gebhart/patrepeval huggingface dataset:
Structure of HAP1-PC7 bound to DNA: implications for DNA recognition and allosteric effects of DNA-binding on transcriptional activation (2000)

HAP1 is a transcription factor in yeast whose DNA-binding domain has been implicated in directly affecting transcriptional activation. Two separate mutations in the DNA-binding domain, S63G (HAP1-PC7) and S63R (HAP1-18), retain wild-type binding affinity. However, HAP1-PC7 is transcriptionally silent while HAP1-18 shows highly elevated levels of transcription. We have determined the X-ray crystal structure of the DNA-binding domain of HAP1-PC7 bound to its DNA target, UAS(CYC7), and compared it to the previously solved HAP1-wt and HAP1-18 complexes to UAS(CYC7). Additionally, we have quantitatively compared the DNA-binding affinity and specificity of the HAP1-PC7, HAP1-18 and HAP1-wt DNA-binding domains. We show that, although the DNA-binding domains of these three proteins bind UAS(CYC7) with comparable affinity and specificity, the protein-DNA interactions are dramatically different between the three complexes. Conserved protein-DNA interactions are largely restricted to an internal DNA sequence that excludes one of the two conserved DNA half-sites of UAS(CYC7) suggesting a mode of recognition distinct from other HAP1 family members. Alternative protein-DNA interactions result in divergent DNA configurations between the three complexes. These results suggest that the differential transcriptional activities of the HAP1, HAP1-18 and HAP1-PC7 proteins are due, at least in part, to alternative protein-DNA contacts, and implies that HAP1-DNA interactions have direct allosteric effects on transcriptional activation.
Microanatomy of Lymphoid Tissue During Humoral Immune Responses: Structure Function Relationships (1989)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
Cardioembolic Stroke in Patients with Patent Foramen Ovale and Implanted Cardiac Leads (2012)

Implanted cardiac devices, including pacemakers, defibrillators, and resynchronization devices, are known to develop thrombus on their intravascular leads. Patent foramen ovale (PFO) occurs in approximately one-quarter of the adult population. It is unclear whether paradoxical cardioembolism and clinically relevant stroke occur in patients with implanted cardiac leads and PFO. We present a case series of four patients with cardioembolic stroke, presumed to arise from intravascular cardiac leads and associated PFO that required device closure of the PFO.
Partition of fatty acids and fluorescent fatty acids into membranes (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPartition of fatty acids and fluorescent fatty acids into membranesW. J. Pjura, A. M. Kleinfeld, and M. J. KarnovskyCite this: Biochemistry 1984, 23, 9, 2039–2043Publication Date (Print):April 24, 1984Publication History Published online1 May 2002Published inissue 24 April 1984https://pubs.acs.org/doi/10.1021/bi00304a024https://doi.org/10.1021/bi00304a024research-articleACS PublicationsRequest reuse permissionsArticle Views116Altmetric-Citations47LEARN 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
Concurrent fatty liver increases risk of hepatocellular carcinoma among patients with chronic hepatitis B (2016)

Concurrent fatty liver is common in HBV-infected patients and an independent risk factor potentiating HBV-associated HCC development by 7.3-fold. The risk of HBV-related HCC is increased by APOC3 gene polymorphism, and further characterization is required by its role.
Webwise (2005)

Mixing business with pleasure, the Traveller Online website is a useful resource for nurses eager to know more about travel and travel health. The site offers expert advice, cheap flights, a traveller magazine and comprehensive healthbook.
Oxidative Stress and Antioxidant Status in High-Risk Prostate Cancer Subjects (2020)

