gebhart/patrepeval huggingface dataset:
Determination of the three-dimensional solution structure of the C-terminal domain of cellobiohydrolase I from Trichoderma reesei. A study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing (1989)

The solution structure of a synthetic 36-residue polypeptide comprising the C-terminal cellulose binding domain of cellobiohydrolase I (CT-CBH I) from Trichoderma reesei was investigated by nuclear magnetic resonance (NMR) spectroscopy. The 1H NMR spectrum was completely assigned in a sequential manner by two-dimensional NMR techniques. A large number of stereospecific assignments for beta-methylene protons, as well as ranges for the phi, psi, and chi 1 torsion angles, were obtained on the basis of sequential and intraresidue nuclear Overhauser enhancement (NOE) and coupling constant data in combination with a conformational data base search. The structure calculations were carried out in an iterative manner by using the hybrid distance geometry-dynamical simulated annealing method. This involved computing a series of initial structures from a subset of the experimental data in order to resolve ambiguities in the assignments of some NOE cross-peaks arising from chemical shift degeneracy. Additionally, this permitted us to extend the stereospecific assignments to the alpha-methylene protons of glycine using information on phi torsion angles derived from the initial structure calculations. The final experimental data set consisted of 554 interproton distance restraints, 24 restraints for 12 hydrogen bonds, and 33 phi, 24 psi, and 25 chi 1 torsion angle restraints. CT-CBH I has two disulfide bridges whose pairing was previously unknown. Analysis of structures calculated with all three possible combinations of disulfide bonds, as well as without disulfide bonds, indicated that the correct disulfide bridge pairing was 8-25 and 19-35. Forty-one structures were computed with the 8-25 and 19-35 disulfide bridges, and the average atomic rms difference between the individual structures and the mean structure obtained by averaging their coordinates was 0.33 +/- 0.04 A for the backbone atoms and 0.52 +/- 0.06 A for all atoms. The protein has a wedgelike shape with an amphiphilic character, one face being predominantly hydrophilic and the other mainly hydrophobic. The principal element of secondary structure is made up of an irregular triple-stranded antiparallel beta-sheet composed of residues 5-9 (beta 1), 24-28 (beta 2), and 33-36 (beta 3) in which strand beta 3 is hydrogen bonded to the other two strands.(ABSTRACT TRUNCATED AT 400 WORDS)
Laser Doppler Imaging in the Investigation of Lower Limb Wounds (2003)

Good blood supply is a primary determinant for the healing of acute and chronic wounds alike. Chronic wounds commonly occur in the lower extremity in man. Scientists are forever looking for objective techniques with which tissue perfusion may be measured with accuracy. Laser Doppler imaging is a very useful technique for measuring microvascular perfusion in wounds because it involves no contact and produces a color image representing flow distribution over an area of tissue. In this article, the authors discuss its application to the assessment of lower limb wounds, and they review published studies in which it has been used to investigate a range of wound types. This review examines the study of healing mechanisms, treatment effects, risk prediction, healing potential, and underlying pathology. It also considers areas in which laser Doppler imaging is still to be exploited fully.
The ?v?6 integrin induces gelatinase B secretion in colon cancer cells (1999)

In human cancers, the co-operative role between cell-adhesion receptors and proteases capable of degrading matrix barriers remains poorly understood. We have previously reported that the epithelium-restricted integrin alpha(v)beta6 becomes highly expressed in colon cancer compared with normal mucosa and that heterologous expression of alpha(v)beta6 in colon cancer cells is associated with enhanced cell growth. Herein, we report that alpha(v)beta6 expression in colon cancer cells leads to a relative increase in secretion of the matrix metalloproteinase gelatinase B over its respective inhibitor and that this secretion parallels the level of cell-surface beta6 expression. The alpha(v)beta6-mediated gelatinase B secretion is associated with increased proteolysis of denatured collagen at the cell surface, and inactivation of gelatinase B in beta6-expressing tumour cells inhibits cell spreading and proliferation within 3-dimensional collagen matrices. Our findings suggest that alpha(v)beta6-mediated gelatinase B secretion is important in the progression of human colon cancer.
Lipid Turnover in Oleaginous Yeasts (1988)

