gebhart/patrepeval huggingface dataset:
Biology, Pathophysiological Role, and Clinical Implications of Exosomes: A Critical Appraisal (2019)

Exosomes are membrane-enclosed entities of endocytic origin, which are generated during the fusion of multivesicular bodies (MVBs) and plasma membranes. Exosomes are released into the extracellular milieu or body fluids; this process was reported for mesenchymal, epithelial, endothelial, and different immune cells (B-cells and dendritic cells), and was reported to be correlated with normal physiological processes. The compositions and abundances of exosomes depend on their tissue origins and cell types. Exosomes range in size between 30 and 100 nm, and shuttle nucleic acids (DNA, messenger RNAs (mRNAs), microRNAs), proteins, and lipids between donor and target cells. Pathogenic microorganisms also secrete exosomes that modulate the host immune system and influence the fate of infections. Such immune-modulatory effect of exosomes can serve as a diagnostic biomarker of disease. On the other hand, the antigen-presenting and immune-stimulatory properties of exosomes enable them to trigger anti-tumor responses, and exosome release from cancerous cells suggests they contribute to the recruitment and reconstitution of components of tumor microenvironments. Furthermore, their modulation of physiological and pathological processes suggests they contribute to the developmental program, infections, and human diseases. Despite significant advances, our understanding of exosomes is far from complete, particularly regarding our understanding of the molecular mechanisms that subserve exosome formation, cargo packaging, and exosome release in different cellular backgrounds. The present study presents diverse biological aspects of exosomes, and highlights their diagnostic and therapeutic potentials.
Thin-film optical initiator (2023)

A thin-film optical initiator having an inert, transparent substrate, a reactive thin film, which can be either an explosive or a pyrotechnic, and a reflective thin film. The resultant thin-film optical initiator system also comprises a fiber-optic cable connected to a low-energy laser source, an output charge, and an initiator housing. The reactive thin film, which may contain very thin embedded layers or be a co-deposit of a light-absorbing material such as carbon, absorbs the incident laser light, is volumetrically heated, and explodes against the output charge, imparting about 5 to 20 times more energy than in the incident laser pulse.
Inositol phosphosphingolipid phospholipase C1 regulates plasma membrane ATPase (Pma1) stability in <i>Cryptococcus neoformans</i> (2014)

Cryptococcus neoformans is a facultative intracellular pathogen, which can replicate in the acidic environment inside phagolysosomes. Deletion of the enzyme inositol-phosphosphingolipid-phospholipase-C (Isc1) makes C. neoformans hypersensitive to acidic pH likely by inhibiting the function of the proton pump, plasma membrane ATPase (Pma1). In this work, we examined the role of Isc1 on Pma1 transport and oligomerization. Our studies showed that Isc1 deletion did not affect Pma1 synthesis or transport, but significantly inhibited Pma1 oligomerization. Interestingly, Pma1 oligomerization could be restored by supplementing the medium with phytoceramide. These results offer insight into the mechanism of intracellular survival of C. neoformans.
Pilot Study of ONCOS-102 and Pembrolizumab: Remodeling of the Tumor Microenvironment and Clinical Outcomes in Anti–PD-1–Resistant Advanced Melanoma (2022)

ONCOS-102 plus pembrolizumab was well tolerated and led to objective responses in patients with anti-PD-1-resistant advanced melanoma. ONCOS-102 promoted T-cell infiltration, particularly cytotoxic CD8+ T cells, which persisted at Week 9, driving clinical benefit. Further investigation of ONCOS-102 plus PD-1 blockade is warranted. See related commentary by Levi and Boland, p. 3.
Piwi Is a Key Regulator of Both Somatic and Germline Stem Cells in the Drosophila Testis (2015)

