gebhart/patrepeval huggingface dataset:
MicroRNAs as powerful diagnostic tools for the differential diagnosis of lung tumors (2008)

11112 Background: Lung cancer is a heterogeneous disease with many histological subtypes, further complicated by the frequent occurrence of lung metastases from various tumor origins. Therefore, determining the correct diagnosis of any lung tumor often poses a difficult diagnostic challenge that may have very significant therapeutic implications. MicroRNAs are short non-coding RNAs that regulate gene expression, and are strongly associated with cancer and development. In the present study we have used microRNAs for differentiating between different primary lung tumors and metastases to the lung. Methods: We used our protocols for extracting RNA from formalin-fixed, paraffin-embedded (FFPE) and fresh/frozen samples, and profiled the RNA on proprietary microRNA microarray. We profiled hundreds of samples from different histological subtypes of lung cancer including small cell carcinoma, different neuroendocrine lung cancers, subtypes of non small cell lung cancer (NSCLC), and metastases to the lung. Expression levels of more than 700 microRNAs were measured and compared between the sample groups. Emerging differences in expression are validated by specific microRNA-based assays using a highly specific qRT-PCR platform we developed. Results: We found that a surprisingly small number of microRNAs can be used as biomarkers for differential diagnosis of various types of lung tumors: 1) a panel of four microRNAs can distinguish between primary lung tumors and metastases to the lung. 2) One microRNA is able to distinguish between squamous cell carcinoma and other NSCLC. 3) A combination of two microRNAs is sufficient to distinguish between carcinoid and other neuroendocrine tumors. 4) A set of two microRNAs distinguishes between neuroendocrine tumors and small cell lung cancer. Conclusions: Combinations of small numbers of microRNAs can successfully answer specific differential diagnosis in lung tumors, and provide a basis for the development of simple and reliable assays in clinical oncology. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Rosetta Genomics Rosetta Genomics
The plasma membrane <scp>NADPH</scp> oxidase <scp>OsRbohA</scp> plays a crucial role in developmental regulation and drought‐stress response in rice (2015)

Plasma membrane NADPH oxidases are major producers of reactive oxygen species (ROS) in plant cells under normal growth and stress conditions. In the present study the total activity of rice NADPH oxidases and the transcription of OsRbohA, which encodes an Oryza sativa plasma membrane NADPH oxidase, were stimulated by drought. OsRbohA was expressed in all tissues examined throughout development. Its mRNA was upregulated by a number of factors, including heat, drought, salt, oxidative stress and methyl jasmonate treatment. Compared with wild-type (WT), the OsRbohA-knockout mutant osrbohA exhibited upregulated expression of other respiratory burst oxidase homolog genes and multiple abnormal agronomic traits, including reduced biomass, low germination rate and decreased pollen viability and seed fertility. However, OsRbohA-overexpressing transgenic plants showed no differences in these traits compared with WT. Although osrbohA leaves and roots produced more ROS than WT, the mutant had lesser intracellular ROS. In contrast, OsRbohA-overexpressing transgenic plants exhibited higher ROS production at the intracellular level and in tissues. Ablation of OsRbohA impaired the tolerance of plants to various water stresses, whereas its overexpression enhanced the tolerance. In addition, a number of genes related to energy supply, substrate transport, stress response and transcriptional regulation were differentially expressed in osrbohA plants even under normal growth conditions, suggesting that OsRbohA has fundamental and broad functions in rice. These results indicate that OsRbohA-mediated processes are governed by complex signaling pathways that function during the developmental regulation and drought-stress response in rice.
The use of molecular genetic markers to demonstrate the effect of organ environment on clonal dominance in a human renal‐cell carcinoma grown in nude mice (1992)

