We propose three different approaches for localized edge detection and present one example scheme for each. In all our approaches, each sensor gathers information from its local neighborhood and determines whether or not it is an edge sensor. We evaluate the performance! of each of the example schemes and compare them with respect to the developed metrics.
Extensive contribution of the multidrug transporters P-glycoprotein and Mrp1 to basal drug resistance. (2000)

Despite accumulating evidence that multidrug resistance transporter proteins play a part in drug resistance in some clinical cancers, it remains unclear whether the relatively low levels of multidrug resistance transporter expression found in most untreated tumors could substantially affect their basal sensitivity to antineoplastic drugs. To shed light on this problem, the drug sensitivities of wild-type mouse cell lines were compared with those of lines in which the Mdr1a and Mdr1b genes encoding P-glycoprotein (P-gp) were inactivated and lines in which the Mrp1 gene was inactivated in addition to Mdr1a and Mdr1b. These models permit a clean dissection of the contribution of each transporter to drug resistance at expression levels similar to those in normal tissues and avoid complications that might arise from previous exposure of cell lines to drug selection. For substrate drugs, we found that these contributions can indeed be very substantial. Lines lacking functional P-gp were, on average, markedly more sensitive to paclitaxel (16-fold), anthracyclines (4-fold) and Vinca alkaloids (3-fold). Lines lacking both P-gp and Mrp1 were (compared with wild-type lines) hypersensitive to an even broader array of drugs, including epipodophyllotoxins (4-7-fold), anthracyclines (6-7-fold), camptothecins (3-fold), arsenite (4-fold) and Vinca alkaloids, especially vincristine (28-fold). Thus, even very low levels of P-gp and Mrp1 expression that may be difficult to detect in tumors could significantly affect their innate sensitivity to a wide range of clinically important substrate drugs. An implication is that the use of resistance reversal agents to sensitize drug-naive tumors may be appropriate in more cases than is presently appreciated.
In Vitro Activities of Piperacillin against β-Lactamase-Negative Ampicillin-Resistant <i>Haemophilus influenzae</i> (2004)

The in vitro activities of piperacillin (PIP) against beta-lactamase-negative ampicillin (AMP)-resistant (BLNAR) Haemophilus influenzae were compared with those of cefotaxime (CTX) and ceftriaxone (CRO), and the potency of PIP as therapy for meningitis caused by BLNAR is also discussed. PIP showed good activity (MIC at which 90% of strains are inhibited, 0.25 micro g/ml) against 69 BLNAR strains, and its activity was comparable to that of CRO and superior to that of CTX. No significant correlation was observed between the MICs of PIP and CTX or CRO or AMP, whereas a high correlation was observed between the MICs of CTX and CRO. In the killing study, PIP showed potent bactericidal activity compared with those of CTX and CRO. By microscopic examination, PIP caused the formation of a spindle and short filamentous cells with bulges and induced cell lysis in BLNAR strains, while treatment with CTX and CRO resulted in the formation of large, spherical cells without any obvious lysis. The affinity of Bocillin FL, a fluorescent penicillin used for determination of the 50% inhibitory concentration (IC(50)s) for penicillin-binding proteins (PBPs), to PBPs 3a and 3b of BLNAR strains was drastically decreased compared with that to an AMP-susceptible strain (ATCC 33391). In the case of the BLNAR strains, the IC(50)s for PBPs 1a, 1b, and 2 were similar to those for the PBPs of ATCC 33391. Since the affinity of binding to PBPs 3a and 3b of the BLNAR strains decreased drastically, the second targets among the PBPs were PBP 2 for PIP, PBP1 (1a and 1b) for CTX and CRO. In conclusion, PIP showed excellent activities against BLNAR strains in a manner different from those of cephem antibiotics, suggesting that it could be a candidate therapeutic agent for the treatment of meningitis caused by BLNAR strains.
Mapping the antigenic epitopes of human dihydrofolate reductase by systematic synthesis of peptides on solid supports. (1990)