The Piwi-piRNA pathway is well known for its germline function, yet its somatic role remains elusive. We show here that Piwi is required autonomously not only for germline stem cell (GSC) but also for somatic cyst stem cell (CySC) maintenance in the Drosophila testis. Reducing Piwi activity in the testis caused defects in CySC differentiation. Accompanying this, GSC daughters expanded beyond the vicinity of the hub but failed to differentiate further. Moreover, Piwi deficient in nuclear localization caused similar defects in somatic and germ cell differentiation, which was rescued by somatic Piwi expression. To explore the underlying molecular mechanism, we identified Piwi-bound piRNAs that uniquely map to a gene key for gonadal development, Fasciclin 3, and demonstrate that Piwi regulates its expression in somatic cyst cells. Our work reveals the cell-autonomous function of Piwi in both somatic and germline stem cell types, with somatic function possibly via its epigenetic mechanism.
Tafamidis Treatment for Patients with Transthyretin Amyloid Cardiomyopathy (2018)

In patients with transthyretin amyloid cardiomyopathy, tafamidis was associated with reductions in all-cause mortality and cardiovascular-related hospitalizations and reduced the decline in functional capacity and quality of life as compared with placebo. (Funded by Pfizer; ATTR-ACT ClinicalTrials.gov number, NCT01994889 .).
A New Relation for ML Estimation in Central Turkey (2017)

Summary Geometrical spreading factor and anelastic attenuation coefficient have been defined for an area of Turkey bounded by coordinates 31° E –35° E and 38.5° N – 41° N. By this way, a new reliable relation estimating typical local magnitudes for earthquakes within this area has been defined. The data used are coming from a local temporary network consisted of six broad-band stations which operated for the period 2007 – 2010. The records of the network have been converted to synthetic Wood-Anderson seismograms and maximum amplitudes of the two horizontal components have been used. The result showed that the seismic wave attenuation is, basically, due to geometrical spreading (n = 1.455) while anelastic attenuation is rather negligible (K = 1.178×10–5). The new local magnitude scale defined here is valid for the study area and holds for hypocentral distances from 8 km up to 200 km, while it can be also used – with caution – for hypocentral distances up to 250 km. The performed evaluation procedure proved the reliability and robustness of the final relation.
Compact and low-loss silicon power splitter based on inverse tapers (2013)

A compact, low-loss, optical power splitter based on inverse tapers is proposed and fabricated on a silicon-on-insulator platform. High efficiency mode evolution between the fundamental mode of the input waveguide and the super mode of the output waveguides is realized using optimized tapers. A 1×4 splitter with insertion loss lower than 0.4 dB and uniformity better than 0.68 dB in a wavelength range from 1510 to 1550 nm are demonstrated within a footprint of only ~75 μm(2). These properties are very promising for ultrahigh density photonic integration applications.
Delineating oil-sand reservoirs with high-resolution PP/PS processing and joint inversion in the Junggar Basin, Northwest China (2010)

Dramatic lateral lithological variations in the fluvial sediments in Chepaizi, in the Junggar Basin of Northwest China, have posed challenges in distinguishing true and false “bright spots” in oil-bearing sand reservoirs. A high-resolution multicomponent seismic survey and joint prestack PP and PS inversion conducted recently provided an effective technique for solving the problem and successfully delineating the characteristics of the reservoir. This is due to the different reflection response of shear waves to the lithology and fluid content, and their ability to resolve thin layers. Surface-consistent amplitude- and resolution-preserving pro-cessing produced high-quality prestack PP and PS migrated gathers and stacks for extracting seismic attributes. Application of joint prestack PP and PS inversion resulted in higher fluid factors and lower VP/VS in oil-bearing sands compared with dry sands. The correlation between the inversion and the existing well data suggests that high-resolution multicomponent AVO can reduce drilling risks and provide more accurate reservoir characterization.
Alternative scaffold proteins (2011)

Review is devoted to the challenging direction in modem molecular biology and bioengineering - the properties of alternative scaffold proteins (ASP) and methods for obtaining ASP binding molecules. ASP molecules incorporate conservative protein core and hypervariable regions, providing for the binding function. Structural classification of ASP includes several types which differ also in their molecular targets and potential applications. Construction of artificial binding proteins on the ASP basis implies a combinatorial library design with subsequent selection of specific binders with the use of phage display or the modem cell-free systems. Alternative binding proteins on non-immunoglobulin scaffolds find broad applications in different fields ofbiotechnology and molecular medicine.
Massively parallel information retrieval for wide area information servers (2002)

