gebhart/patrepeval huggingface dataset:
Effect of polyethylene glycol on the supercoiling free energy of DNA (2000)

The supercoiling free energy of pUC19 DNA [2686 base pairs (bp)] was measured in various concentrations of PEG 8000 (polyethylene glycol; molecular weight 8000) by the topoisomer distribution method. The effective twist energy parameter (E(T)) that governs the supercoiling free energy declined linearly by 1.9-fold with increasing w/v % PEG from 0 to 7.5%, which lies below the threshold for intermolecular condensation. In principle, PEG could affect E(T) either via an osmotic exclusion mechanism or by altering the torsion elastic constant, bending rigidity, or self-repulsions of the DNA. Possible alterations of the DNA secondary structure and torsion elastic constant were assessed by CD spectroscopy and time-resolved fluorescence polarization anisotropy of intercalated ethidium. Up to 7.5% PEG, the secondary structure of the DNA remained largely unaltered, as evidenced by (1) the absence of any significant change in the CD spectrum, (2) an extremely small relative decrease (-0.0013) in intrinsic twist, and (3) a negligibly small change in the torsion elastic constant. The observed reduction in E(T) cannot be ascribed primarily to a decrease in torsion elastic constant, and most likely does not stem from a decrease in bending rigidity either. The decrease in medium dielectric constant due to PEG should increase the self-repulsions, and thereby increase E(T), which is opposite to the observed trend. Instead, the observed decline in E(T) is attributed to an osmotic exclusion mechanism. The change in molar volume excluded to the PEG (Delta V(ex)), when the linking difference converts from Delta l = 0 to Delta l = +/-1, was determined from the observed E(T) value and PEG osmotic pressure at each concentration. The experimental Delta V(ex) values agree well with theoretical estimates reckoned for a simple osmotic exclusion model, in which PEG is excluded by hard-core interactions from a concentric cylindrical volume around every duplex segment. The difference in volume excluded to PEG between the Delta l = 0 and the Delta l = +/-1 topoisomers is attributed entirely to the approximately 0.7 additional writhe "crossing" of two duplex strands at roughly 90 degrees, which is known to occur in the latter species. When the separation between the duplex centers at the "crossing" was adjusted so that the theoretical estimate of Delta V(ex) matched the experimental value at each PEG concentration, a value near 5.7 nm was obtained in each case. The invariance and plausible magnitude of this mean separation at the crossing provide strong support for this simple osmotic exclusion model. An alternative model, in which the PEG is excluded from the entire coil envelope of the DNA out to its radius of gyration, perhaps because it decreases the local dielectric constant, was also considered. The estimated difference in excluded volume in that case exceeds the experimental value by a factor of nearly 10(4), and could be ruled out on that basis.
Power spectrum analysis and heart rate variability in Stage 4 and REM sleep: evidence for state‐specific changes in autonomic dominance (1993)

The present study investigated autonomic activity during NREM and REM sleep stages and wakefulness by spectral analysis of heart rate variability. The results demonstrated that NREM sleep in humans was characterized by a widely different autonomic activation pattern than REM sleep: high parasympathetic activity was found in NREM, while REM was characterized by attenuated vagal tone, and augmented sympathetic activity. The overall pattern during wakefulness showed an intermediate position between NREM and REM patterns; parasympathetic activity was lower than in NREM and higher than in REM, with an opposite trend for sympathetic activity.
Hypophosphatasia: diagnosis and clinical signs – a dental surgeon perspective (2016)

HPP is a rare disease with a wide spectrum of manifestations, with orodental symptoms featuring prominently in the natural history. Dental professionals may be positioned at the beginning of the diagnostic pathway; thus, recognition of HPP features for timely referral and optimal disease management is important.
Preparation and anisotropic mechanical behavior of highly‐oriented electrospun poly(butylene terephthalate) fibers (2006)

Abstract This work describes the effect of the speed of drum‐type rotating collector in an electrospinning process on the orientation of electrospun poly(butylene terephthalate) fiber mats, and its effect on the tensile properties. The degree of orientation increased with the increase in the drum speed (surface velocity) up to a critical level, and thereafter, wavy fibers were observed. The average diameter reduced and its distribution became narrower with increase in the velocity. The mechanical properties in a parallel direction improved about three times with increase in the surface velocity. The anisotropic mechanical behavior could be predicted with a simple classical equation. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 101: 2017–2021, 2006
Increasing 5-lipoxygenase inhibitory activities by oxidative conversion of o-methoxyphenols to catechols using a Cu2+-ascorbic acid-O2 system. (1990)

