gebhart/patrepeval huggingface dataset:
The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast (2008)

The experimental evolution of laboratory populations of microbes provides an opportunity to observe the evolutionary dynamics of adaptation in real time. Until very recently, however, such studies have been limited by our inability to systematically find mutations in evolved organisms. We overcome this limitation by using a variety of DNA microarray-based techniques to characterize genetic changes -- including point mutations, structural changes, and insertion variation -- that resulted from the experimental adaptation of 24 haploid and diploid cultures of Saccharomyces cerevisiae to growth in either glucose, sulfate, or phosphate-limited chemostats for approximately 200 generations. We identified frequent genomic amplifications and rearrangements as well as novel retrotransposition events associated with adaptation. Global nucleotide variation detection in ten clonal isolates identified 32 point mutations. On the basis of mutation frequencies, we infer that these mutations and the subsequent dynamics of adaptation are determined by the batch phase of growth prior to initiation of the continuous phase in the chemostat. We relate these genotypic changes to phenotypic outcomes, namely global patterns of gene expression, and to increases in fitness by 5-50%. We found that the spectrum of available mutations in glucose- or phosphate-limited environments combined with the batch phase population dynamics early in our experiments allowed several distinct genotypic and phenotypic evolutionary pathways in response to these nutrient limitations. By contrast, sulfate-limited populations were much more constrained in both genotypic and phenotypic outcomes. Thus, the reproducibility of evolution varies with specific selective pressures, reflecting the constraints inherent in the system-level organization of metabolic processes in the cell. We were able to relate some of the observed adaptive mutations (e.g., transporter gene amplifications) to known features of the relevant metabolic pathways, but many of the mutations pointed to genes not previously associated with the relevant physiology. Thus, in addition to answering basic mechanistic questions about evolutionary mechanisms, our work suggests that experimental evolution can also shed light on the function and regulation of individual metabolic pathways.
Human amniotic fluid‐derived stem cells have characteristics of multipotent stem cells (2007)

A morphologically homogenous population of fibroblastoid-type (HAFFTs) cells, similar to mesenchymal stem cells from bone marrow (BM-MSCs), was obtained at the third passage. The cells became senescent after 27 passages over a period of 8 months while undergoing 66 population doublings. Under appropriate culture conditions, by the 8th passage they differentiated into adipocytes, osteocytes, chondrocytes and neuronal cells, as revealed by oil red O, von Kossa, Alcian blue and anti-NeuN antibody staining, respectively. Immunophenotype analyses at the 17th passage demonstrated the presence of TRA-1-60; SSEA-3 and-4; collagen types I, II, III, IV and XII; fibronectin; alpha-SMA; vimentin; desmin; CK18; CD44; CD54; CD106; FSP; vWF; CD31; and HLA ABC. Reverse transcriptase-polymerase chain reaction analysis of the HAFFTs from passages 6-20 showed consistent expression of Rex-1, SCF, GATA-4, vimentin, CK18, FGF-5 and HLA ABC genes. Oct-4 gene expression was observed up to the 19th passage but not at the 20th passage. HAFFTs showed telomerase activity at the 5th passage with a decreased level by the 21st passage. Interestingly, BMP-4, AFP, nestin and HNF-4alpha genes showed differential gene expression during ex vivo expansion. Taken together, these observations suggest that HAFFTs are pluripotent stem cells that are less differentiated than BM-MSCs, and that their gene expression profiles vary with passage number during ex vivo expansion.
Compact Quantum Dots for Single-molecule Imaging (2012)

