gebhart/patrepeval huggingface dataset:
In Vivo Reinsertion of Excised Episomes by the V(D)J Recombinase: A Potential Threat to Genomic Stability (2007)

It has long been thought that signal joints, the byproducts of V(D)J recombination, are not involved in the dynamics of the rearrangement process. Evidence has now started to accumulate that this is not the case, and that signal joints play unsuspected roles in events that might compromise genomic integrity. Here we show both ex vivo and in vivo that the episomal circles excised during the normal process of receptor gene rearrangement may be reintegrated into the genome through trans-V(D)J recombination occurring between the episomal signal joint and an immunoglobulin/T-cell receptor target. We further demonstrate that cryptic recombination sites involved in T-cell acute lymphoblastic leukemia-associated chromosomal translocations constitute hotspots of insertion. Eventually, the identification of two in vivo cases associating episomal reintegration and chromosomal translocation suggests that reintegration events are linked to genomic instability. Altogether, our data suggest that V(D)J-mediated reintegration of episomal circles, an event likely eluding classical cytogenetic screenings, might represent an additional potent source of genomic instability and lymphoid cancer.
Methylation-Sensitive Sequence-Specific DNA Binding by the c-Myc Basic Region (1991)

The function of the c-Myc oncoprotein and its role in cell growth control is unclear. A basic region of c-Myc is structurally related to the basic motifs of helix-loop-helix (HLH) and leucine zipper proteins, which provide sequence-specific DNA binding function. The c-Myc basic region was tested for its ability to bind DNA by attaching it to the HLH dimerization interface of the E12 enhancer binding factor. Dimers of the chimeric protein, termed E6, specifically bound an E box element (GGCCACGTGACC) recognized by other HLH proteins in a manner dependent on the integrity of the c-Myc basic motif. Methylation of the core CpG in the E box recognition site specifically inhibited binding by E6, but not by two other HLH proteins. Expression of E6 (but not an E6 DNA binding mutant) suppressed the ability of c-myc to cooperate with H-ras in a rat embryo fibroblast transformation assay, suggesting that the DNA recognition specificity of E6 is related to that of c-Myc in vivo.
Synthesis, Aggregation, and Adsorption Phenomena of Shape-Persistent Macrocycles with Extraannular Polyalkyl Substituents (2001)

The synthesis of shape-persistent macrocycles based on the phenyl-ethynyl backbone containing various extraannular alkyl side chains is described. Although compound solubility increases with increasing size of the side groups, decreasing the solvent polarity induces aggregation of the rings by nonspecific interactions. This was investigated by proton NMR spectroscopy. The magnitude of aggregation can be varied by using solvent mixtures of different hexane content, supporting the model of a solvophobic effect. From 1,2,4-trichlorobenzene solution the macrocycle 1c adsorbs at the surface of highly oriented pyrolitic graphite (HOPG). The two-dimensional order of the structure was investigated by scanning tunneling microscopy (STM) revealing the formation of a two-dimensional lattice of p1(2)mm symmetry with lattice parameters A = 3.6 nm, B = 5.7 nm, and Gamma = 74 degrees.
The effect of liposomal bupivacaine injection during total hip arthroplasty: a controlled cohort study (2014)

Liposomal bupivacaine administration during total hip arthroplasty appears to decrease the need for opioid use post operatively and decrease length of stay. The results of this study justify the need for a well-designed randomized controlled trial utilizing liposomal bupivacaine as part of multimodal analgesia during THA.
Monitoring Strategies for Early Detection of Lepidoptera Resistance to Bacillus thuringiensis Insecticidal Proteins (1996)

