gebhart/patrepeval huggingface dataset:
A novel method to predict protein aggregations using two-dimensional native protein microfluidic chip electrophoresis (2016)

A microfluidic chip native protein electrophoresis was established to predict protein aggregation.
Campylobacter jejuni Infections: Update on Emerging Issues and Trends (2001)

Infection with Campylobacter jejuni is one of the most common causes of gastroenteritis worldwide; it occurs more frequently than do infections caused by Salmonella species, Shigella species, or Escherichia coli O157:H7. In developed countries, the incidence of Campylobacter jejuni infections peaks during infancy and again during early adulthood. Most infections are acquired by the consumption and handling of poultry. A typical case is characterized by diarrhea, fever, and abdominal cramps. Obtaining cultures of the organism from stool samples remains the best way to diagnose this infection. An alarming recent trend is the rapid emergence of antimicrobial agent--resistant Campylobacter strains all over the world. Use of antibiotics in animals used for food has accelerated this trend. It is fortunate that complications of C. jejuni infections are rare, and most patients do not require antibiotics. Guillain-Barré syndrome is now recognized as a post-infectious complication of C. jejuni infection, but its incidence is <1 per 1000 infections. Careful food preparation and cooking practices may prevent some Campylobacter infections.
A New Registration Approach for Dynamic Analysis of Calcium Signals in Organs (2018)

Wing disc pouches of fruit flies are a powerful genetic model for studying physiological intercellular calcium ($Ca^{2+}$) signals for dynamic analysis of cell signaling in organ development and disease studies. A key to analyzing spatial-temporal patterns of $Ca^{2+}$ signal waves is to accurately align the pouches across image sequences. However, pouches in different image frames may exhibit extensive intensity oscillations due to $Ca^{2+}$ signaling dynamics, and commonly used multimodal non-rigid registration methods may fail to achieve satisfactory results. In this paper, we develop a new two-phase non-rigid registration approach to register pouches in image sequences. First, we conduct segmentation of the region of interest. (i.e., pouches) using a deep neural network model. Second, we obtain an optimal transformation and align pouches across the image sequences. Evaluated using both synthetic data and real pouch data, our method considerably outperforms the state-of-the-art non-rigid registration methods.
AMP activated protein kinase: a next generation target for total metabolic control (2007)

Metabolic syndrome is characterized by a cluster of metabolic disorders, such as reduced glucose tolerance, hyperinsulinemia, hypertension, visceral obesity and lipid disorders. The benefit of exercise in maintaining total metabolic control is well known and recent research indicates that AMP-activated protein kinase (AMPK) may play an important role in exercise-related effects. AMPK is considered as a master switch in regulating glucose and lipid metabolism. AMPK is an enzyme that works as a fuel gauge, being activated in conditions of high phosphate depletion. In the liver, activation of AMPK results in decreased production of plasma glucose, cholesterol, triglyceride and enhanced fatty acid oxidation. AMPK is also robustly activated by skeletal muscle contraction and myocardial ischemia, and is involved in the stimulation of glucose transport and fatty acid oxidation by these stimuli. In adipose tissue, activated AMPK inhibits deposition of fat, but enhances breakdown and burning of stored fat, resulting in reduction of body weight. The two leading diabetic drugs, namely metformin and rosiglitazone, and adipokines, such as adiponectin and leptin, show their metabolic effects partially through AMPK. These data suggest that AMPK may be a key player in the development of new treatments for obesity, Type 2 diabetes and the metabolic syndrome. In this review, the author provide insight into the role of AMPK as a probable target for treatment of metabolic syndrome.
The delivery of endocytosed cargo to lysosomes (2009)

In mammalian cells, endocytosed cargo that is internalized through clathrin-coated pits/vesicles passes through early endosomes and then to late endosomes, before delivery to lysosomes for degradation by proteases. Late endosomes are MVBs (multivesicular bodies) with ubiquitinated membrane proteins destined for lysosomal degradation being sorted into their luminal vesicles by the ESCRT (endosomal sorting complex required for transport) machinery. Cargo is delivered from late endosomes to lysosomes by kissing and direct fusion. These processes have been studied in live cell experiments and a cell-free system. Late endosome-lysosome fusion is preceded by tethering that probably requires mammalian orthologues of the yeast HOPS (homotypic fusion and vacuole protein sorting) complex. Heterotypic late endosome-lysosome membrane fusion is mediated by a trans-SNARE (soluble N-ethylmaleimide-sensitive factor-attachment protein receptor) complex comprising Syntaxin7, Vti1b, Syntaxin8 and VAMP7 (vesicle-associated membrane protein 7). This differs from the trans-SNARE complex required for homotypic late endosome fusion in which VAMP8 replaces VAMP7. VAMP7 is also required for lysosome fusion with the plasma membrane and its retrieval from the plasma membrane to lysosomes is mediated by its folded N-terminal longin domain. Co-ordinated interaction of the ESCRT, HOPS and SNARE complexes is required for cargo delivery to lysosomes.
Molecular Findings in Familial Parkinson Disease in Spain (2002)

