gebhart/patrepeval huggingface dataset:
Interaction of thioredoxins with target proteins: Role of particular structural elements and electrostatic properties of thioredoxins in their interplay with 2‐oxoacid dehydrogenase complexes (1999)

The thioredoxin action upon the 2-oxoacid dehydrogenase complexes is investigated by using different thioredoxins, both wild-type and mutated. The attacking cysteine residue of thioredoxin is established to be essential for the thioredoxin-dependent activation of the complexes. Mutation of the buried cysteine residue to serine is not crucial for the activation, but prevents inhibition of the complexes, exhibited by the Clamydomonas reinhardtii thioredoxin m disulfide. Site-directed mutagenesis of D26, W31, F/W12, and Y/A70 (the Escherichia coli thioredoxin numbering is employed for all the thioredoxins studied) indicates that both the active site and remote residues of thioredoxin are involved in its interplay with the 2-oxoacid dehydrogenase complexes. Sequences of 11 thioredoxin species tested biochemically are aligned. The thioredoxin residues at the contact between the alpha3/3(10) and alpha1 helices, the length of the alpha1 helix and the charges in the alpha2-beta3 and beta4-beta5 linkers are found to correlate with the protein influence on the 2-oxoacid dehydrogenase complexes (the secondary structural elements of thioredoxin are defined according to Eklund H et al., 1991, Proteins 11:13-28). The distribution of the charges on the surface of the thioredoxin molecules is analyzed. The analysis reveals the species specific polarization of the thioredoxin active site surroundings, which corresponds to the efficiency of the thioredoxin interplay with the 2-oxoacid dehydrogenase systems. The most effective mitochondrial thioredoxin is characterized by the strongest polarization of this area and the highest value of the electrostatic dipole vector of the molecule. Not only the magnitude, but also the orientation of the dipole vector show correlation with the thioredoxin action. The dipole direction is found to be significantly influenced by the charges of the residues 13/14, 51, and 83/85, which distinguish the activating and inhibiting thioredoxin disulfides.
Effects of Header Configuration on Flow Maldistribution in Plate-Fin Heat Exchangers (2023)

Non-uniform flow distribution among the channels of a heat exchanger (HX) can adversely affect its thermo-hydraulic performance. In this research, various header designs for a plate-fin heat exchanger (PFHX) and a flow data acquisition system were constructed to study the water flow distribution among the channels of the PFHX. These different header configurations were installed at the entrance of the PFHX operating under different flow conditions to evaluate the impact of header structure on flow distribution within the HX and its thermal-hydraulic performance. The conventional header was found to cause severe flow maldistribution at the inlet of the PFHX. The Reynolds number based on channel flow and geometry was seen to significantly affect the flow distribution, which in turn drastically reduced its effectiveness. To improve the conventional header, new headers with different perforated plates were designed and built. Experimental results showed that an improved version of the header is very effective in mitigating the flow maldistribution in the PFHX and thereby enhancing its thermal performance. Engineering correlations relating the flow distribution non-uniformity, HX effectiveness, and the Reynolds number for different header designs were also developed.
The 50 kDa protein subunit of assembly polypeptide (AP) AP-2 adaptor from clathrin-coated vesicles is phosphorylated on threonine-156 by AP-1 and a soluble AP50 kinase which co-purifies with the assembly polypeptides (1993)