The oxidant/antioxidant balance has been implicated in the pathophysiology of prostate cancer. We investigated oxidative damage and antioxidant status in high-risk prostate cancer subjects. Reduced glutathione (GSH) levels were measured in erythrocytes, 8-hydroxydeoxyguanosine (8-OHdG) in leukocytes and plasma levels of catalase (CAT), glutathione peroxidase (GSH-Px), glutathione reductase (GSH-R), glutathione S-transferase (GST), superoxide dismutase (SOD), and lipid peroxide products were measured in high-risk and age-matched healthy subjects. Serum PSA levels were significantly higher (<i>p</i> < 0.0001) in high-risk subjects, whereas GST (<i>p</i> < 0.0001) and GSH (<i>p</i> < 0.002) were higher in healthy controls. Levels of 8-OHdG, an oxidized nucleoside of DNA, were significantly increased (<i>p</i> < 0.0001) in high-risk subjects. No marked difference in the levels of CAT (<i>p</i> = 0.237), GSH-Px (<i>p</i> = 0.74), GSH-R (<i>p</i> = 0.344), SOD (<i>p</i> = 0.109), and lipid peroxide products (<i>p</i> = 0129) were observed between two groups. Pearson's correlation between GST and PSA (r = -0.69 (<i>p</i> < 0.0001)), GST and 8-OHdG (r = -0.62 (<i>p</i> < 0.0004)), GSH and 8-OHdG (r= -0.39 (<i>p</i> = 0.038)), and CAT and GSH-Px (r= -0.33 (<i>p</i> = 0.04)) were found to be negatively correlated, whereas 8-OHdG and PSA were positively associated (r= 0.57 (<i>p</i> < 0.002). These results indicate a significant role of oxidative damage in prostate carcinogenesis, particularly during the early stages of development. In conclusion, our data support the importance of antioxidant defense as a valuable diagnostic and/or prognostic marker in prostate cancer.
Antigen-stimulated apoptotic T-cell death in HIV infection is selective for CD4+T cells, modulated by cytokines and effected by lymphotoxin (1996)

Stimulation of HIV-positive PBMC with CD4-dependent antigens results in selective death of CD4+ T cells that is modulated by cytokines. Our results suggest that apoptotic death is not limited to HIV-infected or HIV-specific T cells, but occurs in bystander cells. Lymphotoxin is a mediator of antigen-stimulated T-cell death in this in vitro model.
Determination of cell viability using acridine orange/propidium iodide dual-spectrofluorometry assay (2019)

In vitro cell viability tests are usually done using 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) method. A new spectrofluorometry method was developed using acridine orange (AO) and propidium iodide (PI) using multi-label microplate reader. Nine biogenic amines (BAs) [histamine (HIM), putrescine (PUT), cadaverine (CAD), 2-phenylethylamine (PHM), tyramine (TYM), tryptamine (TPM), spermine (SPM), spermidine (SPD) and agmatine (AGM)] were exposed to RAW 264.7 macrophage in singles at 37°C with 5% carbon dioxide supplementation for 18–24 hours and cell viability was determined using MTS method and AO/PI developed method using dual-spectrofluorometry. Based on MTS assay, SPM and SPD were found to be cytotoxic and it was supported by AO/PI assay. The precedence of disintegration in the nucleus rather than mitochondria upon cell non-viability was also supported by transmission electron microscopy (TEM). The results showed that AO/PI method could be used as an alternative method to determine cytotoxicity besides usual usage in confocal microscopy.
On regularity and identifiability of blind source separation under constant-modulus constraints (2005)

We investigate the information regularity and identifiability of the blind source separation (BSS) problem with constant modulus (CM) constraints on the sources. We establish for this problem the connection between the information regularity [existence of a finite Crame/spl acute/r-Rao bound (CRB)] and local identifiability. Sufficient and necessary conditions for local identifiability are derived. We also study the conditions under which unique (global) identifiability is guaranteed within the inherently unresolvable ambiguities on phase rotation and source permutation. Both sufficient and necessary conditions are obtained.
Chemotherapy-Induced Monoamine Oxidase Expression in Prostate Carcinoma Functions as a Cytoprotective Resistance Enzyme and Associates with Clinical Outcomes (2014)