When eight strains of the oleaginous yeasts Candida curvata, Lipomyces starkeyi, Rhodosporidium toruloides and Trichosporon cutaneum were starved of carbon after having accumulated lipid up to 34% of their biomass, the lipid was readily converted to new biomass in all cases except the two strains of L. starkeyi. When C. curvata D was grown in a two-stage chemostat with the second stage as a carbon-starvation vessel (but containing NH+ 4) biosynthesis of new biomass reached 1·9 ± 0·2 g per g lipid utilized. Experiments in a single-stage chemostat undergoing transition from lipid accumulation (nitrogen-limited medium) to carbon-starvation conditions showed that the lipid in C. curvata was rapidly mobilized. When the lipid was pre-labelled with 14C, a transitory pool of rapidly metabolizable non-lipid material appeared within 1.5 h of the initiation of starvation. Rates of lipid loss indicated that initiation of lipid degradation occurred immediately carbon was lost from the external medium.
An Unusual Mechanism of Isopeptide Bond Formation Attaches the Collagenlike Glycoprotein BclA to the Exosporium of Bacillus anthracis (2011)

Isopeptide bonds are protein modifications found throughout nature in which amide linkages are formed between functional groups of two amino acids, with at least one of the functional groups provided by an amino acid side chain. Isopeptide bonds generate cross-links within and between proteins that are necessary for proper protein structure and function. In this study, we discovered that BclA, the dominant structural protein of the external nap of Bacillus anthracis spores, is attached to the underlying exosporium basal layer protein BxpB via isopeptide bonds formed through a mechanism fundamentally different from previously described mechanisms of isopeptide bond formation. The most unusual features of this mechanism are the generation of a reactive amino group by proteolytic cleavage and promiscuous selection of acidic side chains. This mechanism, which apparently relies only on short peptide sequences in protein substrates, could be a general mechanism in vivo and adapted for protein cross-linking in vitro.
Increased serum angiogenin concentration in colorectal cancer is correlated with cancer progression. (1999)

We have previously demonstrated that the increased expression of angiogenin (ANG) in pancreatic cancer is related to cancer aggressiveness; however, the relationship between ANG expression and its clinical relevance in colorectal cancer has not been demonstrated. We therefore investigated the correlation between serum ANG (sANG) concentration and colorectal cancer progression or the changes in sANG concentrations before and after cancer resection. To determination sANG concentration by ELISA, sera were obtained from colorectal cancer patients (the cancer group) preoperatively (n = 34) and postoperatively (n = 25), from hernia patients (the nonneoplastic group) preoperatively (n = 9) and postoperatively (n = 4), and from 23 healthy volunteers. The amount of ANG in the colorectal cancer tissues (n = 19) was determined by the same method. Before surgery, the mean sANG concentration in the cancer group (411.8 +/- 106.3 ng/ml) was significantly higher than that in both the nonneoplastic group (344.0 +/- 60.7 ng/ml; P = 0.04) and in the healthy volunteers (321.7 +/- 59.7 ng/ml; P = 0.0001). The degree of elevation of sANG concentration in the cancer group was more significant in the more progressed subgroups as compared with that in the normal group (versus T(is) + T1 + T2 cancer, P = 0.01; versus T3 + T4 cancer, P = 0.002; versus stage 0 + I cancer, P = 0.02; versus >stage III cancer, P = 0.001; versus Dukes' A cancer, P = 0.02; versus Dukes' C cancer, P = 0.006). After cancer resection, the mean sANG concentrations in each subgroup decreased to the same levels as those of the normal group; the degrees of reduction were more significant in the more progressed subgroups. The tissue ANG amount correlated significantly with sANG concentration (P = 0.007). These results suggest that the increased concentration of sANG that is derived from colorectal cancer correlates with cancer progression.
Compared with saturated fatty acids, dietary monounsaturated fatty acids and carbohydrates increase atherosclerosis and VLDL cholesterol levels in LDL receptor-deficient, but not apolipoprotein E-deficient, mice (2001)

