gebhart/patrepeval huggingface dataset:
Wavelet-based synchronization of nongated confocal microscopy data for 4D imaging of the embryonic heart (2005)

With the availability of new confocal laser scanning microscopes, fast biological processes, such as the blood flow in living organisms at early stages of the embryonic development, can be observed with unprecedented time resolution. When the object under study has a periodic motion, e.g. a beating embryonic heart, the imaging capabilities can be extended to retrieve 4D data. We acquire nongated slice-sequences at increasing depth and retrospectively synchronize them to build dynamic 3D volumes. Here, we present a synchronization procedure based on the temporal correlation of wavelet features. The method is designed to handle large data sets and to minimize the influence of artifacts that are frequent in fluorescence imaging techniques such as bleaching, nonuniform contrast, and photon-related noise.
Signal segmentation using self-organizing maps (2002)

Segmenting signals into homogeneous regions is performed in many applications. In geophysical well-log segmentation, the data sets consist of various physical measurements made at different depths down a borehole and the task is to segment the data into geologically meaningful units. The self-organizing map is a realization of an artificial neural network and finds wide application in unsupervised classification and pattern recognition problems. The author proposes using a self-organizing map for signal segmentation and demonstrate the technique by segmenting a bore-hole log.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A system for shotgun DNA sequencing (1981)

A multipurpose cloning site has been introduced into the gene for beta-galactosidase (beta-D-galactosidegalactohydrolase, EC 3.21.23) on the single-stranded DNA phage M13mp2 (Gronenborn, B. and Messing, J., (1978) Nature 272, 375-377) with the use of synthetic DNA. The site contributes 14 additional codons and does not affect the ability of the lac gene product to undergo intracistronic complementation. Two restriction endonuclease cleavage sites in the viral gene II were removed by single base-pair mutations. Using the new phage M13mp7, DNA fragments generated by cleavage with a variety of different restriction endonucleases can be cloned directly. The nucleotide sequences of the cloned DNAs can be determined rapidly by DNA synthesis using chain terminators and a synthetic oligonucleotide primer complementary to 15 bases preceeding the new array of restriction sites.
Discrete Magnesium Hydride Aggregates: A Cationic Mg13H18 Cluster Stabilized by NNNN‐Type Macrocycles (2015)

Large magnesium hydride aggregates [Mg13 (Me3 TACD)6 (μ2 -H12 )(μ3 -H6 )][A]2 ((Me3 TACD)H=1,4,7-trimethyl-1,4,7,10-tetraazacyclododecane; A=AlEt4 , AlnBu4 , B{3,5-(CF3 )2 C6 H3 }4 ) were synthesized stepwise from alkyl complexes [Mg2 (Me3 TACD)R3 ] (R=Et, nBu) and phenylsilane in the presence of additional Mg(II) ions. The central magnesium atom is octahedrally coordinated by six hydrides as in solid α-MgH2 of the rutile type. Further coordination to six magnesium atoms leads to a substructure of seven edge-sharing octahedra as found in the hexagonal layer of brucite (Mg(OH)2 ). Upon protonolysis in the presence of 1,2-dimethoxyethane (DME), this cluster was degraded into a tetranuclear dication [Mg2 (Me3 TACD)(μ-H)2 (DME)]2 [A]2 .
IgM binding protein expressed by activated B cells. (1987)

We have identified an IgM binding protein, a single chain polypeptide of Mr 60,000, that is expressed on the surface of B lymphocytes within 18 hr following their activation with phorbol myristate acetate. The IgM binding protein was also detected on fresh leukemic B cells from individuals with chronic lymphocytic leukemia, and the level of its expression was increased after phorbol myristate acetate activation. Resting and phorbol myristate acetate-activated T cells, monocytes, and polymorphonuclear leucocytes did not express detectable amounts of the IgM binding protein. The 60-kDa protein on activated human B cells could bind secreted IgM molecules of both mouse and human origin, as well as endogenous membrane-bound IgM molecules following their cross-linkage with anti-mu antibodies. The binding of soluble IgM molecules to the surface of activated B cells was also demonstrated by indirect immunofluorescence analysis.
Class Prediction by Nearest Shrunken Centroids, with Applications to DNA Microarrays (2003)

