gebhart/patrepeval huggingface dataset:
A Comparison of Glycopeptides Derived from Soluble and Insoluble Collagens (1968)

Digestion of preparations of insoluble collagen of guinea pig skin with collagenase and trypsin led to the production of two distinct glycopeptide fractions. The lower molecular weight fraction was similar in amount and in composition to the single predominant glycopeptide fraction obtained by similar treatment of soluble collagen. The major component in this fraction had the same chemical and physical characteristics as the glycohexapeptide, Gly-Met-Hyl(-Gal-Glc)-Gly-His-Arg, which had been characterized previously in similar digests of soluble collagen. The second and higher molecular weight glycopeptide fraction (which contained no hydroxylysine) was found only in insoluble collagen. The major amino acids and carbohydrates present in this fraction were aspartic and glutamic acids, glycine, alanine, serine, proline, glucose, galactose, mannose, glucosamine, galactosamine, and sialic acid. The fraction appeared to be quite heterogeneous, and it has not yet been possible to establish whether interpeptide crosslinks were present. This fraction was, however, increased in samples of perchlorate-insoluble collagen identical with those in which Hormann reported evidence for covalent cross-links involving carbohydrate. Alkaline hydrolysis of soluble or insoluble collagen led to the isolation of closely similar quantities of both O-Hyl-(-Gal-Glc) and O-Hyl(-Gal), thus establishing the presence of limited numbers of monosaccharide side chains in both forms of collagen. These analyses, as well as studies of partial acid hydrolysates of purified hydroxylysine-containing glycopeptides, showed the presence in mammalian skin collagen of a disaccharide in which C-1 of D-glucose is linked to D-galactose, and C-1 of D-galactose to the δ-hydroxyl group of hydroxylysine. No evidence was found for the participation of this carbohydrate prosthetic group in crosslinking related to the conversion of soluble collagen to insoluble collagen.
Left Ventricular Deformation Recovery From Cine MRI Using an Incompressible Model (2007)

This paper presents a method for 3-D deformation recovery of the left ventricular (LV) wall from anatomical cine magnetic resonance imaging (MRI). The method is based on a deformable model that is incompressible, a desired property since the myocardium has been shown to be nearly incompressible. The LV wall needs to be segmented in an initial frame after which the method automatically determines the deformation everywhere in the LV wall throughout the cardiac cycle. Two studies were conducted to validate the method. In the first study, the deformation recovered from a 3-D anatomical cine MRI of a healthy volunteer was compared against the manual segmentation of the LV wall and against the corresponding 3-D tagged cine MRI. The average volume agreement between the model and the manual segmentation had a false positive rate of 3%, false negative rate of 3%, and true positive rate of 93%. The average distance between the model and manually determined intersections of perpendicular tag planes was 1.6 mm (1.1 pixel). Another set of 3-D anatomical and tagged MRI scans was taken of the same volunteer four months later. The method was applied to the second set and the recovered deformation was very similar to the one obtained from the first set. In the second study, the method was applied to 3-D anatomical cine MRI scans of three patients with ventricular dyssynchrony and three age-matched healthy volunteers. The LV wall deformations recovered for the three normals agreed well and the recovered strains were similar to those reported by other researchers for normal subjects. Strains and displacements of the three patients were clearly smaller than those of the three normals indicating reduced cardiac function. The deformation recovered for the three normals and the three patients was validated against manual segmentation and corresponding tag cine MRI scans and the agreement was similar to that of the first validation study.
Pulmonary Surfactant, Lung Function, and Endobronchial Inflammation in Cystic Fibrosis (2004)

Cystic fibrosis (CF) lung disease is primarily a disease of the small airways. We hypothesized that even in patients with normal lung function, a reduced surfactant function would be present and favor small airway obstruction. Bronchoalveolar lavages from 76 patients with CF (5-31 years, median 11) with well-conserved lung function (FEV1 94% predicted, range 78-121) and from 10 healthy control subjects were investigated. The deviation of the biophysical surfactant performance from normal, assessed in a bubble surfactometer, was small; however, the ability of the surfactant to maintain the patency of a narrow airway (% open) was significantly reduced. Surfactant protein (SP)-C level was increased, SP-B and SP-D were unchanged, whereas SP-A was decreased. Among the patients with CF, neutrophilic inflammation was modestly related to a poorer surfactant activity, but not to lung function. SP-D was reduced in proportion to the degree of inflammation and in the presence of bacteria. These findings in a large cohort of patients with CF with normal lung function show that the endobronchial airway inflammation is linked to early perturbations of the biophysical properties and immunologic components of pulmonary surfactant and opens fields for novel therapeutic interventions.
Two‐photon molecular excitation provides intrinsic 3‐dimensional resolution for laser‐based microscopy and microphotochemistry (1994)