Heart-healthy dietary recommendations include decreasing the intake of saturated fatty acids (SFA). However, the relative benefit of replacing SFA with monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), or carbohydrates (CARB) is still being debated. We have used two mouse models of atherosclerosis, low density lipoprotein receptor-deficient (LDLRKO) and apolipoprotein E-deficient (apoEKO) mice to measure the effects of four isocaloric diets enriched with either SFA, MUFA, PUFA, or CARB on atherosclerotic lesion area and lipoprotein levels. In LDLRKO mice, compared with the SFA diet, the MUFA and CARB diets significantly increased atherosclerosis in both sexes, but the PUFA diet had no effect. The MUFA and CARB diets also increased very low density lipoprotein-cholesterol (VLDL-C) and LDL-cholesterol (LDL-C) in males and VLDL-C levels in females. Analysis of data from LDLRKO mice on all diets showed that atherosclerotic lesion area correlated positively with VLDL-C levels (males: r = 0.47, P < 0.005; females: r = 0.52, P < 0.001). In contrast, in apoEKO mice there were no significant dietary effects on atherosclerosis in either sex. Compared with the SFA diet, the CARB diet significantly decreased VLDL-C in males and the MUFA, PUFA, and CARB diets decreased VLDL-C and the CARB diet decreased LDL-C in females. In summary, in LDLRKO mice the replacement of dietary SFA by either MUFA or CARB causes a proportionate increase in both atherosclerotic lesion area and VLDL-C. There were no significant dietary effects on atherosclerotic lesion area in apoEKO mice. These results are surprising and suggest that, depending on the underlying genotype, dietary MUFA and CARB can actually increase atherosclerosis susceptibility, probably by raising VLDL-C levels through a non-LDL receptor, apoE-dependent pathway.
Interacting with in-vehicle systems: understanding, measuring, and evaluating attention (2009)

In-vehicle systems research is becoming a significant field as the market for in-vehicle systems continue to grow. As a consequence, researchers are increasingly concerned with opportunities and limitations of HCI in a moving vehicle. Especially aspects of attention constitute a challenge for in-vehicle systems development. This paper seeks to remedy this by defining and exemplifying attention understandings. 100 papers were classified in a two-fold perspective; under what settings are in-vehicle systems evaluated and how is driver attention measured in regard to in-vehicle systems HCI. A breakdown of the distribution of driving settings and measures is presented and the impact of driver attention is discussed. The classification revealed that most of the studies were conducted in driving simulators and real traffic driving, while lateral and longitudinal control and eye behaviour were the most used measures.
The beat spectrum: a new approach to rhythm analysis (2001)

We introduce the beat spectrum, a new method of automatically characterizing the rhythm and tempo of music and audio. The beat spectrum is a measure of acoustic self-similarity as a function of time lag. Highly structured or repetitive music will have strong beat spectrum peaks at the repetition times. This reveals both tempo and the relative strength of particular beats, and therefore can distinguish between different kinds of rhythms at the same tempo. We also introduce the beat spectrogram which graphically illustrates rhythm variation over time. Unlike previous approaches to tempo analysis, the beat spectrum does not depend on particular attributes such as energy or frequency, and thus will work for any music or audio in any genre. We present tempo estimation results which are accurate to within 1% for a variety of musical genres. This approach has a variety of applications, including music retrieval by similarity and automatically generating music videos. Anyone who has ever tapped a foot in time to music has performed rhythm analysis. Though simple for humans, this task is considerably more difficult to automate. We introduce a new measure of tempo analysis called the beat spectrum. This is a measure of acoustic self-similarity versus lag time, computed from a representation of spectrally similarity. Peaks in the beat spectrum correspond to major rhythmic components of the source audio. The repetition time of each component can be determined by the lag time of the corresponding peak, while the relative amplitudes of different peaks reflects the strengths of their corresponding rhythmic components. We also present the beat spectrogram which graphically illustrates rhythmic variation over time. The beat spectrogram is an image formed from the beat spectrum over successive windows. Strong rhythmic components are visible as bright bars in the beat spectrogram, making changes in tempo or time signature visible. In addition, a measure of audio novelty can be computed that measures how novel the source audio is at any time [2]. Instances when this measure is large correspond to significant audio changes. Periodic peaks correspond to rhythmic periodicity in the music. In the final section, we present various applications of the beat spectrum, including music retrieval by rhythmic similarity, an “automatic DJ” that can smoothly sequence music with similar tempos and automatic music video generation.
A novel function for zinc(II) in a nucleic acid-binding protein. Contribution of zinc(II) toward the cooperativity of bacteriophage T4 gene 32 protein binding. (1990)

