gebhart/patrepeval huggingface dataset:
Simulation optimization: multi-response simulation optimization using stochastic genetic search within a goal programming framework (2000)

This study presents a new approach to solve multi-response simulation optimization problems. This approach integrates a simulation model with a genetic algorithm heuristic and a goal programming model. The genetic algorithm technique offers a very flexible and reliable tool able to search for a solution within a global context. This method was modified to perform the search considering the mean and the variance of the responses. In this way, the search is performed stochastically, and not deterministically like most of the approaches reported in the literature. The goal programming model integrated with the genetic algorithm and the stochastic search present a new approach able to lead a search towards a multi-objective solution.
Synthesis and Antimicrobial Activity of Some New 5-Oxo-Imidazolidine Derivatives (2013)

Schiff bases are synthesized from paracetamol. 4-acetamidophenoxyacetylhydrazide is synthesized from paracetamol, which on reaction with various aldehydes gives Schiff bases. Schiff bases treated with amino-acetic acid to produce Imidazolidine derivatives. The entire synthesized compound characterized by physical and analytical data. The chemical structures of synthesized compound were confirmed by means of IR, 1HNMR and MS. Antimicrobial activity of synthesized compounds evaluated by cup-plate method. Synthesized compound showed good antimicrobial activity.
Cholesterol and 25-Hydroxycholesterol Inhibit Activation of SREBPs by Different Mechanisms, Both Involving SCAP and Insigs (2004)

The current paper demonstrates that cholesterol and its hydroxylated derivative, 25-hydroxycholesterol (25-HC), inhibit cholesterol synthesis by two different mechanisms, both involving the proteins that control sterol regulatory element-binding proteins (SREBPs), membrane-bound transcription factors that activate genes encoding enzymes of lipid synthesis. Using methyl-beta-cyclodextrin as a delivery vehicle, we show that cholesterol enters cultured Chinese hamster ovary cells and elicits a conformational change in SREBP cleavage-activating protein (SCAP), as revealed by the appearance of a new fragment in tryptic digests. This change causes SCAP to bind to Insigs, which are endoplasmic reticulum retention proteins that abrogate movement of the SCAP.SREBP complex to the Golgi apparatus where SREBPs are normally processed to their active forms. Direct binding of cholesterol to SCAP in intact cells was demonstrated by showing that a photoactivated derivative of cholesterol cross-links to the membrane domain of SCAP. The inhibitory actions of cholesterol do not require the isooctyl side chain or the Delta5-double bond of cholesterol, but they do require the 3beta-hydroxyl group. 25-HC is more potent than cholesterol in eliciting SCAP binding to Insigs, but 25-HC does not cause a detectable conformational change in SCAP. Moreover, a photoactivated derivative of 25-HC does not cross-link to SCAP. These data imply that cholesterol interacts with SCAP directly by inducing it to bind to Insigs, whereas 25-HC works indirectly through a putative 25-HC sensor protein that elicits SCAP-Insig binding.
Identification of Novel MyoD Gene Targets in Proliferating Myogenic Stem Cells (2002)

A major control point for skeletal myogenesis revolves around the muscle basic helix-loop-helix gene family that includes MyoD, Myf-5, myogenin, and MRF4. Myogenin and MRF4 are thought to be essential to terminal differentiation events, whereas MyoD and Myf-5 are critical to establishing the myogenic cell lineage and producing committed, undifferentiated myogenic stem cells (myoblasts). Although mouse genetic studies have revealed the importance of MyoD and Myf-5 for myoblast development, the genetic targets of MyoD and Myf-5 activity in undifferentiated myoblasts remain unknown. In this study, we investigated the function of MyoD as a transcriptional activator in undifferentiated myoblasts. By using conditional expression of MyoD, in conjunction with suppression subtractive hybridizations, we show that the Id3 and NP1 (neuronal pentraxin 1) genes become transcriptionally active following MyoD induction in undifferentiated myoblasts. Activation of Id3 and NP1 represents a stable, heritable event that does not rely on continued MyoD activity and is not subject to negative regulation by an activated H-Ras G12V protein. These results are the first to demonstrate that MyoD functions as a transcriptional activator in myogenic stem cells and that this key myogenic regulatory factor exhibits different gene target specificities, depending upon the cellular environment.
Quantitative analysis of mRNA amplification by in vitro transcription (2001)

