gebhart/patrepeval huggingface dataset:
A peptide from the eel pancreas with structural similarity to human pancreatic secretory trypsin inhibitor (1988)

The primary structure of a 61-amino-acid residue peptide from the pancreas of the European eel (Anguilla anguilla) has been established as E E K S G(5)L Y R K P(10)S C G E M(15)S A M H A(20)C P M N F(25)A P V C G(30)T D G N T(35)Y P N E C(40)S L C F Q(45)R Q N T K(50)T D I L I(55)T K D D R(60)C. There was no indication of microheterogeneity. This peptide shows structural similarity to pancreatic secretory trypsin inhibitors from several mammalian species and to a cholecystokinin-releasing peptide isolated from rat pancreatic juice. A comparison of the amino acid sequences of the peptides has identified a domain in the central region of the molecules that has been strongly conserved during evolution. In contrast, the amino acid sequence in the region corresponding to the reactive centre of the mammalian trypsin inhibitors is very poorly conserved in the eel peptide. The P1-P1' reactive site lysine-isoleucine (or arginine-isoleucine) bond in the mammalian trypsin inhibitors is replaced by a methionine-asparagine bond. This region does, however, show limited homology to the reactive centre of human alpha 1-protease inhibitor suggesting that the eel peptide may function as an inhibitor of other proteolytic enzymes in the pancreas.
Comparative analysis of the genes UL1 through UL7 of the duck enteritis virus and other herpesviruses of the subfamily Alphaherpesvirinae (2009)

The nucleotide sequences of eight open reading frames (ORFs) located at the 5' end of the unique long region of the duck enteritis virus (DEV) Clone-03 strain were determined. The genes identified were designated UL1, UL2, UL3, UL4, UL5, UL6 and UL7 homologues of the herpes simplex virus 1 (HSV-1). The DEV UL3.5 located between UL3 and UL4 had no homologue in the HSV-1. The arrangement and transcription orientation of the eight genes were collinear with their homologues in the HSV-1. Phylogenetic trees were constructed based on the alignments of the deduced amino acids of eight proteins with their homologues in 12 alpha-herpesviruses. In the UL1, UL3, UL3.5, UL5 and UL7 proteins trees, the branches were more closely related to the genus Mardivirus. However, the UL2, UL4, and UL6 proteins phylogenetic trees indicated a large distance from Mardivirus, indicating that the DEV evolved differently from other viruses in the subfamily Alphaherpesvirinae and formed a single branch within this subfamily.
Culture of Enzymatically Dispersed Anterior Pituitary Cells: Functional Validation of a Method (1972)

A method for preparing short—term enzymatically dispersed pituitary cell cultures is described. It has been used to assay hypothalamic releasing factors. The cells secrete TSH or LH and FSH in amounts directly related to the dose of TRF or LRF respectively. The minimal active doses of synthetic TRF and either synthetic or highly purified ovine LRF is ca. 10-10M. Apparent affinity constants for TRF or LRF receptors are ca. 10-9M. Enhanced secretion rates of TSH or LH of 8– to 20–fold in response to maximal levels of TRF or LRF are routinely observed. The sensitivity of the cultured cells to TRF and LRF is maintained for more than 2 weeks in culture although the magnitude of the secretory response and the intracellular hormone content declines with time in culture. Chronic administration of TRF or LRF depletes the intracellular hormone levels while simultaneously increasing the total TSH or LH content in the culture (tissue and fluid). As has been observed with other in vitro systems, high medium potassium, prostaglandin E2 and theophylline stimulate TSH secretion from the cultured cells. Furthermore, thyroid hormones which suppress the TSH secretion in response to TRF by the anterior pituitary in vivo and in other in vitro methods are similarly effective on these cells. The use of this technique has been applied to pituitary tissues of other species and types of cells, e.g., cells from G1 mouse thyrotropic tumors were shown to respond appropriately to TRF and thyroxine. The enzymatically dispersed cultured cells have been found to behave as would have been expected on the basis of experience with other in vitro methods while having significant advantages over those other procedures. (Endocrinology91: 562, 1972)
Properties And Uses Of Photoreactive Caged Compounds (1989)

