gebhart/patrepeval huggingface dataset:
Rapid and efficient resolution of parentage by amplification of short tandem repeats. (1994)

Short tandem repeat (STR) loci are highly informative polymorphic loci that are gaining popularity for identity testing. We have conducted parentage testing by using nine STR loci on 50 paternity trios that had been previously tested using VNTR loci. These nine unlinked STR loci are amplified in three multiplex reactions and, when examined for genetic informativeness, provide a combined average power of exclusion of 99.73% (Caucasian data). The informative value of the selected loci is based on extensive STR typing of four racial/ethnic populations. In 37 of the 50 cases, paternity could not be excluded by any of the loci. In the remaining 13 cases, paternity was excluded by at least two of the STR markers. The probability of paternity calculated for the alleged father of each matching trio was > 99% in 36 of the 37 inclusion cases. All data agreed with the results reported using VNTR loci and conventional Southern technology. Our studies validate the use of DNA typing with STR loci for parentage testing, thus providing an accurate, highly sensitive, and rapid assay.
xIP-seq Platform: An Integrative Framework for High-Throughput Sequencing Data Analysis (2009)

We report an integrative bioinformatic platform for next-generation sequencing data analysis, xIP-seq, which is built on GenePattern package. The purpose for this tool is to provide analysis pipelines for data derived from next-generation sequencing following a variety of experiments using immunoprecipitation, such as ChIP-seq (chromatin immunoprecipitation following sequencing) for analysis of DNA binding protein, CLIP-seq (cross-linking immunoprecipitation following sequencing) for analysis of RNA binding protein, and MeDIP-seq (methylation DNA immunoprecipitation following sequencing) for DNA methylation profiles. xIP-seq platform provides standardized data pre-processing workflows which prepare raw data from various sequencing platforms for further analysis, and several bioinformatic applications including sequence annotation and analysis of Pol II binding pattern and histone modification.. The tertiary module for sequence annotation is particularly discussed. xIP-seq also allows users to construct new analysis pipelines tailored for individual biological interests by employing currently available modules or creating new ones. As an example, a ldquoCLIP-seq Mapperrdquo pipeline is created to map CLIP-seq-derived data to human genome to identify the genome-wide annotation of SFRS1 binding pattern. This implementation demonstrates the significance of xIP-seq platform to analyze massive amounts of next-generation sequencing data and provide automatic, flexible, and intelligent enterprise-level bioinformatic solutions.
The relationship of gap junctions and compaction in the preimplantation mouse embryo (1992)

In the mouse embryo, gap junctions first appear at the 8-cell stage as compaction is about to take place. Compaction of the embryo is important for the differentiation of the first two cell types; the inner cell mass and the trophectoderm. Our studies examine the contribution of gap junctional communication at this stage of development. We have characterised the normal sequence of appearance of gap junction protein and its distribution. The extent of communication as shown by the passage of dye between cells has been recorded in both normal embryos and embryos treated with drugs that influence gap junctional communication. Comparisons have been made with embryos that express a lethal gap junction defect and attempts were made to rescue such embryos by increasing their gap junction communication.
The high grain protein content gene Gpc-B1 accelerates senescence and has pleiotropic effects on protein content in wheat (2006)

High grain protein content (GPC) is a frequent target of wheat breeding programmes because of its positive effect on bread and pasta quality. A wild wheat allele at the Gpc-B1 locus with a significant impact on this trait was identified previously. The precise mapping of several senescence-related traits in a set of tetraploid recombinant substitution lines (RSLs) segregating for Gpc-B1 is reported here. Flag leaf chlorophyll degradation, change in peduncle colour, and spike water content were completely linked to the Gpc-B1 locus and to the differences in GPC within a 0.3 cM interval corresponding to a physical distance of only 250 kb. The effect of Gpc-B1 was also examined in different environments and genetic backgrounds using a set of tetraploid and hexaploid pairs of isogenic lines. The results were consistent with those observed in the RSLs. The high GPC allele conferred a shorter duration of grain fill due to earlier flag leaf senescence and increased GPC in all four genetic backgrounds. The effect on grain size was more variable, depending on the genotype-environment combinations. These results are consistent with a model in which the wild-type allele of Gpc-B1 accelerates senescence in flag leaves producing pleiotropic effects on nitrogen remobilization, total GPC, and grain size.
Synthesis of fluorine analogues of vitamin E. II. Synthesis of 2-(3-chloropropyl)-2,5,7,8-tetramethyl-6-chromanol and its application for stereocontrolled Wittig reaction with trifluoromethyl ketones. (1988)

