gebhart/patrepeval huggingface dataset:
Ultra-Fast Evaluation of Protein Energies Directly from Sequence (2006)

The structure, function, stability, and many other properties of a protein in a fixed environment are fully specified by its sequence, but in a manner that is difficult to discern. We present a general approach for rapidly mapping sequences directly to their energies on a pre-specified rigid backbone, an important sub-problem in computational protein design and in some methods for protein structure prediction. The cluster expansion (CE) method that we employ can, in principle, be extended to model any computable or measurable protein property directly as a function of sequence. Here we show how CE can be applied to the problem of computational protein design, and use it to derive excellent approximations of physical potentials. The approach provides several attractive advantages. First, following a one-time derivation of a CE expansion, the amount of time necessary to evaluate the energy of a sequence adopting a specified backbone conformation is reduced by a factor of 10(7) compared to standard full-atom methods for the same task. Second, the agreement between two full-atom methods that we tested and their CE sequence-based expressions is very high (root mean square deviation 1.1-4.7 kcal/mol, R2 = 0.7-1.0). Third, the functional form of the CE energy expression is such that individual terms of the expansion have clear physical interpretations. We derived expressions for the energies of three classic protein design targets-a coiled coil, a zinc finger, and a WW domain-as functions of sequence, and examined the most significant terms. Single-residue and residue-pair interactions are sufficient to accurately capture the energetics of the dimeric coiled coil, whereas higher-order contributions are important for the two more globular folds. For the task of designing novel zinc-finger sequences, a CE-derived energy function provides significantly better solutions than a standard design protocol, in comparable computation time. Given these advantages, CE is likely to find many uses in computational structural modeling.
The metabolism of dietary nitrites and nitrates (1996)

Conference Article| August 01 1996 The metabolism of dietary nitrites and nitrates R. Walker R. Walker 1School of Biological Sciences, University of Surrey, Guildford GU2 5XH, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1996) 24 (3): 780–785. https://doi.org/10.1042/bst0240780 Article history Received: April 18 1996 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation R. Walker; The metabolism of dietary nitrites and nitrates. Biochem Soc Trans 1 August 1996; 24 (3): 780–785. doi: https://doi.org/10.1042/bst0240780 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1996 Biochemical Society1996 Article PDF first page preview Close Modal You do not currently have access to this content.
Induction of IgE-mediated cutaneous, cellular, and airway reactivity in rhesus monkeys by Ascaris suum infection. (1983)

In order to maintain a colony of rhesus monkeys with IgE-mediated Ascaris asthma, we evaluated the response of four animals to infection with Ascaris suum ova. All four animals developed immediate-type cutaneous reactivity and airway responses. Serum IgE and IgG antibody responses against Ascaris antigen, as quantitated by the ELISA, were seen in all animals. Peripheral blood histamine release after stimulation with Ascaris antigen was positive in all animals. Airway reactivity to aerosol challenge with Ascaris antigen became positive in all animals and has remained positive for 6 months in three of four animals. Both standard and threshold dose airway types of responses were present. Except for transient eosinophilia, the animals remained in good health. The studies demonstrate that infection with A. suum results in rhesus monkeys with IgE-mediated immediate-type reactivity that simulates the naturally occurring model of asthma.
Low-temperature synthesis of Ge nanocrystals in zeolite Y (1996)

A method for obtaining Ge nanocrystals has been developed using the porous structure of zeolite Y as a matrix. Samples were obtained by reduction of GeO2 nanocrystals, previously grown in zeolite α cages, in H2 at 470 °C. This is apparently the lowest GeO2 reduction temperature reported and is probably due to the influence of the host. Ge crystallites so formed present an absorption edge at 2.2 eV, which is shifted ∼1.4 eV with respect to the bulk value. A softening and an asymmetric broadening of the Raman peak were also observed. We can estimate an average diameter of 3 nm for the Ge nanocrystals from both results.
Immunogenicity of Haemophilus influenzae oligosaccharide-protein and polysaccharide-protein conjugate vaccination of children at 4, 6, and 14 months of age. (1989)

