gebhart/patrepeval huggingface dataset:
Tumor necrosis factor in CHF: a double facet cytokine (1998)

Time for primary review 40 days.

Tumor necrosis factor (TNF) gained its popularity in the world of biology and medicine in a weird way. In 1985, Old in New York City discovered the presence of a protein in blood after lipopolysaccharide (LPS) injection, which is able to induce necrosis of some mouse tumors [1]. He called it ‘tumor necrosis factor’ , a term actually coined in the 1970s. At the same time and, virtually, on the other side of the street, Beutler and Cerami, working at what may appear as an unsurmountable biological distance, discovered that the intriguing state of cachexia is associated with the presence of a protein called ‘cachectin’ in the serum [2]. Its purification made them realize that ‘cachectin’ is an essential mediator of the state of LPS-induced shock and that it is the same molecule of ‘tumor necrosis factor’ [2]. It took some years for these three parents to recognize that their child, whatever called, was unusually gifted. They could not foresee that TNF turned out to be a prodigy molecule eliciting the publication of many papers per day [3].

Two names are not enough to describe TNF, as we now distinguish TNF-α from its twin, TNF-β or ‘lymphotoxin’ (LT), a lymphokine which has only a 30% homology with TNF-α but which binds to the same receptors [4]. Despite similarities, these two proteins do not always transduce identical signals; they have distinct cellular sources and regulation mechanisms. Strangely enough, and without any particular reason, there are many more studies on TNF-α than TNF-β.

Herein the current knowledge on the involvement of TNF-α in congestive heart failure (CHF) is reviewed. For the sake of simplicity, we will refer to TNF-α as TNF.

TNF is a trimeric 17-KDa polypeptide mainly produced by monocytes …
An Association Test of the Spatial Distribution of Rare Missense Variants within Protein Structures Improves Statistical Power of Sequencing Studies (2021)

ABSTRACT Over 90% of variants are rare, and 50% of them are singletons in the Alzheimer’s Disease Sequencing Project Whole Exome Sequencing (ADSP WES) data. However, either single variant tests or unit-based tests are limited in the statistical power to detect the association between rare variants and phenotypes. To best utilize rare variants and investigate their biological effect, we exam their association with phenotypes in the context of protein. We developed a protein structure-based approach, POKEMON (Protein Optimized Kernel Evaluation of Missense Nucleotides), which evaluates rare missense variants based on their spatial distribution on the protein rather than allele frequency. The hypothesis behind this is that the three-dimensional spatial distribution of variants within a protein structure provides functional context and improves the power of association tests. POKEMON identified four candidate genes from the ADSP WES data, namely two known Alzheimer’s disease (AD) genes ( TREM2 and SORL ) and two novel genes ( DUSP18 and CSF1R ). For known AD genes, the signal from the spatial cluster is stable even if we exclude known AD risk variants, indicating the presence of additional low frequency risk variants within these genes. DUSP18 has a cluster of variants primarily shared by case subjects around the ligand-binding domain, and this cluster is further validated in a replication dataset with a larger sample size. POKEMON is an open-source tool available at https://github.com/bushlab-genomics/POKEMON .
UWB receiver for breast cancer detection: Comparison between two different approaches (2013)

In UWB imaging for breast cancer detection, breast-reflected RF signals are processed to create energy images. This method was validated with instrumentation tools, which must be replaced with integrated circuits. We compare two front-end architectures, Direct Conversion (DC) and Coherent Equivalent Time Sampling (CETS). We evaluate the effect—on energy maps and SCR/SMR metrics—of noise sources, phase inaccuracies and non-linearity. DC receiver is more sensitive to phase inaccuracies and so less robust than CETS receiver. The latter can work in time domain with UWB pulses, other than in frequency domain like the DC one, which reduces acquisition time without performance impact.
High-throughput screening technologies for drug glucuronidation profiling (2008)