Mutations in Park2 gene account for 38% of the families with recessive parkinsonism in Spain. We found 2 cases of simple heterozygous Park2 mutation carriers that developed clinical symptoms, either in late adulthood or after brief exposure to parkinsonizing agents. Thus, hereditary Parkinson disease has more variable clinical phenotype and molecular defects than previously thought since heterozygous mutations could be a risk factor for parkinsonism.
Algorithms for bigram and trigram word clustering (1995)

Abstract In this paper, we describe an efficient method for obtaining word classes for class language models. The method employs an exchange algorithm using the criterion of perplexity improvement. The novel contributions of this paper are the extension of the class bigram perplexity criterion to the class trigram perplexity criterion, the description of an efficient implementation for speeding up the clustering process, the detailed computational complexity analysis of the clustering algorithm, and, finally, experimental results on large text corpora of about 1, 4, 39 and 241 million words including examples of word classes, test corpus perplexities in comparison to word language models, and speech recognition results.
Effect of the anastomosis-site after Billroth I gastrectomy on the motility of the remnant stomach. (2004)

Plasma cholecystokinin may explain the difference in motility index between the two groups.
Hydrogen storage in metal–organic frameworks (2009)

New materials capable of storing hydrogen at high gravimetric and volumetric densities are required if hydrogen is to be widely employed as a clean alternative to hydrocarbon fuels in cars and other mobile applications. With exceptionally high surface areas and chemically-tunable structures, microporous metal-organic frameworks have recently emerged as some of the most promising candidate materials. In this critical review we provide an overview of the current status of hydrogen storage within such compounds. Particular emphasis is given to the relationships between structural features and the enthalpy of hydrogen adsorption, spectroscopic methods for probing framework-H(2) interactions, and strategies for improving storage capacity (188 references).
Dual mechanism of daunorubicin-induced cell death in both sensitive and MDR-resistant HL-60 cells (1999)

Exposure of some acute myeloid leukaemia (AML) cells to daunorubicin leads to rapid cell death, whereas other AML cells show natural drug resistance. This has been attributed to expression of functional P-glycoprotein resulting in reduced drug accumulation. However, it has also been proposed that P-glycoprotein-expressing multidrug-resistant (MDR) cells are inherently defective for apoptosis. To distinguish between these different possibilities, we have compared the cell death process in a human AML cell line (HL-60) with a MDR subline (HL-60/Vinc) at doses that yield either similar intracellular daunorubicin concentrations or comparable cytotoxicity. Adjustment of the dose to obtain the same intracellular drug accumulation in the two cell lines did not result in equal cytotoxicity, suggesting the presence of additional resistance mechanisms in the P-glycoprotein-expressing HL-60/Vinc cells. However, at equitoxic doses, similar cell death pathways were observed. In HL-60 cells, daunorubicin induced rapid apoptosis at 0.5-1 microM and delayed mitotic cell death at 0.1 microM. These concentrations are within the clinical dose range. Similarly, HL-60/Vinc cells underwent apoptosis at 50-100 microM daunorubicin and mitotic cell death at 10 microM. These results show, for the first time, that anthracyclines can induce cell death by a dual mechanism in both sensitive and MDR cells. Our results also show that not only the cytotoxicity, but also the kinetics and mechanism of cell death, are dose dependent. Interestingly, regrowth was observed only in association with delayed cell death and the formation of enlarged, often polyploid, cells with micronucleation, suggesting that morphological criteria may be useful to evaluate treatment efficacy in patients with myeloid leukaemias.
Temperature and Concentration Dependence of Density of Model Liquid Foods (2003)

Abstract Density of binary solutions and combinations of sucrose, glucose, fructose, citric acid, malic acid, pectin, and inorganic salts were measured with an oscillating tube density meter in the temperature range from 10° to 60°C, at varying concentrations. Density can be predicted with accuracy better than 5 × 10−5 g cm−3 using predictive equations obtained by fitting the experimental data. Available literature values agreed well with experimental data. Relations for the excess molar volume of these solutions were derived in terms of mole fraction and temperature. A thermodynamic model for the volumetric analysis of multicomponent aqueous solutions containing electrolyte and non‐electrolyte compounds was also proposed. These models can be used for prediction of density of liquid food systems, specially fruit juices and beverages, based on composition and temperature, with high accuracy and without elaborate experimental work.
A Distributed Task Management Solution for Peer-To-Peer and Cloud Environments (2011)