At 4 and 6 months of age, 118 infants were vaccinated with either one of two Haemophilus influenzae type b capsular polysaccharide-protein conjugate vaccines: 72 infants received the polysaccharide coupled to diphtheria toxoid (PRP-D group), and 46 infants received polysaccharide-derived oligosaccharides coupled to CRM197 protein, a nontoxic mutant form of diphtheria toxin (HbOC group). A third dose of the same vaccine was given to 40 children in the PRP-D group and 25 children in the HbOC group at 14 months of age. Antibodies to the H influenzae type b capsular polysaccharide were measured by Farr-type radioimmunoassay in serum samples taken before each vaccination and 1 month after the second and the third doses. Adverse reactions monitored by a questionnaire were mild. After two vaccine doses, the geometric mean concentration of antibodies to H influenzae type b polysaccharide increased from 0.07 micrograms/mL in the prevaccination samples to 0.63 micrograms/mL in the PRP-D group and to 4.32 micrograms/mL in the HbOC group. In the following 7 months, the geometric mean concentrations declined to 0.38 and 1.12 micrograms/mL, respectively. The booster dose given at 14 months elicited a strong antibody response in both groups (to geometric mean concentrations of 29.7 and 58.3 micrograms/mL, respectively). Both vaccines appear to be capable of immunologic priming by immunization in infancy.
Effect of FXR agoniston GW4064 on the proliferation of colorectal cancer cells (2013)

OBJECTIVE:To determine the influence mechanism of farnesoid X receptor(FXR) agoniston GW4064 on proliferation of colorectal cancer cells.METHODS:After HT29 cells were treated with FXR agonist GW4064(0.01,0.1 and 1 μmol/L),the change of HT29 proliferation were detected by MTT.The change of FXR,IBABP and Cyclin D1 expression were determined by the real-time quantitative PCR and Western Blot.RESULST:GW4064 inhibited HT29 proliferation,and when concentration was 0.1-1 μmol/L,GW4064 was in a dose dependent manner(0.1 μmol/L group compared with the control group,t=4.370,P0.05;0.1 μmol/L group compared with 1 μmol/L group,t=8.325,P0.01).GW4064 did not enhance FXR expression of HT29(1 μmol/L group compared with the control group,t=0.392,P0.05),but increased the expression of IBABP,and was in a dose(0.1-1 μmol/L) dependent manner(0.1 μmol/L group compared with the control group,t=13.043,P0.01;0.1 μmol/L group compared with 1 μmol/L group:t=9.001,P0.01).GW4064 reduced the expression of Cyclin D1,and was also in a dose(0.1-1 μmol/L) dependent manner(0.1 μmol/L group compared with the control group,t=4.387,P0.05;0.1 μmol/L group compared with 1 μmol/L group,t=2.790,P0.05).CONCLUSION:GW4064 may inhibit HT29 proliferation by enhancing FXR activity and reducing expression of Cyclin D1,which suggests that FXR ligand may be beneficial for colorectal cancer.
Concatenate feature extraction for robust 3D elliptic object localization (2004)

Developing an efficient object localization system for complicated industrial objects is an important, yet difficult robotic task. To tackle this problem, we have developed a system consisting first of a vision model acquisition editor, where the object salient features are acquired through a human-in-the-loop approach. Subsequently, two feature extraction algorithms, region-growing and edge-grouping, are applied to the object scene. Finally, by Kalman filter estimation of a proper ellipse representation, our object localization system successfully generates ellipse hypotheses by grouping edge fragments in the scene. The proposed system is validated by experiments using actual industrial objects.
A 20MHz BW 68dB DR CT &amp;#x0394;&amp;#x03A3; ADC based on a multi-bit time-domain quantizer and feedback element (2009)

