gebhart/patrepeval huggingface dataset:
Ultrasonic Testing for Determining Dynamic Soil Moduli (1978)

Determination of dynamic E- and G-moduli of a silty clay material were made by measuring directly the velocity of both ultrasonic longitudinal and shear waves transmitted through the material. The equipment, developed at the University of Missouri-Rolla, allows dynamic, nondestructive testing of soil materials to be conducted rapidly and easily.
A micro-watt metal-insulator-solution-transport (MIST) device for scalable digital bio-microfluidic systems (2002)

In this work new data, models, and applications are presented of an ultra-low power, microfluidic device for use in integrated bio-microelectrofluidic systems (Bio-MEFS). The metal-insulator-solution transport (MIST) device is based on the high-speed manipulation of discrete droplets of analytes and reagents under voltage control, and is the MOSFET equivalent for MEFS.
Affinity of the interaction between Fcgamma receptor type III (FcγRIII) and monomeric human IgG subclasses. Role of FcγRIII glycosylation (1997)

Binding of the Fc region of IgG antibodies to low affinity Fc gamma receptors (Fc gammaR) triggers important effector functions in the immune system. The type IIIb Fc gammaR (Fc gammaRIIIb or CD16) is a heavily glycosylated protein anchored to the membrane of neutrophils by a glycosylphosphatidylinositol link. This receptor contributes to cell activation by IgG immune complexes. To better understand the nature of the ligand-receptor association, we have studied the affinity and kinetics of the interaction between human IgG subclasses and two soluble forms of Fc gammaRIIIb (sFc gammaRIIIb or sCD16) corresponding to the 188 N-terminal amino acids of the extracellular region of the receptor, a glycosylated one made in eucaryotic cells (euc.sCD16) and a non-glycosylated one (proc.sCD16) made in Escherichia coli. Experiments using a BIAcore instrument, to measure protein binding in real time, showed that monomeric human IgG1 and IgG3, but not IgG2, IgG4, IgA and divalent antigen-binding fragments (F(ab')2) of IgG1, bound to immobilized euc.sCD16 with an affinity constant (K(A)) of 1.3 +/- 0.6 x 10(6) M(-1) and 2.6 +/- 0.4 x 10(5) M(-1), respectively. The affinity constant of proc.sCD16 for human IgG1 was in the same range (1.1 +/- 0.2 x 10(6) M(-1)), whereas that for human IgG3 was twofold higher (4.2 +/- 0.4 x 10(5) M(-1)). The specificity of the non-glycosylated receptor for human IgG subclasses bound to Sepharose was IgG1 > IgG3 >> IgG4 >>> IgG2. Thus, the extracellular polypeptide of Fc gammaRIIIb dictates the interaction of the receptor with IgG subclasses although glycosylation plays an inhibitory role in the interaction with human IgG3.
Comparative Complete Genome Sequence Analysis of the Amino Acid Replacements Responsible for the Thermostability ofCorynebacterium efficiens (2003)

Corynebacterium efficiens is the closest relative of Corynebacterium glutamicum, a species widely used for the industrial production of amino acids. C. efficiens but not C. glutamicum can grow above 40 degrees C. We sequenced the complete C. efficiens genome to investigate the basis of its thermostability by comparing its genome with that of C. glutamicum. The difference in GC content between the species was reflected in codon usage and nucleotide substitutions. Our comparative genomic study clearly showed that there was tremendous bias in amino acid substitutions in all orthologous ORFs. Analysis of the direction of the amino acid substitutions suggested that three substitutions are important for the stability of the C. efficiens proteins: from lysine to arginine, serine to alanine, and serine to threonine. Our results strongly suggest that the accumulation of these three types of amino acid substitutions correlates with the acquisition of thermostability and is responsible for the greater GC content of C. efficiens.
Local Microcode Compaction Techniques (1980)