AP50 is a subunit of the assembly polypeptide (AP) subclass AP-2 from bovine brain coated vesicles. It can be phosphorylated in vivo and in vitro on a threonine residue by means of the AP50 kinase activity associated with AP. We have undertaken an analysis of the amino acid sequence around the AP50 phosphorylation site. After phosphorylation in vitro of AP50 followed by tryptic cleavage, only one radioactive peptide was isolated following Mono-Q ion-exchange f.p.l.c. and reverse-phase h.p.l.c. The amino acid sequence of this peptide: Glu146-Glu-Gln-Ser-Gln-Ile-Thr-Ser-Gln-Val-Thr*-Gly-Gly-Ile-Gly-Tr p-Arg162, displayed two threonine residues. Analysis of the yield and radioactivity of the product from automated Edman degradation indicated that only Thr-156 was phosphorylated, reflecting the presence of a single phosphorylation site in AP50. AP phosphorylated the corresponding synthetic peptide on the same threonyl residue. We demonstrated that AP50 was a phosphorylation substrate unable to autophosphorylate. The enzyme involved in the AP50 phosphorylation was shown to be associated with AP-1 and with a soluble protein complex co-purified with APs but resolved from the latter by hydroxyapatite-column exclusion chromatography. This AP50 kinase activity corresponded to a 280 kDa protein complex according to gel-filtration data.
Expanding the Peptide β-Turn in αγ Hybrid Sequences: 12 Atom Hydrogen Bonded Helical and Hairpin Turns (2009)

Hybrid peptide segments containing contiguous alpha and gamma amino acid residues can form C(12) hydrogen bonded turns which may be considered as backbone expanded analogues of C(10) (beta-turns) found in alphaalpha segments. Exploration of the regular hydrogen bonded conformations accessible for hybrid alphagamma sequences is facilitated by the use of a stereochemically constrained gamma amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn), in which the two torsion angles about C(gamma)-C(beta) (theta(1)) and C(beta)-C(alpha) (theta(2)) are predominantly restricted to gauche conformations. The crystal structures of the octapeptides Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (1) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (2) reveal two distinct conformations for the Aib-Gpn segment. Peptide 1 forms a continuous helix over the Aib(2)-Aib(6) segment, while the peptide 2 forms a beta-hairpin structure stabilized by four cross-strand hydrogen bonds with the Aib-Gpn segment forming a nonhelical C(12) turn. The robustness of the helix in peptide 1 in solution is demonstrated by NMR methods. Peptide 2 is conformationally fragile in solution with evidence of beta-hairpin conformations being obtained in methanol. Theoretical calculations permit delineation of the various C(12) hydrogen bonded structures which are energetically feasible in alphagamma and gammaalpha sequences.
Effect of operative devascularization on estrogen and progesterone receptor levels in breast cancer specimens. (1985)

To compare estrogen and progesterone receptor values between biopsy and mastectomy specimens, we prospectively studied 29 patients with breast cancer treated by incisional biopsy followed by mastectomy. The average tumor size was 5.4 +/- 0.5 cm and the mean age was 57.6 +/- 3.0 years. Nine patients were premenopausal and 20 were postmenopausal. Biopsies were performed without electrocautery, and tissue samples were promptly frozen and subsequently assayed for estrogen and progesterone receptor levels. After mastectomy, samples of residual tumor were excised from the biopsy site, promptly frozen, and assayed for estrogen and progesterone receptor levels. Operating time averaged 87.7 +/- 6.0 minutes. Estrogen receptor levels averaged 100.0 +/- 24.4 femtomole per mg on biopsy specimens and 29.5 +/- 8.2 fmol/mg on mastectomy specimens, representing a 70% decline (p less than 0.02). Of clinical significance is the fact that eight of 29 (27.6%) tumors changed from positive estrogen receptor values in the biopsy specimen to negative (four) and borderline (four) in the mastectomy specimens. Progesterone receptor levels were more variable, but their mean value decreased by 24.4% from 17.6 +/- 6.4 fmol/mg on biopsy samples to 13.3 +/- 4.3 fmol/mg on mastectomy samples (p, not significant). We conclude that the biopsy specimen is usually a more reliable indicator of hormonal receptor status than the mastectomy specimen and recommend that incisional or excisional biopsy specimens be taken for estrogen and progesterone receptor assays before mastectomy.
Statistical Theory of Asymmetric Damage Segregation in Clonal Cell Populations (2023)

