gebhart/patrepeval huggingface dataset:
Catch me if you can: Mass spectrometry‐based phosphoproteomics and quantification strategies (2011)

Phosphorylation of proteins is one of the most prominent PTMs and for instance a key regulator of signal transduction. In order to improve our understanding of cellular phosphorylation events, considerable effort has been devoted to improving the analysis of phosphorylation by MS-based proteomics. Different enrichment strategies for phosphorylated peptides/proteins, such as immunoaffinity chromatography (IMAC) or titanium dioxide, have been established and constantly optimized for subsequent MS analysis. Concurrently, specific MS techniques were developed for more confident identification and phosphorylation site localization. In addition, more attention is paid to the LC-MS instrumentation to avoid premature loss of phosphorylated peptides within the analytical system. Despite major advances in all of these fields, the analysis of phosphopeptides still remains far from being routine in proteomics. However, to reveal cellular regulation by phosphorylation events, not only qualitative information about the phosphorylation status of proteins but also, in particular, quantitative information about distinct changes in phosphorylation patterns upon specific stimulation is mandatory. Thus, yielded insights are of outstanding importance for the emerging field of systems biology. In this review, we will give an insight into the historical development of phosphoproteome analysis and discuss its recent progress particularly regarding phosphopeptide quantification and assessment of phosphorylation stoichiometry.
Evidence-based interventions to reduce mortality among preterm and low-birthweight neonates in low-income and middle-income countries: a systematic review and meta-analysis (2021)

The findings of this study encourage the implementation of additional, evidence-based interventions in the current (WHO) guidelines and to be selective in usage of antenatal corticosteroids, to reduce mortality among preterm and LBW neonates in LMICs. Given the global commitment to end all preventable neonatal deaths by 2030, continuous evaluation and improvement of the current guidelines should be a priority on the agenda.
Technical Assessment of the National Full Scale Aerodynamic Complex Fan Blades Repair (1998)

This report describes the principal activities of a technical review team formed to address National Full Scale Aerodynamic Complex (NFAC) blade repair problems. In particular, the problem of lack of good adhesive bonding of the composite overwrap to the Hyduliginum wood blade material was studied extensively. Description of action plans and technical elements of the plans are provided. Results of experiments designed to optimize the bonding process and bonding strengths obtained on a full scale blade using a two-step cure process with adhesive primers are presented. Consensus recommendations developed by the review team in conjunction with the NASA Ames Fan Blade Repair Project Team are provided along with lessons learned on this program. Implementation of recommendations resulted in achieving good adhesive bonds between the composite materials and wooden blades, thereby providing assurance that the repaired fan blades will meet or exceed operational life requirements.
Aldehyde and ketone substrate analogs inhibit the collagenase of Clostridium histolyticum (1985)

The collagenase from Clostridium histolyticum is a mixture of several collagenases, all of which are zinc metalloproteases. This enzyme catalyzes the cleavage of the X-Gly peptide bond in the repeating sequence of collagen: -Gly-Pro-X-Gly-Pro-X-. Thus the S3, S2, and S1 subsites on the enzyme appear to be occupied by the sequence -Gly-Pro-X- and the S1', S2', and S3' subsites also by -Gly-Pro-X-. Short peptides up to and including N alpha-acyltetrapeptides containing the repeat sequence do not detectably inhibit the enzyme (IC50 greater than 10 mM). However, peptide aldehydes of the form aminoacyl-X-glycinal, presumably occupying the S1, S2, ..., Sn subsites, are inhibitors. The most potent of these was Pro6-Gly-Pro-glycinal, with an IC50 of 340 +/- 70 microM. The single peptide aldehyde investigated, which could occupy the S1' and S2' subsites, 4-oxobutanoyl-L-proline, did not inhibit collagenase (IC50 greater than 20 mM). The peptide ketone 5-benzamido-4-oxo-6-phenylhexanoyl-Pro-Ala (XXV), which could occupy the S1-S3' subsites, inhibits collagenase with an IC50 of 120 +/- 50 microM, over 80-fold more potently than its parent peptide analogue benzoyl-Phe-Gly-Pro-Ala (XXIII). The alcohol analogue of XXV, 5-benzamido-4-hydroxy-6-phenylhexanoyl-Pro-Ala (XXVI), is over 60-fold less potent with an IC50 of 8 +/- 2mM. Extending the peptide ketone XXV to occupy the S2-S3' subsites gave 5-(N alpha-carbobenzoxy-L-prolinamido)-4-oxo-6-phenylhexanoyl-Pro -Ala (XXVII). Surprisingly, XXVII had an IC50 of only 5.2 +/- 2 mM.(ABSTRACT TRUNCATED AT 250 WORDS)
Буркитбаев М.М., Курманбаева М.С., Бачилова Н.В., Ережепова Н.Ш., Джумаханова Г.Б., Ходжабаева Д.А. Эффективность влияния серосодержащих нанокомпозитов и препаратов на продуктивность пшеницы (Triticum L.) (2018)