In this thesis we introduced the Lightweight Coordination Calculus based logic programming approach to the programming models of the Platform-as-a-Service cloud. By using this approach, PaaS based cloud systems will enable cloud application developers to have more options to implement various kinds of programming models for their distributed tasks. We built a prototype framework based on OpenKnowledge middleware because the OpenKnowledge currently is the only framework that fully supports the LCC based programming model. By adding task control and administrative features such as automated task initiation, task status querying, task termination and input/output message channel, we extended the original usage of the OpenKnowledge framework and made it capable of being used to construct PaaS cloud systems. The automation level of the transformed OpenKnowledge framework is improved and its original advantages are retained simultaneously. All of our work reveals the underlying mechanism of the next generation Platform-as-a-Service cloud system which supports logic programming.
Localization of a mammalian homolog of diaphanous, mDia1, to the mitotic spindle in HeLa cells (2001)

mDia1 is a mammalian homolog of Drosophila diaphanous and works as an effector of the small GTPase Rho. It is a member of the formin homology (FH) proteins and contains the Rho-binding domain and an FH3 region in its N terminus, an FH1 region containing polyproline stretches in the middle and an FH2 region in the C terminus. Several lines of evidence indicate that mDia1 and diaphanous are essential in cytokinesis. mDia1 is present in a large amount in the cytoplasm of both interphase and mitotic cells. Using the instantaneous fixation method that preferentially extracts soluble components, we have analyzed localization of mDia1 in mitotic HeLa cells. Immunocytochemistry using polyclonal anti-mDia1 antibody revealed specific immunofluorescence localized to the mitotic spindle. This localization was seen from prophase to telophase. Western blot analysis also detected anti-mDia1 immunoreactivity in the mitotic spindle fraction isolated from mitotic HeLa cells. Consistently, expression of full-length mDia1 as a fusion protein with green fluorescence protein (GFP) revealed the GFP fluorescence again in the mitotic spindle in HeLa cells. Expression of GFP fusions of various truncated mutants of mDia1 identified that this localization is determined by a 173 amino acid-long sequence between the Rho-binding domain and the FH1 region, which contains the C-terminal part of the FH3 region. Point mutation analysis revealed that Leu(434) and Leu(455) in the FH3 region are essential in localization to the mitotic spindle. Neither electroporation of botulinum C3 exoenzyme nor microinjection of Val14RhoA into mitotic cells affected the localization of endogenous mDia1 to the mitotic spindle, suggesting that mDia1 localizes to the mitotic spindle independent of Rho activity. The present study has thus established the mDia1 localization in the mitotic spindle. This localization suggests a role of mDia1 in the spindle-cleavage furrow interaction during cell division.
Correction to Correlation of Chemical Evaporation Rate with Vapor Pressure (2017)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to Correlation of Chemical Evaporation Rate with Vapor PressureDonald Mackay* and Ian van WesenbeeckCite this: Environ. Sci. Technol. 2017, 51, 17, 10269Publication Date (Web):August 9, 2017Publication History Published online9 August 2017Published inissue 5 September 2017https://pubs.acs.org/doi/10.1021/acs.est.7b03622https://doi.org/10.1021/acs.est.7b03622correctionACS PublicationsCopyright © 2017 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views2005Altmetric-Citations-LEARN 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 PDF (108 KB) Get e-Alertsclose Get e-Alerts
Repeated injections of D-Amphetamine evoke rapid and dynamic changes in phase synchrony between the prefrontal cortex and hippocampus (2013)

Repeated drug use evokes a number of persistent alterations in oscillatory power and synchrony. How synchronous activity in cortico-hippocampal circuits is progressively modified with repeated drug exposure, however, remains to be characterized. Drugs of abuse induce both short-term and long-term adaptations in cortical and hippocampal circuits and these changes are likely important for the expression of the altered behavioral and neurobiological phenotype associated with addiction. The present study explores how the initial (up to 1 h) pharmacological response to D-Amphetamine (AMPH) is altered with repeated injections in the rat. The methods employed herein allow for the progressive changes in synchronized dynamics with repeated intermittent AMPH exposure to be characterized over short time scales (minutes). Specifically, we examined the temporal variations of phase-locking strength in delta and theta bands within the prefrontal cortex (PFC) and between PFC and hippocampus (HC) shortly after drug injection. After the first injection of AMPH synchrony increased within the PFC in the delta band, which was followed, by an increase in theta synchrony between the PFC and HC several minutes later. This relationship switched after repeated AMPH injections, where increases in theta synchrony between the PFC and HC preceded increases in delta synchrony in the PFC. The time-course of increases in synchronous activity were negatively correlated between the PFC delta and the PFC-HC theta. Collectively these data highlight the potential role of PFC-HC circuits in the development of addiction and outline dynamic changes in the time-course that cortico-hippocampal circuits become synchronized with repeated AMPH exposure.
Developing commercial phytoextraction technologies : practical considerations (2001)