Low-power, small-area, 20MHz-BW ADCs that can be integrated in nanoscale CMOS technologies are of immense interest to the wireless communication industry. Implementation of high-performance analog circuits in nanometric technologies faces several challenges [1]. Time-domain digital signal processing (TDSP) [2] can be used as an alternative for some analog circuits to overcome these challenges. The TDSP technique utilizes the high timing resolution available in nanoscale technologies, and can be implemented using digital circuits that are inherently less susceptible to noise. Circuits using this technique also become faster, smaller and consume less power with technology scaling. Hence, solutions using TDSP with as many digital circuits as possible are desired. An ADC architecture that uses a VCO-based time-domain quantizer is presented in [3]. This architecture uses a conventional feedback element (multi-element DAC with DEM) and 950MHz sample rate that leads to high power consumption. In this work, a pulse-width modulator (PWM) and an all-digital time-to-digital converter (TDC) are used to implement the quantizer as well as the feedback element in the time domain. This approach achieves the necessary linearity in the feedback path without DEM or calibration, and allows a low output rate of 250MS/s.
Prediction of Protein Subcellular Locations with Feature Selection and Analysis (2010)

In this paper, we propose a strategy to predict the subcellular locations of proteins by combining various feature selection methods. Firstly, proteins are coded by amino-acid composition and physicochemical properties, then these features are arranged by Minimum Redundancy Maximum Relevance method and further filtered by feature selection procedure. Nearest Neighbor Algorithm is used as a prediction model to predict the protein subcellular locations, and gains a correct prediction rate of 70.63%, evaluated by Jackknife cross-validation. Results of feature selection also enable us to identify the most important protein properties. The prediction software is available for public access on the website http://chemdata.shu.edu.cn/sub22/, which may play a important complementary role to a series of web-server predictors summarized recently in a review by Chou and Shen (Chou, K.C., Shen, H.B. Natural Science, 2009, 2, 63-92, http://www.scirp.org/journal/NS/).
Silicon‐Based Building Blocks for One‐Step <sup>18</sup>F‐Radiolabeling of Peptides for PET Imaging (2008)

Radio-controlled landing of F: The facile 18F labeling of biomolecules has been achieved under mild conditions by using a unique silicon-based one-step approach (see scheme). A di-tert-butylsilyl derivative with an aryl linker was attached to a tetrapeptide. The assembly shows a hydrolytic stability that appears to be within the range required for in vivo positron emission tomography (PET) imaging applications. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z705854_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Clearance of human platelet factor 4 by liver and kidney: its alteration by heparin (1986)

Human 125I-labeled platelet factor 4 (PF4) injected into rabbits showed a biphasic exponential pattern of disappearance from the circulation [half-life of the fast components was 0.75 min, that of the slow components was 20 min] that was not affected by a 1,000-fold excess of unlabeled PF4. Heparin resulted in a single-compartment disappearance of 125I-labeled PF4 (half-life = 25-40 min). Five minutes after injection of 125I-labeled PF4 greater than 40% radioactivity had accumulated in the liver and 4% in the kidney. At that time, accumulation of 125I-labeled beta-thromboglobulin (beta-TG) in the organs was low, approximately 4% in the kidneys and less than 3.0% in the liver. Nuclear imaging studies revealed rapid clearance of 131I-labeled PF4 from blood and its predominant accumulation in the liver. The half-lives of 131I-labeled PF4 radioactivity in liver and kidney were 96 and 252 min, fitting a single-compartment model. 131I-labeled beta-TG accumulated predominantly in the kidney. The half-lives of 131I-labeled beta-TG radioactivity in the kidney and in the liver were 84 and 414 min. Simultaneous or subsequent injection of heparin did not affect the distribution of 131I-labeled beta-TG but caused partial loss of 131I-labeled PF4 radioactivity from the liver and accelerated its appearance in the urinary bladder. Injection of heparin resulted in a 100-fold increase of excretion in the urine of 125I-labeled Pf4 precipitable by 10% trichloroacetic acid.(ABSTRACT TRUNCATED AT 250 WORDS)
Abdominal aorta anastomosis in rats and stable gastric pentadecapeptide BPC 157, prophylaxis and therapy. (2009)