)The problem of increasing the yield of wheat has always been a priority not only for the country,but for the world’s population as a whole, because, bread is an important part of nutrition. All the studies conducted on wheat are aimed at increasing the productivity. Our research also touched this topicalissue. To achieve reliable results, wheat must be grown for at least 3 years in the field, but in the greenhouse conditions, this period can be reduced by half. The greenhouse of Al-Farabi Kazakh National University was first launched in 2016. The use of fertilizer by drip irrigation is an effective and convenientmethod for growing cereal crops. Lately, many different expensive fertilizers, but not all are effective andincrease yields. Sulfur is an essential element like nitrogen, phosphorus and potassium. Sulfur is the active center of many enzymes, is part of proteins and is a participant in their synthesis. The lack of sulfurleads to the accumulation of non-protein nitrogen, resulting in a reduced response to nitrogen fertilizers.In connection with the in-depth study of the effect of sulfur-containing products on wheat productivity, research began in 2017 in greenhouse conditions (Greenhouse of al-Farabi KazNU) for testing newsulfur-containing nanocomposites and preparations obtained by synthesizing. Studies of the influenceof sulfur on the productivity of wheat grains abroad, the aim of our study is to synthesize products usingsulfur resources of Kazakhstan to easily and effectively meet the domestic needs of fertilizers. The studies were conducted in 4 versions, 1-control variant; 2-solution of sulfur nanocomposites; 3-pasty sulfur;4-dry state of sulfur. Since sulfur is important in seed productivity, it was found in the course of the studythat in variants with sulfur-containing preparations, the number of productive shoots, the number andweight of grains increased, compared to the control. The use of a new preparation as a fertilizer showedearly maturing of wheat for 3-4 weeks. Because, sulfur contributes to the rapid growth of wheat. In thenorthern regions of the country, where the winter comes early, the wheat does not have time to ripen.Wheat requires additional sulfur for rapid growth and development. The results of the study show thatnew sulfur-containing preparations are effective and beneficial for obtaining early and high yield, therefore we recommend using tested sulfur preparations in the field of agriculture.Key words: sulfur, solution of the nanosulfur drug, paste-like nanosulfur drug, dry nanosulfur drug,wheat, greenhouse, yield.
A distributed control framework for performance management of virtualized computing environments (2009)

There is growing incentive to reduce the power consumed by data centers. Virtualization is a promising approach to consolidating multiple online services onto a smaller number of computing resources. By dynamically provisioning virtual machines, consolidating the workload, and turning servers on and off as needed, data center operators can maintain desired service-level agreements with end users while achieving higher server utilization and energy efficiency. This paper proposes a distributed cooperative control framework for the power and performance management of virtualized computing environments, and presents some preliminary results aimed at establishing the feasibility of this approach.
Experimental study of anode processes in plasma arc cutting (2013)

Anode processes taking place during pilot arc and cutting phases of plasma arc cutting (PAC) are experimentally studied. The experiments are carried out on commercial equipment so as to bring the studied conditions close to real operating conditions in application areas. The obtained results show the significant role of anode attachment in both process phases. In the pilot arc phase long residence time of the anodic spot results in electrode wear. An increase in the flow rate of the plasma medium facilitates anodic spot movement. In the cutting phase, the anode attachment significantly affects the kerf shape and surface morphology. Lack of its movement deeper inside the kerf leads to different heat transfer conditions at the top and bottom of the material and results in different surface roughness values. Facilitating the anodic spot movement towards the plate bottom is desirable to improve the cut quality
Predictors of Waitlist Mortality in Portopulmonary Hypertension (2017)