Several complicated o-methoxyphenols were oxidized with high selectivity to catechols by a Cu2(+)-ascorbic acid-O2 system. In this way, the RBL-1 5-lipoxygenase inhibitory activities of o-methoxyphenols were greatly increased. [6]-Norgingerol (4), a novel compound derived from [6]-gingerol (3), shows promise as a lead compound for new drugs because of its high inhibitory potency (IC50 = 5.0 x 10(-8) M).
A Visual Tagging Process for Mix and Sort Combinatorial Chemistry (1998)

Colored glass beads and caps provide a simple color-coding strategy adapted to porous plastic containers and allow visual identification of the individual constituents of combinatorial libraries.
IDEC-C2B8 (1994)

Grillo-López, A. J.; Maloney, D. G.; Bodkin, D.; Schilder, R. I.; White, C.; Foon, K.; Janakiraman, N.; Neidhart, J.; Rosenberg, J.; Shen, C. D.; Royston, I.; Levy, R. Author Information
Low-Dose Recombinant Human Growth Hormone as Adjuvant Therapy to Lifestyle Modifications in the Management of Obesity (2004)

Obese individuals are in a reduced GH/IGF-I state that may be maladaptive. Fifty-nine obese men and premenopausal menstruating women (body mass index, 36.9 +/- 5.0 kg/m(2)) were randomized to a double-blind, placebo-controlled trial of low dose recombinant human GH (rhGH). During the 6-month intervention, subjects self-administered daily rhGH or equivalent volume of placebo at 200 micro g (1.9 +/- 0.3 microg/kg for men, 2.0 +/- 0.3 microg/kg for women); after 1 month, the dose was increased to 400 microg (3.8 +/- 0.5 microg/kg) in men and 600 microg (6.0 +/- 0.8 microg/kg) in women. rhGH was then discontinued, and subjects were followed up after 3 months. Forty completed the intervention, and 39 completed the follow-up. Drop-out rates between rhGH vs. placebo groups were not different (chi(2) = 1.45; P = 0.228). One subject discontinued the drug due to an rhGH-related side effect. Body weight (BW) decreased with rhGH from 100.4 +/- 13.2 to 98.0 +/- 15.6 kg at 6 months (P = 0.04) and was sustained at 98.1 +/- 16.6 kg at 9 months (P = 0.02). BW loss was entirely due to loss of body fat (BF). Intention to treat analyses demonstrated changes from baseline between rhGH and placebo in BW (-2.16 +/- 4.48 vs. -0.04 +/- 2.67 kg; P = 0.03) and BF (-2.89 +/- 3.76 vs. -0.68 +/- 2.37 kg; P = 0.01). rhGH increased IGF-I from -0.72 to +0.10 SD (P = 0.0001). rhGH increased high-density lipoprotein cholesterol 19% from 1.11 +/- 0.34 to 1.32 +/- 0.28 mmol/liter (P < 0.001). Neither group had changes in fasting glucose, insulin sensitivity, or resting energy expenditure. In conclusion, in obesity, rhGH normalized IGF-I levels, induced loss of BW from BF, and improved lipid profile without untoward effects on insulin sensitivity.
Aqueous Dispersion Polymerization of 2-Methoxyethyl Acrylate for the Synthesis of Biocompatible Nanoparticles Using a Hydrophilic RAFT Polymer and a Redox Initiator (2011)

Aqueous dispersion polymerization systems mediated by reversible addition–fragmentation chain transfer (RAFT) process have been less studied in comparison with other heterogeneous polymerization systems due to limited number of monomer/polymer pairs that are suitable for such a condition. We report a novel dispersion polymerization system based on 2-methoxyethyl acrylate (MEA) which is highly water-soluble, but its polymer is not. Using a hydrophilic polymer, poly(poly(ethylene glycol) methyl ether methacrylate) (PPEGMA), as the macromolecular chain transfer agent (Macro-CTA), both solution and dispersion polymerization of MEA were studied. Chain extension by MEA from PPEGMA was successfully realized in DMF solution polymerization. In dispersion polymerization of MEA in water, PPEGMA was used as both a RAFT mediating species and a steric stabilizer for the formed nanoparticles. The dispersion polymerization of MEA in water was highly efficient using a redox initiator, potassium persulfate/sodium ascorbate, at low temperatures. Simultaneous control of both colloidal stability and RAFT process was realized. Block copolymers with small polydispersity indices were efficiently produced up to complete monomer conversion at solids content up to 32% w/v, in the form of nanoparticles of 40–60 nm diameter.
Distribution and possible interactions of actin-associated proteins and cell adhesion molecules of nerve growth cones (1989)

