gebhart/patrepeval huggingface dataset:
The potential value of probabilistic tractography-based for MR-guided focused ultrasound thalamotomy for essential tremor (2017)

Magnetic Resonance-guided Focused UltraSound (MRgFUS) offers an incisionless approach to treat essential tremor (ET). Due to lack of evident internal anatomy on traditional structural imaging, indirect targeting must still be used to localize the lesion. Here, we investigate the potential predictive value of probabilistic tractography guided thalamic targeting by defining how tractography-defined targets, lesion size and location, and clinical outcomes interrelate. MR imaging and clinical outcomes from 12 ET patients that underwent MRgFUS thalamotomy in a pilot study at the University of Virginia were evaluated in this analysis. FSL was used to evaluate each patient's voxel-wise thalamic connectivity with FreeSurfer generated pre- and post-central gyrus targets, to generate thalamic target maps. Using Receiver Operating Characteristic curves, the overlap between these thalamic target maps and the MRgFUS lesion was systematically evaluated relative to clinical outcome. To further define the connectivity characteristics of effective MRgFUS thalamotomy lesions, we evaluated whole brain probabilistic tractography of lesions (using post-treatment imaging to define the lesion pre-treatment diffusion tensor MRI). The structural connectivity difference was explored between subjects with the best clinical outcome relative to all others. Ten of twelve patients presented high percentage of overlapping between connectivity-based thalamic segmentation maps and lesion area. The improvement of clinical score was predicted (AUC: 0.80) using the volume of intersection between the thalamic target (precentral gyrus) map and MRgFUS induced lesion as feature. The main structural differences between those with different magnitudes of response were observed in connectivity to the pre- and post-central gyri and brainstem/cerebellum. MRgFUS thalamotomy lesions characterized by strong structural connectivity to precentral gyrus demonstrated better responses in a cohort of patients treated with MRgFUS for ET. The intersection between lesion and thalamic-connectivity maps to motor - sensory targets proved to be effective in predicting the response to the therapy. These imaging techniques can be used to increase the efficacy and consistency of outcomes with MRgFUS and potentially shorten treatment times by identifying optimal targets in advance of treatment.
The T-box transcription factor Brachyury controls tumor cell migration and invasion (2008)

4553 Elevated expression of the T-box transcription factor Brachyury has been demonstrated in various human tumors of epithelial origin and in human cell lines derived from lung, colon, and prostate carcinomas (Clin Cancer Res. 2007;13(8):2471-8). Brachyury9s high expression in tumor cells contrasts with its lack of expression in most human normal adult tissues. The function of Brachyury as a relevant gene for the development of mesoderm during gastrulation is well established; however, no reports exist so far indicating its function in the context of a tumor cell. Formation of mesoderm during embryogenesis is a manifestation of epithelial plasticity where epithelial cells change into mesenchymal cells by triggering an epithelial-to-mesenchymal transition (EMT). Recently, EMT has been recognized as a central process in the progression of primary tumors into metastasis, which involves the acquisition of motility and invasiveness by the tumor cells. Several transcription factors involved in the control of mesoderm such as Twist, Snail and Slug have been identified as controllers or triggers of EMT. Here, we sought to investigate the role of Brachyury in the EMT process during tumor progression. Two experimental approaches were taken in which (1) the expression of Brachyury has been silenced in Brachyury-positive human lung carcinoma cells, or (2) Brachyury has been over-expressed in various human tumor cell lines that are Brachyury-negative. Our results demonstrated that stable silencing of Brachyury expression in carcinoma cells results in down-regulation of mesenchymal markers and up-regulation of epithelial markers with concomitant loss of cell migration and invasion functions. In contrast, the over-expression of Brachyury in several tumor cell lines resulted in up-regulation of mesenchymal markers and down-regulation of epithelial markers, and increased both the migration and invasiveness of the tumor cells. Therefore, our results demonstrate that the transcription factor Brachyury plays a role in the EMT process during tumor progression, conferring on the tumor cells a mesenchymal phenotype as well as migratory and invasive abilities. The high expression of Brachyury in tumor cells and its potential role in the metastatic conversion of tumors make Brachyury an attractive target candidate for anti-tumor mediated therapies.
Potential Protease Inhibitors Based on a Functional Cyclic Sulfamide Scaffold. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Off-resonance correction in MRF using Deep Learning in fingerprint space (2023)

