gebhart/patrepeval huggingface dataset:
High‐throughput profiling of N ‐myristoylation substrate specificity across species including pathogens (2012)

One of the most critical modifications affecting the N-terminus of proteins is N-myristoylation. This irreversible modification affects the membrane-binding properties of crucial proteins involved in signal transduction cascades. This cotranslational modification, catalyzed by N-myristoyl transferase, occurs both in lower and higher eukaryotes and is a validated therapeutic target for several pathologies. However, this lipidation proves very difficult to be evidenced in vivo even with state-of-the-art proteomics approaches or bioinformatics tools. A large part of N-myristoylated proteins remains to be discovered and the rules of substrate specificity need to be established in each organism. Because the peptide substrate recognition occurs around the first eight residues, short peptides are used for modeling the reaction in vitro. Here, we provide a novel approach including a dedicated peptide array for high-throughput profiling protein N-myristoylation specificity. We show that myristoylation predictive tools need to be fine-tuned to organisms and that their poor accuracy should be significantly enhanced. This should lead to strongly improved knowledge of the number and function of myristoylated proteins occurring in any proteome.
The Enzymic Synthesis of l-Cysteine in Escherichia coli and Salmonella typhimurium (1966)

Abstract A two-step pathway from l-serine to l-cysteine is described in Escherichia coli and Salmonella typhimurium. Serine transacetylase, the first enzyme in this pathway, catalyzes the formation of O-acetyl-l-serine from l-serine and acetyl coenzyme A and is inhibited by l-cysteine. The enzyme has been purified approximately 1000-fold and has a spectrum similar to that of pyridoxal phosphate-containing enzymes. O-Acetylserine sulfhydrylase, the second enzyme in the pathway, catalyzes the formation of l-cysteine from O-acetyl-l-serine and sulfide. It is repressed in Salmonella grown on l-cysteine and derepressed when grown on l-djenkolic acid. Cys E mutants in S. typhimurium contain low or undetectable levels of serine transacetylase and variable levels of O-acetylserine sulfhydrylase.
Endostatin inhibits endothelial and tumor cellular invasion by blocking the activation and catalytic activity of matrix metalloproteinase. (2000)

Here we report the inhibition of cellular invasion by a recombinant mouse endostatin and the possible mechanism of the inhibition. Endostatin significantly reduced endothelial as well as tumor cellular invasion into the reconstituted basement membrane in vitro. Gelatin zymographic analysis revealed that the activation of promatrix metalloproteinase-2 (proMMP-2) that was secreted from endothelial cells was blocked upon endostatin treatment. Studies with recombinant MMPs confirmed that endostatin inhibited proMMP-2 activation, mediated by both membrane-type 1 MMP and 4-aminophenylmercuric acetate. Furthermore, enzymatic assays using a peptide substrate demonstrated that endostatin inhibited the catalytic activities of both MMP-2 and membrane-type 1 MMP. Finally, coimmunoprecipitation experiments revealed that endostatin formed a stable complex with proMMP-2. These novel findings would, at least in part, explain the mechanism of the potent antiangiogenic and antitumor activities of endostatin.
Effect of the Duration of Electrical Stimulation on the Analgesic Response in Patients with Low Back Pain (1999)

The recommended duration of electrical stimulation with percutaneous electrical nerve stimulation therapy is 30 min.
2 [ 18 F]F‐A85380: PET imaging of brain nicotinic acetylcholine receptors and whole body distribution in humans (2003)

Noninvasive imaging of nicotinic acetylcholine receptors (nAChRs) in the human brain in vivo is critical for elucidating the role of these receptors in normal brain function and in the pathogenesis of brain disorders. Here we report the first in vivo visualization of human brain areas containing nAChRs by using PET and 2-[18F]fluoro-3-(2(S)azetidinylmethoxy)pyridine (2-[18F]FA). We acquired scans from six healthy non-smoking volunteers after i.v. bolus administration of 2-[18F]FA (1.6 MBq/kg or 0.043 +/- 0.002 mCi/kg). This dose was sufficient for visualizing nAChRs in the thalamus up to 5 h after injection. There were no adverse effects associated with administration of no-carrier-added 2-[18F]FA (1.3-10 pmol/kg). Consistent with the distribution of nAChRs in human brain, accumulated radioactivity was greatest in thalamus, intermediate in the midbrain, pons, cerebellum, and cortex; and least in white matter. As approximately 90% of the injected radioactivity was eliminated via the urine (biological half-life ca. 4 h), the urinary bladder wall received the highest radiation dose. The estimate of radiation dose equivalent to the urinary bladder wall (ca. 180 +/- 30 mSv/MBq or 0.7 rem/mCi with a 2.4 h void interval) suggests that multiple studies could be performed in a single subject. The results predict that quantitative PET imaging of nAChRs in human brain with 2-[18F]FA is feasible.
The Role of Reactive Oxygen Species in Antibiotic-Induced Cell Death in Burkholderia cepacia Complex Bacteria (2016)