To identify molecular alterations in prostate cancers associating with relapse following neoadjuvant chemotherapy and radical prostatectomy patients with high-risk localized prostate cancer were enrolled into a phase I-II clinical trial of neoadjuvant chemotherapy with docetaxel and mitoxantrone followed by prostatectomy. Pre-treatment prostate tissue was acquired by needle biopsy and post-treatment tissue was acquired by prostatectomy. Prostate cancer gene expression measurements were determined in 31 patients who completed 4 cycles of neoadjuvant chemotherapy. We identified 141 genes with significant transcript level alterations following chemotherapy that associated with subsequent biochemical relapse. This group included the transcript encoding monoamine oxidase A (MAOA). In vitro, cytotoxic chemotherapy induced the expression of MAOA and elevated MAOA levels enhanced cell survival following docetaxel exposure. MAOA activity increased the levels of reactive oxygen species and increased the expression and nuclear translocation of HIF1α. The suppression of MAOA activity using the irreversible inhibitor clorgyline augmented the apoptotic responses induced by docetaxel. In summary, we determined that the expression of MAOA is induced by exposure to cytotoxic chemotherapy, increases HIF1α, and contributes to docetaxel resistance. As MAOA inhibitors have been approved for human use, regimens combining MAOA inhibitors with docetaxel may improve clinical outcomes.
Introduction (2006)

In this chapter, we introduce the model of a communication system, as originally proposed by Claude E. Shannon in 1948. We will then focus on the channel portion of the system and define the concept of a probabilistic channel, along with models of an encoder and a decoder for the channel. As our primary example of a probabilistic channel—here, as well as in subsequent chapters—we will introduce the memoryless q-ary symmetric channel, with the binary case as the prevailing instance used in many practical applications. For q = 2 (the binary case), we quote two key results in information theory. The first result is a coding theorem, which states that information through the channel can be transmitted with an arbitrarily small probability of decoding error, as long as the transmission rate is below a quantity referred to as the capacity of the channel. The second result is a converse coding theorem, which states that operating at rates above the capacity necessarily implies unreliable transmission.
Effect of the surfactant pluronic on the stability of lipid-stabilized perfluorocarbon nanobubbles (2017)

Microbubble (MB) contrast agents are widely used in diagnostic and therapeutic ultrasound (US) applications. However, due to their 1-10 μm size range, MBs are constrained to the vasculature and thus this limits applications in cancer diagnosis and therapy. To expand contrast enhanced US capabilities, we have developed sub-micron contrast agents, nanobubbles (NB), stabilized with Pluronic, a nonionic triblock copolymer surfactant, to the phospholipid shell stabilizing perfluoropropane (C3F8) gas. NBs, with diameter of ~200-400 nm are small enough to extravasate from leaky tumor vasculature and accumulate in tumors through the EPR effect. Prior work has shown that bubble echogenicity and stability are, in part, dependent on the surface tension of the stabilizing shell. In this study, we evaluate the effect of Pluronic on surface tension of the lipid films and how its presence in the shell affects NB size, yield, echogenicity and signal decay at clinically-relevant imaging frequencies. To do so, the surface tension of lipid films with varying compositions was measured using pendant drop tensiomentry. Bubble size and concentration were determined using a particle metrology system. Results show a significant decrease in NB surface tension through the incorporation of Pluronic, especially at a molar ratio of 0.2, where this value decreased by 27% (p <; 0.0001). At this concentration, a significant decrease in the signal decay over time resulting in a stability increase of 39% (p <; 0.0001) was observed. The Pluronic had little impact on size; NBs had an average diameter of 165 ± 7 nm. Pluronic also had negligible effect on NB concentration.
Table S2 from <i>Ex Vivo</i> Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids (2023)

&lt;p&gt;In vitro kinase inhibitory activity of Compound 1&lt;/p&gt;
Brief Communication; A Heterologous Oncolytic Bacteria-Virus Prime-Boost Approach for Anticancer Vaccination in Mice (2017)

Anticancer vaccination is becoming a popular therapeutic approach for patients with cancers expressing common tumor antigens. One variation on this strategy is a heterologous virus vaccine where 2 viruses encoding the same tumor antigen are administered sequentially to prime and boost antitumor immunity. This approach is currently undergoing clinical investigation using an adenovirus (Ad) and the oncolytic virus Maraba (MRB). In this study, we show that Listeria monocytogenes can be used in place of the Ad to obtain comparable immune priming efficiency before MRB boosting. Importantly, the therapeutic benefits provided by our heterologous L. monocytogenes-MRB prime-boost strategy are superior to those conferred by the Ad-MRB combination. Our study provides proof of concept for the heterologous oncolytic bacteria-virus prime-boost approach for anticancer vaccination and merits its consideration for clinical testing.
Using Intimate Carbon to Enhance the Performance of NaTi2(PO4)3Anode Materials: Carbon Nanotubes vs Graphite (2014)