Both the severity of liver disease and POPH (as assessed by MELD and PVR, respectively) were significantly associated with waitlist, but not posttransplant, mortality in patients with approved MELD exceptions for POPH. Both factors should potentially be included in the POPH MELD exception score to more accurately reflect waitlist mortality risk.
Figure S4 from Tumor-Associated Fatigue in Cancer Patients Develops Independently of IL1 Signaling (2023)

&lt;p&gt;This file shows burrowing behavior in tumor-bearing mice that were or were not treated with systemic IL-1ra.&lt;/p&gt;
Impact of Human Immunodeficiency Virus Infection on the Etiology and Outcome of Severe Pneumonia in Malawian Children (2010)

PcP is a major barrier in reducing the case-fatality rate of severe pneumonia in infants of HIV-endemic communities. The use of PCR on lung aspirate specimens greatly increased the diagnostic yield.
Determination of Girisopam (2,3-Benzodiazepine Compound) and Its Four Metabolites in Human and Rat Plasma by Gradient RP-HPLC Method (1998)

Abstract A gradient RP-HPLC bioanalytical method has been developed for the human pharmacokinetic studies of girisopam, the new 2,3-benzodiazepine compound with anxiolytic effect that has no myorelaxant and anticonvulsive side effects. The compound is an analogue of tofizopam (Grandaxin®, EGIS Pharmaceuticals Ltd., Budapest, Hungary). The method was found to be appropriate for the purposes of human pharmacokinetic studies performed at 25, 50, 100, 200, 325, and 525 mg dose levels. The method allowed the simultaneous determination of girisopam (G) and its four metabolites (4′-hydroxy-G, 7-demethyl-G, 4-hydroxymethyl-G and 4-demethyl-4-oxo-G) identified in previous studies in human plasma. The solutes were separated on Hypersil BDS C18 column and quantified by UV detection at 238 nm. A solid phase extraction (SPE) method using reversed-phase cartridges was developed for sample processing, whereby girisopam and the much more polar metabolites, as well as the internal standard could be extracted in a single step. The limit of quantitation (LLOQ) was: 1 ng/mL in the case of Girisopam (G), 4-hydroxymethyl-G, 4-demethyl-4-oxo-G and 4′-hydroxy-G. In the case of 7-demethyl-G, LLOQ amounted to 2 ng/mL. The calibration curves showed good linearity; r = 0.9959, 0.9928, 0.9954, and 0.9974 in the concentration range of 1–500 ng/mL and r = 0.9959 in the range of 2–500 ng/mL respectively. The validation results obtained for all the five solutes indicated that the present method complied with internationally accepted criteria and ensured quantitative determinations of appropriate accuracy and reproducibility. After small modification and validation, the developed method was applied for determination of girisopam and its metabolites in rat plasma in a toxicological study (in vivo rat liver micronucleus test) at 600 and 1200 mg/kg dose levels. The LLOQ was 10 ng/mL for girisopam and 50 ng/mL for metabolites in rat plasma. The validation parameters for determination of solutes in rat plasma were internationally acceptable. The linearity was good for all components (r ≥ 0.992) in the wide calibration range of 10–18000 ng/mL and 50–6000 ng/mL in the case of girisopam and its metabolites respectively. The absorption of girisopam was verified by the measuring of girisopam and its metabolite (7-demethyl-G) in the plasma samples of toxicological study (micronucleus test).
Liquid hydrocarbon fuels from fish oil industrial residues by catalytic cracking (2012)

In the present work, catalytic cracking of fish oil industrial residue was investigated to study the effect of temperature, type of catalyst and the heating rate on the yield of organic liquid fraction (OLF) and its acid value. The highest bio-oil yield of 72% (wt.) was obtained at temperature range of 300–500 °C and heating rate of 10 °C/min with the mixture of Al2O3 and Na2CO3 as a catalyst. It was found that the mixture of Na2CO3 and MgSO4 as a catalyst gives lowest acid value of 8.75 mgKOH/goil and 68.1% of OLF yield. Furthermore, the acid value is reduced to 0.36 mgKOH/goil using Na2CO3 as an absorbent. The results show that the catalytic cracking process represents a sustainable method to produce bio-oil from fish oil industrial residues with physicochemical characteristics similar to the diesel fuel. Copyright © 2012 John Wiley & Sons, Ltd.
Identification of Substrates of SMURF1 Ubiquitin Ligase Activity Utilizing Protein Microarrays (2010)