With the development of sensitive and specific fluorescent indicators, modern laser scanning microscopies enable visualization and measurement of submicron, dynamic processes inside living cells and tissues. Here we describe the working principles of new, nonlinear laser microscopies based on two-photon molecular excitation. In these techniques, a pulsed laser produces peak photon densities high enough that when focused into an appropriate medium, excitation by photon energy combinations can occur. For example, two red photons interacting simultaneously with a fluorescent molecule can excite within it a UV electronic transition, one corresponding to twice the energy of each single photon. Because the amount of two-photon excitation depends on the square of the local illumination intensity, this process exhibits a unique localization to the diffraction-limited spot of the beam focus. Elsewhere along the beam, excitation of background and photodamage is virtually nonexistent. Focal point localization of two-photon excitation lends to all visualization, measurement, and photopharmacology studies an intrinsic, three-dimensional resolution. We describe some preliminary biological applications, specifically, imaging of vital DNA stains in developing cells and embryos, imaging of cellular metabolic activity from NADH autofluorescence, spatially resolved measurements of cytoplasmic calcium ion activity, and optically induced micropharmacology using caged bioeffector molecules.
Using Telemetry Data for Video Compression on Unmanned Air Vehicles (2006)

Unmanned Aerial Vehicles in the \mini to \micro size ranges (<6 foot wingspan) are becoming increasingly popular platforms for the collection of video data about an area of interest. Currently, mini-UAV platforms transmit video back to the end user using analog RF transmitters. Transmission of digital video, although it is more desirable on a mini-UAV platform, requires video compression to be performed. Unfortunately, determining the motion information required for digital video compression is a computationally expensive procedure. Hardware capable of performing this task is typically too heavy, too large, and too power intensive to be carried on a mini-UAV. We present an e‐cient algorithm for solving the motion estimation problem which requires far less computation, making it feasible for implementation on-board a mini-UAV. We reduce the amount of computation necessary by using (1) knowledge of camera locations (from available mini-UAV sensor data) and (2) the projective geometry of the camera. We present encouraging initial results, showing that this method reduces computations by almost two orders of magnitude compared to standard methods, and yields comparable or improved compression results.
Diverse Class 2 CRISPR-Cas Effector Proteins for Genome Engineering Applications (2017)

CRISPR-Cas genome editing technologies have revolutionized modern molecular biology by making targeted DNA edits simple and scalable. These technologies are developed by domesticating naturally occurring microbial adaptive immune systems that display wide diversity of functionality for targeted nucleic acid cleavage. Several CRISPR-Cas single effector enzymes have been characterized and engineered for use in mammalian cells. The unique properties of the single effector enzymes can make a critical difference in experimental use or targeting specificity. This review describes known single effector enzymes and discusses their use in genome engineering applications.
Development of the Vault Particle as a Platform Technology (2012)

Vaults are naturally occurring nanoparticles found widely in eukaryotes. The particles can be produced in large quantities and are assembled in situ from multiple copies of the single structural protein following expression. Using molecular engineering, recombinant vaults can be functionally modified and targeted, and their contents can be controlled by packaging. Here, we review the development of engineered vaults as a platform for a wide variety of therapeutic applications and we examine future directions for this unique nanoparticle system.
Continuous appearance-based localisation and mapping (2014)

This thesis presents a novel approach to mobile robot navigation using visual information towards the goal of long-term autonomy. A novel concept of a continuous appearance-based trajectory is proposed in order to solve the limitations of previous robot navigation systems, and two new algorithms for mobile robots, CAT-SLAM and CAT-Graph, are presented and evaluated. These algorithms yield performance exceeding state-of-the-art methods on public benchmark datasets and large-scale real-world environments, and will help enable widespread use of mobile robots in everyday applications.
Spontaneous apoptosis of dendritic cells is efficiently inhibited by TRAP (CD40‐ligand) and TNF‐α, but strongly enhanced by interleukin‐10 (1995)