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific ...Read More
Cell-Demanded Liberation of VEGF 121 From Fibrin Implants Induces Local and Controlled Blood Vessel Growth (2004)

Although vascular endothelial growth factor (VEGF) has been described as a potent angiogenic stimulus, its application in therapy remains difficult: blood vessels formed by exposure to VEGF tend to be malformed and leaky. In nature, the principal form of VEGF possesses a binding site for ECM components that maintain it in the immobilized state until released by local cellular enzymatic activity. In this study, we present an engineered variant form of VEGF, alpha2PI1-8-VEGF121, that mimics this concept of matrix-binding and cell-mediated release by local cell-associated enzymatic activity, working in the surgically-relevant biological matrix fibrin. We show that matrix-conjugated alpha2PI1-8-VEGF121 is protected from clearance, contrary to native VEGF121 mixed into fibrin, which was completely released as a passive diffusive burst. Grafting studies on the embryonic chicken chorioallantoic membrane (CAM) and in adult mice were performed to assess and compare the quantity and quality of neovasculature induced in response to fibrin implants formulated with matrix-bound alpha2PI1-8-VEGF121 or native diffusible VEGF121. Our CAM measurements demonstrated that cell-demanded release of alpha2PI1-8-VEGF121 increases the formation of new arterial and venous branches, whereas exposure to passively released wild-type VEGF121 primarily induced chaotic changes within the capillary plexus. Specifically, our analyses at several levels, from endothelial cell morphology and endothelial interactions with periendothelial cells, to vessel branching and network organization, revealed that alpha2PI1-8-VEGF121 induces vessel formation more potently than native VEGF121 and that those vessels possess more normal morphologies at the light microscopic and ultrastructural level. Permeability studies in mice validated that vessels induced by alpha2PI1-8-VEGF121 do not leak. In conclusion, cell-demanded release of engineered VEGF121 from fibrin implants may present a therapeutically safe and practical modality to induce local angiogenesis.
Reagentless Measurement of Aminoglycoside Antibiotics in Blood Serum via an Electrochemical, Ribonucleic Acid Aptamer-Based Biosensor (2010)

Biosensors built using ribonucleic acid (RNA) aptamers show promise as tools for point-of-care medical diagnostics, but they remain vulnerable to nuclease degradation when deployed in clinical samples. To explore methods for protecting RNA-based biosensors from such degradation we have constructed and characterized an electrochemical, aptamer-based sensor for the detection of aminoglycosidic antibiotics. We find that while this sensor achieves low micromolar detection limits and subminute equilibration times when challenged in buffer, it deteriorates rapidly when immersed directly in blood serum. In order to circumvent this problem, we have developed and tested sensors employing modified versions of the same aptamer. Our first effort to this end entailed the methylation of all of the 2'-hydroxyl groups outside of the aptamer's antibiotic binding pocket. However, while devices employing this modified aptamer are as sensitive as those employing an unmodified parent, the modification fails to confer greater stability when the sensor is challenged directly in blood serum. As a second potentially naive alternative, we replaced the RNA bases in the aptamer with their more degradation-resistant deoxyribonucleic acid (DNA) equivalents. Surprisingly and unlike control DNA-stem loops employing other sequences, this DNA aptamer retains the ability to bind aminoglycosides, albeit with poorer affinity than the parent RNA aptamer. Unfortunately, however, while sensors fabricated using this DNA aptamer are stable in blood serum, its lower affinity pushes their detection limits above the therapeutically relevant range. Finally, we find that ultrafiltration through a low-molecular-weight-cutoff spin column rapidly and efficiently removes the relevant nucleases from serum samples spiked with gentamicin, allowing the convenient detection of this aminoglycoside at clinically relevant concentrations using the original RNA-based sensor.
Molecular potentials and relaxation dynamics (1981)