It was recently proposed that bactericidal antibiotics, besides through specific drug-target interactions, kill bacteria by a common mechanism involving the production of reactive oxygen species (ROS). However, this mechanism involving the production of hydroxyl radicals has become the subject of a lot of debate. Since the contribution of ROS to antibiotic mediated killing most likely depends on the conditions, differences in experimental procedures are expected to be at the basis of the conflicting results. In the present study different methods (ROS specific stainings, gene-expression analyses, electron paramagnetic resonance, genetic and phenotypic experiments, detection of protein carbonylation and DNA oxidation) to measure the production of ROS upon antibiotic treatment in Burkholderia cepacia complex (Bcc) bacteria were compared. Different classes of antibiotics (tobramycin, ciprofloxacin, meropenem) were included, and both planktonic and biofilm cultures were studied. Our results indicate that some of the methods investigated were not sensitive enough to measure antibiotic induced production of ROS, including the spectrophotometric detection of protein carbonylation. Secondly, other methods were found to be useful only in specific conditions. For example, an increase in the expression of OxyR was measured in Burkholderia cenocepacia K56-2 after treatment with ciprofloxacin or meropenem (both in biofilms and planktonic cultures) but not after treatment with tobramycin. In addition results vary with the experimental conditions and the species tested. Nevertheless our data strongly suggest that ROS contribute to antibiotic mediated killing in Bcc species and that enhancing ROS production or interfering with the protection against ROS may form a novel strategy to improve antibiotic treatment.
Vertical continuous flow lithography for fabricating long 3D structures (2013)

We propose an in situ photopolymerization method for three dimensional (3D) microfabrications which we call “Vertical Continuous Flow Lithography” (VCFL). We used a digital micromirror device (DMD) as a dynamic photomask and a vertical flow of polyethylene glycol diacrylate (PEGDA) in a microchannel. VCFL can not only fabricate long (~5 mm) structures but also control 3D geometries of structures. We experimentally demonstrated the fabrication of long fibers whose cross-sectional (diameters and shapes) geometries could be controlled. We believe that VCFL will be useful in bottom up tissue engineering to make long complex structures, such as branched blood vessels.
Stabilization and activation of p53 are regulated independently by different phosphorylation events (1998)

Treatment of mouse or human cells with the protein kinase C (PKC) inhibitors H7 or bisindolylmaleimide I induced an increase in the lifetime of p53, leading to its accumulation. In inhibitor-treated cells, p53 translocated to the nuclei and bound to DNA but was not competent to induce transcription. However, transactivation could be induced by subsequent DNA damage. Phorbol ester, a potent activator of PKC, significantly inhibited the accumulation of p53 after DNA damage. Therefore, constitutive PKC-dependent phosphorylation of p53 itself, or of a protein that interacts with p53, is required for the rapid degradation of p53 in untreated cells. Furthermore, an increase in the lifetime of p53 is not accompanied necessarily by its activation. Treatment with the PKC inhibitors decreased the overall level of p53 phosphorylation but led to the appearance of a phosphopeptide not seen in tryptic digests of p53 from untreated cells. Therefore, the lifetime and activities of p53 are likely to be regulated by distinct alterations of the phosphorylation pattern of p53, probably caused by the actions of different kinases.
Five-Coordinate Silicon in High-Silica Zeolites (1999)