article Free Access Share on Local Microcode Compaction Techniques Authors: David Landskov University of Southwestern Louisiana, Computer Science Department, P.O. Box 44330 U.S.L., Lafayette, Louisiana University of Southwestern Louisiana, Computer Science Department, P.O. Box 44330 U.S.L., Lafayette, LouisianaView Profile , Scott Davidson University of Southwestern Louisiana, Computer Science Department, P.O. Box 44330 U.S.L., Lafayette, Louisiana University of Southwestern Louisiana, Computer Science Department, P.O. Box 44330 U.S.L., Lafayette, LouisianaView Profile , Bruce Shriver University of Southwestern Louisiana, Computer Science Department, P.O. Box 44330 U.S.L., Lafayette, Louisiana University of Southwestern Louisiana, Computer Science Department, P.O. Box 44330 U.S.L., Lafayette, LouisianaView Profile , Patrick W. Mallett Computer Sciences Corporation, 6565 Arlington Boulevard, Falls Church, Virginia Computer Sciences Corporation, 6565 Arlington Boulevard, Falls Church, VirginiaView Profile Authors Info & Claims ACM Computing SurveysVolume 12Issue 3Sept. 1980 pp 261–294https://doi.org/10.1145/356819.356822Published:01 September 1980Publication History 246citation843DownloadsMetricsTotal Citations246Total Downloads843Last 12 Months43Last 6 weeks7 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Apocalmodulin and Ca2+-Calmodulin Bind to Neighboring Locations on the Ryanodine Receptor (2002)

Calmodulin (CaM) binds to the ryanodine receptor/calcium release channel of skeletal muscle (RyR1), both in the absence and presence of Ca(2+), and regulates the activity of the channel activity by activating and inhibiting it, respectively. Using cryo-electron microscopy and three-dimensional reconstruction, we found that one apoCaM binds per RyR1 subunit along the sides of the cytoplasmic assembly of the receptor. This location is distinct from but close to the location found for Ca(2+)-CaM, providing a structural basis for efficient switching of CaM between these two positions with the oscillating intracellular Ca(2+) concentration that generates muscle relaxation/contraction cycles. The locations of apoCaM and Ca(2+)-CaM at a critical region for RYR1-dihydropyridine receptor interaction are suggestive of a direct role for CaM in the mechanism of excitation-contraction coupling.
Studies of seven-membered heterocycles. XXXII. Synthesis of N-unsubstituted 1H-1,4-benzodiazepines stabilized by intramolecular hydrogen bonding. (1990)

The stable N-unsubstituted 1H-1, 4-benzodiazepines (12a-l) having a carbonyl group or its analogue at the 2- or 9-position were prepared from the 4-azidoquinolines (13a-l) by photoreaction in the presence of sodium methoxide.It is known that N-unsubstituetd 1H-1, 4-benzodiazepines having no carbonyl group are too unstable to be isolated.Based on the spectral data, the benzodiazepines (12) isolated are assumed to be stabilized by intramolecular hydrogen bonding between the 1-NH hydrogen and the 2- or 9-carbonyl oxygen, thus allowing their isolation.
TCP-Africa: an adaptive and fair rapid increase rule for scalable TCP (2005)

High capacity data transfers over the Internet routinely fail to meet end-to-end performance expectations. The default transport control protocol for best effort data traffic is currently TCP, which does not scale well to 100 Mbps and higher networks over long distances. In congestion avoidance, TCP is not swift enough to fully utilize resources over paths with a high delay bandwidth product. First attempts to alleviate this problem by equipping TCP with increased aggressiveness have shown the disadvantage of poor fairness with the ubiquitous standard TCP-Reno, or in some cases, even among two connections running over the same path. We propose a new delay sensitive-congestion avoidance mode (TCP-Africa) that allows for scalable, aggressive behavior in large underutilized links, yet falls back to the more conservative TCP-Reno algorithm once links become well utilized and congestion is imminent. Through ns2 simulations we argue for the safety, efficiency, and fairness of TCP-Africa.
Compound Josephson-junction coupler for flux qubits with minimal crosstalk (2009)

An improved tunable coupling element for building networks of coupled rf-superconducting quantum interference device (rf-SQUID) flux qubits has been experimentally demonstrated. This new form of coupler, based on the compound Josephson-junction rf-SQUID, provides a sign and magnitude tunable mutual inductance between qubits with minimal nonlinear crosstalk from the coupler tuning parameter into the qubits. Quantitative agreement is shown between an effective one-dimensional model of the coupler's potential and measurements of the coupler persistent current and susceptibility.
Study effect of Breast Cancer on Some Hematological and Biochemical Parameters in Babylon Province, Iraq (2014)