Asymmetric damage segregation (ADS) is ubiquitous among unicellular organisms: After a mother cell divides, its two daughter cells receive sometimes slightly, sometimes strongly different fractions of damaged proteins accumulated in the mother cell. Previous studies demonstrated that ADS provides a selective advantage over symmetrically dividing cells by rejuvenating and perpetuating the population as a whole. In this work we focus on the statistical properties of damage in individual lineages and the overall damage distributions in growing populations for a variety of ADS models with different rules governing damage accumulation, segregation, and the lifetime dependence on damage. We show that for a large class of deterministic ADS rules the trajectories of damage along the lineages are chaotic, and the distributions of damage in cells born at a given time asymptotically becomes fractal. By exploiting the analogy of linear ADS models with the Iterated Function Systems known in chaos theory, we derive the Frobenius-Perron equation for the stationary damage density distribution and analytically compute the damage distribution moments and fractal dimensions. We also investigate nonlinear and stochastic variants of ADS models and show the robustness of the salient features of the damage distributions.
The Effects of Image Dehazing Methods Using Dehazing Contrast-Enhancement Filters on Image Compression (2016)

To obtain well-dehazed images at the receiver while sustaining low bit rates in the transmission pipeline, this paper investigates the effects of image dehazing methods using dehazing contrast-enhancement filters on image compression for surveillance systems. At first, this paper proposes a novel image dehazing method by using a new method of calculating the transmission function-namely, the direct denoising method. Next, we deduce the dehazing effects of the direct denoising method and image dehazing method based on dark channel prior (DCP) on image compression in terms of ringing artifacts and blocking artifacts. It can be concluded that the direct denoising method performs better than the DCP method for decompressed (reconstructed) images. We also improve the direct denoising method to obtain more desirable dehazed images with higher contrast, using the saliency map as the guidance image to modify the transmission function. Finally, we adjust the parameters of dehazing contrast-enhancement filters to obtain a corresponding composite peak signal-to-noise ratio (CPSNR) and blind image quality assessment (BIQA) of the decompressed images. Experimental results show that different filters have different effects on image compression. Moreover, our proposed dehazing method can strike a balance between image dehazing and image compression.
Synthesis of Gibberellic Acid Derivatives and Their Effects on Plant Growth (2017)

A series of novel C-3-OH substituted gibberellin derivatives bearing an amide group were designed and synthesized from the natural product gibberellic acid (GA₃). Their activities on the plant growth regulation of rice and <i>Arabidopsis</i> were evaluated in vivo. Among these compounds, <b>10d</b> and <b>10f</b> exhibited appreciable inhibitory activities on rice (48.6% at 100 μmol/L) and <i>Arabidopsis</i> (41.4% at 100 μmol/L), respectively. These results provide new insights into the design and synthesis of potential plant growth regulators.
Toward an energy function for the contact map representation of proteins (2000)

We analyzed several energy functions for predicting the native state of proteins from an energy minimization procedure. We derived the parameters of a given energy function by imposing the basic requirement that the energy of the native conformation of a protein is lower than that of any conformation chosen from a set of decoys. Our work is motivated by a recent result which proved that the simple pairwise contact approximation of the energy is insufficient to satisfy simultaneously such a basic requirement for all the proteins in a database. Here, we investigate the reasons of such negative results and show how to improve the predictive power of methods based on energy minimization. We generated decoys by gapless threading, and we derive energy parameters by perceptron learning. We first considered hydrophobic contributions to the energy, defined in several ways, and showed that the additional hydrophobic terms enlarge slightly the number of proteins that can be stabilized together. Next, we performed various modifications of the pairwise energy term. We introduced (1) a distinction between inter-residue contacts on the surface and in the core of a protein and (2) a simple distance-dependent pairwise interaction in which a two-tier definition of contact replaces the original (single-tier) one. Our results suggest that a detailed treatment of the pairwise potential is likely to be more relevant than the consideration of other forces.
FKBP12-rapamycin-associated protein associates with mitochondria and senses osmotic stress via mitochondrial dysfunction (2002)