Single-molecule imaging is an important tool for understanding the mechanisms of biomolecular function and for visualizing the spatial and temporal heterogeneity of molecular behaviors that underlie cellular biology (1-4). To image an individual molecule of interest, it is typically conjugated to a fluorescent tag (dye, protein, bead, or quantum dot) and observed with epifluorescence or total internal reflection fluorescence (TIRF) microscopy. While dyes and fluorescent proteins have been the mainstay of fluorescence imaging for decades, their fluorescence is unstable under high photon fluxes necessary to observe individual molecules, yielding only a few seconds of observation before complete loss of signal. Latex beads and dye-labeled beads provide improved signal stability but at the expense of drastically larger hydrodynamic size, which can deleteriously alter the diffusion and behavior of the molecule under study. Quantum dots (QDs) offer a balance between these two problematic regimes. These nanoparticles are composed of semiconductor materials and can be engineered with a hydrodynamically compact size with exceptional resistance to photodegradation (5). Thus in recent years QDs have been instrumental in enabling long-term observation of complex macromolecular behavior on the single molecule level. However these particles have still been found to exhibit impaired diffusion in crowded molecular environments such as the cellular cytoplasm and the neuronal synaptic cleft, where their sizes are still too large (4,6,7). Recently we have engineered the cores and surface coatings of QDs for minimized hydrodynamic size, while balancing offsets to colloidal stability, photostability, brightness, and nonspecific binding that have hindered the utility of compact QDs in the past (8,9). The goal of this article is to demonstrate the synthesis, modification, and characterization of these optimized nanocrystals, composed of an alloyed HgxCd1-xSe core coated with an insulating CdyZn1-yS shell, further coated with a multidentate polymer ligand modified with short polyethylene glycol (PEG) chains (Figure 1). Compared with conventional CdSe nanocrystals, HgxCd1-xSe alloys offer greater quantum yields of fluorescence, fluorescence at red and near-infrared wavelengths for enhanced signal-to-noise in cells, and excitation at non-cytotoxic visible wavelengths. Multidentate polymer coatings bind to the nanocrystal surface in a closed and flat conformation to minimize hydrodynamic size, and PEG neutralizes the surface charge to minimize nonspecific binding to cells and biomolecules. The end result is a brightly fluorescent nanocrystal with emission between 550-800 nm and a total hydrodynamic size near 12 nm. This is in the same size range as many soluble globular proteins in cells, and substantially smaller than conventional PEGylated QDs (25-35 nm).
Advanced Protocol to Prevent Man-in-the-middle Attack in SCADA System (2014)

SCADA system is a computer system that monitors and controls the national infrastructure or industrial process including transportation facilities, water treatment and distribution, electrical power transmission and distribution, and gas pipelines. If a SCADA system is infected by a malicious worm, such as the Stuxnet, disaster is inevitable. Since the appearance of Stuxnet, researchers focused on detecting this intrusion in SCADA networks. As a result, various methods have been presented by researchers. One of them is to monitor traffic and detect anomalous patterns. However, it is not able to detecting a spoofed packet. This study present three cases of system anomaly by example of pattern based on real data of PROFINET/DCP protocol. And propose protection method using the authentication.
Positive charge of “sticky” peptides and proteins impedes release from negatively charged PLGA matrices (2015)

The influence of electrostatic interactions and/or acylation on release of charged ("sticky") agents from biodegradable polymer matrices was systematically characterized. We hypothesized that release of peptides with positive charge would be hindered from negatively charged poly(lactic-co-glycolic acid) (PLGA) microparticles. Thus, we investigated release of peptides with different degrees of positive charge from several PLGA microparticle formulations, with different molecular weights and/or end groups (acid- or ester-terminated). Indeed, release studies revealed distinct inverse correlations between the amount of positive charge on peptides and their release rates from each PLGA microparticle formulation. Furthermore, we examined the case of peptides with net charge that changes from negative to positive within the pH range observed in degrading microparticles. These charge changing peptides displayed counterintuitive release kinetics, initially releasing faster from slower degrading (less acidic) microparticles, and releasing slower from the faster degrading (more acidic) microparticles. Importantly, trends between agent charge and release rates for model peptides also translated to larger, therapeutically relevant proteins and oligonucleotides. The results of these studies may improve future design of controlled release systems for numerous therapeutic biomolecules exhibiting positive charge, ultimately reducing time-consuming and costly trial and error iterations of such formulations.
Genome sequencing reveals complex secondary metabolome in the marine actinomycete <i>Salinispora tropica</i> (2007)