In the lymphoid tissues, adaptive immune responses are initiated by the interaction of interdigitating dendritic cells (IDC) with naive T cells. To understand this interplay better, we used mature Langerhans cells (mLC), migrating from human epidermis, as the correlate of IDC ex vivo to evaluate the different effects of tumor necrosis factor (TNF)-alpha. TNF-related activation protein (TRAP; CD40-ligand) and interleukin-10 (IL-10) on induction or prevention of apoptotic cell death in these cells. Spontaneous decrease of mLC viability in culture was due to apoptosis, as determined by the appearance of typical morphological changes such as dilatation of the endoplasmic reticulum (ER), chromatin condensation and membrane blebbing. IL-10 strongly reduced mLC viability, whereas TRAP and TNF-alpha facilitated the survival of mLC. Spontaneous DNA fragmentation was detectable after 24 h in culture. IL-10 led to an earlier onset of DNA fragmentation, whereas TRAP and TNF-alpha delayed internucleosomal DNA cleavage. We found that IL-10-treated mLC were readily ingested and removed by macrophages. TNF-alpha and TRAP, in contrast, reduced engulfment of mLC by macrophages. Interestingly, IL-10, even at low concentrations, reverted the effects of TNF-alpha and TRAP in inhibiting mLC apoptosis. Furthermore, IL-10 led to the down-regulation of various surface antigens, especially of CD86 and CD54, whereas TNF-alpha and TRAP enhanced the expression of MHC class I and II antigens and of the accessory molecules CD40, CD54, CD80 and CD86. Taken together, these results show that mLC spontaneously undergo apoptosis in culture and that the progression of mLC to apoptosis is inhibited by TRAP and TNF-alpha, but accelerated by IL-10.
Design of a Modular‐Based Fluorescent Conjugated Polymer for Selective Sensing (2004)

Sensitive and selective, a modular-based fluorescent polymer combines a rigid electron-conducting block (see picture; B) with a flexible binding block (A). The monopyridyl group of the coordinating module has a great affinity for PdII ions and selectively binds them through self-assembly. Thus, the fluorescent conjugated polymer may be used for sensing PdII ions. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z460371_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Minimal Changes of Serum Creatinine Predict Prognosis in Patients after Cardiothoracic Surgery (2004)

Acute renal failure increases risk of death after cardiac surgery. However, it is not known whether more subtle changes in renal function might have an impact on outcome. Thus, the association between small serum creatinine changes after surgery and mortality, independent of other established perioperative risk indicators, was analyzed. In a prospective cohort study in 4118 patients who underwent cardiac and thoracic aortic surgery, the effect of changes in serum creatinine within 48 h postoperatively on 30-d mortality was analyzed. Cox regression was used to correct for various established demographic preoperative risk indicators, intraoperative parameters, and postoperative complications. In the 2441 patients in whom serum creatinine decreased, early mortality was 2.6% in contrast to 8.9% in patients with increased postoperative serum creatinine values. Patients with large decreases (DeltaCrea <-0.3 mg/dl) showed a progressively increasing 30-d mortality (16 of 199 [8%]). Mortality was lowest (47 of 2195 [2.1%]) in patients in whom serum creatinine decreased to a maximum of -0.3 mg/dl; mortality increased to 6% in patients in whom serum creatinine remained unchanged or increased up to 0.5 mg/dl. Mortality (65 of 200 [32.5%]) was highest in patients in whom creatinine increased > or =0.5 mg/dl. For all groups, increases in mortality remained significant in multivariate analyses, including postoperative renal replacement therapy. After cardiac and thoracic aortic surgery, 30-d mortality was lowest in patients with a slight postoperative decrease in serum creatinine. Any even minimal increase or profound decrease of serum creatinine was associated with a substantial decrease in survival.
Kiwifruit improves bowel function in patients with irritable bowel syndrome with constipation. (2010)