Several plant / metal combinations have been identified for the 
phytoextraction of heavy metals from soil. Commercial development 
of technologies for extracting metals from soil has been 
proposed; however, many obstacles must be overcome before 
successful implementation. This paper relates some of the practical 
problems and considerations we have encountered during our 
development of a commercial technology for phytomining of Ni 
from polluted and mineralized soils. Soil conditioning to maximize 
plant growth and metal uptake is first necessary, requiring 
extensive prior knowledge of the influence of soil pH and nutrient 
availability on growth and metal uptake. Seed planting methods 
also need to be determined, such as depth of sowing, potential 
mechanization and planting density. Growth during the year 
requires control of weeds, insects and diseases. Extensive prior 
work is necessary to ensure that the crop is free of these pests and 
regulatory approval may be required for nonlabel use of pesticides. 
Method of harvest is also a concern, as most past researchers have 
harvested material by hand. It is generally hoped that commercial 
forage harvest equipment will be adequate, but this may not be 
practical for some very low-growing hyperaccumulators. All these 
operations require extensive prior testing, often during multi-year 
evaluation, before commercial field operations can be started.
Enteric nervous system neuropathy: repair and restoration (2010)

Emerging knowledge of cell and molecular biology of indwelling stem cells in the gut and strategies for application of pluripotential stem cells in patient-specific organ transplantation reflect an emergent revolution in understanding and treating disordered gut function when the underlying cause is ENS neuropathy.
Feasibility of a bilateral market for load following (2001)

In the ongoing process to create a competitive electricity market, the problem of ancillary services is assuming a fundamental role. Ancillary services are those services performed by generators, transmission and control equipment, which are necessary to support basic services and to maintain reliable operations and system security. In this paper, we focus our attention on one of these services, load following, and propose a competitive way to provide this service through bilateral contracts between supplier and customer. In general, we assume that there will be both a competitive market for the provision of load following and an authority responsible for the amount of load following not met by bilateral contracts.
Inferring dynamic properties of biochemical reaction networks from structural knowledge. (2004)

Functional properties of biochemical networks depend on both the network structure and the kinetic parameters. Extensive data on metabolic network topologies have been collected in databases, but much less information is available about the kinetic constants or metabolite concentrations. Depending on the values of these parameters, metabolic fluxes and control coefficients may vary within a wide range. Nevertheless, some of the parameters may have little influence on the observables of interest. We address the question whether, despite uncertainty about kinetic parameters, probabilistic statements can be made about dynamic network features. To this end, we perform a variability analysis of the parameters: assuming that the parameters follow statistical distributions, we compute the resulting distributions of the network properties like metabolic fluxes, concentrations, or control coefficients by Monte Carlo simulation. In this manner, we study systematically the possible distributions arising from typical topologies of biochemical networks such as linear chains, branched networks, and signaling and gene expression cascades. This analysis reveals how much information about dynamic behavior can be drawn from structural knowledge.
Novel and simple electrochemical biosensor monitoring attomolar levels of miRNA-155 in breast cancer (2016)

This work, describes for the first time, a simple biosensing design to yield an ultrasensitive electrochemical biosensor for a cancer biomarker detection, miRNA-155, with linear response down to the attomolar range. MiRNA-155 was selected for being overexpressed in breast cancer. The biosensor was assembled in two stages: (1) the immobilization of the anti-miRNA-155 that was thiol modified on an Au-screen printed electrode (Au-SPE), followed by (2) blocking the areas of non-specific binding with mercaptosuccinic acid. Atomic force microscopy (AFM) and electrochemical techniques including cyclic voltammetry (CV), impedance spectroscopy (EIS) and square wave voltammetry (SWV) confirmed the surface modification of these devices and their ability to hybridize successfully and stably with miRNA-155. The final biosensor provided a sensitive detection of miRNA-155 from 10 aM to 1.0 nM with a low detection limit (LOD) of 5.7 aM in real human serum samples. Good results were obtained in terms of selectivity towards breast cancer antigen CA-15.3 and bovine serum albumin (BSA). Raw fluid extracts from cell-lines of melanoma did not affect the biosensor response (no significant change of the blank), while raw extracts from breast cancer yielded a positive signal against miRNA-155. This simple and sensitive strategy is a promising alternative for simultaneous quantitative analysis of multiple miRNA in physiological fluids for biomedical research and point-of-care (POC) diagnosis.