We focused on abdominal aorta, clamped and transected bellow renal arteries, and aortic termino-terminal anastomosis created in Albino male rats. We suggested stomach cytoprotection theory holding endothelium protection and peptidergic anti-ulcer cytoprotection therapy to improve management of abdominal aorta anastomosis and thrombus formation. The stable gastric pentadecapeptide BPC 157 (GEPPPGKPADDAGLV, MW 1419) is a small anti-ulcer peptide efficient in inflammatory bowel disease trials (PL 14736) and various wound treatment, no toxicity reported. After 24 h following aortic termino-terminal anastomosis, we shown that BPC 157 (10 microg/kg) may also decrease formation of cloth after aortic termino-terminal anastomosis and preserved walking ability and muscle strength when given as a bath immediately after aortic anastomosis creation. This may be important since aortic termino-terminal anastomosis is normally presenting in rats with a formed cloth obstructing more than third of aortic lumen, severely impaired walking ability, painful screaming and weak muscle strength. Thereby, the effect of BPC 157 (10 microg/kg) was additionally studied at 24 h following aortic termino-terminal anastomosis. Given at the that point, intraperitoneally, within 3 minutes post-application interval the pentadecapeptide BPC 157 rapidly recovered the function of lower limbs and muscle strength while no cloth could be seen in those rats at the anastomosis site.
Neck Length and Processivity of Myosin V (2003)

Myosin V is an unconventional myosin that transports cargo such as vesicles, melanosomes, or mRNA on actin filaments. It is a two-headed myosin with an unusually long neck that has six IQ motifs complexed with calmodulin. In vitro studies have shown that myosin V moves processively on actin, taking multiple 36-nm steps that coincide with the helical repeat of actin. This allows the molecule to "walk" across the top of an actin filament, a feature necessary for moving large vesicles along an actin filament bound to the cytoskeleton. The extended neck length of the two heads is thought to be critical for taking 36-nm steps for processive movements. To test this hypothesis we have expressed myosin V heavy meromyosin-like fragments containing 6IQ motifs, as well as ones that shorten (2IQ, 4IQ) or lengthen (8IQ) the neck region or alter the spacing between 3rd and 4th IQ motifs. The step size was proportional to neck length for the 2IQ, 4IQ, 6IQ, and 8IQ molecules, but the molecule with the altered spacing took shorter than expected steps. Total internal reflection fluorescence microscopy was used to determine whether the heavy meromyosin IQ molecules were capable of processive movements on actin. At saturating ATP concentrations, all molecules except for the 2IQ mutant moved processively on actin. When the ATP concentration was lowered to 10 microm or less, the 2IQ mutant demonstrated some processive movements but with reduced run lengths compared with the other mutants. Its weak processivity was also confirmed by actin landing assays.
Digitally controlled power systems: how much intelligence is needed and where it should be (2002)

The generation of power for telecommunications systems does not inherently require computer control. However, the use of microprocessors can dramatically enhance the capabilities of both power converters and peripheral system functions. Proper application of intelligent control to a power system adds desirable features, improves system reliability, makes the system easier to use, lowers both equipment and operating costs, and pushes performance to levels that would be impossible otherwise. Misapplication of intelligence can have the opposite effects. Intelligent control can be effectively applied to power converters, low voltage disconnect controllers, overall system control, user interfaces, and the monitoring of voltage, current, and temperature. Remote monitoring and full remote control are made possible through the use of intelligent control. Manufacturing, purchasing, installation, inventory, and maintenance information can also be electronically embedded within the system. In practice, the proper application of intelligent control to a power system will seek an optimal balance of the often conflicting design goals of lower cost, higher reliability, greater simplicity, improved performance, and added features. Distributed control, distributed communications, and the use of small, dedicated controllers are effective in achieving these goals. This paper offers some practical examples of where added intelligence has enhanced existing products. It discusses the advantages and disadvantages of intelligent control, the location and extent of the intelligence, and some caveats on how far to push the envelope.
A Closed Form Solution for Flow During the Vacuum Assisted Resin Transfer Molding Process (1999)