A significant number of endogenous and exogenous compounds, including many therapeutic agents, are metabolized in humans via glucuronidation, catalysed by uridine diphosphoglucuronosyltransferases (UGTs). The study of the UGTs is a growing field of research, with constantly accumulated and updated information regarding UGT structure, purification, substrate specificity and inhibition, including clinically relevant drug interactions. Development of reliable UGT assays for the assessment of individual isoform substrate specificity and for the discovery of novel isoform-specific substrates and inhibitors is crucial for understanding the function and regulation of the UGT enzyme family and its clinical and pharmacological relevance. High-throughput screening (HTS) is a powerful technology used to search for novel substrates and inhibitors for a wide variety of targets. However, application of HTS in the context of UGTs is complicated because of the poor stability, low levels of expression, low affinity and broad substrate specificity of the enzymes, combined with difficulties in obtaining individual UGT isoforms in purified format, and insufficient information regarding isoform-specific substrates and inhibitors. This review examines the current status of HTS assays used in the search for novel UGT substrates and inhibitors, emphasizing advancements and challenges in HTS technologies for drug glucuronidation profiling, and discusses possible avenues for future advancement of the field.
Design, Synthesis, and Biological Evaluation of Quercetagetin Analogues as JNK1 Inhibitors (2015)

The recent discovery of c-Jun NH2-terminal kinase JNK1 suppression by natural quercetagetin (1) is a promising lead for the development of novel anticancer agents. Using both X-ray structure and docking analyses we predicted that 5'-hydroxy- (2) and 5'-hydroxymethyl-quercetagetin (3) would inhibit JNK1 more actively than the parent compound 1. Notably, our drug design was based on the active enzyme-ligand complex as opposed to the enzyme's relatively open apo structure. In this paper we test our theoretical predictions, aided by docking-model experiments, and report the first synthesis and biological evaluation of quercetagetin analogues 2 and 3. As calculated, both compounds strongly suppress JNK1 activity. The IC50 values were determined to be 3.4 μM and 12.2 μM, respectively, which shows that 2 surpasses the potency of the parent compound 1 (IC50 =4.6 μM). Compound 2 was also shown to suppress matrix metalloproteinase-1 expression with high specificity after UV irradiation.
Nitric oxide synthase mediates regulation of cell polarity and movement during Drosophila melanogaster morphogenesis (2009)

The effect of expression of the enzyme producing nitric oxide on Drosophila melanogaster morphogenesis was studied using ectopic expression of a truncated splice form of the enzyme that has a dominant negative effect on the full-length enzyme form. The suppressed enzyme expression was shown to affect the cell polarity and movement as well as the structural pattern of organs during Drosophila development. The effect of nitric oxide production on the intercellular distribution of significant factors of cell polarity, protein products of the Strabismus and Prospero genes, has been revealed.
Dynamic network security deployment under partial information (2008)

A network user's decision to start and continue using security products is based on economic considerations. The cost of a security compromise (e.g., worm infection) is compared against the cost of deploying and maintaining a sufficient level of security. These costs are not necessarily the real ones, but rather the perceived costs, which depend on the amount of information available to a user at each time. Moreover, the costs (whether real or perceived) depend on the decisions of other users, too: The probability of a user getting infected depends on the security deployed by all the other users. In this paper, we combine an epidemic model for malware propagation in a network with a game theoretic model of the users' decisions to deploy security or not. Users can dynamically change their decision in order to maximize their currently perceived utility. We study the equilibrium points, and their dependence on the speed of the learning process through which the users learn the state of the network. We find that the faster the learning process, the higher the total network cost.
Development of an effective road management system using web-GIS software (2014)