Recent fermentation studies have identified actinomycetes of the marine-dwelling genus Salinispora as prolific natural product producers. To further evaluate their biosynthetic potential, we sequenced the 5,183,331-bp S. tropica CNB-440 circular genome and analyzed all identifiable secondary natural product gene clusters. Our analysis shows that S. tropica dedicates a large percentage of its genome (≈9.9%) to natural product assembly, which is greater than previous Streptomyces genome sequences as well as other natural product-producing actinomycetes. The S. tropica genome features polyketide synthase systems of every known formally classified family, nonribosomal peptide synthetases, and several hybrid clusters. Although a few clusters appear to encode molecules previously identified in Streptomyces species, the majority of the 17 biosynthetic loci are novel. Specific chemical information about putative and observed natural product molecules is presented and discussed. In addition, our bioinformatic analysis not only was critical for the structure elucidation of the polyene macrolactam salinilactam A, but its structural analysis aided the genome assembly of the highly repetitive slm loci. This study firmly establishes the genus Salinispora as a rich source of drug-like molecules and importantly reveals the powerful interplay between genomic analysis and traditional natural product isolation studies.
Semantic Annotation And Retrieval Of Image Collections (2007)

In order to maximise the benefit of the colossal repository of digital images available both publicly and in private collections, intelligent matchmaking tools are required.Unfortunately, most image search engines rely on free-text search that often returns inaccurate sets of results based on the recurrence of the search keywords in the text accompanying the images.In this paper we present a semantically-enabled image annotation and retrieval engine that relies on methodically structured ontologies for image annotation, thus allowing for more intelligent reasoning about the image content and subsequently obtaining a more accurate set of results and a richer set of alternatives matchmaking the original query.research is to contribute towards the utilisation of semantic web technologies to improve the processes of image annotation and retrieval.The paper begins with an overview of the Semantic web technologies.In section 3 we review the case study that was the motivation for this work.Sections 4, 5, and 6 detail the implementation roadmap of our semanticbased retrieval system, i.e. ontology engineering, annotation, and the retrieval engine.We discuss plans for further work and conclude in chapters 7 and 8 respectively. 2.
SYNTHESIS AND APPLICATIONS OF NOVEL FLUOROALKYL END-CAPPED OLIGOMERS CONTAINING 3,5-DIMETHYL-4-HYDROXYBENZYL AND 3-(2<i>H</i>-BENZOTRIAZOL-2-yl)-4-HYDROXYPHENYL SEGMENTS (2005)

New fluoroalkyl end-capped co-oligomers containing 3,5-dimethyl-4-hydroxybenzyl segments [RF‒(DMHB)x‒(DMAA)y–RF] were prepared by the reactions of fluoroalkanoyl peroxides with N-(3,5-dimethyl-4-hydroxybenzyl)methacrylamide [DMHB] and N,N-dimethylacrylamide (DMAA). Similarly, fluoroalkyl end-capped homo- and co-oligomers containing 3-(2H-benzotriazol-2-yl)-4-hydroxyphenyl segments [RF–(BTRI)x–(Co–M)y–RF] were prepared by the reactions of fluoroalkanoyl peroxides with 2-[3–(2H‒benzotriazol–2–yl)–4–hydroxyphenyl]ethyl methacrylate [BTRI] and co-monomers [Co–M] such as acrylic acid (ACA), DMAA, and acryloylmorpholine (ACMO). The fluoroalkyl end-capped DMHB and BTRI co-oligomers thus obtained were soluble not only in water but also in common organic solvents. In addition, these fluorinated co-oligomers were able to reduce the surface tension of 0.1 N NaOH solutions quite effectively to around 20 mN/mlevels, although the corresponding non-fluorinated co-oligomers were not effective in reducing the surface tension of 0.1 N NaOH solutions. A modified polystyrene film surface treated with these fluoroalkyl end-capped DMHB and BTRI co-oligomers was found to exhibit a good oleophobicity imparted by fluorine with an excellent hydrophilicity. XPS analyses showed that end-capped fluoroalkyl groups in RF-(BTRI)n-RF homo-oligomer were arranged regularly above the modified polystyrene surface. Of particular interest, it was demonstrated that the self-assembled molecular aggregates formed by RF-(DMHB)x-(DMAA)y-RF co-oligomers could interact strongly with 7,7,8,8-tetracyanoquinodimethane (TCNQ) as a guest molecule to form a host–guest intermolecular complex, though such a host–guest interaction was not observed in the corresponding non-fluorinated DMHB co-oligomer.
Factors Affecting Nonenzymatic Browning of Process Cheese (1985)