This is a cross sectional study of variations of Hematological and biochemical parameters among female breast cancer patients and apparently healthy individuals in Babylon province 30 breast cancer patients from daily clinic and private hospitals and 20 control individual were studied between January and June, 2013. Questionnaires for bio data administered to both the patients (cases) and control subjects. Hematological parameters were run on the EDTA samples for packed cell volume (PCV), white blood cell count (WBCs),red blood cell count (RBCs), platelet count, lymphocytes count using (Auto-Hematology Analyzer-, Hungary2011). Erythrocyte sedimentation rate (ESR) also performed on the sodium citrate samples using the Western green method. Significant differences (p < 0.05) were seen in the values for WBCs, RBCs, platelets count, PCV, lymphocyte and ESR (p >0.05) among patients.The mean PCV, RBCs and WBCs,platelet count, lymphocyte value were lower in patients compared to the controls with statistically significant differences (p<0.05). However, the mean ESR value significantly higher than the control subjects (p < 0.05). This study has shown that anemia; leucopenia and thrombocytopenia were common basic features to be considered in breast cancer patients while the biochemical parameters included the level of estrogen, progesterone hormones, cholesterol, triglycerides, lipoproteins (HDL, LDL), some immunoglobulin's (IgG, IgA and IgM) also had been measured in the study. The results demonstrated significantly high values of estrogen, progesterone hormones, triglyceride, LDL, HDL, cholesterol, and significantly high values in immunoglobulin's IgA, IgG,and IgM.in breast cancer in comparison with control group, I.
Vessel tree reconstruction in thoracic CT scans with application to nodule detection (2005)

Vessel tree reconstruction in volumetric data is a necessary prerequisite in various medical imaging applications. Specifically, when considering the application of automated lung nodule detection in thoracic computed tomography (CT) scans, vessel trees can be used to resolve local ambiguities based on global considerations and so improve the performance of nodule detection algorithms. In this study, a novel approach to vessel tree reconstruction and its application to nodule detection in thoracic CT scans was developed by using correlation-based enhancement filters and a fuzzy shape representation of the data. The proposed correlation-based enhancement filters depend on first-order partial derivatives and so are less sensitive to noise compared with Hessian-based filters. Additionally, multiple sets of eigenvalues are used so that a distinction between nodules and vessel junctions becomes possible. The proposed fuzzy shape representation is based on regulated morphological operations that are less sensitive to noise. Consequently, the vessel tree reconstruction algorithm can accommodate vessel bifurcation and discontinuities. A quantitative performance evaluation of the enhancement filters and of the vessel tree reconstruction algorithm was performed. Moreover, the proposed vessel tree reconstruction algorithm reduced the number of false positives generated by an existing nodule detection algorithm by 38%.
Do electromagnetic fields interact directly with DNA? (1997)

The mechanisms whereby electromagnetic (EM) fields stimulate changes in biosynthesis in cells are not known. It has has generally been assumed that EM fields first interact with cell membranes, but this pathway may not be only one. Interactions with membranes are well documented, but recent studies of EM signal transduction in the membrane Na,K-ATPase are best explained by direct interaction of electric and magnetic fields with mobile charges within the enzyme. Interaction with moving charges may be a mechanism that is operative in other biopolymers. Recent studies on DNA have shown that large electron flows are possible within the stacked base pairs of the double helix. Therefore, gene activation by magnetic fields could be due to direct interaction with moving electrons within DNA. Electric fields as well as magnetic fields stimulate transcription, and both fields could interact with DNA directly. The mechanism of EM field-stimulated transcription may be related to the process in striated muscles, where endogenous electrical activity induces the synthesis of new proteins.
SIX1 mutations cause branchio-oto-renal syndrome by disruption of EYA1–SIX1–DNA complexes (2004)