Recently, there has been rapid development of road transportation networks. This situation arises due to the number of vehicles on the road that keeps increasing year by year. Thus, this will increase the possibility of dangerous situations to road users if the roads are not being maintained appropriately. Therefore, in order to keep the roads in safe condition, road management activities should be improved. A complete system for road management has been applied in developed countries for the past decades. However, the usage of application programming interface (API) from commercial geographical information systems (GIS) software has limitations in making modifications in terms of interactivity of the system. In this paper, open source software (OSS) is proposed as a way to assist in reducing the costs in developing a web-GIS road management system. The system can be used by administrators of road networks to update the road information. At the same time, it can be used by road users to view information regarding road-related incidents.
APD readout for Belle II endcap calorimeter upgrade with undoped Cesium Iodide crystals (2014)

The above-mentioned measurements, on crystals, photodetectors and optical couplings, performed at INFN and ENEA laboratories and irradiation facilities, represent a thorough study of options, that will allow the optimal solution for the upgrade of the Belle II end cap calorimeter to be found.
ChemInform Abstract: The Selective Deprotection of Thioesters Using Titanium(IV) Chloride/Zinc. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Legislation against Industrial and Ambient Noise in the US (1976)

Abstract : The Noise Control Act of 1972 established the national policy 'to promote an environment for all Americans free from noise that jeopardizes their public health and welfare.' The Act provides for a division of power between the Federal and State and local Governments: The primary Federal responsibility is for noise source emission control; states and other political sub-divisions retain the rights and authority to control the use of noise sources and the levels of noise permitted in their environment. Although an individual's workplace is a vital component of the overall human environment, the EPA, charged with the execution of the Noise Control Act, does not have jurisdiction over most occupational health and safety matters. They have been traditionally the responsibility of the Departments of Labor and Health, Education and Welfare. The Occupational Safety and Health Act of 1972 gives the Secretary of Labor the responsibility to set standards which adequately assure, to the extent feasible, that no employee will suffer material impairment of health or functional capacity in their working environment. The practical consequences of these legislations, their differences with respect to noise protection standards and their combined overall effectiveness in combating noise-induced health effects will be discussed.
Vesicle-to-Micelle Oscillations and Spatial Patterns (2010)

A pH oscillator is coupled to and controls rhythmic interconversion of nanoscopic vesicles and micelles made of fatty acids. When changes in pH are combined with diffusion, self-assembly produces spatially extended patterns of vesicle/micelle "stripes" or concentric "shells".
Laser Polymer Tattooing: A Versatile Method for Permanent Marking on Polymer Surfaces (2019)

Abstract A versatile and efficient method for the permanent marking of polymer surfaces that combines inkjet deposition and near‐infrared (NIR) laser curing is investigated. The NIR laser treatment forces the ink particles to migrate into the upper layers of the polymer. This results in the fixation of a permanent grayscale image that can be applied to various polymers, such as polypropylene, which is widely used in industry but still difficult to mark. The physiochemical processes induced by laser curing are investigated by electronic and optical microscopy. The dependence of the thickness of the deposited ink and the laser power on the contrast of marking are also studied. A mechanism implying fast laser‐induced melting of the polymer surface followed by displacement of carbon nanoparticles by convection is proposed. Finally, a comparison of the aging properties of samples prepared by this process and standard UV ink is proposed to illustrate the interesting nature of this new polymer marking process. Integrating the ink under the surface of the polymer, as in a skin tattooing procedure, by laser curing is an efficient way to generate permanent images on polymer surfaces.
Contemporary Mapping of Post-Prostatectomy Prostate Cancer Relapse with 11 C-Choline Positron Emission Tomography and Multiparametric Magnetic Resonance Imaging (2016)

Combined choline positron emission tomography and multiparametric magnetic resonance imaging evaluation of biochemical recurrence after prostatectomy reveals an anatomically diverse pattern of recurrence. These findings have implications for optimizing the salvage treatment of patients with prostate cancer with relapse following surgery.
Spin‐spin relaxation of the phosphodiester resonance in the 31P NMR spectrum of human brain (1990)