We discuss assay approaches for monitoring the sensitivity of Lepidoptera to Bacillus thuringiensis (Bt) insecticidal proteins and compare the relative sensitivity of larval feeding bioassays in which, respectively, mortality or growth inhibition were scored. Heliothis virescens (F.) and Helicoverpa zea (Boddie), major lepidopteran pests targeted for control by transgenic cotton, were used for assay comparison. Larval growth inhibition assays using sublethal CryIA(c) protein concentrations were considerably more sensitive than dose-response mortality assays. Growth inhibition assays were easy to set-up and read, and could readily deliver a diagnostic dose allowing for visual discrimination of resistant from susceptible phenotypes. The ability of a larval growth assay, combined with a diagnostic dose, to unambiguously separate resistant from susceptible insects was validated using a CryIA(c) protein resistant strain of H. virescens and F1 hybrids derived by crossing the resistant strain to a susceptible H. virescens strain. Threat of Insect Resistance to Transgenic Plants Producing
Layered Structures Constructed from New Linkages of Ge7(O,OH,F)19 Clusters (2003)

Three new germanate solids, ASU-19, ASU-20-DAPe, and ASU-20-DACH, have been synthesized under hydrothermal conditions using respectively 1,4-diaminobutane (DAB), 1,5-diaminopentane (DAPe), and 1,4-diaminocyclohexane (DACH) as bases. The structures of ASU-19 and ASU-20-DACH have been characterized by single-crystal X-ray diffraction: ASU-19, Ge14O29X4·[GeOX2]·[H2DAB]3·3.8H2O (X = F or OH), space group P1̄, a = 11.4191(5), b = 12.0525(6), c = 18.1847(8) Å, α = 90.704(1)°, β = 92.635(1)°, γ = 91.389(1)°, V = 2499.1(2) Å3; ASU-20-DACH: Ge7O14X3·[H2DACH]1.5·2H2O, space group C2/c, a = 15.9525(11), b = 17.5476(12), c = 19.0027(13) Å, β = 109.446(1)°, and V = 5015.9(6) Å3. The structure of ASU-20-DAPe, Ge7O14X3·[H2DAPe]1.5·H2O, has been determined from X-ray powder diffraction data: space group C2/c, a = 16.3180(5), b = 16.6125(4), c = 17.8898(6) Å, β = 99.684(2)°, V = 4780.5(3) Å3. All three structures are based on the assembly of the same cluster Ge7(O,OH,F)19. The two ASU-20 structures consist of a slab of four-connected clusters. In ASU-19, the same layers are connected pairwise through a GeO2X2 spacer, generating a slab structure, with slab thickness ca. 20 Å. The existence of the same layer in the presence of three different organic bases shows the adaptability of the structures to molecules differing in size, shape, and symmetry.
Flexible Circuit-Based RF MEMS Switches (2001)

Abstract This paper describes a new microelectromechanical systems (MEMS) switch fabricated using flexible circuit technologies. Hundreds of such switches can be laminated onto a large-area printed circuit board (PCB) with other RF devices and circuits. The switches are fabricated using low-cost, low-loss flexible circuit material Kapton-E polyimide film. Switches with actuation voltages as low as 73 V are reported.
Biomolecular prognostic factors in breast cancer (2004)

Rapid translation of laboratory findings to clinical practice was hampered by many difficulties, including technical and statistical concerns, a lack of assay standardization and comparability, and the modest design of translational studies. Many studies are performed on too small series of patients to provide reliable results; the studies are often heterogeneous in terms of treatment, patients and tumor characteristics, and data may be evaluated using different analytical approaches and are thus not easily comparable. Adequately planned prospective studies are required to assess the clinical utility of biomarker determinations.
Water-Soluble β-Sheet Models Which Self-Assemble into Fibrillar Structures (1999)

Self-assembly of beta-sheet domains resulting in the formation of pathogenic, fibrillar protein aggregates (amyloids) is a characteristic feature of various medical disorders. These include neurodegenerative diseases, such as Alzheimer's, Huntington's, and Creutzfeldt-Jacob's. A significant problem in studying such aggregation processes is the poor solubility of these beta-sheet complexes. The present work describes water-soluble de novo beta-sheet peptides which self-assemble into fibrillar structures. The model peptides enable studies of the relationship between beta-sheet stability and association behavior. The peptides [DPKGDPKG-(VT)n-GKGDPKPD-NH2, n = 3-8] are composed of a central beta-sheet-forming domain (VT-sequence), and N- and C-terminal nonstructured octapeptide sequences which promote water solubility. Conformational analyses by circular dichroism and Fourier transform infrared spectroscopy indicate the influence of peptide length, D-amino acid substitution, and concentration on the ability of the peptides to form stable beta-sheet structures. The association behavior investigated by analytical ultracentrifugation and dynamic light scattering was found to correlate strongly with the stability of a beta-sheet conformation. Model peptides with n >/= 6 form stable, water-soluble beta-sheet complexes with molecular masses of more than 2000 kDa, which are organized in fibrillar structures. The fibrils examined by Congo Red staining and electron microscopy show some similarities with naturally occurring amyloid fibrils.
The danger theory: 20 years later (2012)