Urinary tract malformations constitute the most frequent cause of chronic renal failure in the first two decades of life. Branchio-otic (BO) syndrome is an autosomal dominant developmental disorder characterized by hearing loss. In branchio-oto-renal (BOR) syndrome, malformations of the kidney or urinary tract are associated. Haploinsufficiency for the human gene EYA1, a homologue of the Drosophila gene eyes absent (eya), causes BOR and BO syndromes. We recently mapped a locus for BOR/BO syndrome (BOS3) to human chromosome 14q23.1. Within the 33-megabase critical genetic interval, we located the SIX1, SIX4, and SIX6 genes, which act within a genetic network of EYA and PAX genes to regulate organogenesis. These genes, therefore, represented excellent candidate genes for BOS3. By direct sequencing of exons, we identified three different SIX1 mutations in four BOR/BO kindreds, thus identifying SIX1 as a gene causing BOR and BO syndromes. To elucidate how these mutations cause disease, we analyzed the functional role of these SIX1 mutations with respect to protein-protein and protein-DNA interactions. We demonstrate that all three mutations are crucial for Eya1-Six1 interaction, and the two mutations within the homeodomain region are essential for specific Six1-DNA binding. Identification of SIX1 mutations as causing BOR/BO offers insights into the molecular basis of otic and renal developmental diseases in humans.
Trinucleotide repeat disorders in humans: discussions of mechanisms and medical issues (1996)

Several human disorders are now known to be caused by expansion of unstable trinucleotide repeat sequences, including fragile X syndrome (FRAX), myotonic dystrophy (DM), spinal and bulbar muscular atrophy (SBMA, also known as Kennedy disease), Huntington disease (HD), dentatorubral-pallidoluysian atrophy (DRPLA), spinocerebellar ataxia type 1 (SCA1), Machado-Joseph disease (MJD), and Friedreich ataxia. As these diseases are studied in more detail, important differences have emerged in the nature of the unstable repeats and the mechanism by which the repeat expansions cause disease symptoms. There are already animal models of some of these disorders, and these are important resources for studying pathology and therapeutic strategies. Diagnostic procedures for these disorders are only beginning to be standardized, and effective therapy will have to wait for further information on disease mechanisms. Much has been learned since discovery of the fragile X syndrome gene in 1991, but much remains to be done.
Pressure-induced reversible dissociation of enolase (1981)

A study of the polarization of the intrinsic fluorescence and the fluorescence of dansyl conjugates of enolase shows that an increase in hydrostatic pressure, in the range of 1 bar-3 kbar, promotes the dissociation of this protein into dimers. The dissociation of oligomeric proteins under pressure is predicted to be a general phenomenon by a model that assumes the existence of small "free volumes" at the intersubunit boundaries. The same model predicts a dependence of the standard volume change in the dissociation reaction upon the pressure, owing to the additional surface compressibility of the monomers, and numerical analysis of the results clearly shows that dependence for enolase. For a midpoint dissociation pressure of 1.5 kbar the standard volume change in the dissociation reaction is delta V p0 = -65 +/- 8 mL mol-1 and the dependence of the volume change upon pressure (dVp0/dp) is approximately -30 mL mol-1 kbar-1. The reversibility of the pressure effects is shown to be better than 95% by either polarization or fluorescence spectrum recovery. The pressure perturbation of the fluorescence polarization is a method of general applicability to studies of protein aggregation, and it can be also of value in characterizing the effect of ligands on the aggregation of oligomeric proteins.
Ligand identification using electron-density map correlations (2006)

A procedure for the identification of ligands bound in crystal structures of macromolecules is described. Two characteristics of the density corresponding to a ligand are used in the identification procedure. One is the correlation of the ligand density with each of a set of test ligands after optimization of the fit of that ligand to the density. The other is the correlation of a fingerprint of the density with the fingerprint of model density for each possible ligand. The fingerprints consist of an ordered list of correlations of each the test ligands with the density. The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance. The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank. Using a combination of these two characteristics of ligand density, ranked lists of ligand identifications were made for representative (F(o) - F(c))exp(i(phi)c) difference density from entries in the Protein Data Bank. In 48% of the 200 cases, the correct ligand was at the top of the ranked list of ligands. This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule.
Hansch Analysis for Some Antineoplastic Glutarimides (1976)

Department of Pharmacy, Jadavpur University, Calcutta. 700 032 Manuscript received 12 May 1976; accepted 28 May 1976 Hansch analysis has been performed for 38 glutarimide analogs with the help of an IBM 1130 computer. Results of computation reveal that the partition coefficients of these compounds alone can not explain their observed biological activities. This, however, indirectly suggests that the electronic and steric parameters need be considered for explaining their biological acti­vities.
Alternating Donor/Acceptor Repeat Units in Polythiophenes. Intramolecular Charge Transfer for Reducing Band Gaps in Fully Substituted Conjugated Polymers (1998)

