gebhart/patrepeval huggingface dataset:
Tumor Cell–Driven Extracellular Matrix Remodeling Drives Haptotaxis during Metastatic Progression (2016)

Here, we provide new insight into how tumor cell:ECM interactions generate signals and structures that promote directed tumor cell migration, a critical component of metastasis. Our results identify a tumor cell-intrinsic mechanism driven by the actin regulatory protein MENA that promotes ECM remodeling and haptotaxis along FN gradients. Cancer Discov; 6(5); 516-31. ©2016 AACR.See related commentary by Santiago-Medina and Yang, p. 474This article is highlighted in the In This Issue feature, p. 461.
Renal Sympathetic Denervation Provides Ventricular Rate Control But Does Not Prevent Atrial Electrical Remodeling During Atrial Fibrillation (2012)

Renal denervation (RDN) reduces renal efferent and afferent sympathetic activity thereby lowering blood pressure in resistant hypertension. The effect of modulation of the autonomic nervous system by RDN on atrial electrophysiology and ventricular rate control during atrial fibrillation (AF) is unknown. Here we report a reduction of ventricular heart rate in a patient with permanent AF undergoing RDN. Subsequently, we investigated the effect of RDN on AF-induced shortening of atrial effective refractory period, AF inducibility, and ventricular rate control during AF maintained by rapid atrial pacing in 12 pigs undergoing RDN (n=7) or sham procedure (n=5). During sinus rhythm, RDN reduced heart rate (RR-interval, 708±12 versus 577±19 ms; P=0.0021) and increased atrioventricular node conduction time (PQ-interval, 112±12 versus 88±9 ms; P=0.0001). Atrial tachypacing for 30 minutes increased AF inducibility and decreased AF cycle length. This was not influenced by RDN. RDN reduced ventricular rate during AF episodes by ≈24% (119±9 versus 158±19 bpm; P=0.0001). AF episodes were shorter after RDN compared with sham (12±3 versus 34±4 s; P=0.0091), but atrial effective refractory period was not modified by RDN. RDN reduced heart rate and reduced atrioventricular node conduction time during sinus rhythm and provided rate control during AF. AF-induced atrial electrical remodeling, AF inducibility, and AF cycle length were not modified, but duration of AF episodes was shorter after RDN. Modulation of the autonomic nervous system by RDN might provide rate control and reduce susceptibility to AF. Whether RDN may provide rate control in a larger number of patients with AF deserves further clinical studies.
Immunoassay of alpha 1-acid glycoprotein in the Cobas Bio centrifugal analyzer. (1988)

There is an increasing demand for quantification of serum alpha 1-acid glycoprotein (AAG, orosomucoid) in studies evaluating the protein binding of highly bound basic drugs. This paper describes an adaptation of an automated immunoturbidimetric assay for this protein to the Cobas Bio centrifugal analyzer. Replicate analyses of aliquots from six different solutions were used in determining precision. We also analyzed 367 patients' serum samples, in duplicate, to determine the distribution of AAG in hospitalized patients. The intra- and inter-run CVs ranged from 1.3% to 4.4% and from 0.6% to 6.6%, respectively. AAG concentrations in patients' samples ranged from 0.38 to 3.16 g/L. Results by this method correlate well with those by radial immunodiffusion, with no significant amount of bias between the two methods. This immunoturbidimetric procedure is faster and less expensive than currently used radial immunodiffusion techniques, and precision is acceptable.
Epigenomic analysis of lung adenocarcinoma reveals novel DNA methylation patterns associated with smoking (2013)