As the extension of our research to find a biologically active analogue of vitamin E, a more convenient method for the synthesis of fluorine derivatives of 6-chromanol than our previous method was developed. Thus, 2-(3-chloropropyl)-2, 5, 7, 8-tetramethyl-6-chromanol (3) was synthesized by the reaction of 6-chloro-3-methyl-2-hexen-1-ol (2) and trimethylhydroquinone, and the phosphonium ylides (5 and 6) derived from 3 were condensed with trifluoromethylated ketones to give 2-(trifluoroprenyl)-6-chromanol compounds (1a, 1b and 1c) by means of the Wittig reaction as modified by Schlosser. By the use of this revised procedure, the total yields of the chromanols were much improved. Further, the modified Wittig reaction showed higher stereoselectivity than the previous syntheses of these compounds. The double bonds of the side-chain of the products were reduced to give fluorine derivatives of tocopherol analogues. Compound 3 was found to be a useful intermediate for the facile synthesis of vitamin E derivatives.
Synthesis of small molecule inhibitors targeting signal transduction pathways (2009)

The main aim of the study described in this thesis is the development of small molecules as inhibitors targeting signal transduction pathways, thereby treating cancer. We attempted to synthesize compounds based on the hits obtained from high throughput screening of the Chemdiv diversity set compounds. Chapter One is a general introduction to cancer, history of chemotherapeutic drugs and an introduction to signal transduction pathways. The following two chapters briefly introduce the biological targets in the authors study. Chapter Two describes the role of B-cell lymphoma type xL (Bcl-xL), in apoptosis and the development of drugs targeting Bcl-xL. Examples of Bcl-xL drugs relevant to this study have been provided.\nChapter Three introduces Src homology 2 (SH2) domain containing tyrosine phosphatase Shp2, a protein tyrosine phosphatase, as an oncogene, its role in signal transduction pathways and the recent developments in drug development towards the inhibition of this oncogene. Chapter Four gives a general introduction to microwave-assisted organic synthesis and its advantages. This chapter also describes the use of flow reactors in organic synthesis and its advantages. The following two chapters describe the author's own findings. Chapter Five focuses on the design, synthesis and biological evaluation of small molecules as inhibitors of Bcl-xL. Isoquinolinols, NSC-131734 and HL2-100 emerged as lead compounds from high throughput screening for Bcl-xL. Our strategy focused on identifying an isoquinolinol lead with increased potency.\nBased on isatin hits obtained earlier through HTS screen and SAR studies in our lab, more isatin derivatives were synthesized focusing on developing inhibitors with increased cell permeability and improved potency.
Sesquipedalianists, Seek No Longer (2002)

Most actual and incipient logologists seem to pass through of being fascinated by long words, and raising such questions as what is the longest word in English or American. One reason for the eventual passing of this phase, for most of us, is the eventual realization of the fact that, as it is by no means simple to decide what counts as a word.
Factors That Influence Helical Preferences for Singly Charged Gas-Phase Peptide Ions: The Effects of Multiple Potential Charge-Carrying Sites (2009)