We propose a new method for class prediction in DNA microarray studies based on an enhancement of the nearest prototype classifier. Our technique uses "shrunken" centroids as prototypes for each class to identify the subsets of the genes that best characterize each class. The method is general and can be applied to the other high-dimensional classification problems. The method is illustrated on data from two gene expression studies: lymphoma and cancer cell lines.
Messenger RNA sequence and expression of rat pancreatitis-associated protein, a lectin-related protein overexpressed during acute experimental pancreatitis. (1991)

Rat pancreatitis-associated protein (PAP) is an additional protein appearing in pancreatic juice after induction of prancreatic inflammation. Its messenger RNA was cloned and sequenced from pancreas. The deduced amino acid sequence revealed that PAP was synthetized as a preprotein with, in its mature form, a predicted molecular weight of 16,630. A search in protein data bases revealed a marked homology with the carbohydrate binding region of animal lectins; no hemagglutination activity could be shown for PAP, but the protein induced extensive bacterial aggregation. In healthy rats, the very low level of PAP expression in pancreas could be increased up to 4-fold by physiological stimuli such as chronic hormonal or cholinergic stimulation of pancreatic secretion and adaptation of rats to a carbohydrate-rich diet. By contrast, induction of acute experimental pancreatitis by retrograde injection of sodium taurocholate resulted in dramatic overexpression. Pancreatic concentration of PAP mRNA increased more than 300 x within 12 h whereas concentrations of mRNAs encoding major secretory proteins such as amylase decreased. PAP overexpression persisted during the 2 days of the acute phase and then returned to the control level during pancreatic recovery. PAP mRNA could not be evidenced in liver, stomach, salivary glands, brain, kidney, or testis. Its pattern of expression during severe pancreatic aggression suggests that it might be a stress protein involved in the control of bacterial proliferation.
A three base pair deletion encoding the amino acid (lysine-270) in the alpha-cone transducin gene. (2004)

We detected a deletion of a highly conserved lysine at codon 270 in a critical functional area of the alpha-cone transducin molecule. The co-segregation analysis showed that the deletion is not co-inherited with the disease phenotype and therefore is not the disease causing mutation. Apparently the function of this molecule is not altered by this mutation, due to a compensatory effect of aminoacid 271. Taken together, the presence of this deletion in healthy individuals, and our protein modeling results, predict that alpha-cone transducin molecule is able to tolerate structurally and functionally the K270del.
Preparation and characterization of a novel exendin‐4 human serum albumin fusion protein expressed in Pichia pastoris (2007)

A novel recombinant exendin-4 human serum albumin fusion protein (rEx-4/HSA) expressed in Pichia pastoris was prepared and characterized. Ex-4 is a 39-amino acid peptide isolated from the salivary gland of the lizard Heloderma suspectum and is thought to be a novel therapeutic agent for type 2 diabetes. But to gain a continued effect, the peptide has to be injected twice a day owing to its short plasma half-life (t(1/2) = 2.4 h). To extend the half-life of Ex-4 molecule in vivo, we designed a genetically engineered Ex-4/HSA fusion protein. Between Ex-4 and HSA, a peptide linker GGGGS was inserted and the fusion protein was expressed in methylotrophic yeast P. pastoris with native HSA secretion signal sequence. The recombinant protein was secreted correctly and was obtained with high purity (typically > 98%) by a three-step purification procedure. cAMP assay demonstrated that the fusion protein had a bioactivity similar to Ex-4 for interaction with GLP-1 receptors in vitro. Results from oral glucose tolerance test indicated that rEx-4/HSA could effectively improve glucose tolerance in diabetic db/db mice. Pharmacokinetics studies in cynomologus monkeys also showed that rEx-4/HSA had a much longer plasma half-life. Therefore, rEx-4/HSA fusion protein could potentially be used as a new recombinant biodrug for type 2 diabetes therapy.
Diabetes in Elderly Adults (2001)