Actin filaments and their interactions with cell surface molecules have key roles in tissue cell behaviour. Axonal pathfinding during embryogenesis, an especially complex cell behaviour, is based on the migration of nerve growth cones. We have used fluorescence immunocytochemistry to examine the distribution in growth cones, their filopodia and lamellipodia of several actin-associated proteins and nerve cell adhesion molecules. The leading margins of chick dorsal root ganglion nerve growth cones and their protrusions stain strongly for f-actin, filamin, alpha-actinin, myosin, tropomyosin, talin and vinculin. MAP2 is absent from DRG growth cones, and staining for spectrin fodrin extends into growth cones, but not along filopodia. Thus, organization of the leading margins of growth cones may strongly resemble the leading lamella of migrating fibroblasts. The adhesion-mediating molecules integrin, L1, N-CAM and A-CAM are all found on DRG neurites and growth cones. However, filopodia stain relatively more strongly for integrin and L1 than for A-CAM or N-CAM. In fact, the 180 X 10(3) Mr form of N-CAM may be absent from most of the length of filopodia. DRG neurones cultured in cytochalasin B display differences in immunofluorescence staining which further emphasize that these adhesion molecules interact differentially with the actin filament system of migrating growth cones. Several models for neuronal morphogenesis emphasize the importance of regulation of the expression of adhesion molecules. Our results support hypotheses that cellular distribution and transmembrane interactions are key elements in the functions of these adhesion molecules during axonal pathfinding.
Prostate-specific and Androgen-dependent Expression of a Novel Homeobox Gene (1996)

A new member of the mouse NK family of homeobox genes that is related to Drosophila NK-3 has been identified. Expression of this gene, termed Nkx-3.1, is largely restricted to the prostate gland in adult animals. The level of Nkx-3.1 mRNA decreases markedly in response to castration, suggesting that its expression is androgen-dependent. In situ hybridization analyses demonstrated that expression of Nkx-3.1 in the prostate is confined to epithelial cells. In newborns, Nkx-3.1 mRNA is detected in the urethral epithelium that is being induced by the surrounding mesenchyme to invaginate to form prostatic buds. Together, these observations suggest that the Nkx-3.1 protein, which likely functions as a transcription factor, plays a prominent role both in the initiation of prostate development and in the maintenance of the differentiated state of prostatic epithelial cells.
Different cytokine profiles in cryptogenic fibrosing alveolitis and fibrosing alveolitis associated with systemic sclerosis A quantitative study of open lung biopsies (1999)

Differences in the inflammatory response and prognosis of cryptogenic fibrosing alveolitis (CFA) and that associated with systemic sclerosis (FASSc) are beginning to emerge. It is hypothesized that these differences may be reflected in a distinct pattern of T-helper (Th)-1 and Th-2-type cytokines. Open lung biopsies were obtained from clinically well-documented cases of CFA and FASSc and, as a control, compared with grossly and histologically normal parenchyma obtained from smokers whose lungs were resected for cancer (n=5 in each group). In situ hybridization (ISH) was applied to the samples using anti-sense and sense 35S-labelled riboprobes to detect messenger ribonucleic acid (mRNA) for interleukins (IL)-2, IL-4, IL-5 and interferon (IFN)-gamma. Between 52-91% of cells expressing the cytokines studied were present in the alveolar interstitium rather than in lumenal cells or the alveolar epithelial lining. The highest values for all four cytokines were present in the patients with FASSc, i.e., 22-39 ISH positive cells x mm(-2) alveolar tissue compared with 1-19 cells x mm(-2) and 4-5 cell x mm(-2) in CFA and control subjects, respectively. Whereas the proportions of the four cytokines in FASSc were similar to the control subjects, IL-4 and IL-5 predominated significantly in CFA (p<0.001). For example, the ratio of IL-5 to IFN-gamma was 22:1 in CFA, significantly higher than in the cases with FASSc (2:1) or the control subjects (4:1) (p<0.05). In conclusion, cryptogenic fibrosing alveolitis is an inflammatory condition which is characterized, like asthma, by a predominance of gene expression for T-helper-2-type regulatory cytokines, whereas cryptogenic fibrosing alveolitis associated with systemic sclerosis appears to have a distinct mixed T-helper-1/T-helper-2 functional phenotype and a greater number of cells expressing each of these pro-inflammatory cytokines.
Real-Time Three-Dimensional Ultrasound-Assisted Axillary Plexus Block Defines Soft Tissue Planes (2009)