Effective transcript profiling in animal systems requires isolation of homogenous tissue or cells followed by faithful mRNA amplification. Linear amplification based on cDNA synthesis and in vitro transcription is reported to maintain representation of mRNA levels, however, quantitative data demonstrating this as well as a description of inherent limitations is lacking. We show that published protocols produce a template-independent product in addition to amplifying real target mRNA thus reducing the specific activity of the final product. We describe a modified amplification protocol that minimizes the generation of template-independent product and can therefore generate the desired microgram quantities of message-derived material from 100 ng of total RNA. Application of a second, nested round of cDNA synthesis and in vitro transcription reduces the required starting material to 2 ng of total RNA. Quantitative analysis of these products on Caenorhabditis elegans Affymetrix GeneChips shows that this amplification does not reduce overall sensitivity and has only minor effects on fidelity.
Synthesis of Aromatic Chloroberbines (1990)

m t -The introduction of i-hlorhe atoms into aroma/ic rings o i berbines was eilpded lion? an €tho~;viarbJn?id~~yr~?upwhich does not undergo dei-ompositim unJe.r/nz i<ndicions of the B/schler-&&veralsA i reactiun At the end of /he svnthesis of the berbine ring svsten?this group was lrans:>rmipd into a priiiiart dromatii J n i k whim w ~s converted into chlorine by the Sdndn?@pr reaction Thus berbines 6?,b chlorinated in lhr ardmatir ring .A andberblnes IOqb chlorinated in /he aromahi ring0 were prepared The preparation ~1 i thr s t a r t i ~~-~~~?~~~~/ , ~~I .? n i i n e s l a b with an e/houvcarb~3n?ido grdup was also disru.csedBerblne or 56.13.13a-tetrahydro-8H-dibenzo[aag]qulnoI~zine and i t s derivativei have natural or hynthetlr orlglns and several thousand publlcatlons on thelr chernlcal and pharn~acoloqlcal propertiesiiave been reported 1-5 A l l Inown berblnes contain generaly only oxygen function (OH, OMe, O-CH20.)into aromatic rings A small number o f Compounds contalnmg other functions has been describedb-g In fact the dlrect introduction of a withdrawing group on the aromatlc rings prevents the R and C ring closure under the Bischler-Nap~eralski reaction conditions.Previous studies In our laboratory have shown the importance of aroniatic substltution for the o-adrenerglc antaaonist actlvity of berblnes 10-12 In a further.extension of our studies In thls area we describe here the synthesis of same chiormated derivatives of the berblne heterocycle.
The transcription factor interferon regulatory factor-1 is essential for natural killer cell function in vivo. (1996)

The activation of natural killer (NK) cells, cytotoxic lymphocytes capable of major histocompatibility complex (MHC)-unrestricted killing and early antiviral defense, is temporally related to the increased interferon (IFN)-alpha/beta production that is seen in the viral infection of mice. Type I IFN (IFN-alpha/beta) are expressed in many cell types early after primary viral infection and have been shown to mediate resistance against a variety of viruses. In this study, the role of the transcriptional activator IFN regulatory factor-1 (IRF-1) in murine NK cell activity was assessed. IRF-1-deficient mice displayed a normal frequency of NK marker-positive cells, but exhibited greatly reduced NK cell-mediated cytotoxicity after both virus infection and stimulation with the IFN inducer polyinosinic:polycytidilic acid in vivo. In vitro, cytolytic activity in IRF-1-deficient NK cells remained defective after stimulation with IFN-beta, IL-2, and IL-12. IRF-1-deficient mice were unable to eliminate syngeneic MHC class I-negative tumor cells in vivo, and had a reduced ability to reject parental semi-allogeneic donor cells from the circulation. Thus, IRF-1 is essential for the induction of NK cell-mediated cytotoxicity and for the in vivo effector functions that are mediated by this activity.
An empirical Bayes approach to inferring large-scale gene association networks (2004)

Using computer simulations, we investigate the sensitivity (power) and specificity (true negative rate) of the proposed framework to estimate GGMs from microarray data. This shows that it is possible to recover the true network topology with high accuracy even for small-sample datasets. Subsequently, we analyze gene expression data from a breast cancer tumor study and illustrate our approach by inferring a corresponding large-scale gene association network for 3883 genes.
Wolf-Hirschhorn (4P-) syndrome in adults. (2001)