FKBP12-rapamycin associated protein (FRAP, also known as mTOR or RAFT) is the founding member of the phosphatidylinositol kinase-related kinase family and functions as a sensor of physiological signals that regulate cell growth. Signals integrated by FRAP include nutrients, cAMP levels, and osmotic stress, and cellular processes affected by FRAP include transcription, translation, and autophagy. The mechanisms underlying the integration of such diverse signals by FRAP are largely unknown. Recently, FRAP has been reported to be regulated by mitochondrial dysfunction and depletion of ATP levels. Here we show that exposure of cells to hyperosmotic conditions (and to glucose-deficient growth medium) results in rapid and reversible dissipation of the mitochondrial proton gradient. These results suggest that the ability of FRAP to mediate osmotic stress response (and glucose deprivation response) is by means of an intermediate mitochondrial dysfunction. We also show that in addition to cytosolic FRAP a large portion of FRAP associates with the mitochondrial outer membrane. The results support the existence of a stress-sensing module consisting of mitochondria and mitochondrial outer membrane-associated FRAP. This module allows the cell to integrate a variety of stress signals that affect mitochondrial function and regulate a growth checkpoint involving p70 S6 kinase.
[Effect of frostbite under hypoxia on microcirculatory perfusion in rats]. (1997)

Changes of microcirculatory perfusion in rats following cold injury of right hind leg under hypoxia were investigated. Male Wistar rats weighing 200 +/- 20 g were randomly divided into three groups: frostbite at normoxia (FN) group; frostbite during acute hypoxia (4 h at 6000 m simulated altitude, FAH) group and frostbite during hypoxia after acclimation (exposure to hypoxia at 6000 m, 4 h daily for 4 weeks, FHAC) group. The results showed that the microcirculatory perfusion of both hind legs decreased markedly in FN after cold injury. It suggests that the frostbite damage can affect microcirculatory perfusion of another leg besides the region of frostbite. The fall of microcirculatory perfusion before freezing in FAH group indicated that there was a compensatory blood redistribution during acute hypoxia. The changes of microcirculatory perfusion in FAH group post-freezing indicated that acute hypoxia can aggravate the frostbite damage. The microcirculatory perfusion of FHAC group pre-freezing was significantly lower than that of FN and FAH group, and after freezing the perfusion of frostbitten leg in FHAC group was significantly lower than that in FN group, suggesting that hypoxia acclimation may cause disturbance of microcirculation and worsen the frostbite damage at high altitude.
Learning Methods for Evolving Intelligent Systems (2010)

In this work we describe two instruments for introducing evolutionary behavior into intelligent systems.The first is the hierarchical prioritized structure (HPS) and the second is the participatory learning paradigm (PLP).
Direct labelling of the human P2X7receptor and identification of positive and negative cooperativity of binding (2007)

These data demonstrate that human P2X(7) receptors can be directly labelled and provide novel insights into receptor function. The positive cooperativity observed suggests that binding of compound-17 to one subunit in the P2X(7) receptor complex enhances subsequent binding to other P2X(7) subunits in the same complex. The negative cooperative effects of ATP suggest that ATP and compound-17 bind at separate, interacting, sites on the P2X(7) receptor.
Detection of Vancomycin-Resistant Enterococcus Spp. (VRE) from Poultry. (2001)

Twenty-eight isolates of E. faecalis and 5 isolates of E. hirae were isolated from chicken samples obtained from markets in Sri Serdang, Selangor. They were tested for susceptibility to vancomycin and other antimicrobial agents. All of the isolates showed multiple resistance to the antibiotic tested. All Enterococcus spp. were resistant (100%) to ceftaxidime, cephalothin, erythromycin, gentamicin, kanamycin, nalidixic acid and streptomycin. Resistance was also observed to norfloxacin (97%), tetracycline (91%), penicillin (85%), bacitracin (82%), chloramphenicol (61%) and the least resistance was to ampicillin (27%). High prevalence to vancomycin resistance was detected among the E. faecalis (27of 28) and E. hirae (4 of 5) isolates. The multiple antibiotic resistance index ranging between 0.64 to 1.0 showed that all strains tested originated from high-risk contamination. Plasmid profile analysis of Enterococcus spp. revealed plasmid DNA bands ranging in size from 1.3 to 35.8 megadalton but some isolates were plasmidless. No correlation could be made between plasmid patterns and antibiotic resistance.
The Safe Use of Electroconvulsive Therapy in a Patient With a Repaired Arteriovenous Malformation (2015)