The importance of epigenetic regulation has been increasingly recognized in the development of cancer. In this study, we investigated the impact of smoking, a major risk factor of lung cancer, on DNA methylation by comparing the genome-wide DNA methylation patterns between lung adenocarcinoma samples from six smokers and six nonsmokers. We identified that smoking-induced DNA methylations were enriched in the calcium signaling and neuroactive ligand receptor signaling pathways, which are closely related to smoking-induced lung cancers. Interestingly, we discovered that two genes in the mitogen-activated protein kinase signaling pathway (RPS6KA3 and ARAF) were hypomethylated in smokers but not in nonsmokers. In addition, we found that the smoking-induced lung cancer-specific DNA methylations were mostly enriched in nuclear activities, including regulation of gene expression and chromatin remodeling. Moreover, the smoking-induced hypermethylation could only be seen in lung adenocarcinoma tissue but not in adjacent normal lung tissue. We also used differentially methylated DNA loci to construct a diagnostic model to distinguish smoking-associated lung cancer from nonsmoking lung cancer with a sensitivity of 88.9% and specificity of 83.2%. Our results provided novel evidence to support that smoking can cause dramatic changes in the DNA methylation landscape of lung cancer, suggesting that epigenetic regulation of specific oncogenic signaling pathways plays an important role in the development of lung cancer.
Increased Susceptibility of the Left Compared to the Right Ventricle to Remote Ischemia/Reperfusion Injury in Human C1-Inhibitor-Overexpressing Transgene Mice (2002)

Acute myocardial injury has been demonstrated as a remote sequela of severe lower torso ischemia-reperfusion (I/R) due to proinflammatory events. In a model of I/R injury, administration of C1 esterase inhibitor (C1-Inh) reduces myocardial necrosis. We investigated the susceptibility of the left (LV) versus right ventricle (RV) and the protective effect of transgenic C1-Inh-overexpressing mice. Two groups of mice ( n = 6) underwent a 2-h lower torso ischemia followed by 3 h of reperfusion: transgenic and wild type with sham-operated controls. Animals were then injected with 125 I bovine albumin. Heart was removed and samples from right and left ventricular free wall were harvested, weighted, and radioactivity was determined. Permeability index for wild-type animals in the RV was 0.22 - 0.04, compared to 0.17 - 0.07 in controls (NS), and in the LV 0.36 - 0.08, compared to 0.21 - 0.05 in controls ( p < .01). The LV showed a significantly higher value compared to the right (0.22 - 0.04 vs. 0.36 - 0.08, p < .01). No difference was seen in the RV between transgenic and wild-type mice; however, in the LV the values decreased significantly in transgenic animals ( p < .015). Thus, remote myocardial injury after lower torso I/R is present in both ventricles; however, the LV seems to be more susceptible as assessed by albumin permeability. Inhibition of the classic complement cascade may be a promising therapeutic approach for myocardial protection in reperfusion injury.
Changing methods of sterilization as influenced by laparoscopy. (1976)

The introduction of laparoscopic sterilization in a hospital in Basel Switzerland has effected several changes: the type of patients requesting sterilization the numbers of patients and the physicians training programs. With the availability of internal laparoscopic sterilization there has been a shift in the numbers of older women requesting sterilization. Previously becuase the procedure involved laparotomy there was less interest in the procedure. Now more women request sterilization by laparoscopy than men request vasectomy. Traini ng problems that have occurred since the introduction of this method include: 1) a decrease in easy laparotomies for residents to perform; 2) young residents have to start their training by performing laparoscopic operations before they have gained enough experience in doing laparoscopy itself; and 3) older physicians find that they must learn a new technique because of its popularity and have experienced many failed attempts in doing so.
Covalently Dye-Linked, Surface-Controlled, and Bioconjugated Organically Modified Silica Nanoparticles as Targeted Probes for Optical Imaging (2008)

In this paper we report the synthesis and characterization of organically modified silica (ORMOSIL) nanoparticles, covalently incorporating the fluorophore rhodamine-B, and surface-functionalized with a variety of active groups. The synthesized nanoparticles are of ultralow size (diameter approximately 20 nm), highly monodispersed, stable in aqueous suspension, and retain the optical properties of the incorporated fluorophore. The surface of the nanoparticles can be functionalized with a variety of active groups such as hydroxyl, thiol, amine, and carboxyl. The carboxyl groups on the surface were used to conjugate with various bioactive molecules such as transferrin, as well as monoclonal antibodies such as anti-claudin 4 and anti-mesothelin, for targeted delivery to pancreatic cancer cell lines. In vitro experiments have revealed that the cellular uptake of these bioconjugated (targeted) nanoparticles is significantly higher than that of the nonconjugated ones. The ease of surface functionalization and incorporation of a variety of biotargeting molecules, combined with their observed noncytotoxicity, makes these fluorescent ORMOSIL nanoparticles potential candidates as efficient probes for optical bioimaging, both in vitro and in vivo.
Modelling the hydrodynamic sway force exerted on the bare-hull of an axi-symmetric underwater vehicle in lateral acceleration manoeuvres (2008)