The contribution of Zn(II) toward the binding of bacteriophage T4 gene 32 single-stranded nucleic acid-binding protein (gp32) has been examined by the use of two independent approaches. Studies carried out with successively longer oligonucleotides which have the general structure p(dT)n, where n is equal to 8, 16, 24, or 32 nucleotides, suggest that removal of Zn(II) decreases the cooperativity of binding by as much as 30-fold. Hence, whereas apo-gp32 and native gp32 have similar apparent affinities for the single-site lattice p(dT)8, native gp32 has an approximately 10-fold higher affinity compared to apo-gp32 for a two-site lattice, such as p(dT)16. In contrast to native gp32, where full cooperativity (in terms of the strength of a single gp32-gp32 interaction) is reached with only a two-site lattice, the cooperativity of apo-gp32 binding appears to increase approximately 4-fold upon going from a two- to a four-site lattice such as p(dT)32. The conclusion reached from these oligonucleotide studies agrees well with a series of titrations with polyribo(ethenoadenylic) acid, in 0.275-0.40 M NaCl. These latter studies indicate that the 6-38-fold higher affinity of native gp32 as compared to apo-gp32 for polyribo(ethenoadenylic) acid results primarily from the higher cooperativity of binding of native gp32. By stabilizing a specific subdomain within gp32 that is essential along with the NH2-terminal domain (residues 1-9), Zn(II) contributes from 20 to 50% of the free energy of cooperative gp32-gp32 interactions that occur along a polynucleotide lattice.
The PRINTS protein fingerprint database in its fifth year (1998)

PRINTS is a database of protein family 'fingerprints' offering a diagnostic resource for newly-determined sequences. By contrast with PROSITE, which uses single consensus expressions to characterise particular families, PRINTS exploits groups of motifs to build characteristic signatures. These signatures offer improved diagnostic reliability by virtue of the mutual context provided by motif neighbours. To date, 800 fingerprints have been constructed and stored in PRINTS. The current version, 17.0, encodes approximately 4500 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database is accessible via the UCL Bioinformatics World Wide Web (WWW) Server at http://www. biochem.ucl.ac.uk/bsm/dbbrowser/ . We have recently enhanced the usefulness of PRINTS by making available new, intuitive search software. This allows both individual query sequence and bulk data submission, permitting easy analysis of single sequences or complete genomes. Preliminary results indicate that use of the PRINTS system is able to assign additional functions not found by other methods, and hence offers a useful adjunct to current genome analysis protocols.
Studies on cyclodextrin glycosyltransferase. II. Action of cyclodextrin glycosyltransferase from Bacillus megaterium strain No. 5 on starch. (1974)