This paper describes a method to limit the band gap widening that occurs in fully substituted conjugated polymers. This is done by constructing step growth [AB] polymers where the A-units are electron rich and the B-units are electron deficient. The thiophene-based polymers were prepared by modified Stille polymerizations using Pd(0)/CuI catalyst systems in which aryldibromides were coupled with aryldistannanes. The donor units were N,N‘-(bis-tert-butoxycarbonyl)-3,4-diaminothiophene, N,N‘-(bis-tert-butoxycarbonyl)-N,N‘-(dimethyl)-3,4-diaminothiophene, 3,4-diaminothiophene, or 3,4-dialkoxythiophenes while the acceptor units were 3,4-dinitrothiophene, 3,4-(N-n-butylimido)thiophene, or 3,4-diketone-containing thiophenes. The optical spectra showed λmax values ranging from 400 to 676 nm (solution) and 400−768 (film) for these fully substituted polythiophenes, consistent with significant decreases in the band gaps. Intramolecular charge transfer character between the consecutive units explained the lowering of the band gaps. Two polymer systems based solely on electron deficient thiophenes were prepared via an Ullmann coupling which had optical absorption maxima that were in the range of 300−340 nm; considerably smaller than the λmax values for the donor/acceptor systems. Several model trimers were prepared which had significantly shorter wavelength optical absorptions than their corresponding polymers, thus confirming the need for the extended polymeric backbones.
Isolation and Characterization of the Human Chromosomal Gene for Polypeptide Chain Elongation Factor-1α (1989)

The cDNA for human elongation factor-1 alpha was isolated from a cDNA library of human fibroblast cells. Using the cDNA as a probe, a number of chromosomal genes encoding the human elongation factor-1 alpha were isolated. Characterization of the clones by restriction enzyme mapping and nucleotide sequence analysis has revealed that only one of them is an active gene, whereas all of the other genes are processed pseudogenes. The active gene consists of 8 exons and 7 introns spanning about 3.5 kilobases, and the sequence of its exons is completely identical to that of the human elongation factor-1 alpha cDNA. The first non-coding exon of 33 base pairs is separated by a 943-base pair intron from the coding exons. The primer extension of human elongation factor-1 alpha mRNA has indicated that the transcription of human elongation factor-1 alpha gene starts from a C residue, and a "TATA" box was found 24 base pairs upstream of the initiation site. Three and five Sp1 binding sites are present on the 5'-flanking region and the 1st intron, respectively. Furthermore, one Ap-1 binding site is located in the 1st intron. By using nuclear extracts from HeLa cells, the promoter of human elongation factor-1 alpha gene could stimulate in vitro transcription better than the adenovirus major late promoter.
Solid Modeling: A Historical Summary and Contemporary Assessment (1982)

A new generation of industrial geometry systems is emerging based on the technology of the 1970's. The generations of the eighties and nineties will require more research.
Prediction of pH in Model Systems Pressurized with Carbon Dioxide (1992)

Abstract Mathematical models were developed to predict the pH of model liquid food systems (pure water, ascorbic acid‐water, citric acid‐water, and ascorbic acid‐citric acid‐water) pressurized with carbon dioxide, as functions of pressure (0–34.50 MP a ), temperature (32,37, and 42° C), and component concentrations [(0–1.107) X10 −3 M for ascorbic acid, (0 to 6.080) × 10 −4 M for citric acid]. For all simulation systems, predicted pH values closely followed experimentally measured pH values. In the pure water‐CO 2 systems, pH was a strong function of pressure but a weak function of temperature. In ascorbic acid‐water‐CO 2 , citric acid‐water‐CO 2 , and ascorbic acid‐citric acid‐water‐CO 2 systems, pH was relatively insensitive to CO 2 pressure and was a strong function of acid concentrations. This method could be a first step toward predicting the pH of orange juice and other liquid food systems under pressurized CO 2.
Dispersion and nonlinear propagation in air-core photonic band-gap fibers (2003)

We characterize the dispersion and nonlinearity of a recently developed extremely-low-loss, air-core photonic band-gap fiber. We show it can support femtosecond solitons with peak powers greater than 2 MW.