Wolf-Hirschhorn syndrome (WHS) or 4p-deletion syndrome has been extensively described in children. Knowledge on adult WHS patients is still limited due to the small number of published cases. We present 4 adults and review the literature. The phenotype of adult WHS is in general similar to that of childhood WHS. Growth retardation, microcephaly and mental retardation are the rule in both adults and children. Facial dysmorphism also remains similar. The main difference lies in the absence of serious internal (cardiac) abnormalities in adult WHS. Mental retardation ranges from moderate to severe. The nosological overlap between WHS and Pitt-Rogers-Danks syndrome (PRDS) is discussed. More extensive data on adult WHS are needed for appropriate counselling of families with affected young children.
Breast cancer prognosis by combinatorial analysis of gene expression data (2006)

The study shows that LAD provides an accurate and fully explanatory prognostic system for breast cancer using genomic data (that is, a system that, in addition to predicting good or poor prognosis, provides an individualized explanation of the reasons for that prognosis for each patient). Moreover, the LAD model provides valuable insights into the roles of individual and combinatorial biomarkers, allows the discovery of new classes of patients, and generates a vast library of biomedical research hypotheses.
Phase Separation of Liquid Crystals in Polymers (1988)

Abstract New optoelectronic materials based on polymer dispersed liquid crystals (PDLC) show great potential for application in displays, temperature sensors, optical computing and for solar energy control. We report liquid crystal, termoset or thermoplastic materials. PDLC materials may be formed by several different processes. The liquid crystal may be dissolved in low molecular weight polymer precursors, in a thermoplastic melt or with a thermoplastic in a common solvent. Subsequent polymerization, cooling of the polymer melt or solvent evaporation lead to liquid crystal immiscibility, droplet formation and growth, and polymer gelation. The optoelectronic properties of these materials are affected by the droplet morphology. Specific examples are presented for each of these processes and it is demonstrated how the droplet morphology and density, and thus device performance, can be controlled by each method. The thermoplestics are suitable for forming films by a variety of techniques. A range of polymers and liquid crystals may be used to form PDLC materials, allowing them to be tailored for any of a number of applications.
Human Protein Reference Database--2009 update (2008)

Human Protein Reference Database (HPRD--http://www.hprd.org/), initially described in 2003, is a database of curated proteomic information pertaining to human proteins. We have recently added a number of new features in HPRD. These include PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest. Another new feature is a protein distributed annotation system--Human Proteinpedia (http://www.humanproteinpedia.org/)--through which laboratories can submit their data, which is mapped onto protein entries in HPRD. Over 75 laboratories involved in proteomics research have already participated in this effort by submitting data for over 15,000 human proteins. The submitted data includes mass spectrometry and protein microarray-derived data, among other data types. Finally, HPRD is also linked to a compendium of human signaling pathways developed by our group, NetPath (http://www.netpath.org/), which currently contains annotations for several cancer and immune signaling pathways. Since the last update, more than 5500 new protein sequences have been added, making HPRD a comprehensive resource for studying the human proteome.
The impact of oral consumption of Lactobacillus plantarum P-8 on faecal bacteria revealed by pyrosequencing (2015)

Lactobacillus plantarum P-8 (Lp-8) is a novel probiotic bacterium showing beneficial effects in human. The current study is a follow-up work of a previous clinical trial, and it aimed at understanding the mechanism of the observed desirable effects by evaluating the change in faecal bacterial structure at phylogenetic level. The genomic DNAs used for 16S rRNA polymerase chain reaction (PCR)-pyrosequencing were obtained from the previous clinical trial. Briefly, 33 recruited subjects were given a single daily oral dose of Lp-8 (6×10(10) cfu) for 4 weeks. Faecal genomic DNAs were extracted from samples collected before (day 0) and after (day 28) Lp-8 consumption from the subjects. Our results show that the consumption of Lp-8 did not result in major change in the faecal bacterial structure by principal coordinate analysis. However, multivariate analysis of variance and analysis of UniFrac metric distances at day 0 and day 28 revealed significant difference in the faecal bacterial structure upon Lp-8 treatment. Thus, the difference lied on the less abundant rather than the predominant lineages. At genus level, the relative abundance of 5 Firmicutes genera (Leuconostoc, Lactobacillus, Sporacetigenium, Blautia and Staphylococcus) significantly increased after Lp-8 consumption, whereas 3 Proteobacteria genera (Shigella, Escherichia and Enterobacter) decreased (P<0.05). 60 key responding lineages could be identified at operational taxonomic unit (OTU) level by redundancy analysis. Among them, the abundance of 18 OTUs showed significant difference (P<0.05), while 12 OTUs exhibited modest change (0.05<P<0.01) upon treatment. Our study identified a shift in the faecal bacterial structure upon Lp-8 administration, which may explain some of the previously observed beneficial effects.
Use of Earth’s Magnetic Field for Mitigating Gyroscope Errors Regardless of Magnetic Perturbation (2011)