The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X/sup 1/..sigma../sup +/ and a/sup 3/..sigma../sup +/ states of LiH, NaH, KH, RbH, and CsH and the X/sup 2/..sigma../sup +/ states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm/sup -1/ over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500/sup 0/K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy.
Controversies in Sleep Medicine (1994)

Some of the world's best sleep laboratories do not use computerized data acquisition.Some of the world's best sleep laboratories have developed their own homemade computerized data acquisition systems.Many of the world's best sleep laboratories use commercially available acquisition systems.Why don't all laboratories simply purchase such systems?The group from the Sleep Disorders and Research Center from the Baylor College of Medicine have extensive experience in the use of computers in the sleep laboratory.Drs.Hirshkowitz and Moore deal with the issues of computers in the sleep laboratory and help explain the paradox of why some of the world's best sleep laboratories use such systems while other world-class laboratories do not.At the very least, the reader will understand that the issue is a complex one.All of us can drive a car without understanding the nitty gritty of how the car works, but we are not there yet in the computerized sleep field.We still need to know what is going on "under the hood" of our computer systems and only then can we make rational decisions.
Polymer Microcapsules with Programmable Active Release (2013)

We present a new type of microcapsule programmed with a tunable active release mechanism. The capsules are triggered by a plasticizing stimulus that induces a phase change transition of the polymeric membrane from a solid to a fluidized form; thereafter, the cargo is actively driven out of the capsule through a defect at the capsule wall with controllable release kinetics. Tuning the degree of membrane fluidity by tailoring the amount of plasticizing stimulus present allows us to obtain temporal variation of the release kinetics from a subsecond abrupt burst release to a slow sustained release of encapsulant over many minutes. Moreover, we demonstrate tuning of the collective capsule triggering response by adjusting stimulus content, polymer molecular weight, and capsule membrane thickness. For this model system, we use a microfluidic approach to fabricate polystyrene capsules triggered by a toluene stimulus. However, this active release approach is general and is applicable to diverse polymeric capsule systems; this versatility is demonstrated by extension of our trigger-release scheme to capsules fabricated from a rubberlike block copolymer. The utility of our technique further enhances the potential of these active release capsules for practical application.
Prognostic factors of papillary and follicular thyroid cancer: differences in an iodine-replete endemic goiter region. (2004)

Papillary (PTC) and follicular thyroid carcinoma (FTC) are known as differentiated thyroid carcinoma (DTC). Nevertheless, according to the UICC/AJCC (TNM) classification PTC and FTC are frequently analyzed as one cancer. The aim of this study is to show differences in outcome and specific prognostic factors in an iodine-replete endemic goiter region. Six hundred and three patients with DTC treated within a 35-year-period were retrospectively analyzed with respect to carcinoma-specific survival. Prognostic factors were tested for their significance using univariate and multivariate analysis. The histological type (PTC versus FTC) was found to be a highly significant factor - carcinoma-specific survival both in univariate (P<0.001) and multivariate analyses (P=0.003) was significantly different. Univariate analysis revealed patients' age, extra-thyroid tumor spread, lymph node and distant metastases, increasing tumor size, and the tall cell variant to be significant prognostic factors for PTC patients. Age > or =45 years, positive lymph nodes and increasing tumor size were confirmed as independent prognostic factors. Univariate analysis of FTC patients revealed age at presentation, gender, extrathyroidal tumor spread, lymph node and distant metastases, increasing tumor size, multifocality, widely invasive tumor growth and oxyphilic variant to be factors bearing prognostic significance. The presence of distant metastases and increasing tumor size could be identified as independent prognostic factors for FTC patients. This study shows distinctive differences in prognostic factors of PTC and FTC: independent factors predicting poor prognosis are age > or =45 years, positive lymph nodes and increasing tumor size for PTC, and distant metastases and increasing tumor size for FTC. PTC and FTC patients should be analyzed and reported separately.
An Overview of Endosymbiotic Models for the Origins of Eukaryotes, Their ATP-Producing Organelles (Mitochondria and Hydrogenosomes), and Their Heterotrophic Lifestyle (2001)