Variations in manufacturing procedures and the composition of stirred-curd Cheddar cheese were investigated for effects on nonenzymatic browning in process cheese. Using a nongalactosefermenting Streptococcus tbermopbilus culture as an adjunct to mesophiic lactic starter culture resulted in increased galactose concentration in cheese and intensified browning of process cheese. The correlation between galactose content in stirred-curd cheese and brown color intensity in process cheese was very high (r=.929). Higher salt-in-moisture ratios of stirred curd cheese were related to more intense brown color in process cheese. The high salt-in-moisture ratio probably reduced the catabolic activity of the lactic starter and resulted in more residual lactose and galactose in the cheese. Increasing available amino groups in stirred curd cheese by adding casein hydrolysate proved inconclusive. Faster cooling of process cheese from 80 to 37.7C reduced intensity of brown color. Process cheese cooled very rapidly did not develop any brown color, regardless of sugar and salt contents. Browning may be controlled by regulating salt and by using strains of Streptococcus tbermopbilus that ferment galactose.
Conductive Polymer Electrolytes Derived from Poly(norbornene)s with Pendant Ionic Imidazolium Moieties (2007)

Abstract Poly(norbornene)s with pendant imidazolium moieties and three different counter anions, i.e. poly[ exo,endo ‐5‐norbornene‐2‐yl‐carboxyethyl‐3‐ethylimidazolium bis(trifluoromethyl‐sulfonyl)imide], poly( exo,endo ‐5‐norbornene‐2‐yl‐carboxyethyl‐3‐ethylimidazolium tetrafluoroborate), and poly( exo,endo ‐5‐norbornene‐2‐yl‐carboxyethyl‐3‐ethylimidazolium hexafluorophosphate) were prepared via ROMP using ionic liquids as the reaction medium. The ionic polymers possessed $\overline M _{\rm w}$ in the range 8.1–44 × 10 3 and ionic conductivity up to 1.13 × 10 −5 and 1.44 × 10 −4 S · cm −1 at 20 and 50 °C, respectively. The solubility of the new polymeric ionic liquids, their thermal stability and their glass transition temperatures were investigated in detail. Ionic conductivities were found to depend on the nature of the counter‐anion and on the polymers' glass transition temperature rather than its molecular weight. magnified image
Comparative Study on Antioxidant Activity of Lycopene (<i>Z</i>)-Isomers in Different Assays (2011)

Several studies have implicated the potent antioxidant properties of lycopene. However, most of the studies used only the (all-E)-isomer. (Z)-Isomers of lycopene were found in substantial amounts in processed foods and in human tissues. In the present study, we investigated in vitro the antioxidant activity of (5Z)-, (9Z)-, and (13Z)-lycopene compared to the (all-E)-isomer. Additionally, prolycopene, the (7Z,9Z,7'Z,9'Z)-isomer found in tangerine tomatoes, was analyzed. No significant differences were found between the isomers in ferric reducing antioxidant power assay and in bleaching the radical cation of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), both based on ET mechanisms. In contrast, scavenging activity against peroxyl radicals generated by thermal degradation of 2,2'-azobis(2-amidinopropane) (AAPH) was higher in the (Z)-isomers. (5Z)-Lycopene was most antioxidant in scavenging lipid peroxyl radicals, evaluated by analyzing the inhibition of MbFe(III) lipid peroxidation of linoleic acid in mildly acidic conditions (pH 5.8) in a micellar environment, modeling a possible antioxidant action in the gastric compartment.
Feasibility of gated IMRT (2002)

Recent years have seen the development of sophisticated delivery technologies designed to enhance the efficacy of clinical radiotherapy. In this study the authors evaluate the feasibility for combining two pivotal concepts, intensity modulated radiotherapy and respiratory gating, into a single effective therapeutic modality. Respiration is monitored in real-time through the use of cameras which track infrared-reflecting markers placed on the patient's surface. With a sampling rate of 5 Hz, normal breathing produces a simple sinusoidal pattern in three spatial dimensions. A software interface enables gating about exhalation. Radiation is delivered using a Novalis/sup TM/ accelerator and integrated micro-multileaf collimator. The unit is capable of dynamic field shaping and IMRT. Other features making the Novalis ideally suited to gated IMRT include: high output (1200 mu/min) and the ability to start/stop the beam within 0.01 monitor unit. Beam triggering is facilitated through a clinical gating interface provided by the linac manufacturer. To evaluate the performance of the system, dose measurements were performed for dynamically wedged and IMRT fields. Gating frequency was varied from 0.2 to 1.0 Hz and monitor units were varied from 25 to 200. In this manner gating effects could be studied for a wide range of leaf speeds. Two-dimensional dose maps were obtained using an amorphous-silicon detector. Differences relative to gating frequency were observed only for low numbers of monitor units, Above 50 monitor units no variation exceeded 3.5%. In all cases, variations averaged over the entire field were less than 3.5% and less than 1% above 50 monitor units.
Methylenetetrahydrofolate reductase and transcobalamin genetic polymorphisms in human spontaneous abortion: biological and clinical implications (2004)