Magnetic Resonance Fingerprinting (MRF) acquisitions with balanced Steady State Free Precession (bSSFP) and spiral trajectories are prone to off-resonance artifacts. These artifacts affect the reconstruction of the tissue maps (T1 and T2). We propose to use a UNet CNN feed with fingerprints corrupted by off-resonance to generate corrected fingerprints with only aliasing in the bSSFP-MRF sequence. The feasibility of the proposed approach was evaluated in simulations and in-vivo brain data. Our method improved the NRMSE values for both quantitative maps T1 and T2. Considerably reducing the effects of the off-resonance by UNet-MRF in comparison to classical bSSFP-MRF.
Circulating vasoactive intestinal peptide for diagnosis of exacerbation of COPD (2015)

<b>Background:</b> Vasoactive Intestinal Peptide (VIP) is an abundant neuropeptide in the lung, which has been linked to pulmonary arterial hypertension and hypoxia in COPD. We hypothesize that circulating VIP is increased at exacerbation as compared to stable COPD. <b>Methods:</b> In a nested cohort study, 283 patients (mean age 66.31±11.38) with GOLD II-IV (mean post BD FEV1 %pred 47.8±16.37) were examined at stable state and at exacerbation. Serum VIP level, from dedicated frozen samples was determined by ELISA. Diagnostic accuracy was analyzed by receiver-operating characteristic (ROC) curve and area under the curve (AUC). <b>Results:</b> Patients in the stable and exacerbated groups had similar demographics, except for the BORG score (p&lt;0.001). VIP levels did not correlate with oxygen saturation at rest (p=0.722) or exercise (p=0.168). Serum VIP levels were significantly higher at exacerbation (130.25 pg/ml, 95% Confidence Interval, CI 112.19-151.83) as compared to stable COPD (40.07 pg/ml, 95% CI, 37.13-43.96, p&lt;0.001). The association of VIP with exacerbation remained significant after propensity score matching (p&lt;0.001). VIP levels were similar in moderate and severe AECOPD (p=0.805). Serum VIP measurement presented a robust performance to diagnose AECOPD (AUC 0.849, 95% CI 0.779-0.899). According to the Youden index, the optimal cutoff value was 56.6pg/ml. The probability of exacerbation was very low if serum VIP was ≤35pg/ml (sensitivity &gt;90%) and very high if serum VIP was ≥88pg/ml (specificity &gt;90%). Diagnostic performance improved by using a combination of clinical and lung function variables. <b>Conclusion:</b> Increased serum VIP levels are associated with exacerbation of COPD.
Robust Optimal Design of Energy Efficient Series Elastic Actuators:\n Application to a Powered Prosthetic Ankle (2018)

Design of robotic systems that safely and efficiently operate in uncertain\noperational conditions, such as rehabilitation and physical assistance robots,\nremains an important challenge in the field. Current methods for the design of\nenergy efficient series elastic actuators use an optimization formulation that\ntypically assumes known operational conditions. This approach could lead to\nactuators that cannot perform in uncertain environments because elongation,\nspeed, or torque requirements may be beyond actuator specifications when the\noperation deviates from its nominal conditions. Addressing this gap, we propose\na convex optimization formulation to design the stiffness of series elastic\nactuators to minimize energy consumption and satisfy actuator constraints\ndespite uncertainty due to manufacturing of the spring, unmodeled dynamics,\nefficiency of the transmission, and the kinematics and kinetics of the load. In\nour formulation, we express energy consumption as a scalar convex-quadratic\nfunction of compliance. In the unconstrained case, this quadratic equation\nprovides an analytical solution to the optimal value of stiffness that\nminimizes energy consumption for arbitrary periodic reference trajectories. As\nactuator constraints, we consider peak motor torque, peak motor velocity,\nlimitations due to the speed-torque relationship of DC motors, and peak\nelongation of the spring. As a simulation case study, we apply our formulation\nto the robust design of a series elastic actuator for a powered prosthetic\nankle. Our simulation results indicate that a small trade-off between energy\nefficiency and robustness is justified to design actuators that can operate\nwith uncertainty.\n
Design-for-testing for improved remanufacturability (2017)