Two-dimensional (2D) ultrasound is commonly used for regional block of the axillary brachial plexus. In this technical case report, we described a real-time three-dimensional (3D) ultrasound-guided axillary block. The difference between 2D and 3D ultrasound is similar to the difference between plain radiograph and computer tomography. Unlike 2D ultrasound that captures a planar image, 3D ultrasound technology acquires a 3D volume of information that enables multiple planes of view by manipulating the image without movement of the ultrasound probe. Observation of the brachial plexus in cross-section demonstrated distinct linear hyperechoic tissue structures (loose connective tissue) that initially inhibited the flow of the local anesthesia. After completion of the injection, we were able to visualize the influence of arterial pulsation on the spread of the local anesthesia. Possible advantages of this novel technology over current 2D methods are wider image volume and the capability to manipulate the planes of the image without moving the probe.
Detection of DNA strand breaks in individual apoptotic cells by the in situ terminal deoxynucleotidyl transferase and nick translation assays. (1993)

DNA strand breaks which occur in HL-60 cells as a result of activation of endonuclease during apoptosis induced by cell treatment with the DNA topoisomerase I inhibitor camptothecin and topoisomerase II inhibitors teniposide, 4'-(9-acridinylamino)-3-methanesulfon-m-anisidide, and fostriecin were labeled in situ, in individual fixed and permeabilized cells, with biotinylated dUTP (detected by fluoresceinated avidin), using the terminal deoxynucleotidyl transferase or nick translation assays. During the early stage of apoptosis, prior to nuclear fragmentation, the breaks were predominantly localized at the nuclear periphery, close to the nuclear envelope. In more advanced stages, all cellular DNA, then localized within the cell as dense, homogeneous granules of a variety of sizes, was strongly labeled, indicating extensive and more uniform distribution of breaks throughout genomic DNA. Bivariate analysis of the incorporated biotinylated dUTP and cellular DNA content by flow cytometry made it possible to estimate the kinetics of the labeling reaction and relate DNA breaks to cell position in the cycle. The kinetics of biotinylated dUTP incorporation was faster, and the distinction of cells with DNA breaks was more pronounced, using the terminal transferase rather than the nick translation assay. Camptothecin, teniposide, and 4'-(9-acridinylamino)-3-methanesulfon-m-anisidide induced DNA breaks preferentially in S-phase cells, having little effect on cells in the G1 phase of the cycle. In contrast, fostriecin affected cells indiscriminately, in all phases of the cell cycle. The method of detection of DNA strand breaks (3'-hydroxyl termini) in individual cells offers several advantages and can be applied to clinical material (tumor biopsies) to study the induction of apoptosis in tumors during treatment, as a possible prognostic marker. The protein-associated DNA breaks in the "cleavable" DNA-topoisomerase complexes, which are the primary lesions induced by the inhibitors and precede apoptosis, were not detectable by the present methods.
Acquired Ciliary Defects in Nasal Epithelium of Children with Acute Viral Upper Respiratory Infections (1985)

Ciliary function and mucociliary clearance are primary mechanisms of defense in the respiratory tract. We found that infections by several common respiratory viruses in children were associated with ciliary abnormalities that could be detected on ultrastructural examination of the nasal epithelium. Dysmorphic ciliary forms involving microtubular aberrations were observed most often in the early stages of illness in focal sites of the nasal mucosa. Normal epithelial organization and ciliary ultrastructure appeared to be reestablished during the convalescent period, from 2 to 10 weeks after infection. These observations suggest that interference with ciliogenic mechanisms leading to transient, compromised mucociliary clearance may represent a fundamental pathophysiologic disturbance in some respiratory viral infections.
Interaction of Calcium with Bordetella pertussis Adenylate Cyclase Toxin (1995)