The pathogenesis of human spontaneous abortion involves a complex interaction of several genetic and environmental factors. The firm association between increased homocysteine concentration and neural tube defects (NTD) has led to the hypothesis that high concentrations of homocysteine might be embryotoxic and lead to decreased fetal viability. There are several genetic polymorphisms that are associated with defects in folate- and vitamin B12-dependent homocysteine metabolism. The methylenetetrahydrofolate reductase (MTHFR) 677C>T and 1298A>C polymorphisms cause elevated homocysteine concentration and are associated with an increased risk of NTD. Additionally, low concentration of vitamin B12 (cobalamin) or transcobalamin that delivers vitamin B12 to the cells of the body leads to hyperhomocysteinemia and is associated with NTD. This effect involves the transcobalamin (TC) 776C>G polymorphism. Importantly, the biochemical consequences of these polymorphisms can be modified by folate and vitamin B12 supplementation. In this review, I focus on recent studies on the role of hyperhomocysteinemia-associated polymorphisms in the pathogenesis of human spontaneous abortion and discuss the possibility that periconceptional supplementation with folate and vitamin B12 might lower the incidence of miscarriage in women planning a pregnancy.
Multi-class composite n-gram language model using multiple word clusters and word successions (2001)

In this paper, a new language model, the Multi-Class Composite N-gram, is proposed to avoid a data sparseness problem in small amount of training data. The Multi-Class Composite Ngram maintains an accurate word prediction capability and reliability for sparse data with a compact model size based on multiple word clusters, so-called Multi-Classes. In the Multi-Class, the statistical connectivity at each position of the N-grams is regarded as word attributes, and one word cluster each is created to represent positional attributes. Furthermore, by introducing higher order word N-grams through the grouping of frequent word successions, Multi-Class N-grams are extended to Multi-Class Composite N-grams. In experiments, the MultiClass Composite N-grams result in 9.5% lower perplexity and a 16% lower word error rate in speech recognition with a 40% smaller parameter size than conventional word 3-grams.
Automatic actor-based program partitioning (2009)

Software reverse engineering techniques are applied most often to reconstruct the architecture of a program with respect to quality constraints, or non-functional requirements such as maintainability or reusability. In this paper, AOPR, a novel actor-oriented program reverse engineering approach, is proposed to reconstruct an object-oriented program architecture based on a high performance model such as an actor model. Reconstructing the program architecture based on this model results in the concurrent execution of the program invocations and consequently increases the overall performance of the program provided enough processors are available. The proposed reverse engineering approach applies a hill climbing clustering algorithm to find actors.
High frequency heterodyne spectroscopy with current-modulated diode lasers (1984)

The use of current-modulated semiconductor lasers for optical heterodyne spectroscopy has been investigated at modulation frequencies up to 2.6 GHz. The current modulation produces a simultaneous frequency and amplitude modulation of the laser output. A characteristic heterodyne spectrum occurs when the modulated laser probes a narrow absorption line. In order to analyze the measured spectra, a complete line shape theory has been derived for heterodyne spectroscopy with frequency- and amplitude-modulated laser light. The results show how the obtained signals depend on the modulation frequency and the phase difference between the frequency and the amplitude modulation. The measurement technique permits investigation of the FM-AM phase difference of current-modulated semiconductor lasers.
Optimized strings for the Java HotSpot™ virtual machine (2008)

In several Java VMs, strings consist of two separate objects: metadata like the string length are stored in the actual string object, while the string characters are stored in a character array. This separation causes an unnecessary overhead. Each string method must access both objects, which leads to a bad cache behavior and reduces the execution speed.