Transduction of the SN12C human renal-cell carcinoma line with the neoR gene produces a genetically "tagged" cell population within which individual clones can be identified if they dominate the tumor during its growth in vivo. We used this technique to determine whether the clones that dominate the primary local tumor and its metastases are the same or different when the tumor is growing in different organ sites in nude mice. The results show that clonal dominance is influenced by the organ environment in which the primary tumor grows, i.e., distinct clones dominated in the kidney, colon and subcutaneous sites. In addition, tumors grown in the orthotopic site (kidney) were all populated by the same dominant clones, and each distant visceral metastasis retained the same clonality. SN12C neoR-cells grown in an epithelial, ectopic site (colon) produced tumors with uniquely different dominant clones, and their visceral metastases retained the dominant pattern expressed by the parent tumor from which they were derived. In contrast, SN12C tumors growing subcutaneously showed a random pattern of clonal dominance in both their primary and metastatic sites. Parallel cytogenetic analyses could not demonstrate these patterns. We conclude that the organ environment significantly influences clonal dominance of human renal carcinoma and that tumor injection into orthotopic sites may produce a more reproducible selection of dominant clones.
On-Chip Synthesis of Protein Microarrays from DNA Microarrays via Coupled <i>In Vitro</i> Transcription and Translation for Surface Plasmon Resonance Imaging Biosensor Applications (2012)

Protein microarrays are fabricated from double-stranded DNA (dsDNA) microarrays by a one-step, multiplexed enzymatic synthesis in an on-chip microfluidic format and then employed for antibody biosensing measurements with surface plasmon resonance imaging (SPRI). A microarray of dsDNA elements (denoted as generator elements) that encode either a His-tagged green fluorescent protein (GFP) or a His-tagged luciferase protein is utilized to create multiple copies of mRNA (mRNA) in a surface RNA polymerase reaction; the mRNA transcripts are then translated into proteins by cell-free protein synthesis in a microfluidic format. The His-tagged proteins diffuse to adjacent Cu(II)-NTA microarray elements (denoted as detector elements) and are specifically adsorbed. The net result is the on-chip, cell-free synthesis of a protein microarray that can be used immediately for SPRI protein biosensing. The dual element format greatly reduces any interference from the nonspecific adsorption of enzyme or proteins. SPRI measurements for the detection of the antibodies anti-GFP and antiluciferase were used to verify the formation of the protein microarray. This convenient on-chip protein microarray fabrication method can be implemented for multiplexed SPRI biosensing measurements in both clinical and research applications.
In vivo, cAMP stimulates growth and morphogenesis of mouse mammary ducts. (1984)

In culture, cAMP is known to be mitogenic for mammary cells and several other epithelia, but evidence for a similar role in vivo has been only correlative. We have used plastic implants to cause slow release of cholera toxin and other cAMP-active agents to local areas of mammary glands in ovariectomized mice. Elevated levels of intracellular cAMP around the implants promoted vigorous growth and normal ductal morphogenesis, while distant sites were unaffected. Local effects of cAMP included restoration of normal ductal caliber, formation of new end buds, and reinitiation of DNA synthesis in both epithelium and surrounding stroma. Thus, cAMP is both a mitogenic and a morphogenetic factor in this tissue.
ChemInform Abstract: Synthesis of a Rigid Diacylglycerol Analogue Having a Bis‐γ‐ butyrolactone Skeleton Separated by a Cyclopentane Ring. (1995)

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.
Metal-coordination, hydrogen-bond network formation, and protein-solvent interactions in native and complexed human carbonic anhydrase I: a molecular mechanics study (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetal-coordination, hydrogen-bond network formation, and protein-solvent interactions in native and complexed human carbonic anhydrase I: a molecular mechanics studyAngelo Vedani, David W. Huhta, and Stephen P. JacoberCite this: J. Am. Chem. Soc. 1989, 111, 11, 4075–4081Publication Date (Print):May 1, 1989Publication History Published online1 May 2002Published inissue 1 May 1989https://pubs.acs.org/doi/10.1021/ja00193a045https://doi.org/10.1021/ja00193a045research-articleACS PublicationsRequest reuse permissionsArticle Views208Altmetric-Citations40LEARN 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
Technical Report: Time-Activity-Curve Integration in Lu-177 Therapies in Nuclear Medicine (2019)