The amounts of the cyclodextrins G6, G7 and G8 produced by the action of the enzyme from Bacillus megateriian (No. 5 enzyme) and Bacillus macerans amylase (BMA) on starch-14C (U) were determined by the calculation of radioactivity. Both fractions of No. 5 enzyme produced the cyclodextrin G6, G7 and G8 in the proportion of 1:2.4:1. On the other hand, BMA produced the cyclodextrin G6, G7 and G8 in the proportion of 2.7:1:1. The cyclodextrin G6 and G8 which are smaller parts of the reaction products by both fractions of No. 5 enzyme were found to be produced directly from starch, not from the redecomposition of cycledextrin G7. The ratio of the cyclodextrin G6, G7 and G8 were almost constant, regardless of the pH range of the reaction system. By using the maltooligosaccharides terminated at the reducing end by radioactive glucose, the action of both fractions of No. 5 enzyme and BMA on the maltooligosaccharides were compared with each other. The results showed that both fractions of No. 5 enzyme acted on oligosaccharides larger than maltose, producing the radioactive glucose as the major product from each maltooligosaccharide (G2_??_G8). On the other hand, BMA acted on oligosac charides larger than maltotriose, producing the radioactive maltose as the major product.
Metabolism of the anthelmintic drug niclosamide by cytochrome P450 enzymes and UDP-glucuronosyltransferases: metabolite elucidation and main contributions from CYP1A2 and UGT1A1 (2015)

1. Niclosamide is an old anthelmintic drug that shows potential in fighting against cancers. Here, we characterized the metabolism of niclosamide by cytochrome P450 enzymes (CYPs) and UDP-glucuronosyltransferases (UGTs) using human liver microsomes (HLM) and expressed enzymes. 2. NADPH-supplemented HLM (and liver microsomes from various animal species) generated one hydroxylated metabolite (M1) from niclosamide; and UDPGA-supplemented liver microsomes generated one mono-O-glucuronide (M2). The chemical structures of M1 (3-hydroxy niclosamide) and M2 (niclosamide-2-O-glucuronide) were determined through LC-MS/MS and/or NMR analyses. 3. Reaction phenotyping revealed that CYP1A2 was the main enzyme responsible for M1 formation. The important role of CYP1A2 in niclosamide metabolism was further confirmed by activity correlation analyses as well as inhibition experiments using specific inhibitors. 4. Although seven UGT enzymes were able to catalyze glucuronidation of niclosamide, UGT1A1 and 1A3 were the enzymes showed the highest metabolic activities. Activity correlation analyses demonstrated that UGT1A1 played a predominant role in hepatic glucuronidation of niclosamide, whereas the role of UGT1A3 was negligible. 5. In conclusion, niclosamide was subjected to efficient metabolic reactions hydroxylation and glucuronidation, wherein CYP1A2 and UGT1A1 were the main contributing enzymes, respectively.
Fabrication of Titania Nanofibers by Electrospinning (2003)

This paper describes a procedure based on electrospinning for generating nanofibers of anatase with controllable diameters and porous structures. When an ethanol solution containing both poly(vinyl pyrrolidone) (PVP, Mw ≈ 1 300 000) and titanium tetraisopropoxide was injected through a needle under a strong electrical field, composite nanofibers made of PVP and amorphous TiO2 were formed (with lengths up to several centimeters) as a result of electrostatic jetting. These nanofibers could be subsequently converted into anatase without changing their morphology via calcination in air at 500 °C. The average diameter of these ceramic nanofibers could be controlled in the range from 20 to 200 nm by varying a number of parameters such as the ratio between PVP and titanium tetraisopropoxide, their concentrations in the alcohol solution, the strength of the electric field, and the feeding rate of the precursor solution. Both supported and free-standing mats consisting of anatase nanofibers have been successfully fabricated.
Reducing mechanical cross-coupling in phased array transducers using stop band material as backing (2018)

Phased array transducers are widely used for acoustic imaging and surround sensing applications. A major design challenge is the achievement of low mechanical cross-coupling between the single transducer elements. Cross-coupling induces a loss of imaging resolution. In this work, the mechanical cross-coupling between acoustic transducers is investigated for a generic model. The model contains a common backing with two bending elements bonded on top. The dimensions of the backing are small; thus, wave reflections on the backing edges have to be considered. This is different to other researches. The operating frequency in the generic model is set to a low kHz range. Low operating frequencies are typical for surround sensing applications. The influence of the backing on cross-coupling is investigated numerically. In order to reduce mechanical cross-coupling a stop band material is designed. It is shown numerically that a reduction in mechanical cross-coupling can be achieved by using stop band material as backing. The effect is validated with experimental testing.