Diabetes is common in the elderly population. By the age of 75, approximately 20% of the population are afflicted with this illness. Diabetes in elderly adults is metabolically distinct from diabetes in younger patient populations, and the approach to therapy needs to be different in this age group. Diabetes is associated with substantial morbidity from macro- and microvascular complications. Several lines of evidence suggest that optimal glycemic control and risk factor modification can substantially reduce the risk of complications in elderly patients. In the past, treatment options were limited. However, recent studies have delineated several new and exciting therapeutic opportunities for elderly patients with diabetes.
Evidence for large domains of similarly expressed genes in the Drosophila genome (2002)

Groups of adjacent and co-regulated genes that are not otherwise functionally related in any obvious way can be identified by expression profiling in Drosophila. The mechanism underlying this phenomenon is not yet known.
Syntheses and Properties of Some N-Substituted Sulfamides (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSyntheses and Properties of Some N-Substituted SulfamidesANTONIO VANDI, THERALD MOELLER, and LUDWIG F. AUDRIETHCite this: J. Org. Chem. 1961, 26, 4, 1136–1138Publication Date (Print):April 1, 1961Publication History Published online1 May 2002Published inissue 1 April 1961https://doi.org/10.1021/jo01063a039RIGHTS & PERMISSIONSArticle Views339Altmetric-Citations24LEARN 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 InReddit PDF (354 KB) Get e-Alertsclose Get e-Alerts
Discrete-Time Channelizers for Aeronautical Telemetry: Part II - Variable Bandwidth (2012)

ITC/USA 2012 Conference Proceedings / The Forty-Eighth Annual International Telemetering Conference and Technical Exhibition / October 22-25, 2012 / Town and Country Resort & Convention Center, San Diego, California
Novel Styrene−Butadiene Copolymers by Ring-Opening Metathesis Polymerization (2000)

The possibilities offered by the ring-opening metathesis polymerization (ROMP) of macromonomers were exploited to arrange polystyrene (PS) and polybutadiene (PB) subchains in various topologies. PSn-b-PBm and PSn-co-PBm miktoarm stars were obtained by sequential and statistical polymerization of norbornene-terminated PS and PB macromonomers, whereas (PS-b-PB)n star block copolymers were derived by homopolymerization of the corresponding macromonomers via ROMP. Umbrella-type and dumbbell-shaped copolymers are two other architectures that were prepared through the sequential ROMP of ω-norbornenyl PS macromonomer and cyclooctadiene.
Spatially Selective Manipulation of Supported Lipid Bilayers by Laminar Flow:  Steps Toward Biomembrane Microfluidics (2002)

The ability to manipulate supported lipid bilayers after formation on a substrate has made possible new classes of both molecular and cellular level experiments. In this report, we combine the unique properties of these lipid systems with laminar flow concepts to selectively remove, collect, and reconstitute lipid bilayers from specified regions of a surface. A stream of detergent solution was directed over a preformed bilayer, resulting in the removal of bilayer material; mixing between adjacent flows at low Reynolds number is diffusion limited, providing confinement of this stripping solution and, consequently, bilayer removal with precision on the order of several micrometers. The freshly exposed surface allows formation of new connected bilayer when exposed to lipid vesicles. In conjunction with surface micropatterning and electrophoretic manipulation, we further demonstrate a first-generation, membrane-based separation/purification strategy. Flow-based manipulation of lipid bilayers forms the basis of biomembrane microfluidics. In particular, the directed introduction of lipids or other materials provides a route toward dynamic formation and erasure of barriers to lipid diffusion. As examples of future applications of these methods, we discuss the separation of mobile from immobile membrane components and a route toward spatially resolved label-free analysis of composition gradients in patterned supported membranes.
Aminoglycosides: Activity and Resistance (1999)