Most portable systems like smart-phones are equipped with low cost consumer grade sensors, making them useful as Pedestrian Navigation Systems (PNS). Measurements of these sensors are severely contaminated by errors caused due to instrumentation and environmental issues rendering the unaided navigation solution with these sensors of limited use. The overall navigation error budget associated with pedestrian navigation can be categorized into position/displacement errors and attitude/orientation errors. Most of the research is conducted for tackling and reducing the displacement errors, which either utilize Pedestrian Dead Reckoning (PDR) or special constraints like Zero velocity UPdaTes (ZUPT) and Zero Angular Rate Updates (ZARU). This article targets the orientation/attitude errors encountered in pedestrian navigation and develops a novel sensor fusion technique to utilize the Earth's magnetic field, even perturbed, for attitude and rate gyroscope error estimation in pedestrian navigation environments where it is assumed that Global Navigation Satellite System (GNSS) navigation is denied. As the Earth's magnetic field undergoes severe degradations in pedestrian navigation environments, a novel Quasi-Static magnetic Field (QSF) based attitude and angular rate error estimation technique is developed to effectively use magnetic measurements in highly perturbed environments. The QSF scheme is then used for generating the desired measurements for the proposed Extended Kalman Filter (EKF) based attitude estimator. Results indicate that the QSF measurements are capable of effectively estimating attitude and gyroscope errors, reducing the overall navigation error budget by over 80% in urban canyon environment.
A New Method for Arbitrarily-Oriented Text Detection in Video (2012)

Text detection in video frames plays a vital role in enhancing the performance of information extraction systems because the text in video frames helps in indexing and retrieving video efficiently and accurately. This paper presents a new method for arbitrarily-oriented text detection in video, based on dominant text pixel selection, text representatives and region growing. The method uses gradient pixel direction and magnitude corresponding to Sobel edge pixels of the input frame to obtain dominant text pixels. Edge components in the Sobel edge map corresponding to dominant text pixels are then extracted and we call them text representatives. We eliminate broken segments of each text representatives to get candidate text representatives. Then the perimeter of candidate text representatives grows along the text direction in the Sobel edge map to group the neighboring text components which we call word patches. The word patches are used for finding the direction of text lines and then the word patches are expanded in the same direction in the Sobel edge map to group the neighboring word patches and to restore missing text information. This results in extraction of arbitrarily-oriented text from the video frame. To evaluate the method, we considered arbitrarily-oriented data, non-horizontal data, horizontal data, Hua's data and ICDAR-2003 competition data (Camera images). The experimental results show that the proposed method outperforms the existing method in terms of recall and f-measure.
Synthesis and Characterization of Defined Branched Poly(propylene)s with Different Microstructures by Copolymerization of Propylene and Linear Ethylene Oligomers (Cn = 26–28) with Metallocenes/MAO Catalysts (2006)