The effect of intermixed carbon nanotubes and graphite on the electrochemical functionality of NaTi2(PO4)3 was examined. Specifically, the performance of NaTi2(PO4)3 made with "intimate carbons" containing carbon nanotubes (or graphite) introduced at the precursor stage was compared to the performance of similar materials made with the carbons added post synthesis. Specifically, different combinations of carbon nanotubes and graphite were used as carbon sources both in the precursor blend prior to sintering as well as conductive additives in the test electrodes. Graphite-coated NaTi2(PO4)3 with additional carbon nanotubes added (post synthesis) as conductive agent exhibited the best overall performance: the first cycle discharge specific capacity is 130 mAh/g (close to theoretical value 133 mAh/g) at 0.1C rate. The combination also exhibits good cycling stability in aqueous electrolyte: 86% capacity retention under continuous charge/discharge without relaxation at 1C rate for 100 cycles. This suggests that fully coating the precursor material with carbon is critical for performance, and that a graphite additive in the precursor phase is more effective than nanotubes at performing this function.
Stereopagnosia: Fooling Stereo Networks with Adversarial Perturbations (2021)

This work studies the effect of adversarial perturbations of images on the estimates of disparity by deep learning models trained for stereo. We show that imperceptible additive perturbations can significantly alter the disparity map, and correspondingly the perceived geometry of the scene. These perturbations not only affect the specific model they are crafted for, but transfer to models with different architecture, trained with different loss functions. We show that, when used for adversarial data augmentation, our perturbations result in trained models that are more robust, without sacrificing overall accuracy of the model. This is unlike what has been observed in image classification, where adding the perturbed images to the training set makes the model less vulnerable to adversarial perturbations, but to the detriment of overall accuracy. We test our method using the most recent stereo networks and evaluate their performance on public benchmark datasets.
Solid state neutron detector array (2023)

A neutron detector array is capable of measuring a wide range of neutron fluxes. The array includes multiple semiconductor neutron detectors. Each detector has a semiconductor active region that is resistant to radiation damage. In one embodiment, the array preferably has a relatively small size, making it possible to place the array in confined locations. The ability of the array to detect a wide range of neutron fluxes is highly advantageous for many applications such as detecting neutron flux during start up, ramp up and full power of nuclear reactors.
Use of an anti‐CD16 antibody for in vivo depletion of natural killer cells in rhesus macaques (2008)

Summary Non‐human primates serve as key animal models for a variety of viral infections. To evaluate the contribution of natural killer (NK) cells to the immune‐mediated control of these viruses in macaque monkeys, we have described a method for depleting NK cells in vivo by administration of anti‐human CD16 mouse monoclonal antibody. Using a fluorometric NK‐cell cytotoxicity assay, we show that most NK‐cell cytotoxicity in rhesus monkey peripheral blood mononuclear cells resides in the CD16 + and/or CD159A + subset of lymphocytes. The anti‐human CD16 antibody, 3G8, binds to subsets of rhesus monkey lymphocytes and monocytes but not to neutrophils. Intravenous administration of 10–50 mg/kg of 3G8 to normal rhesus monkeys resulted in anti‐CD16 antibody persistence in the plasma for 1–3 weeks. This treatment also depleted 80–90% of CD3 – CD159A + lymphocytes, putative NK cells, from blood for at least 1 week and was associated with the loss of NK‐cell cytotoxicity when evaluated by in vitro assays. Using this method, transient depletion of NK cells from two rhesus monkeys chronically infected with simian immunodeficiency virus failed to cause changes in virus replication. These studies describe a non‐human primate model for in vivo NK‐cell depletion and suggest a limited role for cytotoxic CD16 + NK cells in controlling AIDS virus replication during chronic infection.
MEMS-based Imaging LIDAR (2018)