Currently, there is a high interest in Lu-177 targeted radionuclide therapies, which could be attributed to favourable results obtained from Lu-177 compounds targeting neuroendocrine and prostate tumours. Generally, it has been recognized that a transition from dosimetry based on planar images towards based on fully-quantitative SPECT is beneficial in terms of increased accuracy. SPECT based dosimetry could not only be used for achieving accurate absorbed dose per-organ, but even for deriving dose values for individual voxels. However, a voxel-wise determination of TACs is problematic since several confounding factors exist, such as e.g. poor count-statistics or registration inaccuracies. A particle filter (PF) is a class of methods which applies regularization based on a model of a state's evolution over time. We applied PFs for de-noising the TACs of 26 patients, who underwent Lu-177-DOTATOC or -PSMA therapy. The TACs were obtained from four serial SPECT(/CT) data. The model used in the PF was a mono-exponential decay. The time-integrated activities (TIA) resulting from the PF were compared to the results of a monoexponential fit of the individual voxels in several volumes of interest. Optimal values for noise of observations and noise of the model were 0.25 and 0.5, respectively. The distribution of voxel-wise halflives resulting from the PFFit method were considerably closer to the organ average value and the number of implausibly long halflives was reduced. However, one has to admit that voxel-wise fitting generally lead to considerable deviations from the organ-average TIA as obtained by conventional whole-organ evaluation. Unfortunately, we did not have ground-truth TIA of our patient data and proper ground-truth could even be impossible to obtain. Nevertheless, there are strong indicators that Particle Filtering can be used for reducing voxel-wise TAC noise.
Chemical Characterization of Gilsonite Bitumen (2014)

This research provides new insights into the chemical composition of the Gilsonite in order to ascertain its properties which can assist in the refining and processing paths of the natural resource. Gilsonite, naturally occurring asphaltite bitumen, consists of a complex mixture of organic compounds. It was collected in the Uinta Basin near the town of Bonanza, Utah. The aim of this work is to obtain a more complete picture of molecular structure of Gilsonite, very important in fuel processing industry, matching and interpreting the results from different techniques. The Gilsonite was characterized by elemental analysis (EA) to determine the concentrations of C, H, N, S, and O, by Fourier transform infrared spectroscopy (FTIR) for comparative analysis of the chemical structures, by Nuclear magnetic resonance spectroscopy of hydrogen ( 1 H NMR) to ascertain the aliphatic and aromatic hydrogen fractions, and by Thin layer chromatography-flame ionization detection (Iatroscan TLC-FID) to quantify saturated and aromatic hydrocarbons, and resin/asphaltene fractions. The results were evaluated in combination with the available geological data and with some bitumens to evaluate, chemically, possible mechanisms of Gilsonite formation. Low hydrogen to carbon atomic ratio (1.44), low sulfur (0.27 wt.%) and high nitrogen (3.25 wt.%) contents were the main characteristics of the Gilsonite from Uinta Basin. FTIR revealed the presence of alkane, aromatic rings, phenyl rings, alcohols, carbonyl groups, organic sulfoxides, and sulfate salts, confirming the fact that Gilsonite is composed of high molecular weight polycyclic constituents comprising of nitrogen, sulfur and oxygen heteroatoms. Likewise, FTIR proved that Gilsonite includes fingerprint of clay minerals. Iatroscan data showed interestingly that Gilsonite contains considerable amount of asphaltenes (79.7 wt.%) and nil amount of aromatics (0 wt.%). While, the yields of saturates and resins account only for 1.6 wt.% and 18.7 wt.%, respectively. Furthermore, SARA method estimated that Gilsonite is extremely instable (Colloidal instability index, CII = 4.34). Proton NMR measurements indicated that the aliphatic hydrogen portion is approximately 95.38% and the aromatic hydrogen fraction is about 4.62%.
Two rhombomeres are altered in <i>Hoxa-1</i> mutant mice (1993)