Abstract Summary: Copolymers of propylene and hexacosene (C n = 26–28) were synthesized in the presence of three different metallocene catalysts activated by methylaluminoxane. The poly(propylene) copolymers were prepared with iso‐, syndio‐, and atactic backbone microstructures by using different symmetric metallocenes such as rac ‐{Me 2 Si[2‐Me‐4‐(1‐Naph)Ind] 2 }ZrCl 2 ( 1 ), [Ph 2 C(Cp)(Flu)]ZrCl 2 ( 2 ), and [(H 3 C) 2 Si(9‐Flu) 2 ]ZrCl 2 ( 3 ) and up to 46.6 mol‐% comonomer content in the feed. The influence of the incorporated linear, ethylene‐based side chains into the poly(propylene) backbone were investigated by DSC, GPC, and 13 C NMR. Generally, a decreasing content of comonomer in the feed enhances the activity of metallocene based catalysts. The determination of the branched microstructure by 13 C NMR of the copolymers allows a smart identification of the amount of inserted hexacosene because of the separated backbone and side chain signals. Moreover, the relationship between the population of the side chains and the melting behavior of resulting copolymers were discussed. The melting point of the syndiotactic and isotactic poly(propylene) backbone decreases with increasing hexacosene content. When the inserted comonomer content exceeds 2 mol‐%, a second melting point of the crystallized ethylene based side chains can be observed which increases with an increasing amount of hexacosene. Thermal behavior of isospecific hexacosene/propylene copolymers in dependence on the incorporation of hexacosene. magnified image Thermal behavior of isospecific hexacosene/propylene copolymers in dependence on the incorporation of hexacosene.
Isolation of additional polymorphic clones from the cystic fibrosis region, using chromosome jumping from D7S8. (1989)

The cystic fibrosis (CF) locus has been located, by both linkage analysis and physical mapping, to a 900-kb region of 7q22-31 flanked by D7S8 (J3.11) and D7S23 (XV-2c). Using a 100-kb general jumping library, we isolated two sequential jump clones, J31 and J29, to one side of the D7S8 region and one jump clone, J32, to the other side of D7S8, so that the total region covered is about 300 kb. Three new RFLPs were detected by J29 and J32. Using PFGE mapping and the three jump clones, we found it possible to orient D7S8 on the chromosome and, by linkage analysis, to further narrow the CF region by 100 kb. The orientation of D7S8 will be useful for directing the isolation of other jump clones toward the CF locus. Though the newly described RFLPs are in considerable linkage disequilibrium with D7S8 polymorphisms, they increase the informativeness of genetic markers in the D7S8 region and should be useful in prenatal diagnosis.
Effects of Alum Adjuvant or a Booster Dose on Immunogenicity during Clinical Trials of Group B Streptococcal Type III Conjugate Vaccines (2001)

Phase 1 and 2 clinical trials of group B streptococcal (GBS) capsular polysaccharide (CPS)-protein conjugate vaccines in healthy adults have demonstrated their safety and improved immunogenicity compared with uncoupled CPSs. Two recent trials sought to determine (i) whether adsorption of conjugate vaccine to aluminum hydroxide would improve immunogenicity and (ii) whether the CPS-specific immunoglobulin G (IgG) response could be boosted by administration of a second dose. Adsorption of GBS type III CPS-tetanus toxoid (III-TT) conjugate vaccine to alum did not improve the immune response to a 12.5-microg dose in healthy adult recipients. Four weeks after vaccination, the geometric mean antibody concentrations (GMCs) for the 15 recipients of III-TT with or without alum were 3.3 and 3.6 microg/ml, respectively. In the second trial, 36 healthy adults vaccinated previously with GBS III-TT conjugate were given a second 12.5-microg dose 21 months later. At 4 weeks after the second dose, the GMCs of type III CPS-specific IgG were similar to those measured 4 weeks after the primary vaccination, suggesting a lack of a booster response. However, 8 (22%) of the 36 participants who had undetectable III CPS-specific IgG (<0.05 microg/ml) before the first dose of III-TT conjugate exhibited a booster response to the second dose, with a fourfold-greater GMC of type III CPS-specific IgG than after the initial immunization. These results suggest that prior natural exposure to type III GBS or a related antigen may be responsible for the brisk IgG response to CPS noted in most adults after vaccination. However, a second dose of GBS III-TT conjugate vaccine may be required for adults whose initial CPS-specific IgG concentrations are very low and would also restore the initial peak-specific III CPS-IgG in responders to previous vaccination.
Genomic sequence correction by single‐stranded DNA oligonucleotides: role of DNA synthesis and chemical modifications of the oligonucleotide ends (2005)

We show that, on a chromosomal level, the orientation of the replication fork towards the targeted locus is not central in the strand bias of ssODN-based targeted sequence correction. We demonstrate the importance of accessible ssODN ends for sequence alteration. Finally, we provide evidence for the involvement of DNA synthesis in the process.