Most text is stored in electronic form at one point or another in its file. Computers have made relatively little impact on how it is stored and retrieved. The wide area information service project (WAIS) seeks to alleviate this problem by making text databases widely accessible via a common user interface and wide area networking. The ultimate success of the effort depends, in part, on the availability of high-performance text search engines. Such engines can be implemented on massively parallel machines, using either signature file or inverted file database structures. Inverted files are particularly appealing, and permit databases as large as 8192 Gbytes to be searched in under 15 s, using currently available hardware.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Does a betaretrovirus infection trigger primary biliary cirrhosis? (2003)

Patients with primary biliary cirrhosis develop progressive ductopenia associated with the production of antimitochondrial antibodies that react with a protein aberrantly expressed on biliary epithelial cells and peri-hepatic lymph nodes. Although no specific microbe has been identified, it is thought that an infectious agent triggers this autoimmune liver disease in genetically predisposed individuals. Previous serologic studies have provided evidence to suggest a viral association with primary biliary cirrhosis. Here we describe the identification of viral particles in biliary epithelium by electron microscopy and the cloning of exogenous retroviral nucleotide sequences from patients with primary biliary cirrhosis. The putative agent is referred to as the human betaretrovirus because it shares close homology with the murine mammary tumor virus and a human retrovirus cloned from breast cancer tissue. In vivo, we have found that the majority of patients with primary biliary cirrhosis have both RT-PCR and immunohistochemistry evidence of human betaretrovirus infection in lymph nodes. Moreover, the viral proteins colocalize to cells demonstrating aberrant autoantigen expression. In vitro, we have found that lymph node homogenates from patients with primary biliary cirrhosis can induce autoantigen expression in normal biliary epithelial cells in coculture. Normal biliary epithelial cells also develop the phenotypic manifestation of primary biliary cirrhosis when cocultivated in serial passage with supernatants containing the human betaretrovirus or the murine mammary tumor virus, providing a model to test Koch's postulates in vitro.
Enhanced strength and temperature dependence of mechanical properties of Li at small scales and its implications for Li metal anodes (2016)

Most next-generation Li ion battery chemistries require a functioning lithium metal (Li) anode. However, its application in secondary batteries has been inhibited because of uncontrollable dendrite growth during cycling. Mechanical suppression of dendrite growth through solid polymer electrolytes (SPEs) or through robust separators has shown the most potential for alleviating this problem. Studies of the mechanical behavior of Li at any length scale and temperature are limited because of its extreme reactivity, which renders sample preparation, transfer, microstructure characterization, and mechanical testing extremely challenging. We conduct nanomechanical experiments in an in situ scanning electron microscope and show that micrometer-sized Li attains extremely high strengths of 105 MPa at room temperature and of 35 MPa at 90 °C. We demonstrate that single-crystalline Li exhibits a power-law size effect at the micrometer and submicrometer length scales, with the strengthening exponent of -0.68 at room temperature and of -1.00 at 90 °C. We also report the elastic and shear moduli as a function of crystallographic orientation gleaned from experiments and first-principles calculations, which show a high level of anisotropy up to the melting point, where the elastic and shear moduli vary by a factor of ∼4 between the stiffest and most compliant orientations. The emergence of such high strengths in small-scale Li and sensitivity of this metal's stiffness to crystallographic orientation help explain why the existing methods of dendrite suppression have been mainly unsuccessful and have significant implications for practical design of future-generation batteries.
Enhanced results for web search (2011)

