gebhart/patrepeval huggingface dataset:
Prediction of Protein Retention Times in Anion-Exchange Chromatography Systems Using Support Vector Regression (2002)

Quantitative Structure-Retention Relationship (QSRR) models are developed for the prediction of protein retention times in anion-exchange chromatography systems. Topological, subdivided surface area, and TAE (Transferable Atom Equivalent) electron-density-based descriptors are computed directly for a set of proteins using molecular connectivity patterns and crystal structure geometries. A novel algorithm based on Support Vector Machine (SVM) regression has been employed to obtain predictive QSRR models using a two-step computational strategy. In the first step, a sparse linear SVM was utilized as a feature selection procedure to remove irrelevant or redundant information. Subsequently, the selected features were used to produce an ensemble of nonlinear SVM regression models that were combined using bootstrap aggregation (bagging) techniques, where various combinations of training and validation data sets were selected from the pool of available data. A visualization scheme (star plots) was used to display the relative importance of each selected descriptor in the final set of "bagged" models. Once these predictive models have been validated, they can be used as an automated prediction tool for virtual high-throughput screening (VHTS).
Structural and Rheological Properties of Pectins Extracted from Industrial Sugar Beet By-Products (2019)

In this work, the efficient extraction of pectin from sugar beet by-products (pressed, ensiled and dried pulp), by using an acid method or a commercial cellulose, is accomplished. The extraction method had an impact on the pectin monomeric composition, mainly in xylose, arabinose, and galacturonic acid content, as determined by GC-FID. FTIR and SEC analyses allowed the determination of similar degrees of methoxylation and molecular weights, respectively, in the extracted pectins. The acid extraction of pectin in the ensiled by-product led to the highest yield (19%) with a galacturonic acid content of 46%, whereas the application of the enzymatic extraction method resulted in a lower yield (13%) but higher galacturonic acid content (72%). Moreover, the stability in aqueous solution as well as the emulsifying activity index was higher for pectin extracted by the acid method, whereas the viscosity was higher in pectin extracted by the enzymatic method. To the best of our knowledge, this is the first study analyzing the physicochemical properties and exploring the potential reuse of ensiled and dried by-products from sugar beet industry for the extraction of pectin to be further used in the food and pharmaceutical areas.
PHIFACT-a Boolean preprocessor for multi-level logic synthesis (2002)

PHIFACT is a multi-level Boolean optimization program characterized by a controlled time-area trade-off. Its first phase, the Boolean phase, uses Boolean techniques of decomposition and merging to carry out a structural analysis and, in particular, to detect shared circuit parts. Its second phase, the restructuring phase, carries out a systematic exploration of the area-time design space by applying a user controlled sequence of transformations minimizing a parameterized cost function. The obtained results show the feasibility of full Boolean computations and open the way to an important family of new structural analysis techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Enhanced spin pumping at yttrium iron garnet/Au interfaces (2012)

Spin injection across the ferrimagnetic insulator yttrium iron garnet (YIG)/normal metal Au interface was studied using ferromagnetic resonance. The spin mixing conductance was determined by comparing the Gilbert damping parameter α in YIG/Au and YIG/Au/Fe heterostructures. The main purpose of this study was to correlate the spin pumping efficiency with chemical modifications of the YIG film surface using in situ etching and deposition techniques. By means of Ar+ ion beam etching, one is able to increase the spin mixing conductance at the YIG/Au interface by a factor of 5 compared to the untreated YIG/Au interface.
Glucocorticoid-stimulated increase in chemotactic peptide receptors on differentiating human myeloid leukemia (HL-60) cells. (1981)