Irritable bowel syndrome (IBS) is a common functional disorder of the gastrointestinal system, and is characterized by abdominal pain, diarrhea (IBS/D), constipation (IBS/C), and alternating diarrhea and constipation (IBSC/A). The purpose of this study was to examine the impact of a four week kiwifruit intervention on bowel function in patients diagnosed with IBS/C. Fifty-four patients with IBS/C and 16 healthy adults participated in this study. All subjects participated in the 6 week, three phase study, which included a baseline phase (1 week), a dietary intervention period (4 weeks), and a post-intervention phase (1 week). Forty-one IBS/C patients and all healthy adults consumed two Hayward green (Actinida deliciosa var) kiwifruits per day for 4 weeks. Thirteen IBS/C patients in the control group took two placebo capsules per day for 4 weeks. Colon transit time was measured immediately prior to and following the intervention period. All subjects completed daily defecation records. After the 4-week intervention, weekly defecation frequency significantly increased in the IBS/C group of participants who consumed kiwifruit (p<0.05). Colon transit time significantly decreased (p=0.026) in the IBS/C group that consumed kiwi fruit. These findings suggest that kiwifruit consumption for 4 weeks shortens colon transit time, increases defecation frequency, and improves bowel function in adults diagnosed with IBS/C.
Biochemical and Functional Properties of Lysine-Specific Cysteine Proteinase (Lys-Gingipain) as a Virulence Factor of Porphyromonas gingivalis in Periodontal Disease (1998)

The oral anaerobic bacterium Porphyromonas gingivalis has been implicated as a major etiologic agent of progressive periodontal disease. A novel lysine-specific cysteine proteinase, termed "Lys-gingipain," was purified from the culture supernatant of the Arg-gingipain-deficient mutant of P. gingivalis (KDP112) by a simple method including immunoaffinity chromatography. The purified enzyme was found to be composed of a single polypeptide of Mr=51,000. Analysis of the enzymatic properties revealed several distinctive features of this enzyme. The proteolytic activity was remarkably activated by thiol-reducing agents and inhibited by idoacetamide, idoacetic acid, and leupeptin. The enzyme was also inhibited by the chloromethyl ketones of tosyl-L-lysine and tosyl-L-phenylalanine. However, internal protease inhibitors, such as cystatins and alpha1-antichymotrypsin, had no effect on the activity, suggesting its resistance to normal host defense systems in vivo. Despite its narrow specificity for synthetic substrates containing Lys in the P1 site, the enzyme extensively degraded human type I collagen and immunoglobulins G and A (both serum and secretory types). Most important, the enzyme was able to disrupt the functions of polymorphonuclear leukocytes, as shown by its inhibitory effect on the generation of active oxygen species from the activated cells. These results suggest that Lys-gingipain, like Arg-gingipain, plays a crucial role as a virulence factor from P. gingivalis in the development of periodontal disease via the direct destruction of periodontal tissue components and the disruption of normal host defense mechanisms.
Receptor-mediated regulation of the TRPM7 channel through its endogenous protein kinase domain (2004)

TRPM7 is a ubiquitously expressed and constitutively active divalent cation-selective ion channel, whose basal activity is regulated by intracellular levels of Mg(2+) and Mg.ATP. We have investigated receptor-mediated mechanisms that may actively regulate TRPM7 activity. We here report that TRPM7 currents are suppressed by intracellular GTPgammaS, suggesting the involvement of heterotrimeric G proteins. TRPM7 currents are also inhibited by stimulating endogenous muscarinic receptors, which is mediated by G(i) because the inhibitory effect is blunted by pertussis toxin. Conversely, stimulation of endogenous G(s)-coupled beta-adrenergic receptors potentiates TRPM7 currents, whereas G(q)-coupled thrombin receptors have little effect. Consistent with the involvement of G(s)/G(i) in controlling adenylyl cyclase activity, elevations of intracellular cAMP levels enhance TRPM7 activity and prevent receptor-mediated modulation of TRPM7 activity by muscarinic and adrenergic agonists. This cAMP-dependent effect requires the functional integrity of both protein kinase A (PKA) and the endogenous kinase domain of TRPM7 because cAMP-mediated effects are abolished when treating cells with the PKA inhibitors H89 or KT5720 as well as in cells expressing phosphotransferase-deficient TRPM7 constructs. These mutant channels are also much less susceptible to GTPgammaS-mediated inhibition, suggesting that the main regulatory effect occurs through G(i)- and G(s)-mediated changes in cAMP. Taken together, our results demonstrate that TRPM7 activity is up- and down-regulated through its endogenous kinase in a cAMP- and PKA-dependent manner.
Effects of indole-3-carbinol on lung tumorigenesis and DNA methylation induced by 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and on the metabolism and disposition of NNK in A/J mice. (1990)