The ubiquitin proteasome pathway (UPP) has been implicated in a number of pathogenic diseases: cancer, inflammation, metabolic disorders, and viral infection. The human genome contains well over 500 genes encoding proteins involved in the UPP. Ubiquitin ligases (E3s) comprise the largest subset of these genes, and together with an E2 partner, provide the substrate selectivity required for regulating cellular proteins through the covalent attachment of ubiquitin. Many ligases that have been identified in critical cellular pathways have no known substrates. Even those E3s with known substrates may have a yet unidentified role in the pathways on which they lie and as such may have additional substrates. It is critical to identify these substrates for discovery of selective small molecule inhibitors aimed at therapeutic intervention. Other methods, such as mass spectrometry, have been utilized for identifying ligase substrates, but these are labor-intensive and require a significant investment. In this study, we utilized protein microarrays for the identification of substrates of the HECT domain E3, Smurf1. Smurf1 is a critical regulator of TGF-beta and bone morphogenic protein signaling, and has been demonstrated to play a role in regulating cell polarity through the degradation of RhoA. We set out to identify novel Smurf1 substrates involved in the regulation of the aforementioned pathways. Proof-of-principle experiments with known Smurf1 substrates demonstrated efficient ubiquitination thereby validating this approach. Assaying a human protein microarray for ubiquitination with Smurf1 and the partner E2 ubiquitin ligase Ubch5 or Ubch7 identified 89 potential substrates of the Smurf1 E3 activity, which spanned a number of different biological pathways. Substrates identified utilizing protein microarray technology have been validated in vitro. Here we demonstrate the utility of this approach for identifying substrates of particular E2/E3 complexes.
Role of mitochondrial calcium transport in failing heart. (1975)

Mitochondrial calcium uptake, but not binding, like microsomal calcium uptake in failing human hearts, was less than the control values for dog, rabbit, and hamster hearts. Decrease in mitochondrial calcium binding and uptake was observed in genetically myopathic hamsters (BIO 14.6) at early, moderate, and late stages of congestive heart failure. Inhibitors of mitochondrial calcium transport, Dicumarol, dinitrophenol, and sodium azide, were found to produce a rapid fall in contractility of the isolated rat heart. Inability of rat hearts to generate contractile force on perfusion with Na+- or K+-free medium was associated with an increase in mitochondrial calcium uptake. A dramatic increase in mitochondrial calcium uptake was observed on perfusing rat hearts with control medium after CA++-free medium. No change in mitochondrial calcium uptake was noted in acute ischemic dog myocardium or hypoxic rat heart in which contractile force was severely depressed. Both mitochondrial calcium transport and contractility were decreased on perfusing rat hearts with substrate-free medium; however, the change in calcium uptake was secondary to the fall in contractile force. Decrease in pH, ATP:ADP ratio, ATP6AMP ratio, and K+:Na+ ratio were found to reduce the dog heart mitochondrial calcium uptake. It is likely that various factors such as pH, ATP:ADP ration, ATP:AMP ratio, and K+ :Na+ ration, in addition to damage in mitochondrial structure, play an important role in inhibiting mitochondrial calcium transport in failing hearts. The results also suggest that alterations in mitochondrial calcium transport are dependent upon the degree and type of heart failure.
Process and outlook of the acoustic intensity technique (1983)

The development of electronic instrumentation and microphone technology as well as statistical methods of signal processing allows us to measure the acoustic intensity vector with good precision in a broad freqeuncy range. The ability to measure acoustic intensity allows us to improve or simplify some basic measurements as, for instance, the sound power radiated by complex sources, absorption coefficient, transmission loss, etc. The determination of sound power flow makes it possible to improve the efficiency of noise control treatments. Another area of intensity measurement application is the exploration of basic properties of complex acoustic radiators and fields with complex boundary conditions. This paper presents a summary of achievements and projections in future applications.
Suppression of heat‐ and polyglutamine‐induced cytotoxicity by nonsteroidal anti‐inflammatory drugs (2004)