Pentacoordinated silicon units, SiO4/2F-, were found by solid-state NMR experiments in various as-made high-silica zeolites (Beta, SSZ-23, ITQ-3, ITQ-4, ZSM-12, Silicalite-1) that are prepared in the presence of fluoride ions as mineralizing agents. The SiO4/2F- units are part of the framework, being connected, through sharing of the four O atoms, with four neighboring tetracoordinated SiO4/2 units. These five-coordinate silicon units balance the charge of the cationic organic structure-directing agent. The 29Si chemical shift of these sites is between −140 and −150 ppm, and the 19F chemical shifts are between −56 and −78 ppm. The zeolites SSZ-23, ITQ-4, and Silicalite-1 show a dynamic motion of the fluoride ions at room temperature which is frozen out at a temperature of 130−140 K. In the case of fluoride motion, the 29Si chemical shifts are between −120 and −150 ppm, indicating an exchange between four- and five-coordinate silicon, which means that the fluoride ions exchange between different framework silicon sites. The rigid SiO4/2F- units show a characteristic parameter of the 19F chemical shift anisotropy: the span value, Ω = δ11 − δ33, is between 80 and 87 ppm.
The murine homolog of the interleukin-8 receptor CXCR-2 is essential for the occurrence of neutrophilic inflammation in the air pouch model of acute urate crystal-induced gouty synovitis (1998)

Chemokines that bind the IL-8 receptor CXCR-2 are essential for the development of acute neutrophilic inflammation in response to urate crystals in the subcutaneous air pouch model.
Tumors and the heart: molecular genetic advances (2001)

Recent molecular genetic investigations of primary cardiac tumors (myxomas, lipomas, rhabdomyomas, and fibromas) have provided insight into fundamental mechanisms of cardiac cell growth. Myxomas are the most common adult cardiac tumor, and familial cardiac myxomas are now appreciated to be caused by mutations in the PRKAR1alpha gene that encodes a regulatory subunit of protein kinase A. Cytogenetic studies have targeted candidate chromosomal loci that may be perturbed during cardiac lipoma pathogenesis. Rhabdomyomas, the most common pediatric cardiac neoplasm, are frequently associated with tuberous sclerosis, caused by mutations in the TSC-1 and TSC-2 genes. The study of Gorlin syndrome has shed light on the etiology of cardiac fibromas. This disorder is caused by mutation of the PTC gene, which regulates cell growth, commitment and differentiation. In the future, manipulation of PRKAR1alpha-, TSC-, and PTC-dependent pathways may foster new strategies to regenerate myocardium in the ischemic or myopathic heart.
A preliminary study (2018)

The aim of this study was to explore the sequential use of risk malignancy index (RMI) combined with contrast-enhanced ultrasonography (CEUS) in identification diagnosis of adnexal masses.This study contained 2 steps: first, 151 patients were analyzed retrospectively with RMI 1, RMI 2, and RMI 3 indices; receiver operating characteristic (ROC) curves were plotted to analyze area under the curves (AUC), and then RMI cut-off value was obtained according to maximum Youden index (YI, Sensitivity + Specificity - 1) and calculating diagnostic sensitivity, specificity, positive/negative predictive value, and accuracy. Second, 151 cases were divided into 2 groups randomly (105 in study group and 46 in test group); in the study group, the lower cut-off value (LC), upper cut-off value (UC), CEUS cut-off value according to maximum YI, and then these cut-offs were validated in test group.There was no statistical significance in 3 RMI models (P = .35), and RMI1 model was established randomly for following study. When the RMI1 cut-off value was 149, the YI was maximal (0.53), and the sensitivity, specificity, positive/negative predictive value, and accuracy were 71.0%, 81.7%, 77.1%, 75.6%, and 76.2%, respectively. The LC was 15 (sensitivity was 98.0%), the UC was 3000 (specificity was 98.0%), and the CEUS cut-off value was 7 (maximal YI was 0.81). In the test group (46 cases), combining RMI1 LC (15) and UC (3000) with CEUS cut-off value (7), the sensitivity, specificity, positive/negative predictive value, and accuracy were up to 85.7%, 92.0%, 90.0%, 88.5%, and 89.1%, respectively.CEUS can help RMI to make a more effective differential diagnosis of the adnexal mass. Further validation by additional multicenter prospective trials is required.
Genomic analysis of the host response to hepatitis B virus infection (2004)