Experimental data from pure sway tests on a series of five axi-symmetric bare-hulls for a slender underwater vehicle were used to study and model the sway force in lateral-plane sway manoeuvres. The sway force is represented with two components, one in phase with the sway acceleration and the other in phase with the sway velocity. The test data reveal that there is a variation in the apparent mass with both the sway frequency and amplitude. Although the present study provides some insight into this phenomenon, further experimental and analytical work will be required to acquire an improved understanding of the phenomena.
Error Estimation in Large Spreadsheets using Bayesian Statistics (2009)

Spreadsheets are ubiquitous in business with the financial sector particularly heavily reliant on the technology. It is known that the level of spreadsheet error can be high and that it is often necessary to review spreadsheets based on a structured methodology which includes a cell by cell examination of the spreadsheet. This paper outlines the early research that has been carried out into the use of Bayesian Statistical methods to estimate the level of error in large spreadsheets during cell be cell examination based on expert knowledge and partial spreadsheet test data. The estimate can aid in the decision as to the quality of the spreadsheet and the necessity to conduct further testing or not.
Structural context for protein <i>N</i>‐glycosylation in bacteria: The structure of PEB3, an adhesin from <i>Campylobacter jejuni</i> (2007)

Campylobacter jejuni is unusual among bacteria in possessing a eukaryotic-like system for N-linked protein glycosylation at Asn residues in sequons of the type Asp/Glu-Xaa-Asn-Xaa-Ser/Thr. However, little is known about the structural context of the glycosylated sequons, limiting the design of novel recombinant glycoproteins. To obtain more information on sequon structure, we have determined the crystal structure of the PEB3 (Cj0289c) dimer. PEB3 has the class II periplasmic-binding protein fold, with each monomer having two domains with a ligand-binding site containing citrate located between them, and overall resembles molybdate- and sulfate-binding proteins. The sequon around Asn90 is located within a surface-exposed loop joining two structural elements. The three key residues are well exposed on the surface; hence, they may be accessible to the PglB oligosaccharyltransferase in the folded state.
Monoclonal antibodies to the human immunodeficiency virus p18 protein cross-react with normal human tissues. (1988)

The immunohistochemical reactivity of four monoclonal antibodies (MAbs): CVK, 49-5, 49-6 and 63-FH2, raised against the p18 protein of HIV-1 was assessed in tissues obtained from HIV-infected and uninfected individuals. As already reported, all the MAbs specifically labelled follicular dendritic cells (FDC) in lymph nodes from HIV-infected patients with lymphadenopathy, and cells of microglial nodules in the brain from patients with AIDS-related encephalopathy. However, cross-reactivity with normal uninfected tissues was also observed: epithelial cells of the skin, the thymus and tonsils with CVK, and astrocytes in the brain of 49-6 and 63-FH2. Such cross-reactivities suggest that 'molecular mimicry' could exist between p18 of HIV and normal constituents of human cells. This phenomenon could be relevant for the diagnostic use of anti-p18 MAbs on pathological specimens, and it could be of importance in the pathophysiology of HIV infection.
Automatic detection of malignant prostatic gland units in cross-sectional microscopic images (2010)

Prostate cancer is the second most frequent cause of cancer deaths among men in the US. In the most reliable screening method, histological images from a biopsy are examined under a microscope by pathologists. In an early stage of prostate cancer, only relatively few gland units in a large region become malignant. Discovering such sparse malignant gland units using a microscope is a labor-intensive and error-prone task for pathologists. In this paper, we develop effective image segmentation and classification methods for automatic detection of malignant gland units in microscopic images. Both segmentation and classification methods are based on carefully designed feature descriptors, including color histograms and texton co-occurrence tables.
Development and implementation of an automated wafer transport system (2002)