Aminoglycosides are highly potent, broad-spectrum antibiotics with many desirable properties for the treatment of life-threatening infections ([28][1]). Their history begins in 1944 with streptomycin and was thereafter marked by the successive introduction of a series of milestone compounds (
Concomitant suppression of hyperlipidemia and intestinal polyp formation in Apc-deficient mice by peroxisome proliferator-activated receptor ligands. (2003)

Epidemiological studies have shown a positive association of colon cancer with hyperlipidemia. Furthermore, signaling generated by peroxisome proliferator-activated receptor (PPAR) alpha and gamma ligands, suggested to be candidate tumor preventive agents, has been shown to lower serum triglyceride levels. In the present study, we assessed hyperlipidemia in Apc-deficient mice, model animals for human familial adenomatous polyposis, and examined the effects of pioglitazone and bezafibrate, respectively, PPARgamma and PPARalpha agonists, on both hyperlipidemia and intestinal polyposis. Serum lipid levels in Apc(1309) mice and Min mice from 6 to 15 weeks of age were measured. Although serum levels of triglyceride and cholesterol were low in both Apc(1309) and wild-type mice at 6 weeks, triglycerides were elevated 10-fold in Apc(1309) mice by the age of 12 weeks but not in their wild-type counterparts. Cholesterol was also increased significantly, and marked centrilobular-restricted steatosis was observed in the livers of aged Apc(1309) mice. Similar findings were observed for Min mice at 15 weeks of age. Moreover, lipoprotein lipase mRNA levels in the liver and small intestine of Apc(1309) and Min mice were demonstrated to be lower than those in wild-type mice. Treatment of Apc(1309) mice with 100 and 200 ppm pioglitazone or bezafibrate for 6 weeks from 6 weeks of age caused dose-dependent reduction in serum triglycerides and cholesterol, along with reduction in the numbers of intestinal polyps to 67% of the control value. The present study clearly demonstrated a hyperlipidemic state in Apc gene-deficient mice and a potential of PPARalpha and PPARgamma ligands to suppress both hyperlipidemia and polyp formation. Hyperlipidemia in these mice may thus be associated with their intestinal lesion development.
Toroidal hollow-core microcavities produced by self-rolling of strained polymer bilayer films (2008)

Hollow-core toroidal micro-cavities are obtained by self-rolling of double-layer (polyvinyl pyridine/polystyrole) polymer films. Rolling of the bilayer is due to preferential swelling of the polyvinyl pyridine in water solution of dodecyl benzene sulfonic acid. The tube formation proceeds from a circular opening in the film made by photolithography or by mechanical scratching. The toroid equilibrium dimensions are determined by the balance of the elastic energy relaxation via the film scrolling and the work of the in-plane stretching that is due to increasing radius of the toroid. The principal features of the micro-toroid formation process are captured by a simple analytical model. The inner walls of the cavities can be made metal coated. To this aim, the polymer bilayer can be metallized by vacuum sputtering prior to lithographic patterning and rolling of the bilayer. The toroids with metallic inner surface are promising for the future research as IR-frequency range resonators.
Specification of the germ cell lineage in mice: A process orchestrated by the PR-domain proteins, Blimp1 and Prdm14 (2008)

Germ cell specification in mice, which generates primordial germ cells (PGCs), the common source of the oocytes and spermatozoa, from the epiblast, integrates three key events: repression of the somatic program, re-acquisition of potential pluripotency, and genome-wide epigenetic reprogramming. A PR-domain containing protein, Blimp1 (also known as Prdm1), has been identified as a critical factor for PGC specification. Using a highly representative single-cell microarray technology, we identified a complex but highly ordered genome-wide transcription dynamics associated with PGC specification. This analysis not only demonstrated a dominant role of Blimp1 for the repression of the genes normally downregulated in PGCs relative to their somatic neighbors, but also revealed the presence of gene expression programs initiating independently from Blimp1. Among such programs, we identified Prdm14, another PR-domain containing protein, as a key regulator for the re-acquisition of potential pluripotency and genome-wide epigenetic reprogramming. The launch of the germ cell lineage in mice, therefore, is orchestrated by two independently acquired, PR domain-containing transcriptional regulators, Blimp1 and Prdm14.
Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis (1998)