"Ten blue links" have defined web search results for the last fifteen years -- snippets of text combined with document titles and URLs. In this paper, we establish the notion of enhanced search results that extend web search results to include multimedia objects such as images and video, intent-specific key value pairs, and elements that allow the user to interact with the contents of a web page directly from the search results page. We show that users express a preference for enhanced results both explicitly, and when observed in their search behavior. We also demonstrate the effectiveness of enhanced results in helping users to assess the relevance of search results. Lastly, we show that we can efficiently generate enhanced results to cover a significant fraction of search result pages.
CS-HOG: Color similarity-based HOG (2013)

Conventional object detection methods often use local features based on object shape, of which the HOG feature is typical. In recent years, Color Self-Similarity (CSS) has been proposed as a local feature that uses color information. CSS involves computing color similarity as a basis for deciding the sameness of objects, and thus represent a feature that is effective for object detection. It has also been reported that detection performance can be improved by using the CSS feature together with the HOG feature or other shape-based feature. We propose a Color Similarity-based HOG (CS-HOG) feature that is based on color similarity for object detecting shapes. The CS-HOG feature enables clarification of the object shape by using color similarity to calculate the degree of object sameness, thus achieving highly-accurate object detection. Evaluation experiments show that the CS-HOG feature improves performance from 22.5% and 27.2% compared to the HOG feature and the CSS feature, and by 4.2% compared to the HOG feature and the CSS feature used together.
Reversible Oxidative Modification (2009)

Angiotensin II (Ang II) inhibits the cardiac sarcolemmal Na(+)-K(+) pump via protein kinase (PK)C-dependent activation of NADPH oxidase. We examined whether this is mediated by oxidative modification of the pump subunits. We detected glutathionylation of beta(1), but not alpha(1), subunits in rabbit ventricular myocytes at baseline. beta(1) Subunit glutathionylation was increased by peroxynitrite (ONOO(-)), paraquat, or activation of NADPH oxidase by Ang II. Increased glutathionylation was associated with decreased alpha(1)/beta(1) subunit coimmunoprecipitation. Glutathionylation was reversed after addition of superoxide dismutase. Glutaredoxin 1, which catalyzes deglutathionylation, coimmunoprecipitated with beta(1) subunit and, when included in patch pipette solutions, abolished paraquat-induced inhibition of myocyte Na(+)-K(+) pump current (I(p)). Cysteine (Cys46) of the beta(1) subunit was the likely candidate for glutathionylation. We expressed Na(+)-K(+) pump alpha(1) subunits with wild-type or Cys46-mutated beta(1) subunits in Xenopus oocytes. ONOO(-) induced glutathionylation of beta(1) subunit and a decrease in Na(+)-K(+) pump turnover number. This was eliminated by mutation of Cys46. ONOO(-) also induced glutathionylation of the Na(+)-K(+) ATPase beta(1) subunit from pig kidney. This was associated with a approximately 2-fold decrease in the rate-limiting E(2)-->E(1) conformational change of the pump, as determined by RH421 fluorescence. We propose that kinase-dependent regulation of the Na(+)-K(+) pump occurs via glutathionylation of its beta(1) subunit at Cys46. These findings have implications for pathophysiological conditions characterized by neurohormonal dysregulation, myocardial oxidative stress and raised myocyte Na(+) levels.
Field Investigation of Vapor‐Phase‐Based Groundwater Monitoring (2011)