The move to 300 mm wafers has prompted IC manufacturers to demand a reliable automated material handling system (AMHS). Hewlett Packard's Inkjet Supplies Business Unit has worked with a supplier to develop a system using overhead rails and vehicles with hoist mechanisms to perform direct-to-tool delivery of 200 mm podded wafers. The system is intended to increase throughput by providing just-in-time material delivery and improve safety by minimizing manual handling. The system has a near zero footprint, leaving valuable floor space for process tools. While the system was built specifically for 200 mm material, most of this effort is directly applicable to 300 mm systems, and tests on the new system are very promising. Tool-to-tool delivery time was approximately 38 s, and pod placement accuracy was satisfactory regardless of pod load or vertical hoisting distance. Long term reliability tests indicated mean cycles between interrupts (MCBI) per vehicle of approximately 3,286 cycles (where a cycle is a pod move from between tools). All but one of the incidents encountered during reliability testing were recovered in 1 minute or less. A third party failure mode analysis identified a small number of potential safety hazards, which the supplier is addressing. Our study also identified issues to be addressed prior to production implementation, including improved vehicle maintenance procedures and better methods of identifying, troubleshooting and resolving system errors. Further modeling and scenario testing may need to be performed to better estimate system benefits and potential integration issues for specific applications.
γδ T cells in cancer: a small population of lymphocytes with big implications (2019)

γδ T cells are a small population of mostly tissue-resident lymphocytes, with both innate and adaptive properties. These unique features make them particularly attractive candidates for the development of new cellular therapy targeted against tumor development. Nevertheless, γδ T cells may play dual roles in cancer, promoting cancer development on the one hand, while participating in antitumor immunity on the other hand. In mice, γδ T-cell subsets preferentially produce IL-17 or IFN-γ. While antitumor functions of murine γδ T cells can be attributed to IFN-γ<sup>+</sup> γδ T cells, recent studies have implicated IL-17<sup>+</sup> γδ T cells in tumor growth and metastasis. However, in humans, IL-17-producing γδ T cells are rare and most studies have attributed a protective role to γδ T cells against cancer. In this review, we will present the current knowledge and most recent findings on γδ T-cell functions in mouse models of tumor development and human cancers. We will also discuss their potential as cellular immunotherapy against cancer.
Nonplanar Butterfly‐Shaped π‐Expanded Pyrrolopyrroles (2016)

Large aza-analogues of curved polycyclic aromatic hydrocarbons with a double-helicene structure present unique features for molecular photonics. We present the preparation and characterization of three such structures. The synthesis of these heterocyclic nanographenes involves only a few high-yield steps that use readily available starting materials. X-ray analysis revealed that each of these new dyes has three conformational isomers: one diastereoisomer in a meso form and two enantiomers in twisted forms [(P,P)] and [(M,M)]. The low energy barriers between the conformers, however, prevent their separation by using chiral HPLC, and the NMR spectra show only one set of signals for each of these curved compounds. Density functional theory (DFT) calculations quantify the small energy difference and the small energy barriers between the chiral and meso forms, which fully supports the experimental results. Their optical absorption lacks any sensitivity to the solvent environment, whereas their fluorescence features exhibit pronounced solvatochromism. This rarely observed solvatofluorochromism of centrosymmetric molecules without either electron-withdrawing groups or -donating substituents was probed by using time-resolved spectroscopy. These studies suggest that, similar to 9,9'-bianthryl, the nonpolar locally excited state shows negligible solvatochromism, whereas the charge-transfer state is sensitive to solvent polarity.
What Is an Antidepressant Binding Site Doing in a Bacterial Transporter? (2007)

LeuT is a bacterial amino acid transporter belonging to a large family of membrane proteins, including the neurotransmitter transporters that are targets for antidepressant drugs. The high-resolution structure of LeuT has provided an important model for understanding structure and function in this family. Two recent papers found that LeuT can bind tricyclic antidepressants, raising the possibility that it may also serve as a model for the pharmacological properties of neurotransmitter transporters.
Macrostructure of petroleum asphaltenes by small angle neutron scattering (2007)

The size and shape of petroleum asphaltenes in solvents have been determined by small angle neutron scattering. Their most likely morphology is a membrane like particle. Their size decreases with temperatur, this change being quite reversible. It is very solvent dependent: the more polar the solvent the smaller the aggregates. Similarly, the more polar the asphaltene the larger the particles.
Experimental and simulation studies of hard contact in force reflecting teleoperation (2003)