The effect of dexamethasone on the HL-60 human promyelocytic leukemia cell line was studied using a radioligand-binding assay for a chemotactic peptide receptor that is found on the surface of mature polymorphonuclear leukocytes. When dimethyl sulfoxide (DMSO) is added to cultures, HL-60 cells undergo morphological and functional differentiation over a period of 6 to 7 days. Differentiation is accompanied by increased binding of the synthetic N-formylated chemotactic peptide N-formylmethionylleucyl[3H]phenylalanine. Binding of N-formylmethionylleucyl[3H]phenylalanine to cells induced to differentiate with DMSO was temperature dependent, specific, saturable, of high affinity, reversible, and proportional to cell number. Dexamethasone increased the number of N-formylated chemotactic peptide receptors in cultures of differentiating HL-60 cells without affecting the affinity of the receptors for the tritiated peptide. This steroid response was dose dependent, proportional in magnitude to glucocorticoid activity, and abolished by cycloheximide. Dexamethasone had little effect on N-formylmethionylleucyl[3H]phenylalanine binding unless DMSO was also present in culture or the cells were first induced by DMSO to differentiate. These results suggest that the glucocorticoid stimulated increase in number of N-formylated chemotactic peptide receptors was mediated by the high-affinity glucocorticoid receptor, involved protein synthesis, and was apparently dependent on differentiation.
Spatial QBE Interface for Web GIS (2005)

Many applications use geographic data, such as land management, urban planning, tourism, vehicle guidance and navigation, and e-commerce. A related research problem is to define user-friendly interfaces for Web GIS. There is a need for the definition of simple and user-friendly interfaces to allow the users to pose ad-hoc queries. Query-by-example (QBE) is a user-friendly language developed for a RDBMS. However, many RDBMS have included support for spatial extensions in SQL. QBE has not been extended in line with these extensions. In this paper, we make an effort to create extensions for QBE to support spatial queries and thus calling it spatial QBE. We show that spatial QBE is a simple and user-friendly interface for Web users. It can cater to both spatial and common database queries. The main strengths of this interface are its simplicity to express a query and its expressive power
Amidation or esterification of bovine .beta.-lactoglobulin to form positively charged proteins (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAmidation or esterification of bovine .beta.-lactoglobulin to form positively charged proteinsNina L. Mattarella, Lawrence K. Creamer, and Thomas RichardsonCite this: J. Agric. Food Chem. 1983, 31, 5, 968–972Publication Date (Print):September 1, 1983Publication History Published online1 May 2002Published inissue 1 September 1983https://pubs.acs.org/doi/10.1021/jf00119a012https://doi.org/10.1021/jf00119a012research-articleACS PublicationsRequest reuse permissionsArticle Views222Altmetric-Citations38LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Techniques for Cache and Memory Simulation Using Address Reference Traces. (1991)

Simulation using address reference traces is one of the primary methods for the performance evaluation of the memory hierarchy of computer systems. In this paper we survey the techniques used in such a simulation. In both the uniprocessor and shared-memory multiprocessor cases, the issues can be divided into trace collection, trace storage, and trace usage. Trace collection can employ several hardware or software methods. Common concerns are that the collection method capture all of the address references of interest, that the execution overhead of the collection method is not excessive, and that the trace is of adequate length. The increasing size of caches heightens the adequate length concern. Trace storage is of concern because of the large size of traces. Techniques for trace compression and trace reduction have been developed. Trace usage is of concern because of the length of a simulation. Under some circumstances it is possible to evaluate multiple cache sizes in a si...
Countering security information overload through alert and packet visualization (2006)

This article presents a framework for designing network security visualization systems as well as results from the end-to-end design and implementation of two highly interactive systems. In this article, we provide multiple contributions: we present the results of our survey of security professionals, the design framework, and lessons learned from the design of our systems as well as an evaluation of their effectiveness. Our results indicate that both systems effectively present significantly more information when compared to traditional textual approaches. We believe that the interactive, graphical techniques that we present will have broad applications in other domains seeking to deal with information overload.
Matrix metalloproteinase expression in the olfactory epithelium (2003)