This study provides a detailed description of the anatomical defects in the Hoxa-1-/- mutant mice previously generated in our laboratory (T. Lufkin, A. Dierich, M. LeMeur, M. Mark and P. Chambon, 1991; Cell 66, 1105-1119). Three-dimensional reconstructions of the Hoxa-1-/- rhombencephalon reveals that it bears only five rhombomeric structures (ie. morphological segments) instead of the normal seven. The first three of these rhombomeres appear normal as judged from the distribution pattern of CRABPI transcripts in the neurectoderm and from the histological analysis of the cranial nerve components derived from these structures. In contrast, the neural-crest-cell-free region normally located opposite rhombomere 5 is lacking in Hoxa-1-/- embryos, and motor neurons of the facial and abducens nerves, which normally differentiate within rhombomeres 4, 5 and 6, are missing in Hoxa-1-/- fetuses. These morphological data, combined with the determination of the molecular positional identities of the rhombomeres 4 and 5 (P. Dollé, T. Lufkin, R. Krumlauf, M. Mark, D. Duboule and P. Chambon, 1993; Proc. Natl. Acad. Sci. USA, in press), suggest that rhombomere 4 is markedly reduced, whereas rhombomere 5 is almost absent. Thus, the remnants of rhombomeres 4 and 5 appear to be fused caudally with rhombomere 6 to form a single fourth rhombomeric structure. Moreover, the migration of neural crest cells contributing to the glossopharyngeal and vagus nerves occurs in a more rostral position, resulting in abnormalities of these cranial nerves, which were visualized by whole-mount anti-neurofilament immunostaining. The mutual relationship along the rostrocaudal axis between the otic pit and the neuroepithelial site of int-2 protein secretion (a putative otogenic cue) is not significantly changed in Hoxa-1-/- embryos. However, the abnormal relationship between the rhombencephalon and the epithelial inner ear may account for the aplasia and faulty differentiation of the membranous labyrinth, the disruption of the cartilaginous otic capsule and the disorganisation of some middle ear structures. This phenotype is compared with that of the Hoxa-1-/- mutants generated by O. Chisaka, T. S. Musci and M. R. Capecchi, 1992 (Nature 335, 516-520) and with that of the mice homozygous for the kreisler mutation.
Coupled Object Detection and Tracking from Static Cameras and Moving Vehicles (2008)

We present a novel approach for multi-object tracking which considers object detection and spacetime trajectory estimation as a coupled optimization problem. Our approach is formulated in a Minimum Description Length hypothesis selection framework, which allows it to recover from mismatches and temporarily lost tracks. Building upon a state-of-the-art object detector, it performs multiview/multicategory object recognition to detect cars and pedestrians in the input images. The 2D object detections are checked for their consistency with (automatically estimated) scene geometry and are converted to 3D observations which are accumulated in a world coordinate frame. A subsequent trajectory estimation module analyzes the resulting 3D observations to find phyically plausible spacetime trajectories. Tracking is achieved by performing model selection after every frame. At each time instant, our approach searches for the globally optimal set of spacetime trajectories which provides the best explanation for the current image and for all evidence collected so far, while satisfying the constraints that no two objects may occupy the same physical space, nor explain the same image pixels at any point in time. Successful trajectory hypotheses are then fed back to guide object detection in future frames. The optimization procedure is kept efficient throught incremental computation and conservative hypothesis pruning. We evaluate our approach on several challenging video sequences and demonstrate its performance on both a surveillance-type scenario and a scenario where the input videos are taken from inside a moving vehicle passing through crowded city areas.
Optimal constellation distortion for PAR reduction in MIMO-OFDM systems (2008)