By definition, a remanufactured product must perform to the same (or higher) level as the original product, and must therefore be issued a warranty of the same (or longer) duration. However, many components of remanufactured products will have been subjected to regular stresses in their first cycle of use and may exhibit unseen signs of damage at a microstructural level. This may not affect the remanufactured product’s performance initially but could cause it to fail before its renewed warranty expires. To combat this, we propose that the integrity of individual components is assessed non-destructively before storage. However, lack of remanufacture specific tools and techniques; particularly non-destructive tools, are major hindrances. Furthermore, ease of non-destructive testing (NDT) is not currently a consideration in the design of components; components with complex geometries may therefore be difficult to test. This paper presents, for the first time, a framework for including NDT suitability as a design criterion at the outset in the component’s lifecycle, where the geometry and surface accessibility of the component are optimised for future assessment. Ensuring that components can be easily inspected would not only allow increased confidence in the structural integrity of remanufactured products, but it would also extend the range of products suitable for remanufacturing. This paper serves as a proof of concept, examining simple inspection scenarios in order to demonstrate how the shape of components and data acquisition geometries can adversely affect the coverage of ultrasonic NDT.
Influence of Surface Morphology on Wetting Behaviors of Liquid Metal during Aluminum Heat Exchanger Fabrication (2014)

The market demand for aluminum brazed exchangers in air conditioning and refrigeration industry is continually growing owing mostly to the cost and weight savings of aluminum materials, with undisputed compactness and low charge. Manufacturing of aluminum heat exchangers requires reliable metal bonding technology to join together various components, such as tubes, fins and header manifolds. Controlled atmosphere brazing (CAB) of aluminum is the state-of-the-art technology for mass production of compact aluminum heat exchangers. Traditionally, the development of a brazing process relies on trial and error in practice. However, modern manufacturing process requires good understanding of scientific principles involved in the brazing operations. It is well known that a brazing process is assisted by the capillary flow of liquid filler metal on the base surfaces of various heat exchanger components. Therefore a good understanding of the molten flow behavior on aluminum surfaces is critical in quality assurance of the brazed heat exchangers. Capillary flow occurring at high temperature level during brazing is usually much more complicated than the wetting in an inert system with a smooth solid surface. For example, the flow of liquid is not only controlled by surface tension force, but also influenced by interactions between liquid and base metal materials. In addition, the metal surface of a heat exchanger component to be brazed is usually not smooth due to the fabrication process such as extrusion or hot/cold rolling. In this paper, the phenomena closely related to liquid filler metal wetting behaviors on base metal with different surface morphologies are presented. Experimental facilities such as heating stage microscopy system and transparent furnace are used to visualize the capillary flow of molten filler metal under typical CAB brazing conditions. The influence of the base metal surface morphology on wetting behavior as well as brazed joint quality are examined, assisted by metallographic analysis of re-solidified brazing joints. The physical and chemical phenomena in the interaction between liquid (molten flux and filler metal) and solid (base metal) are described. The results from this study provide useful insights on how material selection and surface treatment can affect the brazing process and brazed heat exchanger quality.
Loop Diuretics - Infusion or Bolus? (1982)