The evolutionary processes underlying the differentness of prokaryotic and eukaryotic cells and the origin of the latter's organelles are still poorly understood. For about 100 years, the principle of endosymbiosis has figured into thoughts as to how these processes might have occurred. A number of models that have been discussed in the literature and that are designed to explain this difference are summarized. The evolutionary histories of the enzymes of anaerobic energy metabolism (oxygen-independent ATP synthesis) in the three basic types of heterotrophic eukaryotes those that lack organelles of ATP synthesis, those that possess mitochondria and those that possess hydrogenosomes--play an important role in this issue. Traditional endosymbiotic models generally do not address the origin of the heterotrophic lifestyle and anaerobic energy metabolism in eukaryotes. Rather they take it as a given, a direct inheritance from the host that acquired mitochondria. Traditional models are contrasted to an alternative endosymbiotic model (the hydrogen hypothesis), which addresses the origin of heterotrophy and the origin of compartmentalized energy metabolism in eukaryotes.
Antialiasing for automultiscopic 3D displays (2006)

Automultiscopic displays show stereoscopic images that can be viewed from any viewpoint without special glasses. They hold great promise for the future of television and digital entertainment. However, the image quality on these 3D displays is currently not sufficient to appeal to the mass market. In this paper, we extend the frequency analysis of light fields to address some of the major issues in 3D cinematography for automultiscopic displays. First, we derive the bandwidth of 3D displays using ray-space analysis, and we introduce a method to quantify display depth of field. We show that this approach provides solid foundations to analyze and distinguish various aspects of aliasing. We then present an anti-aliasing technique for automultiscopic displays by combining a reconstruction and a display prefilter. Next, we show how to reparameterize multi-view inputs to optimally match the depth of field of a display to improve the image quality. Finally, we present guidelines for 3D content acquisition, such as optimal multi-view camera configuration and placement.
Improved Automatic Analysis of Architectural Floor Plans (2011)

This paper proposes a novel complete system for automated floor plan analysis. Besides applying and improving state-of-the-art processing methods, we introduce novel preprocessing methods, e.g., the differentiation between thick, medium, and thin lines and the removal of components outside the convex hull of the outer walls. Especially the latter method increases the performance of the final system. In our experiments on a reference data set we compare our approach to other approaches available in the literature. We show that our system outperforms previous systems. The final room recognition accuracy is 79% that is 10% higher than the 69% achieved by a state-of-the-art approach from the literature.
Architectural and Performance Evaluation of GigaNet and Myrinet Interconnects on Clusters of Small-Scale SMP Servers (2000)

GigaNet and Myrinet are two of the leading interconnects for clusters of commodity computer systems. Both provide memory-protected user-level network interface access, and deliver low-latency and high-bandwidth communication to applications. GigaNet is a connection-oriented interconnect based on a hardware implementation of Virtual Interface (VI) Architecture and Asynchronous Transfer Mode (ATM) technologies. Myrinet is a connection-less interconnect which leverages packet switching technologies from experimental Massively Parallel Processors (MPP) networks. This paper investigates their architectural differences and evaluates their performance on two commodity clusters based on two generations of Symmetric Multiple Processors (SMP) servers. The performance measurements reported here suggest that the implementation of Message Passing Interface (MPI) significantly affects the cluster performance. Although MPICH-GM over Myrinet demonstrates lower latency with small messages, the polling-driven implementation of MPICH-GM often leads to tight synchronization between communication processes and higher CPU overhead.
ANGPTL4 regulates the metastatic potential of oral squamous cell carcinoma (2014)