The olfactory epithelium contains neuronal progenitor cells capable of continuous neurogenesis and is a unique model for studying neural degeneration, regeneration, axon outgrowth and recovery from injury. Matrix metalloproteinases (MMPs), and tissue inhibitors of metalloproteinases (TIMPs), have been implicated in cell turnover, development, migration, and metastatic processes. We used Western blot and immunohistochemistry to determine whether MMP-2 and associated proteins TIMP-2 and membrane type 1 matrix metalloproteinase (MT1-MMP) are present in the olfactory epithelium of mice. We found MMP-2 expression localized to the olfactory basal cells and immature neurons. After injury-induced neural degeneration, MMP-2 and MT1-MMP levels decreased while TIMP-2 levels increased. However, following 35 days of neurogenesis and cell replacement TIMP-2 and MT1-MMP returned to control levels. The results show a correlation between MMP and TIMP levels and the stages of neural degeneration, regeneration and recovery of the olfactory epithelium following injury.
Evaluation of a Mechanical Grader to Separate Fingerling Channel Catfish,<i>Ictalurus punctatus,</i>into Length Groups (1994)

A Fischtechnik fingerling grader and bioscanner counter were evaluated for speed and accuracy in grading and counting channel catfish, "Ictalurus punctatus," fingerlings. Channel catfish fingerlings ranging in total length from 90 to 280 mm were graded into 110- to 140-mm, 140- to 170-mm, 170- to 200-mm and >200-mm length groups and counted. A sample of the fingerlings was manually separated through grader boxes with 109 mm (7/16 inch), 141 mm (9/16 inch) and 172 mm (11/16 inch) bar spaces to compare length variation within size groups with the mechanical grader. The accuracy of the bioscanner counter was tested by comparison with hand countintg. Fingerlings weighing 679 kg were mechanically graded and counted in 56 minutes, a rate of 12.1 kg/minute. Standard deviation for length within size groups was 10.9, 13.5, and 24.0 mm for the 109-mm, 141-mm, and 172-mm grader boxes, respectively; and 13.4, 12.6, 13.0, and 16.4 mm for the 110- to 140-mm, 140- to 170-mm, 170- to 200-mm and >200-mm mechanical grader length categories, respectively. Length variance within size groups was statistically lower for the mechanical grader compared with the box graders (P < 0.05). The bioscanner counter averaged a 5% overcount of channel catfish fingerlings compared with the manual count (P < 0.05).
Metal artifact reduction in CT based on adaptive steering filter and nonlocal sinogram inpainting (2010)

This paper proposed a novel metal artifact reduction strategy for computerized tomography (CT). Firstly, an adaptive steering filter is applied to suppress noise and smooth artifacts in the original CT image with metal artifacts. Secondly, the metal component and artifact component is extracted from the filtered image using Mutual Information Maximized Segmentation (MIMS) with different maximum class number. With tagged projection sinogram from the metal artifact part in original CT image, we complete the subtracted sinogram using a novel nonlocal means inpainting method. Then, a corrected image is obtained using the filtered back-projection of the completed sinogram. The final image is formed from a combination of the corrected image and the image component free of artifacts. Experiment with both phantom and clinical images show that CT metal artifacts can be significantly reduced using our proposed method.
Age-Dependent Effects of A53T Alpha-Synuclein on Behavior and Dopaminergic Function (2013)

Expression of A53T mutant human alpha-synuclein under the mouse prion promoter is among the most successful transgenic models of Parkinson's disease. Accumulation of A53T alpha-synuclein causes adult mice to develop severe motor impairment resulting in early death at 8-12 months of age. In younger, pre-symptomatic animals, altered motor activity and anxiety-like behaviors have also been reported. These behavioral changes, which precede severe neuropathology, may stem from non-pathological functions of alpha-synuclein, including modulation of monoamine neurotransmission. Our analysis over the adult life-span of motor activity, anxiety-like, and depressive-like behaviors identifies perturbations both before and after the onset of disease. Young A53T mice had increased distribution of the dopamine transporter (DAT) to the membrane that was associated with increased striatal re-uptake function. DAT function decreased with aging, and was associated with neurochemical alterations that included increased expression of beta-synuclein and gamma synuclein. Prior to normalization of dopamine uptake, transient activation of Tau kinases and hyperphosphorylation of Tau in the striatum were also observed. Aged A53T mice had reduced neuron counts in the substantia nigra pars compacta, yet striatal medium spiny neuron dendritic spine density was largely maintained. These findings highlight the involvement of the synuclein family of proteins and phosphorylation of Tau in the response to dopaminergic dysfunction of the nigrostriatal pathway.
First-Principles Study of Phenol Hydrogenation on Pt and Ni Catalysts in Aqueous Phase (2014)