The effects of indole-3-carbinol (I3C) on lung neoplasia induced by the tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) were assessed in an A/J mouse pulmonary adenoma bioassay. Mice were administered corn oil or I3C (25 or 125 mumol/mouse/day) by gavage for 4 consecutive days. Two h after the final pretreatment, mice were administered a single dose of NNK (10 mumol/mouse) i.p. Pulmonary adenomas were quantitated 16 wk after NNK dosing. Mice pretreated with corn oil developed 10.7 tumors/mouse; I3C pretreatment at either dose level inhibited tumor multiplicity by approximately 40%. The effects of I3C on NNK-induced DNA methylation in the lungs and livers of A/J mice were assessed using the same dosing regimen as in the bioassay. Both dose levels of I3C inhibited pulmonary O6-methylguanine formation by at least 50%, but enhanced hepatic DNA methylation at 2 or at 6 h after NNK administration. The effects of I3C pretreatment on NNK metabolism were also investigated. Hepatic microsomes of I3C-pretreated mice showed increased formation of alpha-hydroxylation products, while no significant effect of I3C pretreatment was observed in pulmonary microsomes. The effects of I3C on [5-3H]NNK disposition were also evaluated. I3C pretreatment produced lower levels of total radioactivity in the lung when compared with controls. Additionally, lower proportions of NNK and its carcinogenic metabolite 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol were found in the lungs of I3C-pretreated mice. These results demonstrate that I3C inhibits NNK-induced lung neoplasia in A/J mice and suggest that the basis of this inhibition is the decrease in O6-methylguanine formation in A/J lung caused by I3C pretreatment. This decrease in lung DNA methylation appears to be due to the decreased bioavailability of NNK and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol in the lungs of I3C-treated mice which, in turn, may be a result of increased metabolic alpha-hydroxylation of NNK by the liver.
Systemic Antitumor Immunity in Experimental Brain Tumor Therapy Using a Multimutated, Replication-Competent Herpes Simplex Virus (1999)

Replication-competent, attenuated herpes simplex virus (HSV) vectors have been developed for viral oncolytic therapy of primary and metastatic malignant brain tumors. However, the role of the host immune responses in the brain has not been elucidated. N18 neuroblastoma cells were used as a tumor model in syngeneic A/J mice to test the therapeutic efficacy of G207, a conditionally replicating HSV vector, in an immunocompetent condition. G207 inoculated intraneoplastically exhibited a prominent oncolytic antitumor effect in mice harboring N18 tumors in the brain or subcutaneously, and, in addition, elicited a systemic antitumor immune response. Subcutaneous tumor therapy with G207 caused regression of a remote, established tumor in the brain or in the periphery, which was potentially mediated by the systemic antitumor immune response, and provided persistent tumor-specific protection against N18 tumor rechallenge in the brain as well as in the periphery. Antitumor immunity was associated with an elevation of specific CTL activity against N18 tumor cells that persisted for at least 13 months. The results suggest that the oncolytic antitumor action of replication-competent HSV may be augmented by induction of specific and systemic antitumor immunity effective both in the periphery and in the brain.
Rapid turnover of low density lipoprotein receptor in human monocytic THP‐1 cells (1991)

We examined whether human monocyte-derived macrophages had low density lipoprotein (LDL) receptors with a short life span. The human monocytic leukemia cell line, THP-1, was highly differentiated when treated with phorbol ester. LDL receptors degraded rapidly with half-lives of 3-4 h in THP-1 cells before phorbol ester treatment. During the transition into monocytic cells, expression of the LDL receptor gene was not affected. However, relative degradation rates of LDL receptors normalized by those of cellular total proteins were about twice as fast in phorbol ester-treated THP-1 cells compared to untreated cells.