The self-non-self theory has dominated immunology since the 1950s. In the 1990s, Matzinger and her colleagues suggested a new, competing theory, called the "danger theory." This theory has provoked mixed acclaim: enthusiasm and criticism. Here we assess the danger theory vis-à-vis recent experimental data on innate immunity, transplantation, cancers and tolerance to foreign entities, and try to elucidate more clearly whether danger is well defined.
Refined 1.89-.ANG. Structure of the Histidine-Binding Protein Complexed with Histidine and Its Relationship with Many Other Active Transport/Chemosensory Proteins (1994)

The structure of the histidine-binding protein (HBP, M(r) = 26,100), involved solely in active transport, has been determined by the molecular replacement technique and refined to 1.89-A resolution and to an R-factor of 0.199. The structure is that of two protein molecules, each with a bound L-histidine, in the asymmetric unit. Replacement solution was achieved by using a model of the crystal structure of the ligand-free, open-cleft form of the lysine/arginine/ornithine-binding protein which was modified so that the two domains are close to each other by bending the hinge connecting the two domains. The bound histidine is held in place by 10 hydrogen bonds, 2 salt links, and about 60 van der Waals contacts. Elucidation of the HBP structure brings a total of eight different binding proteins structures determined in our laboratory, including those with specificities for monosaccharides, maltodextrins (linear and cyclic), aliphatic amino acids, and inorganic oxyanions. These structures comprise about a third of the entire family of periplasmic binding proteins which act as initial primary high-affinity receptors of active transport in Gram-negative bacteria. Two of the binding proteins with specificities for glucose/galactose and maltodextrins also serve in a similar capacity in chemotaxis. Though these proteins have different molecular weights (ranging from 26,000 to 40,000), amino acid sequences, and ligand specificities, their three-dimensional structures are similar overall. They are elongated (axial ratios of 2:1) and composed of two similar globular domains separated by a deep cleft wherein the ligand-binding site is located. These structures provide understanding of molecular recognition of a variety of ligands at the atomic level and functional roles of the binding proteins.
The use of vasopressin in the setting of recalcitrant hypotension due to calcium channel blocker overdose (2007)

Treatment of hypotension caused by calcium channel blocker overdose (CCB) remains a challenge. We describe the successful use of vasopressin in two patients with massive CCB overdoses in whom hypotension was unresponsive to calcium, glucagon, insulin, and conventional vasopressor therapies. While various modes of treatments have been used to treat the hypotension of CCB overdose, this is the first report to our knowledge of the successful use of vasopressin in this clinical setting.
A critical role for p59fyn in CD2-based signal transduction (2000)

TCR- but not CD2-triggered IL-2 production is p56(lck) dependent. To test the hypothesis that p59(fyn), a second src-family protein tyrosine kinase (PTK) expressed in T lymphocytes, might be an essential upstream component of the CD2 signaling pathway, we generated human (h) CD2 transgenic (tg) fyn(+/+) and fyn(-/-) mice. Clustering of hCD2 molecules on resting peripheral T lymphocytes results in Ca(2+) mobilization, activation of MAPK and cellular proliferation. In contrast, in the absence of p59(fyn), these CD2-initiated activities are markedly reduced, while TCR-triggered proliferation is unaffected. Several CD2 pathway components regulated by p59(fyn) have been identified including phospholipase C-gamma1 (PLC-gamma1), Vav, protein kinase C-theta isoform (PKC-theta), docking protein (Dok), focal adhesion kinase (FAK) and Pyk2. Decreased inducible PKC-theta catalytic activity and Vav phosphorylation likely account for diminished p38 and JNK activation in hCD2tg fyn(-/-) mice. Moreover, deficiency in fyn-dependent PLC-gamma1 catalytic activity may contribute to reduced PKC-alpha-dependent ERK activation. Of note, CD2-dependent Dok but not linker from activated T cells (LAT) tyrosine phosphorylation requires p59(fyn). Furthermore, that FAK and Pyk2 are target substrates implies that p59(fyn) may be an important regulator of T cell adhesion as well. Collectively, these data identify p59(fyn) as a key PTK in CD2-mediated activation of mature T lymphocytes.
Revised structure for the phenazine antibiotic from Pseudomonas fluorescens 2-79 (NRRL B-15132) (1987)