The effect of an aqueous phase on phenol hydrogenation over Pt and Ni catalysts was investigated using density functional theory-based ab initio molecular dynamics calculations. The adsorption of phenol and the addition of the first and second hydrogen adatoms to three, ring carbon positions (ortho, meta, and para with respect to the phenolic OH group) were explored in both vacuum and liquid water. The major change in the electronic structure of both Pt(111) and Ni(111) surfaces, between a gaseous and liquid phase environment, results from a repulsion between the electrons of the liquid water and the diffuse tail of electron density emanating from the metal surface. The redistribution of the metal's electrons toward the subsurface layer lowers the metal work function by about 1 eV. The lower work function gives the liquid-covered metal a higher chemical reduction strength and, in consequence, a lower oxidation strength, which, in turn lowers the phenol adsorption energy, despite the stabilizing influence of the solvation of the partly positively charged adsorbate. At both the solid/vapor and the solid/water interface, H adatom addition involves neutral H atom transfer hence the reaction barriers for adding H adatoms to phenol are lowered by only 10-20 kJ/mol, due to a small stabilizing at the transition state. More importantly, the liquid environment significantly influences the relative energetics of charged, surface-bound intermediates and of proton-transfer reactions like keto/enol isomerization. For phenol hydrogenation, solvation in water results in an energetic preference to form ketones as a result of tautomerization of surface-bound enol intermediates.
Synergy of molecular targeted approaches and immunotherapy in melanoma: preclinical basis and clinical perspectives (2015)

Clinical applications of immunotherapy strategies have recently changed the therapeutic mainstay for metastatic melanoma. Biologic and initial preclinical data support their integration with innovative molecular targeted therapies, opening enormous perspectives for researchers in the effort of finding a definitive cure. Main open challenges are the definition of reliable research models, assessment of effective schedules, safety issues and designing of personalized approaches.
Safety, feasibility, and potential efficacy of intraarterial selective cooling infusion for stroke patients treated with mechanical thrombectomy (2018)

This is a prospective non-randomized cohort study of 113 consecutive patients to investigate the safety and efficacy of a short-duration intraarterial selective cooling infusion (IA-SCI) targeted into an ischemic territory combined with mechanical thrombectomy (MT) in patients with large vessel occlusion-induced acute ischemic stroke (AIS); 45/113 patients underwent IA-SCI with 350 ml 0.9% saline at 4℃ for 15 min at the discretion of the interventionalist. Key parameters such as vital signs and key laboratory values, symptomatic and any intracranial hemorrhage, coagulation abnormalities, pneumonia, urinary tract infections and mortality were not significantly different between the two groups. Final infarct volume (FIV) was assessed on noncontrast CT performed at three to seven days. After an adjusted regression analysis, the between-group difference in FIV (19.1 ml; 95% confidence interval (CI) 3.2 to 25.2; P = 0.038) significantly favored the IA-SCI group. At 90 days, no differences were found in the proportion of patients who achieved functional independence (mRS 0-2) (51.1% versus. 41.2%, adjusted odd ratio (aOR) 1.9, 95% CI 0.8-2.6, P = 0.192). Combining short-duration IA-SCI with MT was safe. There was a smaller FIV and trend towards clinical benefit that will need to be further evaluated in randomized control trials.
Effects of Quercetin in a Mouse Model of Experimental Dry Eye (2015)