The use of in‐field analysis of vapor‐phase samples to provide real‐time volatile organic compound (VOC) concentrations in groundwater has the potential to streamline monitoring by simplifying the sample collection and analysis process. A field validation program was completed to (1) evaluate methods for collection of vapor samples from monitoring wells and (2) evaluate the accuracy and precision of field‐portable instruments for the analysis of vapor‐phase samples. The field program evaluated three vapor‐phase sample collection methods: (1) headspace samples from two locations within the well, (2) passive vapor diffusion (PVD) samplers placed at the screened interval of the well, and (3) field vapor headspace analysis of groundwater samples. Two types of instruments were tested: a field‐portable gas chromatograph (GC) and a photoionization detector (PID). Field GC analysis of PVD samples showed no bias and good correlation to laboratory analysis of groundwater collected by low‐flow sampling (slope = 0.96, R 2 = 0.85) and laboratory analysis of passive water diffusion bag samples from the well screen (slope = 1.03; R 2 = 0.96). Field GC analysis of well headspace samples, either from the upper portion of the well or at the water‐vapor interface, resulted in higher variability and much poorer correlation (consistently biased low) relative to laboratory analysis of groundwater samples collected by low‐flow sample or passive diffusion bags (PDBs) (slope = 0.69 to 0.76; R 2 = 0.60 to 0.64). These results indicate that field analysis of vapor‐phase samples can be used to obtain accurate measurements of VOC concentrations in groundwater. However, vapor samples collected from the well headspace were not in equilibrium with water collected from the well screen. Instead, PVD samplers placed in the screened interval represent the most promising approach for field‐based measurement of groundwater concentrations using vapor monitoring techniques and will be the focus of further field testing.
Transcriptional Regulatory Networks in <i>Saccharomyces cerevisiae</i> (2002)

We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in living cells. Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, this network of regulator-gene interactions describes potential pathways yeast cells can use to regulate global gene expression programs. We use this information to identify network motifs, the simplest units of network architecture, and demonstrate that an automated process can use motifs to assemble a transcriptional regulatory network structure. Our results reveal that eukaryotic cellular functions are highly connected through networks of transcriptional regulators that regulate other transcriptional regulators.
Reservoir Connectivity Evaluation and Upscaled Model Screening Using Streamline Simulation (2013)

Abstract Significant gas potential has been identified in both conventional and unconventional reservoirs in emerging gas projects in Algeria, south-western Sahara. This study is focused on Lower Devonian reservoirs, which overall depositional model is characterized by shallow marine shelfal to tidal sandstones and mudstones in a range of depositional settings, with thin thickness (less than 10 m) and low porosity and permeability, at 3000–4000 m depth. The analysis of eight exploratory wells drilled in the area, has shown that the field under study presents high lateral and vertical heterogeneity, with an important connectivity uncertainty. Geological models were performed with the objective to evaluate the structural complexity and high reservoir heterogeneity. In order to account for the properties variation uncertainty in the inter-well distribution, and the impact in upscaled models and resulting reservoir simulation, different geological model approaches were evaluated using streamline simulation, concentrating the study on some of the most important parameters that control the number of wells and recovery: reservoir quality, distribution and connectivity. Streamline simulation allowed us to optimize the simulation grid, with the objective to capture the critical reservoir features of the fine-grid geological model. Streamline simulation can be used to analyze and rank different geological models based on certain dynamic performance parameters that effectively reflect the reservoir connectivity, which cannot be easily analyzed with finite difference simulations. The volumetric sweep efficiency and the water cut response can be used to understand the reservoir connection and heterogeneity, and the optimum level of upscaling comparing with fine-grid models. Relatively few real field case examples of this technique have been documented in the past and this paper presents a clear workflow which helped to improve the knowledge of upscaled models screening and resulting reservoir connectivity evaluation.
Web scraping technologies in an API world (2013)

Web services are the de facto standard in biomedical data integration. However, there are data integration scenarios that cannot be fully covered by Web services. A number of Web databases and tools do not support Web services, and existing Web services do not cover for all possible user data demands. As a consequence, Web data scraping, one of the oldest techniques for extracting Web contents, is still in position to offer a valid and valuable service to a wide range of bioinformatics applications, ranging from simple extraction robots to online meta-servers. This article reviews existing scraping frameworks and tools, identifying their strengths and limitations in terms of extraction capabilities. The main focus is set on showing how straightforward it is today to set up a data scraping pipeline, with minimal programming effort, and answer a number of practical needs. For exemplification purposes, we introduce a biomedical data extraction scenario where the desired data sources, well-known in clinical microbiology and similar domains, do not offer programmatic interfaces yet. Moreover, we describe the operation of WhichGenes and PathJam, two bioinformatics meta-servers that use scraping as means to cope with gene set enrichment analysis.