A closed form solution to the flow of resin in vacuum assisted resin transfer molding process (VARTM) has been derived. VARTM is used extensively for affordable manufacturing of large composite structures. During the VARTM process, a highly permeable distribution medium is incorporated into the preform as a surface layer. During infusion, the resin flows preferentially across the surface and simultaneously through the preform giving rise to a complex flow front. The analytical solution presented here provides insight into the scaling laws governing fill times and resin inlet placement as a function of the properties of the preform, distribution media and resin. The formulation assumes that the flow is fully developed and is divided into two regimes: a saturated region with no crossflow and a flow front region where the resin is infiltrating into the preform from the distribution medium. The flow front region moves with a uniform velocity. The law of conservation of mass and Darcy’s Law for flow through porous media are applied in each region. The resulting equations are nondimensionalized and are solved to yield the flow front shape and the development of the saturated region. It is found that the flow front is parabolic in shape and the length of the saturated region is proportional to the square root of the time elapsed. The results thus obtained are compared to data from full scale simulations and an error analysis of the solution was carried out. It was found that the time to fill is determined with a high degree of accuracy while the error in estimating the flow front length, d, increases with a dimensionless parameter ε=K2xxh22/K2yyd2. The solution allows greater insight into the process physics, enables parametric and optimization studies and can reduce the computational cost of full-scale 3-dimensional simulations. A parametric study is conducted to establish the sensitivity of flow front velocity to the distribution media/preform thickness ratio and permeabilities and preform porosity. The results provide insight into the scaling laws for manufacturing of large scale structures by VARTM. [S1087-1357(00)02002-5]
Multiresolution Subband Blind Source Separation: Models and Methods (2009)

The goal of this paper is to review the multiresolution subband Blind Source Separation (MRSBSS) methods, classify them into different categories, and identify new trends. After the perspective of MRSBSS is briefly presented, the general and detailed definition of the MSBSS model is given, the relationships among BSS, Independent Component Analysis (ICA) and MRSBSS method are discussed simultaneously. Then, the state-of-theart MRSBSS algorithms: adaptive filter based method and sparsity based multiscale ICA method are constructed and overviewed in detail from different theory base. The paper concludes by discussing the impact of multiresolution subband on BSS research and outlining potential future research directions and applications.
New hormonal therapy in prostatic carcinoma: combined treatment with an LHRH agonist and an antiandrogen. (1982)

In order to block the influence of androgens from all sources on the growth of prostatic cancer, we have used a new hormonal therapy based on medical castration achieved with the potent LHRH agonist [D-Ser(TBU)6, des-Gly-NH2(10)]LHRH ethylamide (HOE-766) combined with the administration of a pure antiandrogen that neutralizes the action of adrenal androgens as well as those still secreted in low amounts by the testis during LHRH agonist treatment. This study was performed in ten patients with advanced prostatic carcinoma (9 at stage D2 and one at stage C). Bone pain, prostatism and general well-being were 60 to 90% improved within one month after starting treatment in all patients. After 2 months of treatment, minimal bone pain remained only in one patient who was originally bedridden. Bone scanning showed a 70 to 90% decrease in uptake after 3 to 5 months of treatment in the patients studied. Acid phosphatase levels were 60 to 90% reduced after 2 months of treatment in 3 out of the 4 patients who had elevated levels before therapy. Marked objective and subjective improvement was thus rapidly observed in 9 out of 10 patients treated with the combined therapy, while, in the other patient at stage C, subjective improvement could be documented. Although preliminary, this study indicates that a combined hormonal therapy which neutralizes all androgenic influences on peripheral tissues is of potential benefit in prostatic cancer. Moreover, the ease of application as well as the lack of secondary effects of the present approach should make possible its use early in the disease and should thus minimize the development of metastases and androgen-resistant cell clones. Randomized prospective studies on this potentially beneficial therapy are warranted.