Experiments and simulations of a single-axis force-reflecting teleoperation system have been conducted to investigate the problem of contacting a hard environment and maintaining a controlled force in teleoperation in which position is fed forward from the hand controller (master) to the manipulator (slave), and force is fed back to the human operator through motors in the master. The simulations, using an electrical circuit model, reproduce the behavior of the real system, including effects of human operator biomechanics. It is shown that human operator properties, which vary as a result of different types of grasp of the handle, affect the stability of the system in the hard-contact task. The effect of a heavier grasp on the handle is equivalent to increased hand-controlled velocity damping in terms of the systems stability in the contact task, but control system damping sufficient to guarantee stable contact results in perceptible sluggishness of the control handle's response in free motion. These results suggest that human operator biomechanics must be taken into account to guarantee stable and ergonomic performance of advanced teleoperators.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Statin Therapy and Risk of Developing Type 2 Diabetes: A Meta-Analysis (2009)

Although statin therapy greatly lowers vascular risk, including among those with and at risk for diabetes, the relationship of statin therapy to incident diabetes remains uncertain. Future statin trials should be designed to formally address this issue.
Effects of zidovudine on Friend virus complex infection in Rfv-3r/s genotype-containing mice used as a model for HIV infection. (1990)

Infection with the Friend virus complex (FV) in (B10.A x A/WySn)F1 mice containing the Rfv-3r/s genotype results in several disease manifestations analogous to those seen in patients with acquired immune deficiency syndrome, predominantly high levels of specific antibody and low levels of infectious virus with eventual retroviral disease-induced death of the host. Other immunologic manifestations of FV infection in this murine host included inhibition of percent total T, T-helper, and T-suppressor/cytotoxic cells of total splenic lymphocytes and phytohemagglutinin-induced response of spleen cells. Interleukin-1 production was not affected but the numbers of splenic B cells were increased by the infection. 3'-Azido-3'-deoxythymidine (zidovudine, AZT) administered (a) intraperitoneally three times daily for 24 days beginning 4 h after virus inoculation in doses of 60 to 480 mg/kg/day, (b) in drinking water for 22 days beginning 4 h after virus inoculation in doses of 22 to 216 mg/kg/day, or (c) in drinking water for 29 days beginning 6 days after virus inoculation in doses of 22 to 216 mg/kg/day markedly inhibited FV-induced disease. In the mice receiving early-initiated AZT therapy, FV-induced splenomegaly and hematocrit values were inhibited and infectious centers in the spleen and FV titers in the plasma were reduced to below detectable levels at the higher AZT dosage levels. The percent of total T cells in splenic lymphocytes was increased in the infected, AZT-treated mice. In the intraperitoneal experiment, FV disease-induced death was prevented by treatment with all doses of AZT. Neutralizing antibody to FV was significantly reduced in all AZT-treated groups. Toxicologic manifestations of these AZT treatments included splenic enlargement and reduced hematocrit, although all treated, uninfected mice survived the treatments, gained weight, and displayed no significant effects on enumeration of T and B cells.
Gene Cloning, Purification, and Characterization of NfsB, a Minor Oxygen-Insensitive Nitroreductase from Escherichia coli, Similar in Biochemical Properties to FRase I, the Major Flavin Reductase in Vibrio fischeri (1996)

nfsB, encoding a minor oxygen-insensitive nitroreductase, was isolated by PCR using primers corresponding to two amino acid sequences conserved among the major flavin reductase from Vibrio fischeri and classical nitroreductases from Salmonella typhimurium and Enterobacter cloacae. The gene product, NfsB, was purified to homogeneity from extracts of Escherichia coli cells overexpressing it. NfsB was found to be situated at 13 min on the E. coli map. Biochemical analysis indicated NfsB to be a polypeptide having a calculated molecular weight of 23,904, capable of forming a homodimer and associated tightly with FMN as a prosthetic group. Although it exhibited a lower affinity to the NfsB apoenzyme than FMN, FAD could serve as an effective substitute for FMN. It was also shown that NfsB has a broad electron acceptor specificity and is associated with a low level of the NAD(P)H-flavin oxidoreductase. The NfsB catalysis obeys the ping pong Bi-Bi mechanism. The Km value for NADH varied depending on the second substrate used.