The adenylate cyclase (CyaA) secreted by Bordetella pertussis is a toxin that is able to enter eukaryotic cells and cause a dramatic increase in cAMP level. In addition, the toxin also exhibits an intrinsic hemolytic activity that is independent from the ATP cycling catalytic activity of the toxin. Both the cytotoxic and hemolytic activities are calcium-dependent. In this work, we have analyzed the calcium interacting properties of CyaA. We have shown that CyaA exposed to CaCl2 could retain membrane binding capability and hemolytic activity when it was further assayed in the presence of an excess of EGTA. Determination of the calcium content of CyaA exposed first to calcium and subsequently to EGTA indicated that some (3-5) calcium ions remained bound to the protein, suggesting the existence of Ca2+ binding sites of high affinity. Binding of Ca2+ to these sites might be necessary for both the membrane binding capability and the hemolytic activity of the toxin. In addition, CyaA possesses a large number (about 45) of low affinity (KD = 0.5-0.8 mM) Ca2+ binding sites that are located in the C terminus of the toxin, between amino acids 1007 and 1706. This region mainly consists of about 45 repeated sequences of the type GGXGXDXLX (where X represents any amino acid) that are characteristic of the RTX (Repeat in ToXin) bacterial protein family. Our data suggest that each one can bind one calcium ion. Circular dichroism spectroscopy analysis showed that calcium binding to the low affinity sites induces a large conformational change of CyaA, as revealed by an important increase in the content of alpha-helical structures. This conformational change might be directly involved in the Ca(2+)-dependent translocation of the catalytic domain of CyaA through the plasma membrane of target cells.
Phase Behavior of Poly(n‐butyl acrylate) and Poly(2‐ethylhexyl acrylate) in Nematic Liquid Crystal E7 (2011)

Abstract Summary: This paper reports on the phase behavior of photochemically crosslinked poly( n ‐butyl acrylate) (PABu) and poly(2‐ethylhexyl acrylate) (PEHA) networks in a nematic liquid crystal (LC) solvent. The swelling properties of these networks were studied as a function of temperature using a low molecular weight LC (LMWLC), which is an eutectic mixture of cyanoparaphenylenes named E7. To obtain different polymer network densities, the ratio of the reactive monomers ABu (or EHA) to the crosslinking agent hexanedioldiacrylate (HDDA) was varied prior to polymerization/crosslinking reactions. Immersion of these networks in an excess of LC solvent allowed for the measurement of size increase by polarizing optical microscopy in terms of temperature. Diameter ratios were calculated considering swollen to dry network states of the samples. The uptake of LMWLC inside the network preferentially takes place around the nematic to isotropic transition temperature of the solvent. Phase diagrams in the concentration‐temperature framework were given and discussed as a function of crosslinking degree of the polymer network and temperature and phase behavior of the solvent.
First in-vivo studies of presbyopia treatment with ultrashort laserpulses (2003)

The most probable reason for presbyopia, the age-related loss of the accomodation-ability of the eye, is an age-related loss of the elasticity of the lens. To increase the elasticity, resp. regain elasticity we performed different fs-laser-induced cuts with an near-infrared 5 kHz femtosecond laser inside ex-vivo and in-vivo rabbit lenses. Sagittal and annulus cutting patterns in the lens were produced by focusing the laser beam through the cornea inside the lens and creating a laser induced optical breakdown. The cutting results were recorded with light microscopy and finally, after euthanization, changes in the optical fibers of the lens tissue were described.
Minimizing Position Error in a Car Navigation System by fusing GPS and Dead-Reckoning (1994)

The CNS(Car Navigation System) is used more generally in driver aid system than ALV(Auto nomous Land Vehicle) research area. In this paper we developed a new position tracking algorithm for the Global Path Planning in the CNS. In japan, CNS is already well developed and, thesedays they sell CNS products about thousands per year, and USA and European Communications(EC), too. In Korea, studies of the first generation CNS, which finds current location of a navigating vehicle and displays its location in a Digital-Map with real-time are progressing but still in the beginning step. Therefore a new position tracking algorithm is presented, which reduces vehicle position error dramatically by fusing GPS and dead-reckoning sensors. And the validity of our algorithm is demonstrated by the experimental results with the real car.