Ion mobility-mass spectrometry is used to investigate the structure(s) of a series of model peptide [M + H](+) ions to better understand how intrinsic properties affect structure in low dielectric environments. The influence of peptide length, amino acid sequence, and composition on gas-phase structure is examined for a series of model peptides that have been previously studied in solution. Collision cross sections for the [M + H](+) ions of Ac-(AAKAA)(n)Y-NH(2) (n = 3-6) and Ac-Y(AEAAKA)(n)F-NH(2) (n = 2-5) are reported and correlated with candidate structures generated using molecular modeling techniques. The [M + H](+) ions of the AAKAA peptide series each exhibit a single, dominant ion mobility arrival time distribution (ATD) which correlates to partial helical structures, whereas the [M + H](+) ions of the AEAAKA ion series are composed of ATDs which correlate to charge-solvated globules (i.e., the charge is coordinated or solvated by polar peptide functional groups). These data raise numerous questions concerning intrinsic properties (amino acid sequence and composition as well as charge location) that dictate gas-phase peptide ion structure, which may reflect trends for peptide ion structure in low dielectric environments, such as transmembrane segments.
Ab initio computational modeling of loops in G‐protein‐coupled receptors: Lessons from the crystal structure of rhodopsin (2006)

With the help of the crystal structure of rhodopsin an ab initio method has been developed to calculate the three-dimensional structure of the loops that connect the transmembrane helices (TMHs). The goal of this procedure is to calculate the loop structures in other G-protein coupled receptors (GPCRs) for which only model coordinates of the TMHs are available. To mimic this situation a construct of rhodopsin was used that only includes the experimental coordinates of the TMHs while the rest of the structure, including the terminal domains, has been removed. To calculate the structure of the loops a method was designed based on Monte Carlo (MC) simulations which use a temperature annealing protocol, and a scaled collective variables (SCV) technique with proper structural constraints. Because only part of the protein is used in the calculations the usual approach of modeling loops, which consists of finding a single, lowest energy conformation of the system, is abandoned because such a single structure may not be a representative member of the native ensemble. Instead, the method was designed to generate structural ensembles from which the single lowest free energy ensemble is identified as representative of the native folding of the loop. To find the native ensemble a successive series of SCV-MC simulations are carried out to allow the loops to undergo structural changes in a controlled manner. To increase the chances of finding the native funnel for the loop, some of the SCV-MC simulations are carried out at elevated temperatures. The native ensemble can be identified by an MC search starting from any conformation already in the native funnel. The hypothesis is that native structures are trapped in the conformational space because of the high-energy barriers that surround the native funnel. The existence of such ensembles is demonstrated by generating multiple copies of the loops from their crystal structures in rhodopsin and carrying out an extended SCV-MC search. For the extracellular loops e1 and e3, and the intracellular loop i1 that were used in this work, the procedure resulted in dense clusters of structures with Calpha-RMSD approximately 0.5 angstroms. To test the predictive power of the method the crystal structure of each loop was replaced by its extended conformations. For e1 and i1 the procedure identifies native clusters with Calpha-RMSD approximately 0.5 angstroms and good structural overlap of the side chains; for e3, two clusters were found with Calpha-RMSD approximately 1.1 angstroms each, but with poor overlap of the side chains. Further searching led to a single cluster with lower Calpha-RMSD but higher energy than the two previous clusters. This discrepancy was found to be due to the missing elements in the constructs available from experiment for use in the calculations. Because this problem will likely appear whenever parts of the structural information are missing, possible solutions are discussed.
Impact of management guidelines on the outcome of severe community acquired pneumonia (1997)

Management guidelines for severe community acquired pneumonia have been widely adopted but without a reduction in mortality in our hospital. Factors other than early diagnosis, appropriate antibiotics, or prompt ICU transfer may influence the outcome in severe community acquired pneumonia.
Shell-less culture of the chick embryo as a model system in the study of developmental neurobiology (2004)