The phosphodiester peak in 31P nuclear magnetic resonance spectra of human brain in vivo is often the most prominent feature of the spectrum. We have demonstrated that this resonance exhibits bi-exponential spin-spin relaxation, giving relaxation times of 2 and 10 ms. We interpret this in terms of the two components which make up the peak, bilayer lipids and the small cytosolic phosphates glycerophosphoethanolamine and glycerophosphocholine. Using the relaxation times and the relative peak heights of the two components we have also been able to quantitate the concentration of the bilayer lipids as 20-40 times that of ATP.
A novel approach to extract colon lumen from CT images for virtual colonoscopy (2000)

An automatic method has been developed for segmentation of abdominal computed tomography (CT) images for virtual colonoscopy obtained after a bowel preparation of a low-residue diet with ingested contrast solutions to enhance the image intensities of residual colonic materials. Removal of the enhanced materials was performed electronically by a computer algorithm. The method is a multistage approach that employs a modified self-adaptive on-line vector quantization technique for a low-level image classification and utilizes a region-growing strategy for a high-level feature extraction. The low-level classification labels each voxel based on statistical analysis of its three-dimensional intensity vectors consisting of nearby voxels. The high-level processing extracts the labeled stool, fluid and air voxels within the colon, and eliminates bone and lung voxels which have similar image intensities as the enhanced materials and air, but are physically separated from the colon. This method was evaluated by volunteer studies based on both objective and subjective criteria. The validation demonstrated that the method has a high reproducibility and repeatability and a small error due to partial volume effect. As a result of this electronic colon cleansing, routine physical bowel cleansing prior to virtual colonoscopy may not be necessary.
Genetic Factors Associated with Elevated Carbapenem Resistance in KPC-Producing Klebsiella pneumoniae (2010)

In the United States, the most prevalent mechanism of carbapenem resistance among Enterobacteriaceae is the production of a Klebsiella pneumoniae carbapenemase (KPC). KPC-producing isolates often exhibit a range of carbapenem MICs. To better understand the factors that contribute to overall carbapenem resistance, we analyzed 27 KPC-producing K. pneumoniae isolates with different levels of carbapenem resistance, 11 with low-level (i.e., meropenem or imipenem MIC ≤ 4 μg/ml), 2 with intermediate-level (i.e., meropenem and imipenem MIC = 8 μg/ml), and 14 with high-level (i.e., imipenem or meropenem MIC ≥ 16 μg/ml) carbapenem resistance, that were received from throughout the United States. Among 14 isolates that exhibited high-level carbapenem resistance, Western blot analysis indicated that 10 produced an elevated amount of KPC. These isolates either contained an increased bla(KPC) gene copy number (n = 3) or had deletions directly upstream of the bla(KPC) gene (n = 7). Four additional isolates lacked elevated KPC production but had high-level carbapenem resistance. Porin sequencing analysis identified 22 isolates potentially lacking a functional OmpK35 and three isolates potentially lacking a functional OmpK36. The highest carbapenem MICs were found in two isolates that lacked both functioning porins and produced elevated amounts of KPC. The 11 isolates with low-level carbapenem resistance contained neither an upstream deletion nor increased bla(KPC) copy number. These results suggest that both bla(KPC) copy number and deletions in the upstream genetic environment affect the level of KPC production and may contribute to high-level carbapenem resistance in KPC-producing K. pneumoniae, particularly when coupled with OmpK36 porin loss.
Aesthetic quality classification of photographs based on color harmony (2011)