All of the 181 possible overlapping hexapeptides as well as 179 octapeptides covering the amino acid sequence of human dihydrofolate reductase (hDHFR) were synthesized on polyethylene supports. The synthetic procedure of Geysen et al. (Geysen, H. M., Rodda, S. J., Mason, T. J., Tribbick, G., and Schoofs, P. G. (1987) J. Immunol. Methods 102, 259-274) was modified to obtain up to 100 nmol of peptide on each pin. Peptides constituting antigenic epitopes on hDHFR were identified by examining the binding of antibodies raised against both native and denatured hDHFR to these peptides by enzyme-linked immunosorbent assay. The peptides bound in a similar pattern to polyclonal antibodies against both native and denatured dihydrofolate reductase (DHFR). Six major epitopes were located corresponding to residues 27-33, 45-51, 67-74, 133-139, 153-158, and 176-181 using both hexapeptides and octapeptides. An additional epitope, constituting residues 14-21, was found by the use of octapeptides. Most of the epitopes are hydrophilic and reside largely in "loop" regions at the boundaries of secondary structural elements of hDHFR. This observation is consistent with our previous results which suggested that ligand binding at the active site of the enzyme can cause a dramatic reduction in antibody binding to DHFR due to conformational constraints in flexible loop regions in various parts of the molecule. The similarity of the immunogenic profiles of native versus denatured hDHFR indicates that the two forms of the antigen share the same amino acid sequence-specific epitopes. Competitive enzyme-linked immunosorbent assay showed that the binding of anti-hDHFR antiserum to both native and denatured hDHFR was inhibited by approximately 30% by the seven antigenic peptides, indicating that a significant proportion of the antibodies elicited by this enzyme is specific for short peptides. Besides revealing the antigenic structure of DHFR our results provide a rational basis for the design of mutant DHFRs to study the importance of loop residues in the conformational dynamics of the enzyme.
Visible/Near‐Infrared Spectroscopy: A New Tool for the Evaluation of Fish Freshness? (2002)

ABSTRACT: The freshness as storage time in ice of cod ( Gadus morhua ) and salmon ( Salmo salar ) was estimated by visible/near infrared (VIS/NIR) spectroscopy. The correlation between spectral data and storage time was modeled by multivariate statistics. For cod, the best‐fit model was found by using the visible wavelength range, giving correlation of prediction of 0.97 with an error value of 1.04 d. For salmon, the best‐fit model was made with data from the NIR range giving correlation of prediction of 0.98 and an error value of 1.20 d. Hence, VIS/NIR spectroscopy proved useful for the evaluation of fish freshness.
Properties of Amorphous Si:F:H Film and Its Photovoltaic Characteristics (1981)

The optical and electrical properties of a-Si:F:H films deposited by an R.F. glow discharge in (SiF 4 +SiH 4 ) and the photovoltaic properties of a-Si solar cells using the a-Si:F:H film were investigated. The dark conductivity and the activation energy of phosphorous doped a-Si:F:H film were 8.22 (Ω cm) -1 and 0.014 eV, respectively. The Staebler and Wronski effect for a-Si:H and a-Si:F:H films was investigated. The change in the dark conductivity of the a-Si:F:H film was smaller than that in the a-Si:H film. The best conversion efficiency for a Glass/ITO/p(H)-i(F:H)-n + (H) cell and a Glass/ITO/p(H)-i(F:H)-n + (F:H) cell were 2.1% and 2.5%, respectively. The change in the conversion efficiency of the a-Si:F:H and a-Si: H cells which occurs with an increase in the intensity of the incident light was measured. A decrease in the conversion efficiency of the a-Si:F:H cell was scarcely recognized.
Elastase Activity of some Purified Proteinase Preparations as Related to their Depilatory Action (1965)

Relation between the elastolytic and depilatory activities was examined using various highly purified proteinase preparations. Elastolytic activity of the enzymes did not correlates well with their depilatory action. Among 11 proteinase preparations tested, Pseudomonas aeruginosa elastase showed the highest depilatory activity.
Electrocutaneous Pulse Rate and Pulse Width Psychometric Functions for Sensory Communications (1979)

Psychometric functions of pulse rate (PR) and pulse width (PW) from electrocutaneous stimuli were determined using the method of comparative judgments. The study revealed that changes in PR were more easily detected than changes in PW, as measured by the percent of just noticeable difference (jnd). The PR jnd data from test subjects indicated that maximum frequency discrimination occurred near 20 pulses per second. Using the PR and PW psychometric curves, compensatory transfer functions can be determined which will improve the efficacy of sensory communication systems based on electrocutaneous stimulation.
Investigation of the effect of large x-ray fluences on multilayer structures (1992)

The use of multilayer mirrors in x-ray laser cavities is complicated by extremely intense optical and x-ray pulses that damage the multilayer mirror before it has done its job. The issue of damage of the mirror by x-ray emission from the plasma amplifier has been studied experimentally using short duration (500 psec) bursts of soft x-rays from a laser produced Au plasma. Different damage/failure mechanisms have been observed and identified for Mo/Si, MoSi 2 /Si, W/C, WC/C and Cr 3 C 2 /C multilayers and damage thresholds quantified. The effect of the x-ray flux on the peak mirror reflectivity together with the position and shape of the bandpass has been resolved both temporally and spec­trally. The shape of the bandpass has been fitted to solutions to the Fresnel equations for aperiodic stacks in order to infer the time history of the stack. Rapid diffusion of Mo into Si in Mo/Si multilayers has been observed to occur in time scales of order 70 psec.