We present images showing surgical clips from a remotely repaired cerebral arteriovenous malformation in a patient treated safely with electroconvulsive therapy.
Evaluating hospital performance in antibiotic stewardship to guide action at national and local levels in a lower-middle income setting (2019)

Only one hospital had an official ABS programme, but many facilities had existing structures and resources that could be used to improve antibiotic use. Thus, ABS Strategies should be built upon existing practices with national ABS policies taking maximum advantage of existing structures to manage the supply and prescription of antimicrobials. We conclude that ABS interventions that build on established responsibilities, methods and practices would be more efficient than interventions that presume a need to establish new ABS apparatus.
Prestressed Fiber Bragg Grating With High Temperature Stability (2011)

A prestressed fiber Bragg grating with high temperature stability has been successfully fabricated by use of 800 nm femtosecond laser pulse irradiation through high-temperature annealing, followed by a rapid cooling treatment. The reflectivity and the resonant wavelength of the grating are maintained constants for more than 26 h in an isothermal measurement up to 1200°C, showing significant improvement over conventional femtosecond laser pulse induced fiber gratings. Longitudinal tension tests demonstrate that the prestressed fiber exhibits enhanced mechanical robustness compared with the residual stress relaxed fiber. This paper reveals that residual stress plays an important role and essentially provides a new solution to enhance the thermal stability of fiber gratings at elevated temperatures and offering high reliability.
Emodin Bidirectionally Modulates Macrophage Polarization and Epigenetically Regulates Macrophage Memory (2016)

Macrophages are pleiotropic cells capable of performing a broad spectrum of functions. Macrophage phenotypes are classified along a continuum between the extremes of proinflammatory M1 macrophages and anti-inflammatory M2 macrophages. The seemingly opposing functions of M1 and M2 macrophages must be tightly regulated for an effective and proper response to foreign molecules or damaged tissue. Excessive activation of either M1 or M2 macrophages contributes to the pathology of many diseases. Emodin is a Chinese herb-derived compound and has shown potential to inhibit inflammation in various settings. In this study, we tested the ability of emodin to modulate the macrophage response to both M1 and M2 stimuli. Primary mouse macrophages were stimulated with LPS/IFNγ or IL4 with or without emodin, and the effects of emodin on gene transcription, cell signaling pathways, and histone modifications were examined by a variety of approaches, including microarray, quantitative real-time PCR, Western blotting, chromatin immunoprecipitation, and functional assays. We found that emodin bidirectionally tunes the induction of LPS/IFNγ- and IL4-responsive genes through inhibiting NFκB/IRF5/STAT1 signaling and IRF4/STAT6 signaling, respectively. Thereby, emodin modulates macrophage phagocytosis, migration, and NO production. Furthermore, emodin inhibited the removal of H3K27 trimethylation (H3K27m3) marks and the addition of H3K27 acetylation (H3K27ac) marks on genes required for M1 or M2 polarization of macrophages. In conclusion, our data suggest that emodin is uniquely able to suppress the excessive response of macrophages to both M1 and M2 stimuli and therefore has the potential to restore macrophage homeostasis in various pathologies.
Single-Molecule Charge Transfer and Bonding at an Organic/Inorganic Interface:  Tetracyanoethylene on Noble Metals (2007)

We have studied the structural and electronic properties of tetracyanoethylene (TCNE) molecules on different noble-metal surfaces using scanning tunneling spectroscopy and density functional theory. Striking differences are observed in the TCNE behavior on Au, Ag, and Cu substrates in the submonolayer limit. We explain our findings by a combination of charge-transfer and lattice-matching properties for TCNE across substrates that results in a strong variation of molecule-molecule and molecule-substrate interactions. These results have significant implications for future organic/inorganic nanoscopic devices incorporating molecule-based magnetism.