Conference Abstract| September 01 1982 Loop Diuretics - Infusion or Bolus? G.T. McINNES; G.T. McINNES 1Departments of Medicine and Pharmacy, Western Infirmary, Glasgow Search for other works by this author on: This Site PubMed Google Scholar A.H. Thomson; A.H. Thomson 1Departments of Medicine and Pharmacy, Western Infirmary, Glasgow Search for other works by this author on: This Site PubMed Google Scholar W.G. Rapeport; W.G. Rapeport 1Departments of Medicine and Pharmacy, Western Infirmary, Glasgow Search for other works by this author on: This Site PubMed Google Scholar A. Cook A. Cook 1Departments of Medicine and Pharmacy, Western Infirmary, Glasgow Search for other works by this author on: This Site PubMed Google Scholar Clin Sci (Lond) (1982) 63 (3): 33P–34P. https://doi.org/10.1042/cs063033Pc Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation G.T. McINNES, A.H. Thomson, W.G. Rapeport, A. Cook; Loop Diuretics - Infusion or Bolus?. Clin Sci (Lond) 1 September 1982; 63 (3): 33P–34P. doi: https://doi.org/10.1042/cs063033Pc Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsClinical Science Search Advanced Search This content is only available as a PDF. © 1982 The Biochemical Society and the Medical Research Society1982 Article PDF first page preview Close Modal You do not currently have access to this content.
Mapping genetic determinants of host susceptibility to Pseudomonas aeruginosa lung infection in mice (2016)

We propose a set of genes involved in the pathogenesis of P. aeruginosa infection that may be explored to complement human studies.
Photonic BiCMOS technology — Enabler for Si-based, monolithically integrated transceivers towards 400 Gbps (2016)

We present a photonic BiCMOS process enabling for monolithically integrated Si-based transceiver front-ends towards single-wavelength 400 Gb/s data rate by combining segmented Mach-Zehnder-Interferometer modulators and high-speed germanium photo detectors with high-performance electronics.
Estimating the Confidence Level of White Matter Connections Obtained with MRI Tractography (2008)

Our results demonstrate that whereas we can have a strong confidence in mid- and long-range connections obtained by a tractography experiment, it is difficult to distinguish between short connections traced due to diffusion coherence contrast from those produced by chance due to the other uncontrolled factors of the tractography methodology.
A Comprehensive Enumeration of the Human Proteostasis Network. 2. Components of the Autophagy-Lysosome Pathway (2023)

The condition of having a healthy, functional proteome is known as protein homeostasis, or proteostasis. Establishing and maintaining proteostasis is the province of the proteostasis network, approximately 2,700 components that regulate protein synthesis, folding, localization, and degradation. The proteostasis network is a fundamental entity in biology that is essential for cellular health and has direct relevance to many diseases of protein conformation. However, it is not well defined or annotated, which hinders its functional characterization in health and disease. In this series of manuscripts, we aim to operationally define the human proteostasis network by providing a comprehensive, annotated list of its components. We provided in a previous manuscript a list of chaperones and folding enzymes as well as the components that make up the machineries for protein synthesis, protein trafficking into and out of organelles, and organelle-specific degradation pathways. Here, we provide a curated list of 838 unique high-confidence components of the autophagy-lysosome pathway, one of the two major protein degradation systems in human cells.
Crystal structure of (perchlorato-κ<i>O</i>)(1,4,7,10-tetraazacyclododecane-κ<sup>4</sup><i>N</i>)copper(II) perchlorate (2016)

The crystal structure of the title salt, [Cu(ClO<sub>4</sub>)(C<sub>8</sub>H<sub>20</sub>N<sub>4</sub>)]ClO<sub>4</sub>, is reported. The Cu<sup>II</sup> ion exhibits a square-pyramidal geometry and is coordinated by the four N atoms of the neutral 1,4,7,10-tetra-aza-cyclo-dodecane (cyclen) ligand and an O atom from one perchlorate anion, with the second perchlorate ion hydrogen-bonded to one of the amine N atoms of the cyclen ligand. Additional N-H⋯O hydrogen bonds between the amine H atoms and the coordinating and non-coordinating perchlorate groups create a three-dimensional network structure. Crystals were grown from a concentrated methanol solution at ambient temperature, resulting in no co-crystallization of solvent.
Screens for Mutations Affecting Embryogenesis in <i>Xenopus tropicalis</i> (2000)