A phenazine antibiotic (mp, 243 to 244 degrees C), isolated in a yield of 134 micrograms/ml from cultures of Pseudomonas fluorescens 2-79 (NRRL B-15132), was indistinguishable in all of its measured physicochemical (melting point, UV and infrared spectra, and gas chromatography-mass spectrometry data) and biological properties from synthetic phenazine-1-carboxylic acid. Gurusiddaiah et al. (S. Gurusiddaiah, D. M. Weller, A. Sarkar, and R. J. Cook, Antimicrob. Agents Chemother. 29:488-495, 1986) attributed a dimeric phenazine structure to an antibiotic with demonstrably similar properties obtained from the same bacterial strain. Direct comparison of the physicochemical properties of the authentic antibiotic obtained from D. M. Weller with synthetic phenazine-1-carboxylic acid and with the natural product from the present study established that all three samples were indistinguishable within the experimental error of each method. No evidence to support the existence of a biologically active dimeric species was obtained. Phenazine-1-carboxylic acid has a pKa of 4.24 +/- 0.01 (25 degrees C; I = 0.09), and its carboxylate anion shows no detectable antimicrobial activity compared with the active uncharged carboxylic acid species. These data suggest that phenazine-1-carboxylic acid is probably not an effective biological control agent for phytopathogens in environments with a pH greater than 7.
Deblurring for non‐2D fourier transform magnetic resonance imaging (1992)

For several non-2D Fourier transform imaging methods, off-resonant reconstruction does not just cause geometric distortion, but changes the shape of the point spread function and causes blurring. This effect is well known for projection reconstruction and spiral k-space scanning sequences. We introduce here a method that automatically removes blur introduced by magnetic field inhomogeneity and susceptibility without using a resonant frequency map, making these imaging methods more useful. In this method, the raw data are modulated to several different frequencies and reconstructed to create a series of base images. Determination of degree of blur is done by calculating a focusing measure for each point in each base image and a composite image is then constructed using only the unblurred regions from each base image. This method has been successfully applied to phantom and in vivo images using projection-reconstruction and spiral-scan sequences.
Pattern generation with SLM imaging (2002)

Pattern generation founded on micro-mirror spatial light modulator (SLM) imaging presents a way to manage the decreasing feature sizes and increasing pattern complexities dictated by Moore's law. This paper identifies the critical elements of the imaging in the implementation of such a pattern generator. We show how the laser illumination, SLM chip, and optics collectively generate the image, and in particular, that these elements can be manufactured and integrated to specification. Expected deficiencies and variations in image quality are then effectively countered with calibration routines that bring final performance to within lithographic requirements, while also being manageable in design and turn-around-times.
A Review of Localization Systems for Robotic Endoscopic Capsules (2012)

Obscure gastrointestinal (GI) bleeding, Crohn disease, Celiac disease, small bower tumors, and other disorders that occur in the GI tract have always been challenging to be diagnosed and treated due to the inevitable difficulty in accessing such a complex environment within the human body. With the invention of wireless capsule endoscope, the next generation of the traditional cabled endoscope, not only a dream has come true for the patients who have experienced a great discomfort and unpleasantness caused by the conventional endoscopic method, but also a new research field has been opened to develop a complete miniature robotic device that is swallowable and has full functions of diagnosis and treatment of the GI diseases. However, such an ideal device needs to be equipped with a highly accurate localization system to be able to exactly determine the location of lesions in the GI tract and provide essential feedback to an actuation mechanism controlling the device's movement. This paper presents a comprehensive overview of the localization systems for robotic endoscopic capsules, for which the motivation, challenges, and possible solutions of the proposed localization methods are also discussed.
Specific toxicity of 2-chlorodeoxyadenosine toward resting and proliferating human lymphocytes (1983)