Previous studies in hepatitis B virus (HBV)-infected humans and chimpanzees suggest that control of HBV infection involves the cells, effector functions, and molecular mediators of the immune response. The objective of the current study was to identify, in the liver of acutely HBV-infected chimpanzees, the spectrum of virus-induced and immune response-related genes that regulate the infection. The results demonstrate that HBV does not induce any genes during entry and expansion, suggesting it is a stealth virus early in the infection. In contrast, a large number of T cell-derived IFN-γ-regulated genes are induced in the liver during viral clearance, reflecting the impact of an adaptive T cell response that inhibits viral replication and kills infected cells, thereby terminating the infection.
3-D Scene Representation as a Collection of Images and Fundamental Matrices (1994)

&lt;p&gt;The problem we solve in this paper is the following. Suppose we are given N views of a static scene obtained from different viewpoints, perhaps with different cameras. These viewpoints we call reference viewpoints since they are all we know of the scene. We would like to decide if it is possible to predict ano- ther view of the scene taken by a camera from a viewpoint which is arbitrary and a priori di erent from all the reference viewpoints. One method for doing this would be to use these viewpoints to construct a three-dimensional representation of the scene and reproject this representation on the retinal plane of the virtual camera. In order to achieve this goal, we would have to establish some sort of calibration of our system of cameras, fuse the three-dimensional representations obtained from, say, pairs of cameras thereby obtaining a set of 3-D points, the scene. We would then have to approximate this set of points by surfaces, a segmentation problem which is still mostly unsolved, and then intersect the optical rays from the virtual camera with these surfaces. This is the most straightforward way of going from a set of images to a new image using the current computer vision paradigm of rst building a three-dimensional representation of the environment from which the rest is derived. We do not claim that there does not exist any simpler way of using the three-dimensional representation than the one we just sketched, but this is just simply not our point. Our point is that it is possible to avoid entirely the explicit three-dimensional reconstruction process: the scene is represented by its images and by some ba- sically linear relations that govern the way points can be put in correspondence between views when they are the images of the same scene-point. These images and their algebraic relations are all we need for predicting a new image. This approach is similar in spirit to the one that has been used in trinocular stereo. Hypotheses of correspondences between two of the images are used to predict features in the third. These predictions can then be checked to validate or invalidate the initial correspondence. This approach has proved to be quite e cient and accurate. Related to these ideas are those developed in the photogrammetric community under the name of transfer methods which nd for one or more image points in a given image set, the corresponding points in some new image set.&lt;/p&gt;
Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm (2001)

The finite mixture (FM) model is the most commonly used model for statistical segmentation of brain magnetic resonance (MR) images because of its simple mathematical form and the piecewise constant nature of ideal brain MR images. However, being a histogram-based model, the FM has an intrinsic limitation--no spatial information is taken into account. This causes the FM model to work only on well-defined images with low levels of noise; unfortunately, this is often not the the case due to artifacts such as partial volume effect and bias field distortion. Under these conditions, FM model-based methods produce unreliable results. In this paper, we propose a novel hidden Markov random field (HMRF) model, which is a stochastic process generated by a MRF whose state sequence cannot be observed directly but which can be indirectly estimated through observations. Mathematically, it can be shown that the FM model is a degenerate version of the HMRF model. The advantage of the HMRF model derives from the way in which the spatial information is encoded through the mutual influences of neighboring sites. Although MRF modeling has been employed in MR image segmentation by other researchers, most reported methods are limited to using MRF as a general prior in an FM model-based approach. To fit the HMRF model, an EM algorithm is used. We show that by incorporating both the HMRF model and the EM algorithm into a HMRF-EM framework, an accurate and robust segmentation can be achieved. More importantly, the HMRF-EM framework can easily be combined with other techniques. As an example, we show how the bias field correction algorithm of Guillemaud and Brady (1997) can be incorporated into this framework to achieve a three-dimensional fully automated approach for brain MR image segmentation.
NLOS detection algorithms for Ultra-Wideband localization (2007)