Topical application of quercetin can help to improve ocular surface disorders of dry eye not only by decreasing the corneal surface irregularity but also by increasing the tear volume and goblet cell density. Moreover, quercetin has the potential for use in eye drops as a treatment for dry eye disease with antiinflammatory effects on the lacrimal functional unit.
Capillary Electrophoresis−Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Using a Vacuum Deposition Interface (2000)

An improved vacuum deposition interface for coupling capillary electrophoresis with MALDI-TOF MS has been developed. Liquid samples consisting of analyte and matrix were deposited on a moving tape in the evacuated source chamber of a TOF mass spectrometer, enabling 24 h of uninterrupted analysis. The vacuum deposition procedure was compared with the dried-droplet method, and it was found that vacuum deposition generated significantly more reproducible signal intensity, eliminating the need for "sweet spot" searching. A concentration detection limit in the low-nanomolar range has been achieved with a low-attomole amount of sample consumed per spectrum. In addition, ion suppression caused by hydrophobicity differences in the analytes was reduced. To minimize ion suppression further, separation prior to MALDI MS analysis was employed. The performance of capillary electrophoresis (CE)-MALDI-TOF MS using the vacuum deposition interface was evaluated with a peptide mixture injected at low-femtomole levels. All peptides were baseline resolved with separation efficiencies in the range of 250000-400000 plates/m (2-3-s band half-width), demonstrating the high separation efficiency of the CE-MALDI MS coupling. A fast (approximately 40 s) CE separation of a mixture of angiotensins was found to reduce significantly ion suppression and enable trace level detection. It was also shown, for the analysis of an enolase digest, that sequence coverage of 65% was obtained using CE separation compared to 52% using step-elution solid-phase extraction and 44% in the control experiment using an unseparated mixture.
Hypomethylation of retrotransposable elements correlates with genomic instability in non‐small cell lung cancer (2008)

LINE-1 and Alu elements are non-LTR retrotransposons, constituting together over 30% of the human genome and they are frequently hypomethylated in human tumors. A relationship between global hypomethylation and genomic instability has been shown, however, there is little evidence to suggest active role for hypomethylation-mediated reactivation of retroelements in human cancer. In our study, we examined by Pyrosequencing the methylation levels of LINE-1 and Alu sequences in 48 primary nonsmall cell carcinomas and their paired adjacent tissues. We demonstrate a significant reduction of the methylation levels of both elements (p = 7.7 x 10(-14) and 9.6 x 10(-7), respectively). The methylation indices of the 2 elements correlated (p = 0.006), suggesting a possible common mechanism for their methylation maintenance. Genomic instability was measured utilizing 11 fluorescent microsatellite markers located on lung cancer hot-spot regions such as 3p, 5q 9p, 13q and 17p. Hypomethylation of both transposable elements was associated with increased genomic instability (LINE, p = 7.1 x 10(-5); Alu, p = 0.008). The reduction of the methylation index of LINE-1 and Alu following treatment of 3 lung cell lines with 5-aza-2'-deoxycitidine, consistently resulted in increased expression of both elements. Our study demonstrates the strong link between hypomethylation of transposable elements with genomic instability in non-small cell lung cancer and provides early evidence for a potential active role of these elements in lung neoplasia. As demethylating agents are now entering lung cancer trials, it is imperative to gain a greater insight into the potential reactivation of silent retrotransposons in order to advance for the clinical utilization of epigenetics in cancer therapy.
Electro-optic switching in spin-coated ferroelectric mesomorphic polymer films and its analysis (1996)

Thin films of a chiral side-chain polymer with a ferroelectric phase were deposited on a substrate by spin coating. Electro-optic switching in the films were observed by applying an external field using in-plane electrodes. Characteristics of the switching are presented, together with an analysis of the switching dynamics that takes into account the inhomogenous field distribution in the active area.