Experimental studies on animal models play essential roles in the development of preventive, diagnostic and therapeutic procedures for diseases in a wide spectrum of fields including neurological sciences. The goal of this study was to demonstrate the shell-less culture system of the chick embryo as a potential experimental model in the field of developmental neurobiology. We were able to observe and record the central nervous system development of a vertebrate embryo in an artificial experimental culture container starting from an early, three-vesicle brain stage up to a well-developed five-vesicle brain stage with an embryo survival rate of 100%. Thus, this model system has the potential to enhance our knowledge on molecular and developmental neurobiology at both basic and clinical science level. © neuroanatomy.org.
Efficient and precise interactive hand tracking through joint, continuous optimization of pose and correspondences (2016)

Fully articulated hand tracking promises to enable fundamentally new interactions with virtual and augmented worlds, but the limited accuracy and efficiency of current systems has prevented widespread adoption. Today's dominant paradigm uses machine learning for initialization and recovery followed by iterative model-fitting optimization to achieve a detailed pose fit. We follow this paradigm, but make several changes to the model-fitting, namely using: (1) a more discriminative objective function; (2) a smooth-surface model that provides gradients for non-linear optimization; and (3) joint optimization over both the model pose and the correspondences between observed data points and the model surface. While each of these changes may actually increase the cost per fitting iteration, we find a compensating decrease in the number of iterations. Further, the wide basin of convergence means that fewer starting points are needed for successful model fitting. Our system runs in real-time on CPU only, which frees up the commonly over-burdened GPU for experience designers. The hand tracker is efficient enough to run on low-power devices such as tablets. We can track up to several meters from the camera to provide a large working volume for interaction, even using the noisy data from current-generation depth cameras. Quantitative assessments on standard datasets show that the new approach exceeds the state of the art in accuracy. Qualitative results take the form of live recordings of a range of interactive experiences enabled by this new approach.
Identification of a Cytoplasmic-Retention Sequence in ERK2 (1999)

A key step in the signaling mechanism of the mitogen-activated protein kinase/extracellular signal-responsive kinase (ERK) cascade is its translocation into the nucleus where it regulates transcription and other nuclear processes. In an attempt to characterize the subcellular localization of ERK2, we fused it to the 3'-end of the gene expressing green fluorescent protein (GFP), resulting in a GFP-ERK2 protein. The expression of this construct in CHO cells resulted in a nuclear localization of the GFP-ERK2 protein. However, coexpression of the GFP-ERK2 with its upstream activator, MEK1, resulted in a cytosolic retention of the GFP-ERK2, which was the result of its association with MEK1, and was reversed upon stimulation. We then examined the role of the C-terminal region of ERK2 in its subcellular localization. Substitution of residues 312-319 of GFP-ERK2 to alanine residues prevented the cytosolic retention of ERK2 as well as its association with MEK1, without affecting its activity. Most important for the cytosolic retention are three acidic amino acids at positions 316, 319, and 320 of ERK2. Substitution of residues 321-327 to alanines impaired the nuclear translocation of ERK2 upon mitogenic stimulation. Thus, we conclude that residues 312-320 of ERK2 are responsible for its cytosolic retention, and residues 321-327 play a role in the mechanism of ERK2 nuclear translocation.
The chloroplast import receptor is an integral membrane protein of chloroplast envelope contact sites. (1990)