The ability to accurately predict gene function based on gene sequence is an important tool in many areas of biological research. Such predictions have become particularly important in the genomics age in which numerous gene sequences are generated with little or no accompanying experimentally determined functional information. Almost all functional prediction methods rely on the identification, characterization, and quantification of sequence similarity between the gene of interest and genes for which functional information is available. Because sequence is the prime determining factor of function, sequence similarity is taken to imply similarity of function. There is no doubt that this assumption is valid in most cases. However, sequence similarity does not ensure identical functions, and it is common for groups of genes that are similar in sequence to have diverse (although usually related) functions. Therefore, the identification of sequence similarity is frequently not enough to assign a predicted function to an uncharacterized gene; one must have a method of choosing among similar genes with different functions. In such cases, most functional prediction methods assign likely functions by quantifying the levels of similarity among genes. I suggest that functional predictions can be greatly improved by focusing on how the genes became similar in sequence (i.e., evolution) rather than on the sequence similarity itself. It is well established that many aspects of comparative biology can benefit from evolutionary studies (Felsenstein 1985), and comparative molecular biology is no exception (e.g., Altschul et al. 1989; Goldman et al. 1996). In this commentary, I discuss the use of evolutionary information in the prediction of gene function. To appreciate the potential of a phylogenomic approach to the prediction of gene function, it is necessary to first discuss how gene sequence is commonly used to predict gene function and some general features about gene evolution.
Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence (2004)

Discrete RNA secondary and higher-order structures, typically local in extent, play a fundamental role in RNA virus replication. Using new bioinformatics analysis methods, we have identified genome-scale ordered RNA structure (GORS) in many genera and families of positive-strand animal and plant RNA viruses. There was remarkably variability between genera that possess this characteristic; for example, hepaciviruses in the family Flaviviridae show evidence for extensive internal base-pairing throughout their coding sequences that was absent in both the related pestivirus and flavivirus genera. Similar genus-associated variability was observed in the Picornaviridae, the Caliciviridae, and many plant virus families. The similarity in replication strategies between genera in each of these families rules out a role for GORS in a fundamentally conserved aspect of this aspect of the virus life cycle. However, in the Picornaviridae, Flaviviridae, and Caliciviridae, the existence of GORS correlated strongly with the ability of each genus to persist in their natural hosts. This raises the intriguing possibility of a role for GORS in the modulation of innate intracellular defense mechanisms (and secondarily, the acquired immune system) triggered by double-stranded RNA, analogous in function to the expression of structured RNA transcripts by large DNA viruses. Irrespective of function, the observed evolutionary conservation of GORS in many viruses imposes a considerable constraint on genome plasticity and the consequent narrowing of sequence space in which neutral drift can occur. These findings potentially reconcile the rapid evolution of RNA viruses over short periods with the documented examples of extreme conservatism evident from their intimate coevolution with their hosts.
Filamentous hemagglutinin of Bordetella pertussis: nucleotide sequence and crucial role in adherence. (1989)

Filamentous hemagglutinin is a surface-associated adherence protein of Bordetella pertussis, which is a component of some new acellular pertussis vaccines. The nucleotide sequence of an open reading frame that encompasses the filamentous hemagglutinin structural gene, fhaB, suggests that proteolytic processing is necessary to generate the mature 220-kDa filamentous hemagglutinin product. An Arg-Gly-Asp (RGD) tripeptide is found within filamentous hemagglutinin that may be involved in its adherence properties. An internal in-frame deletion in fhaB, encompassing the RGD region, causes loss of B. pertussis-binding to ciliated eukaryotic cells, confirming a potential role for this protein in host-cell binding and infection.