2-Chlorodeoxyadenosine (CdA), an adenosine-deaminase-resistant purine deoxynucleoside, is markedly toxic toward human T-lymphoblastoid cell lines in vitro and is an effective agent against L1210 leukemia in vivo. The present studies have examined the toxicity, and in some cases, metabolism, of CdA in (1) multiple established human cell lines of varying phenotype, (2) leukemia and lymphoma cells taken directly from patients, (3) normal bone marrow cells, and (4) normal peripheral blood lymphocytes. Nanomolar concentrations of CdA blocked the proliferation of lymphoblastoid cell lines with a high ratio of deoxycytidine kinase to deoxynucleotidase. The drug had virtually no effect on the growth of cell lines derived from solid tissues. The CdA inhibited the spontaneous uptake of tritiated thymidine by many T and non-T, non-B acute lymphoblastic leukemia cell specimens at concentrations less than or equal to 5 nM. The same concentrations did not impair either thymidine uptake or granulocyte-monocyte colony formation by normal bone marrow cells. In common with deoxyadenosine, but unlike several other agents affecting purine and purine metabolism, CdA was lethal to resting normal T lymphocytes and to slowly dividing malignant T cells. In both resting and proliferating lymphocytes, the CdA was phosphorylated by deoxycytidine kinase and entered a rapidly turning over nucleotide pool. Dividing lymphocytes also incorporated abundant CdA into DNA. The selective toxicity of CdA toward both dividing and resting lymphocytes may render the drug useful as an immunosuppressive or antileukemic agent.
The ecdysone response enhancer of the Fbp1 gene of Drosophila melanogaster is a direct target for the EcR/USP nuclear receptor. (1994)

The transcription of the Drosophila melanogaster Fbp1 gene is induced by the steroid hormone 20-hydroxyecdysone and restricted to the late-third-instar fat body tissue. In a previous study we showed that the -68 to -138 region relative to the transcription start site acts as an ecdysone-dependent third-instar fat body-specific enhancer in a transgenic assay. Here we report that seven nucleoprotein complexes are formed in vitro on this enhancer when a nuclear extract from late-third-instar fat body is used in a gel shift assay. Accurate mapping of the binding sites of the complexes revealed a remarkably symmetrical organization. Using specific antibodies, one of the complexes was identified as a heterodimer consisting of the ecdysone receptor (EcR) and Ultraspiracle (USP) proteins. The binding site of the heterodimer as defined by mutagenesis and methylation interference experiments bears strong sequence similarity to the canonical hsp27 ecdysone response element, including an imperfect palindromic structure. The two elements diverge at three positions in both half-sites, indicating that the structure of an active EcR/USP binding site allows considerable sequence variations. In vivo footprinting experiments using ligation-mediated PCR and wild-type or ecdysteroid-deficient larvae show that occupancy of the Fbp1 EcR/USP binding site and adjacent region is dependent on a high concentration of ecdysteroids. These results provide strong evidence for a direct role of the EcR/USP heterodimer in driving gene expression in response to changes of the ecdysteroid titer during Drosophila larval development.
Distributed dynamic carrier allocations in mobile cellular networks: search vs. update (2002)

There are two approaches to distributed implementation of dynamic carrier allocation (DCA) strategies: the update approach and the search approach. We first investigate the fundamental differences between the two approaches: two simple and representative schemes, namely the basic update scheme and the basic search scheme, are presented and compared. We argue that the update approach is more appropriate than the search approach for mobile cellular networks. Then we propose an advanced update scheme that is more efficient than the basic update scheme in terms of message complexity and carrier acquisition delay. The advanced update scheme can support a group of DCA strategies which require resource planning.