We have shown that sodium salicylate activates the heat shock promoter and induces the expression of heat shock proteins (hsps), with a concomitant increase in the thermotolerance of cells. To determine whether these effects are generally displayed by nonsteroidal anti-inflammatory drugs (NSAIDs), we examined the effects of a cyclooxygenase inhibitor, indomethacin, and a lipoxygenase inhibitor, nordihydroguaiaretic acid. Both inhibitors up-regulated the hsp promoter at 37 degrees C through the activation of heat shock factors, and increased cellular levels of hsps in mammalian cells, although the degree of the expression of hsps and thermotolerance of cells differed depending on the drugs. Furthermore, NSAIDs such as sodium salicylate and indomethacin suppressed the protein aggregation and apoptosis caused by an expanded polyglutamine tract in a cellular model of polyglutamine disease. These findings suggest that NSAIDs generally induce the expression of hsps in mammalian cells and may be used for the protection of cells against deleterious stressors and neurodegenerative diseases.
Electronic properties of low‐field‐emitting ultrananocrystalline diamond films (2004)

Abstract This work reports on electronic properties of nitrogen‐doped, n‐type ultrananocrystalline diamond (UNCD) films grown on p‐type Si substrates from CH 4 –Ar–N 2 gas mixtures using a microwave plasma chemical vapor deposition technique. Films ∼1 µm thick were grown with 5%N 2 and 10%N 2 in the plasmas. Charge‐based deep‐level transient spectroscopy showed a shallow level of point defects with an activation energy of ∼0.05 eV. The density of these shallow defects was increased with increasing nitrogen content in the plasma. Complex scanning probe microscopy methods were applied to study the film microstructure. Generally it was found that the nitrogen‐doped UNCD films showed a periodic ‘cell‐like’ structure in which the cell with a lateral size of several nanometers was less conducting than the boundary between the cells. The boundary width was found to be 0.5–1 nm. The observed details of the periodic structure can be associated with diamond nanocrystallites (grains) and grain boundaries, respectively. In addition, 2–5 nm high‐conducting inclusions clustered on the film surface were observed. It was noted that the emission field was inversely proportional to the film electroconductivity, and the lowest emission field of F ∼ 10 V µm −1 was detected near the high‐conducting inclusions. Moreover, the surface electron potential at the emission sites was lowered. The reasons why the shallow donor center is predominantly introduced by nitrogen incorporated into the grain boundaries and the possible mechanisms of low‐field electron emission from the nitrogen‐doped UNCD films have been discussed. Copyright © 2004 John Wiley &amp; Sons, Ltd.
The protein quality of mycoprotein (2010)

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Dearomatization Reactions Using Phthaloyl Peroxide (2015)

A new oxidative dearomatization reaction has been developed using phthaloyl peroxide to chemoselectively install two oxygen-carbon bonds into aromatic precursors. The oxidation reaction proceeds only once; addition of superstoichiometric equivalents of phthaloyl peroxide does not react further with the newly generated 1,3-cyclohexadiene. The reaction has been challenged by the addition of different functional groups and shown to maintain chemoselectivity. Due to the broad reactivity with 1,2-methylenedioxybenzene derivatives, linear free energy correlations were determined and support a mechanism proceeding through diradicals analogous to arene-hydroxylation reactions using phthaloyl peroxide.
Improving the constituent codes of turbo encoders (2002)

The performance of turbo codes can be improved by choosing the best constituent encoder. Previous lists of the best constituent codes were found based on maximising the input weight, two effective free distance d/sub 2/. We show that minimising the number of nearest neighbours N/sub 2/ is also an important requirement. If there are multiple codes having the same d/sub 2/ and N/sub 2/, we show that the minimum distance d/sub min/ can be a useful criteria to identify the best code. A list of generator polynomials suitable for turbo codes are presented in this paper which satisfy the criteria mentioned above. The previously published results are also extended to include larger memory.
Modeling, design and performance of integrated power electronics using MEMS toroidal inductors (2014)

This paper presents the design and optimization of MEMS-microfabricated toroidal inductors targeted for use in integrated power electronics. The process is based on Monte-Carlo inductor synthesis, performance evaluation based on analytic inductor models and circuit simulation, and Pareto-optimal filtering. The models and simulation are verified through comparison with magnetic finite element analysis and measurements. The design process is illustrated through the development of a buck converter in a 25-W LED driver that uses air-core toroidal inductors and GaN transistors. Design results indicate that efficiencies higher than 90% and power densities higher than 100 W/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> are possible. In the resulting designs the inductors are no longer the physically largest part of the converter.