Micro Electro Mechanical System (MEMS) is a pathway for high performance yet cost effective Time-of-Flight based LIDARs while satisfying trade-offs in performances, such as field-of-view, angular and range resolution, scanning speed and power consumption.
Galectin-3 Is Associated with Restrictive Lung Disease and Interstitial Lung Abnormalities (2016)

Elevated Gal-3 concentrations are associated with interstitial lung abnormalities coupled with a restrictive pattern, including decreased lung volumes and altered gas exchange. These findings suggest a potential role for Gal-3 in early stages of pulmonary fibrosis.
Activation of the Contact System at the Surface of Fusobacterium necrophorum Represents a Possible Virulence Mechanism in Lemièrre's Syndrome (2011)

Fusobacterium necrophorum causes Lemièrre's syndrome, a serious disease with septic thrombophlebitis of the internal jugular vein, pulmonary involvement, and systemic inflammation. The contact system is a link between inflammation and coagulation, and contact activation by the bacteria could therefore contribute to the abnormal coagulation and inflammation seen in patients with Lemièrre's syndrome. In this study, F. necrophorum was found to bind radiolabeled high-molecular-weight kininogen (HK), a central component of the contact system. Binding was inhibited by the addition of unlabeled HK and domain D5 of HK but not other components of the contact system, indicating a specific interaction mediated through the D5 region. Binding of HK was significantly reduced after pretreatment of the bacteria with trypsin, suggesting that surface proteins are involved in HK binding. Incubation of the bacteria with human plasma resulted in an HK breakdown pattern suggestive of bradykinin release, and bradykinin was also detected in the supernatant. In addition, we show that factor XI (FXI), another component of the contact system, binds to F. necrophorum and that the bound FXI reconstitutes the activated partial thromboplastin time of FXI-deficient plasma. Thrombin activity was detected at the surface of the bacteria following incubation with plasma, indicating that the intrinsic pathway of coagulation is activated at the surface. This activity was completely blocked by inhibitors of the contact system. The combined results show that the contact system is activated at the surface of F. necrophorum, suggesting a pathogenic role for this system in Lemièrre's syndrome.
Mesoporous Biomaterials: a Lexicon andStructured Bibliography of Reviews (2016)

Accessing mesoporous and nanostructured biomaterial information can be particularly time-consuming and problematic due to the interdisciplinary nature of the field. Relevant papers can be found across a broad range of journals and various key words are needed to comprehensively retrieve information. A keyword lexicon and themed bibliography of over 250 review articles from more than 100 different journals has therefore been assembled to aid students and researchers in this expanding field. Reviews dedicated to fabrication of mesoporous materials and some key characterisation techniques are grouped together. Reviews focussed on specific medical issues like biocompatibility and toxicological testing are also provided. Medical applications that have been the focus of reviews include drug delivery, cancer therapy, medical imaging, orthopaedics, tissue engineering, biofiltration, biosensing and bioanalysis. The following mesoporous materials also have had dedicated reviews on biomedical uses: silica, silicon, silicates, metallic biomaterials, metal organic frameworks, carbonaceous materials, calcium phosphates, titania, and alumina.
Genome-wide association study identifies new locus associated with OCD (2021)

Obsessive-compulsive disorder (OCD) is a heritable disorder, but no definitive, replicated OCD susceptibility loci have yet been identified by any genome-wide association study (GWAS). Here, we report results from a GWAS in the largest OCD case-control sample (N = 14,140 OCD cases and N = 562,117 controls) to date. We explored the genetic architecture of OCD, including its genetic relationships to other psychiatric and non-psychiatric phenotypes. In the GWAS analysis, we identified one SNP associated with OCD at a genome-wide significant level. Subsequent gene-based analyses identified additional two genes as potentially implicated in OCD pathogenesis. All SNPs combined explained 16% of the heritability of OCD. We show sub-stantial positive genetic correlations between OCD and a range of psychiatric disorders, including anxiety disorders, anorexia nervosa, and major depression. We thus for the first time provide evidence of a genome-wide locus implicated in OCD and strengthen previous literature suggesting a polygenic nature of this disorder.