A chloroplast import receptor from pea, previously identified by antiidiotypic antibodies was purified and its primary structure deduced from its cDNA sequence. The protein is a 36-kD integral membrane protein (p36) with eight potential transmembrane segments. Fab prepared from monospecific anti-p36 IgG inhibits the import of the ribulose-1,5-bisphosphate carboxylase small subunit precursor (pS) by interfering with pS binding at the chloroplast surface. Anti-p36 IgGs are able to immunoprecipitate a Triton X-100 soluble p36-pS complex, suggesting a direct interaction between p36 and pS. This immunoprecipitation was specific as it was abolished by a pS synthetic transit peptide, consistent with the transit sequence receptor function of p36. Immunoelectron microscopy localized p36 to regions of the outer chloroplast membrane that are in close contact with the inner chloroplast membrane. Comparison of the deduced sequence of pea p36 to that of other known proteins indicates a striking homology to a protein from spinach chloroplasts that was previously suggested to be the triose phosphate-3-phosphoglycerate-phosphate translocator (phosphate translocator) (Flügge, U. I., K. Fischer, A. Gross, W. Sebald, F. Lottspeich, and C. Eckerskorn. 1989. EMBO (Eur. Mol. Biol. Organ.) J. 8:39-46). However, incubation of Triton X-100 solubilized chloroplast envelope material with hydroxylapatite indicated that p36 was quantitatively absorbed, whereas previous reports have shown that phosphate translocator activity does not bind to hydroxylapatite (Flügge, U. I., and H. W. Heldt. 1981. Biochim. Biophys. Acta. 638:296-304. These data, in addition to the topology and import inhibition data presented in this report support the assignment of p36 as a receptor for chloroplast protein import, and argue against the assignment of the spinach homologue of this protein as the chloroplast phosphate translocator.
Molecular cloning of seven mouse immunoglobulin .kappa. chain messenger ribonucleic acids (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular cloning of seven mouse immunoglobulin .kappa. chain messenger ribonucleic acidsNicholas M. Gough, Elizabeth A. Webb, Suzanne Cory, and Jerry M. AdamsCite this: Biochemistry 1980, 19, 12, 2702–2710Publication Date (Print):June 10, 1980Publication History Published online1 May 2002Published inissue 10 June 1980https://pubs.acs.org/doi/10.1021/bi00553a026https://doi.org/10.1021/bi00553a026research-articleACS PublicationsRequest reuse permissionsArticle Views44Altmetric-Citations22LEARN 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
Towards Location Based QoS-Aware Network Selection Mechanism for the Nomadic Mobile Services (2009)

The advances in the area of location based computing will soon make it feasible to predict the availability of wireless networks and their application level Quality of Service (QoS) characteristics along the location and time dimensions. Such predictions are referred to as QoS predictions which are provided by the QoS Context Source (QoSCS) hosted in the fixed network. Herewith we present a network selection mechanism on the mobile device which requests QoS predictions as needed and uses these predictions combined with the current location and time to select the wireless network which satisfies QoS requirements of the services hosted on a mobile device. We evaluate the performance of the proposed scheme using simulations and compare the results with the other mechanism that only uses information locally available on the mobile device for the network selection. The results obtained from the simulations encourage further system development and prototyping.
An insulin-like growth factor I/insulin hybrid exhibiting high potency for interaction with the type I insulin-like growth factor and insulin receptors of placental plasma membranes. (1990)

We have prepared by semisynthetic methods a two-chain insulin/insulin-like growth factor I hybrid that contains a synthetic peptide related to residues 22-41 of insulin-like growth factor I linked via peptide bond to ArgB22 of des-octapeptide-(B23-B30)-insulin and have applied the analog to the analysis of ligand interactions with the type I insulin-like growth factor and insulin receptors of placental plasma membranes. Relative potencies for the inhibition of 125I-labeled insulin-like growth factor I binding to type I insulin-like growth factor receptors were 1.0:0.20:0.003 for insulin-like growth factor I, the hybrid analog, and insulin, respectively. Corresponding relative potencies for the inhibition of 125I-labeled insulin binding to insulin receptors were 0.007:0.28:1 for the three respective peptides. Additional studies identified that the hybrid analog interacts with only one of two populations of insulin-like growth factor I binding sites on placental plasma membranes and permitted the analysis of insulin-like growth factor I interactions with the separate populations of binding sites. We conclude that (a) des-octapeptide-(B23-B30)-insulin can serve well as a scaffold to support structural elements of insulin-like growth factor I and insulin necessary for high affinity binding to their receptors, (b) major aspects of structure relevant to the conferral of receptor binding affinity lie in the COOH-terminal region of the insulin B chain and in the COOH-terminal region of the insulin-like growth factor I B domain and in its C domain, and (c) the evolution of ligand-receptor specificity in these systems has relied as much on restricting interactions (through the selective introduction of negative structural elements) as it has on enhancing interactions (through the introduction of affinity conferring elements of structure).