Aesthetic quality classification plays an important role in how people organize large photo collections. In particular, color harmony is a key factor in the various aspects that determine the perceived quality of a photo, and it should be taken into account to improve the performance of automatic aesthetic quality classification. However, the existing models of color harmony take only simple color patterns into consideration-e.g., patches consisting of a few colors-and thus cannot be used to assess photos with complicated color arrangements. In this work, we tackle the challenging problem of evaluating the color harmony of photos with a particular focus on aesthetic quality classification. A key point is that a photograph can be seen as a collection of local regions with color variations that are relatively simple. This led us to develop a method for assessing the aesthetic quality of a photo based on the photo's color harmony. We term the method `bags-of-color-patterns.' Results of experiments on a large photo collection with user-provided aesthetic quality scores show that our aesthetic quality classification method, which explicitly takes into account the color harmony of a photo, outperforms the existing methods. Results also show that the classification performance is improved by combining our color harmony feature with blur, edges, and saliency features that reflect the aesthetics of the photos.
Fine Needle Aspiration Biopsy (2002)

Fine needle aspiration biopsy (FNAB) is a diagnostic procedure that is a form of point-of-care testing in anatomic pathology. It is a minimally invasive procedure that uses a fine (<22-gauge) needle to aspirate tissue from mass lesions. Any trained physician can aspirate superficial palpable masses, but the procedure is optimally performed by an experienced cytopathologist who will follow the procedure with a rapid microscopic interpretation. This paper reviews the 10-year experience of the Massachusetts General Hospital's pathology-run FNAB service (1991 to 2001). A total of 5633 FNABs were performed, most from the breast (32%). On average, two-thirds of patients were spared unnecessary surgery due to either a benign biopsy result (64%), or the documentation of a nonsurgical malignancy such as lymphoma or a metastasis (20%). Using only those cases with histologic follow-up, the accuracy rate averaged 94% (1994 to 2000). The vast majority of cytohistologic discrepancies were due to FNAB sampling error (79%). Fine-needle aspiration biopsy is highly accurate and efficient, resulting in rapid triage of patient management in most cases, reducing overall hospital costs, decreasing workload for various hospital departments, and reducing delays in the diagnosis-therapeutic cycle.
Mechanism of formation of 1,2,3,4-tetramethylnaphthalene from 2-butyne and triphenyltris(tetrahydrofuran) chromium(III) (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanism of formation of 1,2,3,4-tetramethylnaphthalene from 2-butyne and triphenyltris(tetrahydrofuran) chromium(III)George M. Whitesides and William J. EhmannCite this: J. Am. Chem. Soc. 1970, 92, 19, 5625–5640Publication Date (Print):September 1, 1970Publication History Published online1 May 2002Published inissue 1 September 1970https://pubs.acs.org/doi/10.1021/ja00722a015https://doi.org/10.1021/ja00722a015research-articleACS PublicationsRequest reuse permissionsArticle Views460Altmetric-Citations56LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The prognostic relevance of tumor hypoxia markers in resected carcinoma of the gallbladder (2010)

In gallbladder cancer high expression of EGFR is an independent predictor of survival.
Carboxyhemoglobin Levels in Neonatal Immune Hemolytic Jaundice Treated with Intravenous Gammaglobulin (1995)

In order to examine the effect of intravenous immunoglobulin (IVIG) on the rate of hemolysis in immune hemolytic hyperbilirubinemia, we measured the carboxyhemoglobin levels of 5 newborn infants who were subjected to IVIG treatment. The pretreatment rate of hemolysis, in the 5 patients with isoimmune hemolytic jaundice (3 patients with Rh hemolytic disease of the newborn and 2 patients with ABO hemolytic disease of the newborn), as reflected by carboxyhemoglobin levels was higher than the rate of hemolysis in normal newborn infants. In 4 out of the 5 patients treated with IVIG, there was a rapid decline ( > 30%) of carboxyhemoglobin levels, a pattern which was different from that observed in normal newborn infants with no hemolytic jaundice and in 3 untreated patients with ABO hemolytic disease of the newborn. None of the treated patients required an exchange transfusion. Our preliminary results support the theory that the attenuation of jaundice observed following IVIG treatment in patients with immune hemolytic hyperbilirubinemia is caused, at least in part, by the reduction in hemolysis.