One of the main problems with orthogonal frequency division multiplexing (OFDM) modulation is the high peak-to-average-ratio (PAR) of the transmitted time-domain signal. Optimally distorting the transmitted constellation for peak reduction in OFDM systems was introduced and shown to be a convex optimization problem. This work advantageously extends this approach to multiple-input multiple-output (MIMO) systems. While the problem is still convex, solving the problem using standard convex optimization techniques quickly becomes computationally prohibitive for a large number of tones and/or antennas. This paper therefore also proposes solving the optimization problem using an interior-point method (IPM) based on the conjugate-gradient (CG) algorithm.
Microservices in IoT clouds (2016)

The current Internet of Things technology landscape is admittedly plagued with fragmentation. Fragmentation in IoT seems to be abundant ranging from the device hardware, operating system and software to device-to-device and device-to-cloud-based infrastructure protocols, to the actual cloud-based infrastructure and tools used for developing and operating software that runs on these two opposite ends of the system. As such it is challenging for a developer to decide the development, deployment and operational technologies for a complete end-to-end IoT solution. In this paper we focus on the performance evaluation and technology selection of the cloud end of the system. Given that a modern IoT cloud infrastructure is based on a microservices platform, we tackle the challenge of the selection of a Microservice Application Server (MAS) among several available in the developer community for the task of data collection from IoT devices. This paper provides two key contributions. First of all we present an empirical evaluation between different JVM-based MASs and corresponding client/frameworks taking into consideration throughput (req/s), memory footprint and binary footprint. Secondly we provide an open-source testbed that can be used for reproducing the current evaluation and for extending the evaluation towards additional MASs that have been implemented in different runtimes/programming languages.
Progressive oxidative damage in the central nervous system of a murine model for juvenile Batten disease (2007)

Oxidative damage is a known contributor to the pathogenesis of neurodegenerative diseases. Juvenile Batten disease is a progressive neurodegenerative disorder of childhood that results from mutation in Cln3. We have performed an initial characterization of the oxidative burden throughout the CNS in a Cln3(-/-) mouse model for juvenile Batten disease. A survey of multiple regions of the Cln3(-/-) mouse brain revealed a specific reduction of total glutathione, a tripeptide antioxidant molecule, in the cerebellum. Further analysis revealed an increase in protein oxidation not only in the cerebellum but also in the thalamus and primary motor cortex. Additionally, the thalamus was found to have an increase in the amount of a potent antioxidant enzyme, manganese superoxide dismutase (MnSOD), which may be in response to an increase in deleterious superoxide radicals. Colocalization studies indicate that microglia are localized directly adjacent to neurons expressing MnSOD, indicating that microglial activation may be related to the observed oxidative damage. This study helps to provide an initial measure of regions within the CNS of Cln3(-/-) mice that are specifically affected by the loss of CLN3 function and may serve to identify at the neuroanatomical level, the sequence of events that plays a role in the pathogenesis and clinical course of juvenile Batten disease.
Leishmaniasis: Current Treatment and Prospects for New Drugs and Vaccines (2009)

Leishmaniasis is a disease that ranges in severity from skin lesions to serious disfigurement and fatal systemic infection. WHO estimates that the disease results in 2 million new cases a year, threatens 350 million people in 88 countries and that there are 12 million people currently infected worldwide. Current treatment is based on chemotherapy, which relies on a handful of drugs with serious limitations such as high cost, toxicity, difficult route of administration and lack of efficacy in endemic areas. Pentavalent antimonials have been the mainstay of antileishmanial therapy for over 70 years with second line drugs, Amphotericin B and Pentamidine, used in case of antimonial failure. Since the introduction of miltefosine at the beginning of this century, no new antileishmanial compounds have been approved for human treatment. Leishmaniasis is considered one of a few parasitic diseases likely to be controllable by vaccination. However, to date no such vaccine is available despite substantial efforts by many laboratories. The development of a safe, effective and affordable antileishmanial vaccine is a critical global public-health priority. This review outlines the current status of vaccine development and looks at the currently available chemotherapy as well as examples of drugs in development and different approaches to antileishmanial drug discovery and identification of novel antiparasitic compounds.