Lymph node metastasis is a major factor for poor prognosis in oral squamous cell carcinoma (OSCC). However, the molecular mechanisms of lymph node metastasis are unclear. We determined that angiopoietin-like protein 4 (ANGPTL4) mRNA and protein expression were increased in OSCC cells established from the primary site in metastatic cases. In addition, ANGPTL4 expression in biopsy specimens was correlated with the presence of lymph node metastasis. Therefore, our initial findings suggest that OSCC cells expressing ANGPTL4 may possess metastatic ability. Furthermore, cell culture supernatants from OSCC cells that metastasized to the lymph node contain ANGPTL4 and promote invasive ability. These findings suggest that secreted ANGPTL4 may affect the invasive ability of OSCC. Moreover, the rates of positive ANGPTL4 expression at the primary site were significantly higher in the lymph node metastasis group. These results demonstrate that ANGPTL4 contributes to OSCC metastasis by stimulating cell invasion. Therefore, ANGPTL4 is a potential therapeutic target for preventing cancer metastasis.
Molecular Biology of Erythropoietin (2004)

The glycoprotein hormone erythropoietin (EPO) is an essential viability and growth factor for the erythrocytic progenitors. EPO is mainly produced in the kidneys. EPO gene expression is induced by hypoxia-inducible transcription factors (HIF). The principal representative of the HIF-family (HIF-1, -2 and -3) is HIF-1, which is composed of an O2-labile alpha-subunit and a constant nuclear beta-subunit. In normoxia, the alpha-subunit of HIF is inactivated following prolyl- and asparaginyl-hydroxylation by means of alpha-oxoglutarate and Fe(2+)-dependent HIF specific dioxygenases. While HIF-1 and HIF-2 activate the EPO gene, HIF-3, GATA-2 and NFkappaB are likely inhibitors of EPO gene transcription. EPO signalling involves tyrosine phosphorylation of the homodimeric EPO receptor and subsequent activation of intracellular antiapoptotic proteins, kinases and transcription factors. Lack of EPO leads to anemia. Treatment with recombinant human EPO (rHuEPO) is efficient and safe in improving the management of the anemia associated with chronic renal failure. RHuEPO analogues with prolonged survival in circulation have been developed. Whether the recent demonstration of EPO receptors in various non-hemopoietic tissues, including tumor cells, is welcome or ominous still needs to be clarified. Evidence suggests that rHuEPO may be a useful neuroprotective agent.
Surface plasmon resonance properties of DC magnetron sputtered Ag nanoislands on ITO‐glass and In 2 O 3 ‐PET substrates (2014)

Films of Ag nanoislands (NIs) were successfully grown on two different transparent conducting oxide coated substrates (indium tin oxide (ITO) coated glass and indium oxide (In 2 O 3 ) coated polyethylene terephthalate (PET) flexible film) by direct current (DC) magnetron sputtering. The morphology of the Ag NIs was studied using transmission electron microscopy (TEM) and scanning electron microscopy (SEM). Both SEM and TEM confirm the formation of silver NIs. To amplify the localised surface plasmon resonance (SPR) effect, post‐deposition annealing was performed at 200°C for 30 minutes in a nitrogen atmosphere, resulting in tuning the shape and size of the NIs. Optical transmission spectroscopy was performed in the ultraviolet–visible–near‐infrared spectral region to examine the SPR characteristics of the Ag NIs deposited on ITO‐glass and In 2 O 3 ‐PET. Post‐deposition annealing is found to tune the SPR wavelength and results in strong enhancement of the SPR of the Ag NIs on both ITO‐glass and In 2 O 3 ‐PET. DC magnetron sputtering and the post‐deposition annealing technique can be applied for the growth of size‐controlled Ag NIs. The result can be applied to the enhancement of the efficiency of organic light emitting diodes and solar cells.