Conference Abstract| October 01 2000 Screens for Mutations Affecting Embryogenesis in Xenopus tropicalis D. L. Stemple D. L. Stemple 1Div. of Dev. Biol., National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (2000) 28 (5): A141. https://doi.org/10.1042/bst028a141 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation D. L. Stemple; Screens for Mutations Affecting Embryogenesis in Xenopus tropicalis. Biochem Soc Trans 1 October 2000; 28 (5): A141. doi: https://doi.org/10.1042/bst028a141 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 2000 Biochemical Society2000 Article PDF first page preview Close Modal You do not currently have access to this content.
Multifunctional Nanovehicles for Combined 5-Fluorouracil and Gold Nanoparticles Based on the Nanoprecipitation Method (2011)

To facilitate the administration of combined 5-Fluorouracil (5-FU) and gold nanoparticles (for photothermal treatment purposes), we developed 5-FU-gold-poly(lactide-co-glycolic acid) (5-FU-Au-PLGA) nanovehicles, via the nanoprecipitation method. The gold nanoparticles were incorporated inside the 5-FU-PLGA carriers using a roller mixer. Morphological analysis using atomic force microscopy (AFM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM), indicated uniform, singly separated spherical nanoparticles (NPs). Drug content, recovery and entrapment in the NPs were approximated using UV-spectrophotometer data. Approximately 26% of nanoparticles were recovered after drying. The percentage of total drug content was about 30%, and the percentage of drug entrapment reached 57%. Electrostatic Force Microscopy images confirmed the presence of gold inside the drug-loaded nanoparticles. We speculate that the 20-nm gold particles were able to diffuse, after 12 hours of mixing (using the roller mixer), into the PLGA matrix through the 100-nm pores (observed by SEM) without affecting the integrity of the drug delivery vehicle. These synthesized nanoparticles show promise as multimodal vehicles in the delivery of chemotherapeutic agents.
A retrospective comparison of three sequential groups of patients with Recurrent/Refractory chronic lymphocytic leukemia treated with fludarabine‐based regimens (2005)

The results of this retrospective comparison of patients with recurrent and refractory CLL indicated a higher complete remission rate and the longest estimated survival for patients who were treated with FCR, providing the basis for randomized clinical trials of this regimen.
Analysis of SOCS-3 Promoter Responses to Interferon γ (2004)

SOCS-3 (suppressor of cytokine signaling 3) is an intracellular protein that is selectively and rapidly induced by appropriate agonists and that modulates responses of immune cells to cytokines by interfering with the Janus kinase/signal transducer and activator of transcription (Jak/STAT) pathway. On the basis of the observations that interferon gamma (IFNgamma) up-regulates SOCS-3 gene and protein expression in primary mouse macrophages, J774 macrophage cell line and embryonal fibroblasts, we investigated which sequences of the 5' SOCS-3 gene are responsive to IFNgamma. By promoter deletion analysis we identified a functional IFNgamma-responsive element, located at nucleotides -72/-64 upstream from the transcription initiation, whose presence and integrity is necessary to ensure responsiveness to IFNgamma. This element contains a STAT consensus binding sequence (SOCS-3/STAT-binding element (SBE)) whose specific mutation totally abolished the responsiveness to IFNgamma. In contrast, discrete deletion of other 5' regions of the SOCS-3 promoter did not substantially modify the inducibility by IFNgamma. Electromobility shift assay analyses revealed that IFNgamma promotes specific DNA binding activities to an oligonucleotide probe containing the SOCS-3/SBE sequence. Even though IFNgamma triggered tyrosine phosphorylation of both STAT1 and STAT3 in macrophages and J774 cells, only STAT1 was appropriately activated and thus found to specifically bind to the SOCS-3/SBE oligonucleotide probe. Accordingly, IFNgamma-induced SOCS-3 protein expression was not impaired in STAT3-deficient embryonal fibroblasts. Taken together, these results demonstrate that the induction of SOCS-3 by IFNgamma depends upon the presence of a STAT-binding element in the SOCS-3 promoter that is specifically activated by STAT1.