Non Line of Sight (NLOS) channels are one of the major drawbacks for accurate ranging and localization with Ultra-Wideband (UWB) technology. Whereas several proposals exist to detect these situations, a comprehensive overview, investigation and testing of these methods has to the authors' knowledge not yet been prepared. This paper tries to fill this gap with a classification of the algorithms proposed of the UWB and mobile phone community. In addition, one novel method based on the signal power variation is suggested. Afterwards, the methods are evaluated regarding their practicability for real UWB localization systems, which excludes some of them from further investigation. For the remaining algorithms thresholds are proposed, which are strived to be as independent of the system and environment as possible. Finally, the NLOS detection algorithms are tested and compared with both an UWB simulation environment and an UWB localization test bed.
Bacteria and Bacterial Toxins as Therapeutic Agents for Solid Tumors (2004)

Patients with advanced solid tumors frequently relapse and succumb to their metastatic disease after developing resistance to conventional treatment modalities such as chemotherapy and radiotherapy. In these patients, novel strategies of targeting widespread tumors are urgently needed. The increasing knowledge of the underlying pathogenetic mechanisms has led to the identification of numerous molecules that are overexpressed in various tumors and accumulate at the cell surface. The use of genetically modified bacteria and their toxins targeting these surface molecules has emerged as a promising new treatment strategy in refractory cancers. This review focuses on bacterial toxins such as Diphtheria toxin (DT), Pseudomonas exotoxin A (PE) and Clostridium perfringens enterotoxin (CPE). In addition, the use of anaerobic bacteria such as Clostridium, Salmonella and Bifidobacterium spp. as drug-delivery systems targeting hypoxic tumor areas will be discussed as a new therapeutic modality of advanced solid tumors.
Serial Analysis of Gene Expression as a Tool to Assess the Human Thyroid Expression Profile and to Identify Novel Thyroidal Genes (2000)

The assessment of the expression profile of normal human thyroid tissue using serial analysis of gene expression (SAGE) generated a collection of 10,994 sequence transcripts (tags). Each tag represented a messenger RNA transcript, and, in total, 6099 different tags could be distinguished. The presence and abundance of thyroid-specific transcripts showed the overall expression profile to be from a normal thyroid cell. The expression level of several transcripts was confirmed on Northern blot. Seventy percent of tags could not be attributed to a known human gene and, therefore, possibly correspond to novel genes putatively involved in thyroid function. The tag sequence generated by the SAGE technique can be used to further characterize these novel genes. In this way, application of the SAGE technique to thyroid tissue gives insight in the expression profile of a normal thyroid gland and provides the information to characterize novel genes involved in thyroid pathology, such as congenital hypothyroidism and thyroid neoplasia
Holographic optical elements (1996)

Diffraction gratings formed by recording an interference pattern in a suitable light-sensitive medium (commonly called holographic diffraction gratings) have replaced conventional ruled gratings for many applications. While Burch and Palmer [1961] first showed that transmission gratings could be made by photographing interference fringes using silver halide emulsions, it was the use of photoresist layers coated on optically worked blanks which finally led to the production of spectrographic gratings of high quality [Rudolph & Schmahl, 1967; Labeyrie & Flamand, 1969]. After processing, the photoresist layer yields a relief image (see section 7.3) which can be coated with an evaporated metal layer and used as a reflection grating.
Mutations of factor VIII cleavage sites in hemophilia A (1988)

Hemophilia A is caused by a defect in coagulation factor VIII, a protein that undergoes extensive proteolysis during its activation and inactivation. To determine whether some cases of hemophilia are caused by mutations in important cleavage sites, we screened patient DNA samples for mutations in these sites by a two-step process. Regions of interest were amplified from genomic DNA by repeated rounds of primer- directed DNA synthesis. The amplified DNAs were then screened for mutations by discriminant hybridization using oligonucleotide probes. Two cleavage site mutations were found in a survey of 215 patients. A nonsense mutation in the activated protein C cleavage site at amino acid 336 was discovered in a patient with severe hemophilia. In another severely affected patient, a mis-sense mutation results in a substitution of cysteine for arginine in the thrombin activation site at amino acid 1689. This defect is associated with no detectable factor VIII activity, but with normal levels of factor VIII antigen. The severe hemophilia in this patient was sporadic; analysis of the mother suggested that the mutation originated in her gametes or during her embryogenesis. The results demonstrate that this approach can be used to identify factor VIII gene mutations in regions of the molecule known to be important for function.